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Ali Z, Khan I, Iqbal MS, Shi H, Ding L, Hong M. Impact of copper stress in the intestinal barriers and gut microbiota of Chinese stripe-necked turtle (Mauremys sinensis). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2025; 290:117723. [PMID: 39827614 DOI: 10.1016/j.ecoenv.2025.117723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 01/07/2025] [Accepted: 01/10/2025] [Indexed: 01/22/2025]
Abstract
Copper is used to treat algal blooms, macrophyte infestations and other environmental issues, but its rising ambient levels harm aquatic animals, especially their intestines. However, its impact on turtles' digestive health is not well understood, and the risks are unclear. This study investigates the effects of copper on the intestinal health of Chinese stripe-necked turtle, focusing on histomorphology, mucosal barrier function, gene expression, and gut microbiota. Copper stress caused intestinal damage, characterized by shortened villi, inflammatory cell infiltration, and reduced epithelial layer thickness, as well as decreased acidic mucins, increased villi edema and inflammation. The mRNA expression level of bacteriostatic enzymes significantly reduced. Furthermore, This study found that copper exposure increases gut permeability by suppressing tight junction genes and triggers an inflammatory response in the gut, as indicated by elevated inflammatory cytokines. At the phylum level, Firmicutes exhibited a significant decrease, whereas Bacteroidota displayed a notable increase, and Fusobacteriota showed a substantial reduction in relative abundance in copper-treated groups. Similarly, at genus level Romboutsia, Cetobacterium decreased, while Turicibacter and Sarcina significantly increases in copper-treated groups compared to the control. This indicating the unique properties of copper including its essentiality, reactivity, and accumulation enables it to profoundly impact gut bacteria, altering both their composition and function. Copper's dual role as a nutrient and toxicant uniquely impacts gut microbes. Our findings suggest that copper stress compromises the intestinal physical, immune, chemical, and microbial barrier in M. sinensis, all of which contribute to the turtle's poor health.
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Affiliation(s)
- Zeeshan Ali
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Ijaz Khan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Muhammad Shahid Iqbal
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Meiling Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
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Fernandez-Jalao I, Siles-Sánchez MDLN, Santoyo S, Tamargo A, Relaño de la Guía E, Molinero N, Moreno-Arribas V, Jaime L. Modulation of Gut Microbiota Composition and Microbial Phenolic Catabolism of Phenolic Compounds from Achillea millefolium L. and Origanum majorana L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:478-494. [PMID: 39699532 DOI: 10.1021/acs.jafc.4c07910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2024]
Abstract
The impact of the nonbioaccessible fraction of two phenolic-rich extracts from Achillea millefolium L. (yarrow) and Origanum majorana L. (marjoram) on the modulation of the human gut microbiota was investigated in vitro. Microbial metabolism of the phenolic compounds was also addressed. In general, phenolic acids or O-glycosidic flavones quickly disappeared, in contrast to methoxy- or C-glycosidic flavonoids. This colonic metabolism yielded phloroglucinol, 3,4-dimethoxyphenylacetic acid, 3-(4-hydroxyphenyl)-propionic acid, and 4-hydroxybenzoic acid as the main metabolites of the microbial catabolism of rosmarinic acid or caffeoylquinic acids, among others. The 16S rRNA gene sequencing showed that the most promising modulatory effect was related to the increase in Bifidobacterium spp., Collinsella spp., Romboutsia, and Akkermansia muciniphila for both plant extracts, along with Blautia spp. and Dialister for yarrow extract. This beneficial modulation was accompanied by the increase in butyric acid production, highlighting the potential prebiotic-like effect on the gut microbiota of these two previously unstudied edible plants.
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Affiliation(s)
- Irene Fernandez-Jalao
- Departmental Section of Food Science, Faculty of Science, Universidad Autónoma de Madrid, Madrid 28049, Spain
- Department of Production and Characterization of Novel Food, Food Science Research Institute (CIAL), CEI UAM+CSIC, Madrid 28049, Spain
| | - María de Las Nieves Siles-Sánchez
- Departmental Section of Food Science, Faculty of Science, Universidad Autónoma de Madrid, Madrid 28049, Spain
- Department of Production and Characterization of Novel Food, Food Science Research Institute (CIAL), CEI UAM+CSIC, Madrid 28049, Spain
| | - Susana Santoyo
- Departmental Section of Food Science, Faculty of Science, Universidad Autónoma de Madrid, Madrid 28049, Spain
- Department of Production and Characterization of Novel Food, Food Science Research Institute (CIAL), CEI UAM+CSIC, Madrid 28049, Spain
| | - Alba Tamargo
- Department of Food Biotechnology and Microbiology, Food Science Research Institute (CIAL), CEI UAM+CSIC, Madrid 28049, Spain
| | - Edgard Relaño de la Guía
- Department of Food Biotechnology and Microbiology, Food Science Research Institute (CIAL), CEI UAM+CSIC, Madrid 28049, Spain
| | - Natalia Molinero
- Department of Food Biotechnology and Microbiology, Food Science Research Institute (CIAL), CEI UAM+CSIC, Madrid 28049, Spain
| | - Victoria Moreno-Arribas
- Department of Food Biotechnology and Microbiology, Food Science Research Institute (CIAL), CEI UAM+CSIC, Madrid 28049, Spain
| | - Laura Jaime
- Departmental Section of Food Science, Faculty of Science, Universidad Autónoma de Madrid, Madrid 28049, Spain
- Department of Production and Characterization of Novel Food, Food Science Research Institute (CIAL), CEI UAM+CSIC, Madrid 28049, Spain
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Hu J, Bai M, Xing Y, Liu J, Xu K, Xiong X, Liu H, Yin Y. Artemisia annua Residue Regulates Immunity, Antioxidant Ability, Intestinal Barrier Function, and Microbial Structure in Weaned Piglets. Animals (Basel) 2024; 14:3569. [PMID: 39765473 PMCID: PMC11672813 DOI: 10.3390/ani14243569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 12/04/2024] [Accepted: 12/06/2024] [Indexed: 01/11/2025] Open
Abstract
Artemisia annua residue (AR), as the byproduct of industrial extraction of artemisinin, contains rich nutrients and active ingredients. This study was conducted to determine the effects of AR as an unconventional feed material on growth performance, immunity, and intestinal health in weaned piglets. Thirty-two piglets weaned at 21 days (7.53 ± 0.31 kg average BW) were fed with a corn-soybean basal diet (BD) and a basal diet with 1% (LAR), 2% (MAR), and 4% (HAR) AR diets for 28 days. AR diets increased the serum IgA and complement component 3 levels, superoxide dismutase activity, and villus height in the duodenum (p < 0.05). The MAR group increased the ADG, serum total protein, and mRNA expression levels of Claudin-1 in the duodenum and zonula occludens-1 (ZO-1) and the mucin 2 (MUC2) in the colon, as well as colonic Romboutsia and Anaerostipes abundances, and decreased the Proteobacteria abundance (p < 0.05). To sum up, dietary AR supplementation may enhance growth performance by improving serum immunoglobulin and antioxidant enzyme activity, intestinal morphology, tight junction protein expression, and gut microbiota of weaned piglets. Regression analysis showed that the optimal AR supplemental level for growth performance, immunity, antioxidant ability, and intestinal health of weaned piglets was 2.08% to 4.24%.
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Affiliation(s)
- Jinjie Hu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (Y.X.); (Y.Y.)
| | - Miaomiao Bai
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (K.X.); (X.X.)
| | - Yueyao Xing
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (Y.X.); (Y.Y.)
| | - Junhong Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China;
| | - Kang Xu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (K.X.); (X.X.)
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha 410219, China
| | - Xia Xiong
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (K.X.); (X.X.)
| | - Hongnan Liu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (K.X.); (X.X.)
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (Y.X.); (Y.Y.)
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (K.X.); (X.X.)
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Prapa I, Yanni AE, Kompoura V, Mitropoulou G, Panas P, Kostomitsopoulos N, Kourkoutas Y. Functional Modulation of Gut Microbiota and Blood Parameters in Diabetic Rats Following Dietary Intervention with Free or Immobilized Pediococcus acidilactici SK Cells on Pistachio Nuts. Nutrients 2024; 16:4221. [PMID: 39683613 DOI: 10.3390/nu16234221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Revised: 12/01/2024] [Accepted: 12/02/2024] [Indexed: 12/18/2024] Open
Abstract
BACKGROUND/OBJECTIVES The gut microbiota is linked to the pathogenesis of type 1 diabetes mellitus (T1DM), while supplementation with probiotics may result in positive alterations in the composition of the gut microbiome. This research aimed to map the changes in the gut microbiome and blood markers of streptozotocin-induced diabetic rats after a dietary intervention with free or immobilized cells of the presumptive probiotic Pediococcus acidilactici SK on pistachio nuts. METHODS Twenty-four male Wistar rats were studied and divided into four groups (healthy or diabetic) which received the free or the immobilized P. acidilactici SK cells on pistachio nuts for 4 weeks. Blood, fecal, and intestinal tissue samples were examined. RESULTS The diabetic rats exhibited an elevated concentration of HDL-c, while the inflammatory IL-1β levels were significantly lower in the diabetic animals that received the immobilized cells compared to the group that received the free cells. The dietary intervention with immobilized cells led to decreased counts of fecal staphylococci and enterococci in the diabetic animals, while the diet with both free and immobilized P. acidilactici SK cells rendered levels of these populations in normal values in the feces and intestinal tissue of the diabetic animals. Noticeably, the Lactobacillus and Bifidobacterium genera were elevated after the supplementation with immobilized P. acidilactici SK cells on pistachio nuts. CONCLUSIONS Dietary supplementation with P. acidilactici SK cells (in free or in immobilized form) beneficially affected the gut microbiota/microbiome of streptozotocin-induced diabetic rats, leading to the alleviation of dysbiosis and inflammation and control over their lipid levels.
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Affiliation(s)
- Ioanna Prapa
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Amalia E Yanni
- Laboratory of Chemistry, Biochemistry, Physical Chemistry of Foods, Department of Nutrition and Dietetics, Harokopio University of Athens, 17671 Athens, Greece
| | - Vasiliki Kompoura
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Gregoria Mitropoulou
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | | | - Nikolaos Kostomitsopoulos
- Laboratory Animal Facility, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Yiannis Kourkoutas
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
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Yang KC, Tien WY, Cheng MF. Gut microbiota compositions in the carriers and noncarriers of third-generation cephalosporin-resistant Escherichia coli: A study among children in southern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:896-905. [PMID: 39261124 DOI: 10.1016/j.jmii.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND Antimicrobial resistance, particularly in third-generation cephalosporin-resistant (3GC-R) Escherichia coli (E. coli), poses major global health challenges and has various clinical implications. Researchers have explored the relationship between extended-spectrum β-lactamase-producing E. coli and gut microbiota composition, which influence host health and disease susceptibility, in adults. In this study, we analyzed gut microbiota composition in Taiwanese children by the colonization status of 3GC-R E. coli. METHODS This cross-sectional study included children (age, 0-6 years) from Kaohsiung, Taiwan. Fecal samples were subjected to microbiological and gut microbiome (full-length 16S rRNA sequencing) analyses. The antimicrobial susceptibility of E. coli colonies isolated from the samples was tested. Furthermore, gut microbiota compositions and diversity indices were compared between 3GC-R E. coli carriers and noncarriers. RESULTS Approximately 46% of all children aged <6 years carried 3GC-R E. coli. The abundances of Drancourtella, Romboutsia, and Desulfovibrio (genus level) were higher in carriers than in noncarriers. By contrast, the abundances of Odoribacteraceae (family level) and Sutterella (genus level) were higher in noncarriers than in carriers. No significant between-group difference was observed in alpha diversity. However, a significant between-group difference was noted in beta diversity (unweighted UniFrac analysis). CONCLUSION This is the first study that investigated differences in the gut microbiota between healthy 3GC-R E. coli carriers and noncarriers in children, suggesting potential mechanisms involving altered utilization of short-chain fatty acids and elevated succinate levels contributing to increased colonization of 3GC-R E. coli. The other taxa identified in this study may contribute to colonization resistance in the pediatric population.
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Affiliation(s)
- Keng-Chin Yang
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wan-Yu Tien
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ming-Fang Cheng
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Kaohsiung Veterans General Hospital Tainan Branch, Tainan, Taiwan.
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6
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Li Z, Lv J, Chen J, Sun F, Sheng R, Qin Y, Rao L, Lu T, Sun L. Comparative study of gut content microbiota in freshwater fish with different feeding habits: A case study of an urban lake. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39567260 DOI: 10.1111/jfb.16002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 11/06/2024] [Accepted: 11/07/2024] [Indexed: 11/22/2024]
Abstract
The gut microbiota plays a crucial role in various physiological functions of the host and can be modulated by numerous factors, including feeding habit or trophic level. In this study, the impact of host feeding habits on the gut microbiota of freshwater fish was explored. Ten fish species, classified into four feeding habit categories (herbivorous, omnivorous, planktivorous, and carnivorous) were sampled from West Lake, a renowned urban scenic lake, and their gut content microbiota was analysed using 16S ribosomal RNA gene sequencing. A total of 2531 operational taxonomic units, belonging to 34 bacterial phyla, were identified, with 33.4% shared across all feeding habits. Firmicutes and Proteobacteria were the predominant phyla. However, at the family level, Peptostreptococcaceae and Clostridiaceae_1 were the most dominant. Microbiota composition diversity was highest in herbivorous fish, followed by omnivores, carnivores, and planktivores. Statistically significant differences in microbiota diversity were found between different feeding categories, except for the omnivores, which did not differ from the carnivores or planktivores. The most abundant predicted metabolic pathways across all feeding habits were similar, with amino acid metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, and metabolism of other amino acids being dominant. However, comparing the relative abundance of gene functions between different feeding habits revealed notable variations across most comparisons. Co-occurrence network analysis for each feeding habit revealed that all networks were dominated by the strong positive correlation among pairs of bacterial genera abundances, while the basic properties varied, implying differences in gut microbiota interactions based on the feeding habit. In conclusion, these results confirmed that the feeding habit could affect the structure and composition of the gut content microbiota but also changed their functions and interactions.
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Affiliation(s)
- Zaitian Li
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Junsheng Lv
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jun Chen
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou, China
| | - Fengzhu Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Ruozhu Sheng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yueyun Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Lihua Rao
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, China
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Garcés-Ordóñez O, Córdoba-Meza T, Sáenz-Arias S, Blandón L, Espinosa-Díaz LF, Pérez-Duque A, Thiel M, Canals M. Potentially pathogenic bacteria in the plastisphere from water, sediments, and commercial fish in a tropical coastal lagoon: An assessment and management proposal. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135638. [PMID: 39217937 DOI: 10.1016/j.jhazmat.2024.135638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 08/06/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Microplastics in aquatic ecosystems harbor numerous microorganisms, including pathogenic species. The ingestion of these microplastics by commercial fish poses a threat to the ecosystem and human livelihood. Coastal lagoons are highly vulnerable to microplastic and microbiological pollution, yet limited understanding of the risks complicates management. Here, we present the main bacterial groups, including potentially pathogenic species, identified on microplastics in waters, sediments, and commercial fish from Ciénaga Grande de Santa Marta (CGSM), the largest coastal lagoon in Colombia. DNA metabarcoding allowed identifying 1760 bacterial genera on microplastics, with Aeromonas and Acinetobacter as the most frequent and present in all three matrices. The greatest bacterial richness and diversity were recorded on microplastics from sediments, followed by waters and fish. Biochemical analyses yielded 19 species of potentially pathogenic culturable bacteria on microplastics. Aeromonas caviae was the most frequent and, along with Pantoea sp., was found on microplastics in all three matrices. Enterobacter roggenkampii and Pseudomonas fluorescens were also found on microplastics from waters and fish. We propose management strategies for an Early Warning System against microbiological and microplastic pollution risks in coastal lagoons, illustrated by CGSM. This includes forming inter-institutional alliances for research and monitoring, accompanied by strengthening governance and health infrastructures.
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Affiliation(s)
- Ostin Garcés-Ordóñez
- Instituto de Investigaciones Marinas y Costeras "José Benito Vives de Andréis" -INVEMAR, calle 25 No. 2-55 Rodadero, Santa Marta, Colombia; Sustainable Blue Economy Chair, GRC Geociències Marines, Departament de Dinàmica de la Terra i de l'Oceà, Universitat de Barcelona, Martí i Franquès s/n, 08028 Barcelona, Spain; Grupo de Investigación Territorios Semiáridos del Caribe, Universidad de La Guajira, Colombia.
| | - Tania Córdoba-Meza
- Instituto de Investigaciones Marinas y Costeras "José Benito Vives de Andréis" -INVEMAR, calle 25 No. 2-55 Rodadero, Santa Marta, Colombia
| | - Sol Sáenz-Arias
- Instituto de Investigaciones Marinas y Costeras "José Benito Vives de Andréis" -INVEMAR, calle 25 No. 2-55 Rodadero, Santa Marta, Colombia
| | - Lina Blandón
- Instituto de Investigaciones Marinas y Costeras "José Benito Vives de Andréis" -INVEMAR, calle 25 No. 2-55 Rodadero, Santa Marta, Colombia
| | - Luisa F Espinosa-Díaz
- Instituto de Investigaciones Marinas y Costeras "José Benito Vives de Andréis" -INVEMAR, calle 25 No. 2-55 Rodadero, Santa Marta, Colombia
| | - Alejandra Pérez-Duque
- Centro de Bioinformática y Biología Computacional de Colombia - BIOS, Manizales, Colombia
| | - Martin Thiel
- MarineGEO Program, Smithsonian Environmental Research Center (SERC), Edgewater, USA; Facultad Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile; Center for Ecology and Sustainable Management of Oceanic Island (ESMOI), Coquimbo, Chile
| | - Miquel Canals
- Sustainable Blue Economy Chair, GRC Geociències Marines, Departament de Dinàmica de la Terra i de l'Oceà, Universitat de Barcelona, Martí i Franquès s/n, 08028 Barcelona, Spain; Reial Acadèmia de Ciències i Arts de Barcelona (RACAB), La Rambla 115, 08002 Barcelona, Spain; Institut d'Estudis Catalans (IEC), Secció de Ciències i Tecnologia, Carme 47, 08001 Barcelona, Spain
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Jeong JY, Kim J, Kim M, Shim SH, Park C, Jung S, Jung H. Effects of Increasing Oral Deoxynivalenol Gavage on Growth Performance, Blood Biochemistry, Metabolism, Histology, and Microbiome in Rats. BIOLOGY 2024; 13:836. [PMID: 39452144 PMCID: PMC11505534 DOI: 10.3390/biology13100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 10/15/2024] [Accepted: 10/17/2024] [Indexed: 10/26/2024]
Abstract
Mycotoxin-contaminated feed or food can affect physiological responses and cause illnesses in humans and animals. In this study, we evaluated the effects of deoxynivalenol (DON) toxicity on the growth performance, blood biochemistry, histology, microbiome, and metabolism of rats fed with different toxin concentrations. After 1 week of acclimatization, seven-week-old male rats received 0.9% saline as a control, 0.02 mg/kg DON as T1, and 0.2 mg/kg DON as T2 via oral gavage for 4 weeks. The final body weight of the T2 group was significantly lower than that of the control and T1; however, the average daily gain, feed intake, and feed conversion ratio did not differ. Fibrosis and apoptosis were observed in various tissues as DON concentration increased. Creatinine and alkaline phosphatase levels were significantly lower in the DON-treated group than in the control. Firmicutes and Desulfobacterota phyla dominated the cecum, whereas those in the feces were Proteobacteria and Bacteroidetes. Metabolomic profiling showed phenylalanine, tyrosine, and tryptophan biosynthesis as the most prominent pathways. Overall, our results suggest that low-dose and short-term DON exposure can trigger several adverse effects in rats. Dietary toxicants in rats may explain the physiological effects associated with the metabolism commonly reported in animals.
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Affiliation(s)
- Jin-Young Jeong
- Animal Nutrition and Physiology Division, National Institute of Animal Science, Wanju 55365, Republic of Korea; (J.K.); (M.K.); (S.-H.S.); (H.J.)
| | - Junsik Kim
- Animal Nutrition and Physiology Division, National Institute of Animal Science, Wanju 55365, Republic of Korea; (J.K.); (M.K.); (S.-H.S.); (H.J.)
| | - Minji Kim
- Animal Nutrition and Physiology Division, National Institute of Animal Science, Wanju 55365, Republic of Korea; (J.K.); (M.K.); (S.-H.S.); (H.J.)
| | - Seong-Hoon Shim
- Animal Nutrition and Physiology Division, National Institute of Animal Science, Wanju 55365, Republic of Korea; (J.K.); (M.K.); (S.-H.S.); (H.J.)
| | - Cheolju Park
- Division of Animal Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea; (C.P.); (S.J.)
| | - Sungju Jung
- Division of Animal Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea; (C.P.); (S.J.)
| | - Hyunjung Jung
- Animal Nutrition and Physiology Division, National Institute of Animal Science, Wanju 55365, Republic of Korea; (J.K.); (M.K.); (S.-H.S.); (H.J.)
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Larsson A, Ericson U, Jönsson D, Miari M, Athanasiadis P, Baldanzi G, Brunkwall L, Hellstrand S, Klinge B, Melander O, Nilsson PM, Fall T, Maziarz M, Orho-Melander M. New connections of medication use and polypharmacy with the gut microbiota composition and functional potential in a large population. Sci Rep 2024; 14:23723. [PMID: 39390025 PMCID: PMC11467196 DOI: 10.1038/s41598-024-71571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/29/2024] [Indexed: 10/12/2024] Open
Abstract
Medication can affect the gut microbiota composition and function. The aim of this study was to investigate connections between use of common non-antibiotic medicines and the gut microbiota composition and function in a large Swedish cohort (N = 2223). Use of 67 medications and polypharmacy (≥ 5 medications), based on self-reported and prescription registry data, were associated with the relative abundance of 881 gut metagenomic species (> 5% prevalence) and 103 gut metabolic modules (GMMs). Altogether, 97 associations of 26 medications with 40 species and of four medications with five GMMs were observed (false discovery rate < 5%). Several earlier findings were replicated like the positive associations of proton pump inhibitors (PPIs) with numerous oral species, and those of metformin with Escherichia species and with lactate consumption I and arginine degradation II. Several new associations were observed between, among others, use of antidepressants, beta-blockers, nonsteroidal anti-inflammatory drugs and calcium channel blockers, and specific species. Polypharmacy was positively associated with Enterococcus faecalis, Bacteroides uniformis, Rothia mucilaginosa, Escherichia coli and Limosilactobacillus vaginalis, and with 13 GMMs. We confirmed several previous findings and identified numerous new associations between use of medications/polypharmacy and the gut microbiota composition and functional potential. Further studies are needed to confirm the new findings.
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Affiliation(s)
- Anna Larsson
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Ulrika Ericson
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Daniel Jönsson
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
- Public Dental Service of Skåne, Lund, Sweden
- Department of Periodontology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Mariam Miari
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Paschalis Athanasiadis
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Gabriel Baldanzi
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Louise Brunkwall
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Sophie Hellstrand
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Björn Klinge
- Department of Periodontology, Faculty of Odontology, Malmö University, Malmö, Sweden
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Solna, Sweden
| | - Olle Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Peter M Nilsson
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Tove Fall
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Marlena Maziarz
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden.
- Clinical Research Center, Diabetes and Cardiovascular Disease, Box 50332, 202 13, Malmö, Sweden.
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10
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Chen Q, Peng C, Xie R, Xu H, Su Z, Yilihan G, Wei X, Yang S, Shen Y, Ye C, Jiang C. Placental and fetal enrichment of microplastics from disposable paper cups: implications for metabolic and reproductive health during pregnancy. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135527. [PMID: 39151363 DOI: 10.1016/j.jhazmat.2024.135527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
The disposable paper cups (DPCs) release millions of microplastics (MPs) when used for hot beverages. However, the tissue-specific deposition and toxic effects of MPs and associated toxins remain largely unexplored, especially at daily consumption levels. We administered MPs and associated toxins extracted from leading brand DPCs to pregnant mice, revealing dose-responsive harmful effects on fetal development and maternal physiology. MPs were detected in all 13 examined tissues, with preferred depositions in the fetus, placenta, kidney, spleen, lung, and heart, contributing to impaired phenotypes. Brain tissues had the smallest MPs (90.35 % < 10 µm). A dose-responsive shift in the cecal microbiome from Firmicutes to Bacteroidetes was observed, coupled with enhanced biosynthesis of microbial fatty acids. A moderate consumption of 3.3 cups daily was sufficient to alter the cecal microbiome, global metabolic functions, and immune health, as reflected by tissue-specific transcriptomic analyses in maternal blood, placenta, and mammary glands, leading to neurodegenerative and miscarriage risks. Gene-based benchmark dose framework analysis suggested a safe exposure limit of 2 to 4 cups/day in pregnant mice. Our results highlight tissue-specific accumulation and metabolic and reproductive toxicities in mice at DPC consumption levels presumed non-hazardous, with potential health implications for pregnant women and fetuses.
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Affiliation(s)
- Qiong Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China.
| | - Chen Peng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Ruwen Xie
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Haoteng Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Zhuojie Su
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Gulimire Yilihan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Xin Wei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Sen Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Yueran Shen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Cunqi Ye
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China.
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11
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Wang M, Ma W, Wang C, Li D. Lactococcus G423 improve growth performance and lipid metabolism of broilers through modulating the gut microbiota and metabolites. Front Microbiol 2024; 15:1381756. [PMID: 38939183 PMCID: PMC11210191 DOI: 10.3389/fmicb.2024.1381756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/15/2024] [Indexed: 06/29/2024] Open
Abstract
This study aimed to explore whether Lactococcus G423 could improve growth performance and lipid metabolism of broilers by the modulation of gut microbiota and metabolites. A total of 640 1-day-old AA broilers were randomly divided into 4 groups [Control (CON), Lac_L, Lac_H, and ABX]. Average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR), breast muscle, thigh muscle, and abdominal fat pad were removed and weighed at 42 days of age. Serum was obtained by centrifuging blood sample from jugular vein (10 mL) for determining high-density lipoprotein (HDL), total cholesterol (TC), low-density lipoprotein (LDL), and triglyceride (TG) using ELISA. The ileal contents were harvested and immediately frozen in liquid nitrogen for 16S rRNA and LC-MS analyses. Then, the results of 16S rRNA analysis were confirmed by quantitative polymerase chain reaction (qPCR). Compared with the CON group, FCR significantly decreased in the Lac_H group (p < 0.05) in 1-21 days; ADG significantly increased and FCR significantly decreased in the Lac_H group (p < 0.05) in 22-42 days. 42 days weight body and ADG significantly increased in the Lac_H group (p < 0.05) in 42 days. Abdominal fat percentage was significantly decreased by Lactococcus G423 (p < 0.05), the high dose of Lactococcus G423 significantly decreased the serum of TG, TC, and LDL level (p < 0.05), and the low dose of Lactococcus G423 significantly decreased the serum of TG and TC level (p < 0.05). A significant difference in microbial diversity was found among the four groups. Compared with the CON group, the abundance rates of Firmicutes and Lactobacillus in the Lac_H group were significantly increased (p < 0.05). The global and overview maps and membrane transport in the Lac_L, Lac_H, and ABX groups significantly changed versus those in the CON group (p < 0.05). The results of LC-MS demonstrated that Lactococcus could significantly improve the levels of some metabolites (6-hydroxy-5-methoxyindole glucuronide, 9,10-DiHOME, N-Acetyl-l-phenylalanine, and kynurenine), and these metabolites were involved in four metabolic pathways. Among them, the pathways of linoleic acid metabolism, phenylalanine metabolism, and pentose and glucuronate interconversions significantly changed (p < 0.05). Lactococcus G423 could ameliorate growth performance and lipid metabolism of broilers by the modulation of gut microbiota and metabolites.
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Affiliation(s)
| | | | | | - Desheng Li
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
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12
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Wang R, Bai B, Huang Y, Degen A, Mi J, Xue Y, Hao L. Yaks Are Dependent on Gut Microbiota for Survival in the Environment of the Qinghai Tibet Plateau. Microorganisms 2024; 12:1122. [PMID: 38930503 PMCID: PMC11205922 DOI: 10.3390/microorganisms12061122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai-Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai-Tibetan plateau.
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Affiliation(s)
- Runze Wang
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; (R.W.); (B.B.)
| | - Binqiang Bai
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; (R.W.); (B.B.)
| | - Yayu Huang
- PEGASE, INRAE, Institut Agro, 35590 Saint-Gilles, France;
| | - Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 8410500, Israel;
| | - Jiandui Mi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China;
| | - Yanfeng Xue
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; (R.W.); (B.B.)
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13
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Wang L, Li Y, Zhang YJ, Peng LH. Intestinal microecological transplantation for a patient with chronic radiation enteritis: A case report. World J Gastroenterol 2024; 30:2603-2611. [PMID: 38817661 PMCID: PMC11135409 DOI: 10.3748/wjg.v30.i19.2603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND The gut microbiota is strongly associated with radiation-induced gut damage. This study aimed to assess the effectiveness and safety of intestinal microecological transplantation for treating patients with chronic radiation enteritis. CASE SUMMARY A 64-year-old female with cervical cancer developed abdominal pain, diarrhea, and blood in the stool 1 year after radiotherapy. An electronic colonoscopy was performed to diagnose chronic radiation enteritis. Two courses of intestinal microecological transplantation and full-length 16S rRNA microbiological analysis were performed. The patient experienced short- and long-term relief from symptoms without adverse effects. Whole 16S rRNA sequencing revealed significant differences in the intestinal flora's composition between patient and healthy donors. Pathogenic bacteria, such as Escherichia fergusonii and Romboutsia timonensis, were more in the patient. Beneficial bacteria such as Faecalibacterium prausnitzii, Fusicatenibacter saccharivorans, Ruminococcus bromii, and Bifidobacterium longum were more in the healthy donors. Intestinal microbiota transplantation resulted in a significant change in the patient's intestinal flora composition. The composition converged with the donor's flora, with an increase in core beneficial intestinal bacteria, such as Eubacterium rectale, and a decrease in pathogenic bacteria. Changes in the intestinal flora corresponded with the patients' alleviating clinical symptoms. CONCLUSION Intestinal microecological transplantation is an effective treatment for relieving the clinical symptoms of chronic radiation enteritis by altering the composition of the intestinal flora. This study provides a new approach for treating patients with chronic radiation enteritis.
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Affiliation(s)
- Lin Wang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- Department of Gastroenterology and Hepatology, Chinese PLA Medical School, Beijing 100853, China
| | - Yan Li
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yu-Jing Zhang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- Department of Gastroenterology and Hepatology, Chinese PLA Medical School, Beijing 100853, China
| | - Li-Hua Peng
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
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Bonilla-Espadas M, Zafrilla B, Lifante-Martínez I, Camacho M, Orgilés-Calpena E, Arán-Aís F, Bertazzo M, Bonete MJ. Selective Isolation and Identification of Microorganisms with Dual Capabilities: Leather Biodegradation and Heavy Metal Resistance for Industrial Applications. Microorganisms 2024; 12:1029. [PMID: 38792858 PMCID: PMC11124520 DOI: 10.3390/microorganisms12051029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium's oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products' end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications.
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Affiliation(s)
- Manuela Bonilla-Espadas
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Basilio Zafrilla
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
| | - Irene Lifante-Martínez
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Mónica Camacho
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
| | - Elena Orgilés-Calpena
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Francisca Arán-Aís
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Marcelo Bertazzo
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - María-José Bonete
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
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15
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Zhang Y, Yang B, Peng S, Zhang Z, Cai S, Yu J, Wang D, Zhang W. Mechanistic insights into chemical conditioning on transformation of dissolved organic matter and plant biostimulants production during sludge aerobic composting. WATER RESEARCH 2024; 255:121446. [PMID: 38489963 DOI: 10.1016/j.watres.2024.121446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
Inorganic coagulants (aluminum and iron salt) are widely used to improve sludge dewaterability, resulting in numerous residues in dewatered sludge. Composting refers to the controlled microbial process that converts organic wastes into fertilizer, and coagulant residues in dewatered sludge can affect subsequent compost efficiency and resource recycling, which remains unclear. This work investigated the effects of two typical metal salt coagulants (poly aluminum chloride [PAC] and poly ferric sulfate [PFS]) conditioning on sludge compost. Our results revealed that PAC conditioning inhibited composting with decreased peak temperature, microbial richness, enzymatic reaction intensities, and compost quality, associated with decreased pH and microbial toxicity of aluminum. Nevertheless, PFS conditioning selectively enriched Pseudoxanthomonas sp. and resulted in more fertile compost with increased peak temperature, enzymatic reaction intensities, and humification degree. Spectroscopy and mass difference analyses indicated that PFS conditioning enhanced reaction intensities of labile biopolymers at the thermophilic stage, mainly comprising hydrolyzation (H2O), dehydrogenation (-H2, -H4), oxidation (+O1H2), and other reactions (i.e., +CH2, C2H4O1, C2H6O1). Unlike the common composting process primarily conducts humification at the cooling stage, PFS conditioning changed the main occurrence stage to the thermophilic stage. Non-targeted metabolomics revealed that indole (a humification intermediate) is responsible for the increased humification degree and indoleacetic acid content in the PFS-conditioned compost, which then promoted compost quality. Plant growth experiments further confirmed that the dissolved organic matter (DOM) in PFS-conditioned compost produced the maximum plant biomass. This study provided molecular-level evidence that PFS conditioning can promote humification and compost fertility during sludge composting, enabling chemical conditioning optimization for sustainable management of sludge.
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Affiliation(s)
- Yu Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Boyuan Yang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Siwei Peng
- Datang Environmental Industry Group Co., Ltd, Haidian District, Beijing 100097, China
| | - Ziwei Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Siying Cai
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Junxia Yu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Dongsheng Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Weijun Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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16
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Liang Y, Wang Z, Gao N, Qi X, Zeng J, Cui K, Lu W, Bai S. Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season. Microorganisms 2024; 12:800. [PMID: 38674744 PMCID: PMC11052518 DOI: 10.3390/microorganisms12040800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.
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Affiliation(s)
- Yangyang Liang
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Zijia Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Gao
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Xiaoxue Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
| | - Juntao Zeng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cui
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Wenxuan Lu
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Shijie Bai
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
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17
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Maguey-González JA, Liu J, Zhang G, Latorre JD, Hernández-Ramírez JO, de Jesús Nava-Ramírez M, Senas-Cuesta R, Gómez-Rosales S, de Lourdes Ángeles M, Stein A, Solís-Cruz B, Hernández-Patlán D, Merino-Guzmán R, Hernandez-Velasco X, Castellanos-Huerta I, Uribe-Diaz S, Vázquez-Durán A, Méndez-Albores A, Petrone-Garcia VM, Tellez Jr. G, Hargis BM, Téllez-Isaías G. Assessment of the Impact of Humic Acids on Intestinal Microbiota, Gut Integrity, Ileum Morphometry, and Cellular Immunity of Turkey Poults Fed an Aflatoxin B 1-Contaminated Diet. Toxins (Basel) 2024; 16:122. [PMID: 38535788 PMCID: PMC10975313 DOI: 10.3390/toxins16030122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 04/13/2024] Open
Abstract
A recent study published data on the growth performance, relative weights of the organs of the gastrointestinal tract, liver histology, serum biochemistry, and hematological parameters for turkey poults fed an experimental diet contaminated with aflatoxin B1 (AFB1) and humic acids (HA) extracted from vermicompost. The negative effects of AFB1 (250 ng AFB1/g of feed) were significantly reduced by HA supplementation (0.25% w/w), suggesting that HA might be utilized to ameliorate the negative impact of AFB1 from contaminated diets. The present study shows the results of the remaining variables, as an extension of a previously published work which aimed to evaluate the impact of HA on the intestinal microbiota, gut integrity, ileum morphometry, and cellular immunity of turkey poults fed an AFB1-contaminated diet. For this objective, five equal groups of 1-day-old female Nicholas-700 turkey poults were randomly assigned to the following treatments: negative control (basal diet), positive control (basal diet + 250 ng AFB1/g), HA (basal diet + 0.25% HA), HA + AFB1 (basal diet + 0.25% HA + 250 ng AFB1/g), and Zeolite (basal diet + 0.25% zeolite + 250 ng AFB1/g). In the experiment, seven replicates of ten poults each were used per treatment (n = 70). In general, HA supplementation with or without the presence of AFB1 showed a significant increase (p < 0.05) in the number of beneficial butyric acid producers, ileum villi height, and ileum total area, and a significant reduction in serum levels of fluorescein isothiocyanate-dextran (FITC-d), a marker of intestinal integrity. In contrast, poults fed with AFB1 showed a significant increase in Proteobacteria and lower numbers of beneficial bacteria, clearly suggesting gut dysbacteriosis. Moreover, poults supplemented with AFB1 displayed the lowest morphometric parameters and the highest intestinal permeability. Furthermore, poults in the negative and positive control treatments had the lowest cutaneous basophil hypersensitivity response. These findings suggest that HA supplementation enhanced intestinal integrity (shape and permeability), cellular immune response, and healthier gut microbiota composition, even in the presence of dietary exposure to AFB1. These results complement those of the previously published study, suggesting that HA may be a viable dietary intervention to improve gut health and immunity in turkey poults during aflatoxicosis.
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Affiliation(s)
- Jesús A. Maguey-González
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (J.D.L.); (R.S.-C.); (A.S.); (I.C.-H.); (S.U.-D.); (B.M.H.); (G.T.-I.)
| | - Jing Liu
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA;
| | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA;
| | - Juan D. Latorre
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (J.D.L.); (R.S.-C.); (A.S.); (I.C.-H.); (S.U.-D.); (B.M.H.); (G.T.-I.)
| | - Juan O. Hernández-Ramírez
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores (FES) Cuautitlán, UNAM, Cuautitlán Izcalli 54740, Mexico; (J.O.H.-R.); (M.d.J.N.-R.); (A.V.-D.); (A.M.-A.)
| | - María de Jesús Nava-Ramírez
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores (FES) Cuautitlán, UNAM, Cuautitlán Izcalli 54740, Mexico; (J.O.H.-R.); (M.d.J.N.-R.); (A.V.-D.); (A.M.-A.)
| | - Roberto Senas-Cuesta
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (J.D.L.); (R.S.-C.); (A.S.); (I.C.-H.); (S.U.-D.); (B.M.H.); (G.T.-I.)
| | - Sergio Gómez-Rosales
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal (CENID-INIFAP), Km1 Carretera a Colon Ajuchitlán, Querétaro 76280, Mexico; (S.G.-R.); (M.d.L.Á.)
| | - María de Lourdes Ángeles
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal (CENID-INIFAP), Km1 Carretera a Colon Ajuchitlán, Querétaro 76280, Mexico; (S.G.-R.); (M.d.L.Á.)
| | - Andressa Stein
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (J.D.L.); (R.S.-C.); (A.S.); (I.C.-H.); (S.U.-D.); (B.M.H.); (G.T.-I.)
| | - Bruno Solís-Cruz
- Laboratorio 5: LEDEFAR, Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores (FES) Cuautitlán, UNAM, Cuautitlán Izcalli 54740, Mexico; (B.S.-C.); (D.H.-P.)
- División de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de México, Tultitlan 54910, Mexico
| | - Daniel Hernández-Patlán
- Laboratorio 5: LEDEFAR, Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores (FES) Cuautitlán, UNAM, Cuautitlán Izcalli 54740, Mexico; (B.S.-C.); (D.H.-P.)
- División de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de México, Tultitlan 54910, Mexico
| | - Rubén Merino-Guzmán
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, UNAM, Ciudad de México 04510, Mexico; (R.M.-G.); (X.H.-V.)
| | - Xochitl Hernandez-Velasco
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, UNAM, Ciudad de México 04510, Mexico; (R.M.-G.); (X.H.-V.)
| | - Inkar Castellanos-Huerta
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (J.D.L.); (R.S.-C.); (A.S.); (I.C.-H.); (S.U.-D.); (B.M.H.); (G.T.-I.)
| | - Santiago Uribe-Diaz
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (J.D.L.); (R.S.-C.); (A.S.); (I.C.-H.); (S.U.-D.); (B.M.H.); (G.T.-I.)
| | - Alma Vázquez-Durán
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores (FES) Cuautitlán, UNAM, Cuautitlán Izcalli 54740, Mexico; (J.O.H.-R.); (M.d.J.N.-R.); (A.V.-D.); (A.M.-A.)
| | - Abraham Méndez-Albores
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores (FES) Cuautitlán, UNAM, Cuautitlán Izcalli 54740, Mexico; (J.O.H.-R.); (M.d.J.N.-R.); (A.V.-D.); (A.M.-A.)
| | | | - Guillermo Tellez Jr.
- Department of Developmental Biology, Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK;
| | - Billy M. Hargis
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (J.D.L.); (R.S.-C.); (A.S.); (I.C.-H.); (S.U.-D.); (B.M.H.); (G.T.-I.)
| | - Guillermo Téllez-Isaías
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (J.D.L.); (R.S.-C.); (A.S.); (I.C.-H.); (S.U.-D.); (B.M.H.); (G.T.-I.)
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18
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Lau CHF, Capitani S, Tien YC, Verellen LA, Kithama M, Kang H, Kiarie EG, Topp E, Diarra MS, Fruci M. Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens. Anim Microbiome 2024; 6:6. [PMID: 38360706 PMCID: PMC10868003 DOI: 10.1186/s42523-024-00293-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND We had earlier described the growth-promoting and -depressive effects of replacing soybean meal (SBM) with low (12.5% and 25%) and high (50% and 100%) inclusion levels of black soldier fly larvae meal (BSFLM), respectively, in Ross x Ross 708 broiler chicken diets. Herein, using 16S rRNA gene amplicon sequencing, we investigated the effects of replacing SBM with increasing inclusion levels (0-100%) of BSFLM in broiler diets on the cecal bacterial community composition at each growth phase compared to broilers fed a basal corn-SBM diet with or without the in-feed antibiotic, bacitracin methylene disalicylate (BMD). We also evaluated the impact of low (12.5% and 25%) inclusion levels of BSFLM (LIL-BSFLM) on the prevalence of selected antimicrobial resistance genes (ARGs) in litter and cecal samples from 35-day-old birds. RESULTS Compared to a conventional SBM-based broiler chicken diet, high (50 to100%) inclusion levels of BSFLM (HIL-BSFLM) significantly altered the cecal bacterial composition and structure, whereas LIL-BSFLM had a minimal effect. Differential abundance analysis further revealed that the ceca of birds fed 100% BSFLM consistently harbored a ~ 3 log-fold higher abundance of Romboutsia and a ~ 2 log-fold lower abundance of Shuttleworthia relative to those fed a BMD-supplemented control diet at all growth phases. Transient changes in the abundance of several potentially significant bacterial genera, primarily belonging to the class Clostridia, were also observed for birds fed HIL-BSFLM. At the finisher phase, Enterococci bacteria were enriched in the ceca of chickens raised without antibiotic, regardless of the level of dietary BSFLM. Additionally, bacitracin (bcrR) and macrolide (ermB) resistance genes were found to be less abundant in the ceca of chickens fed antibiotic-free diets, including either a corn-SBM or LIL-BSFLM diet. CONCLUSIONS Chickens fed a HIL-BSFLM presented with an imbalanced gut bacterial microbiota profile, which may be linked to the previously reported growth-depressing effects of a BSFLM diet. In contrast, LIL-BSFLM had a minimal effect on the composition of the cecal bacterial microbiota and did not enrich for selected ARGs. Thus, substitution of SBM with low levels of BSFLM in broiler diets could be a promising alternative to the antibiotic growth promoter, BMD, with the added-value of not enriching for bacitracin- and macrolide-associated ARGs.
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Affiliation(s)
- Calvin Ho-Fung Lau
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.
| | - Sabrina Capitani
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Yuan-Ching Tien
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Lou Ann Verellen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Munene Kithama
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Hellen Kang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- School of Medicine, Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Elijah G Kiarie
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Agroécologie research unit, INRAE, Université de Bourgogne, Dijon, France
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Michael Fruci
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada.
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19
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Ankudavicius V, Nikitina D, Lukosevicius R, Tilinde D, Salteniene V, Poskiene L, Miliauskas S, Skieceviciene J, Zemaitis M, Kupcinskas J. Detailed Characterization of the Lung-Gut Microbiome Axis Reveals the Link between PD-L1 and the Microbiome in Non-Small-Cell Lung Cancer Patients. Int J Mol Sci 2024; 25:2323. [PMID: 38396998 PMCID: PMC10889071 DOI: 10.3390/ijms25042323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Next-generation sequencing technologies have started a new era of respiratory tract research in recent years. Alterations in the respiratory microbiome between healthy and malignant conditions have been revealed. However, the composition of the microbiome varies among studies, even in similar medical conditions. Also, there is a lack of complete knowledge about lung-gut microbiome interactions in lung cancer patients. The aim of this study was to explore the lung-gut axis in non-small-cell lung cancer (NSCLC) patients and the associations between lung-gut axis microbiota and clinical parameters (CRP, NLR, LPS, CD8, and PD-L1). Lung tissue and fecal samples were used for bacterial 16S rRNA sequencing. The results revealed, for the first time, that the bacterial richness in lung tumor tissue gradually decreased with an increase in the level of PD-L1 expression (p < 0.05). An analysis of β-diversity indicated a significant positive correlation between the genera Romboutsia and Alistipes in both the lung tumor biopsies and stool samples from NSCLC patients (p < 0.05). Survival analysis showed that NSCLC patients with higher bacterial richness in their stool samples had prolonged overall survival (HR: 2.06, 95% CI: 1.025-4.17, p = 0.0426).
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Affiliation(s)
- Vytautas Ankudavicius
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Darja Nikitina
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Deimante Tilinde
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Violeta Salteniene
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Skaidrius Miliauskas
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Marius Zemaitis
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
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20
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Zhang Z, Zhang G, Huang Z, Shi Y, Wang D. Application of Mendelian randomization to assess host gene-gut microbiota correlations in patients with esophageal cancer. Front Microbiol 2023; 14:1309596. [PMID: 38179450 PMCID: PMC10764629 DOI: 10.3389/fmicb.2023.1309596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Background Increasing evidence suggests that esophageal cancer (ESCA) may be correlated with gut flora. However, their causal connection remains unclear. This study aimed to evaluate potential causal linkages and gene-gut microbiome associations between the gut microbiota and ESCA using Mendelian randomization (MR). Methods We analyzed the data using genome-wide association studies. The exposure factor and outcome variable were the gut microbiota and ESCA, respectively. The MR-Egger method, weighted median, inverse-variance weighted method, heterogeneity test, sensitivity analysis, and multiplicity analysis were used for the MR analysis. And it was validated using an external dataset. Further meta-analysis was performed to validate the robustness of this relationship. Finally, we annotated single nucleotide polymorphisms in the gut microbiota that were causally associated with ESCA to explore possible host gene-gut microbiota correlations in patients with ESCA. Results We identified four species with potential associations with ESCA. Three of these species had a negative causal relationship with ESCA (odds ratio (OR): 0.961; 95% confidence interval (CI): 0.923-0.971; p = 0.047 for Romboutsia; OR: 0.972; 95% CI: 0.921-0.961; p = 0.018 for Lachnospira; OR: 0.948; 95% CI: 0.912-0.970; p = 0.032 for Eubacterium). A positive causal relationship was observed between one bacterial group and ESCA (OR: 1.105; 95% CI: 1.010-1.072; p = 0.018 for Veillonella). External datasets show the same trend. This is further supported by meta-analysis. None of the data showed pleiotropy, and leave-one-out analysis indicated the reliability of these findings. The gut microbiomes of patients with ESCA may correlate with the 19 identified genes. Conclusion Our data indicate a potential causal link between these four gut bacteria and ESCA and identify a correlation between host genes and gut microbiota in ESCA, offering novel therapeutic options.
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Affiliation(s)
- Zhenhu Zhang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Guodong Zhang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhulan Huang
- Department of Ultrasound Medicine, Longgang District Maternity and Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong, China
| | - Yamin Shi
- Department of Foreign Languages, Shandong University of Finance and Economics, Jinan, China
| | - Dong Wang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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21
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Bao R, Cheng Z, Peng L, Mehmood T, Gao L, Zhuo S, Wang L, Su Y. Effects of biodegradable and conventional microplastics on the intestine, intestinal community composition, and metabolic levels in tilapia (Oreochromis mossambicus). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 265:106745. [PMID: 37944327 DOI: 10.1016/j.aquatox.2023.106745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/03/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
Despite growing interest in conventional microplastics (CMPs) and their toxicological effects on aquatic species, little is known about biodegradable microplastics (BMPs) and their corresponding implications for aquatic life. Here, tilapia (Oreochromis mossambicus) were semi-statically exposed for 14 days to the bio-based plastic polylactic acid (PLA, 100 μg/L, 2.52 ± 0.46 μm) and the petroleum-based plastic polyvinyl chloride (PVC, 100 μg/L, 1.58 ± 0.36 μm). The results showed that ingesting the above two types of microplastics (MPs) led to oxidative stress in the fish gut, and damage to gut tissues and organelles, and PLA resulted in more obvious gut tissue edema than PVC. Furthermore, PLA caused increased levels of gut microbiota dysbiosis and a decrease in the abundance of the genus Cetobacterium, which is linked to vitamin B-12 synthesis, whereas an opposite relationship was observed on PVC. Metabolomic analysis indicated that PVC caused a significant down-regulation of orotic acid, co-metabolite of folic acid with vitamin B-12, while PLA did not affect orotic acid, which may lead to the accumulation of folic acid in fish. The joint analysis found that MPs disturbed gut metabolism homeostasis, implying that abnormal gut microbiota metabolites may be a key mechanism for MPs to induce tissue damage and oxidative stress in the gut. Overall, this study systematically illustrates the differential toxic effects of BMPs and CMPs on tilapia through gut microbiota and metabolite interactions, which will contribute to assessing the risks of BMPs to organismal health.
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Affiliation(s)
- Ruiqi Bao
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province (Hainan University), Haikou, Hainan Province 570228, PR China
| | - Zhiruo Cheng
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province (Hainan University), Haikou, Hainan Province 570228, PR China
| | - Licheng Peng
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province (Hainan University), Haikou, Hainan Province 570228, PR China; College of Ecology and Environment, Hainan University, Haikou, Hainan Province 570228, PR China.
| | - Tariq Mehmood
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province (Hainan University), Haikou, Hainan Province 570228, PR China
| | - Liu Gao
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province (Hainan University), Haikou, Hainan Province 570228, PR China
| | - Shengchi Zhuo
- Eternal Materials Co., Ltd. Suzhou, Jiangsu Province 215000, PR China
| | - Li Wang
- Eternal Materials Co., Ltd. Suzhou, Jiangsu Province 215000, PR China
| | - Yuanyuan Su
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province (Hainan University), Haikou, Hainan Province 570228, PR China
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22
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Wang M, Zheng H, Wang S, Luo H, Li Z, Song X, Xu H, Li P, Sun S, Wang Y, Yuan Z. Comparative analysis of changes in diarrhea and gut microbiota in Beigang pigs. Microb Pathog 2023; 185:106441. [PMID: 37944676 DOI: 10.1016/j.micpath.2023.106441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Increasing evidence indicated that the gut microbiota is a large and complex organic combination, which is closely related to the host health. Diarrhea is a disease with devastating effects on livestock that has been demonstrated to be associated with gut microbiota. Currently, studies on gut microbiota and diarrhea have involved multiple species, but changes in gut microbiota of Beigang pigs during diarrhea have not been characterized. Here, we described gut microbial changes of Beigang pigs during diarrhea. Results indicated that a total of 4423 OTUs were recognized in diarrheic and healthy Beigang pigs, and Firmicutes and Bacteroidota were the most dominant phyla regardless of health status. However, the major components of the gut microbiota changed between diarrheic and healthy Beigang pigs. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla (Synergistota, Actinobacteriota and Spirochaetota) and 30 genera increased significantly during diarrhea, whereas the relative abundances of 3 phyla (Patescibacteria, Bacteroidota and Fibrobacterota) and 41 genera decreased significantly. In conclusion, this study found significant changes in the gut microbiota of Beigang pigs during diarrhea. Meanwhile, this also lays the foundation for the prevention and treatment of diarrhea in Beigang pigs and the further discovery of more anti-diarrhea probiotics.
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Affiliation(s)
- Meng Wang
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hao Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Shuaiwei Wang
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Houqiang Luo
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Ziwei Li
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Xianzhang Song
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Hongxi Xu
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Peide Li
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Siyu Sun
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Yan Wang
- Tibet Livestock Research Institute, Tibet Academy of Agriculture and Animal Science, Lhasa, 850009, China.
| | - Zhenjie Yuan
- Tibet Livestock Research Institute, Tibet Academy of Agriculture and Animal Science, Lhasa, 850009, China.
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23
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Hu X, Meng LJ, Liu HD, Guo YS, Liu WC, Tan HX, Luo GZ. Impacts of Nile Tilapia (Oreochromis niloticus) exposed to microplastics in bioflocs system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165921. [PMID: 37527718 DOI: 10.1016/j.scitotenv.2023.165921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/03/2023]
Abstract
Microplastics (MPs) are abundant in aquaculture water, including in bioflocs aquaculture systems. Compared with other aquaculture systems, biofloc technology systems have the richest microbes and are beneficial to cultivated organisms. Therefore, this study provides a comprehensive assessment of the potential effects of MPs on aquaculture organisms in bioflocs systems. Here, Nile Tilapia (Oreochromis niloticus) were exposed to MPs (polystyrene; 32-40 μm diameter) with 0, 80 items/L (30 μg/L), and 800 items/L (300 μg/L) for 28 days in a bioflocs aquaculture system. The results showed that the MPs generally had no apparent effect on water quality, tilapia growth, or digestive enzyme activity. However, MPs accumulated the most in the liver (5.65 ± 0.74 μg/mg) and significantly increased the hepato-somatic index of tilapia and reduced the crude protein and lipid of tilapia muscle (p < 0.05). The levels of the antioxidant enzymes catalase and glutathione S-transferase increased significantly in response to MPs (p < 0.05). In contrast, MPs did not affect the content of glutathione, glutathione peroxidase, oxidized glutathione, and malondialdehyde, or the enzyme activity of Na+/K+-ATPase. Moreover, using an improved integrated biomarker response index, growth performance was found to be less responsive to MPs than to oxidative stress and digestive activity. Exposure to MPs did not significantly influence the microbial communities of the bioflocs and tilapia guts (p < 0.05). These results suggest that MPs barely affected tilapia in the bioflocs system. This study contributes to the evaluation of the ecological risk of MPs in aquaculture systems and a better understanding of the integrated response of cultivated vertebrates to MPs in biofloc technology systems.
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Affiliation(s)
- Xin Hu
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Liu-Jiang Meng
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Han-Dan Liu
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Yan-Shuo Guo
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Wen-Chang Liu
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-culture of Aquaculture Animals, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Hong-Xin Tan
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-culture of Aquaculture Animals, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Guo-Zhi Luo
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-culture of Aquaculture Animals, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.
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24
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Huang X, Gao Y, Zhang Y, Wang J, Zheng N. Strontium Chloride Improves Reproductive Function and Alters Gut Microbiota in Male Rats. Int J Mol Sci 2023; 24:13922. [PMID: 37762223 PMCID: PMC10531462 DOI: 10.3390/ijms241813922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Strontium (Sr) is an essential trace element in the human body and plays an important role in regulating male reproductive health. Recent studies have shown that gut flora plays a key role in maintaining spermatogenesis, as well as testicular health, through the gut-testis axis. At present, it is unclear whether gut microbiota can mediate the effects of Sr on sperm quality, and what the underlying mechanisms may be. We investigated the effects of different concentrations of strontium chloride (SrCl2) solutions (0, 50, 100, and 200 mg/kg BW) on reproductive function and gut microbiota in male Wistar rats (6-8 weeks, 250 ± 20 g). All the animals were euthanized after 37 days of treatment. The Sr-50 group significantly increased sperm concentration, sperm motility, and sperm viability in rats. After Sr treatment, serum and testicular testosterone (T) and Sr levels increased in a dose-dependent manner with increasing Sr concentration. At the same time, we also found that testicular marker enzymes (ACP, LDH) and testosterone marker genes (StAR, 3β-HSD, and Cyp11a1) increased significantly in varying degrees after Sr treatment, while serum NO levels decreased significantly in a dose-dependent manner. Further investigation of intestinal flora showed that SrCl2 affected the composition of gut microbiome, but did not affect the richness and diversity of gut microbiota. Sr treatment reduced the number of bacteria with negative effects on reproductive health, such as Bacteroidetes, Tenericutes, Romboutsia, Ruminococcaceae_UCG_014, Weissella, and Eubacterium_coprostanoligenes_group, and added bacteria with negative effects on reproductive health, such as Jeotgalicoccus. To further explore the Sr and the relationship between the gut microbiota, we conducted a Spearman correlation analysis, and the results showed that the gut microbiota was closely correlated with Sr content in serum and testicular tissue, sex hormone levels, and testicular marker enzymes. Additionally, gut microbiota can also regulate each other and jointly maintain the homeostasis of the body's internal environment. However, we found no significant correlation between intestinal flora and sperm quality in this study, which may be related to the small sample size of our 16S rDNA sequencing. In conclusion, the Sr-50 group significantly increased T levels and sperm quality, and improved the levels of testicular marker enzymes and testosterone marker genes in the rats. Sr treatment altered the gut flora of the rats. However, further analysis of the effects of gut microbiota in mediating the effects of SrCl2 on male reproductive function is needed. This study may improve the current understanding of the interaction between Sr, reproductive health, and gut microbiota, providing evidence for the development of Sr-rich foods and the prevention of male fertility decline.
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Affiliation(s)
- Xulai Huang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Laboratory of Quality and Safety Risk Assessment for Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanan Gao
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Laboratory of Quality and Safety Risk Assessment for Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yangdong Zhang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Laboratory of Quality and Safety Risk Assessment for Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiaqi Wang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Laboratory of Quality and Safety Risk Assessment for Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Zheng
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Laboratory of Quality and Safety Risk Assessment for Dairy Products, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Milk and Milk Products Inspection Center, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Yao S, Zhao Y, Chen H, Sun R, Chen L, Huang J, Yu Z, Chen S. Exploring the Plasticity of Diet on Gut Microbiota and Its Correlation with Gut Health. Nutrients 2023; 15:3460. [PMID: 37571397 PMCID: PMC10420685 DOI: 10.3390/nu15153460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Dietary habits have been proven to help alter the composition of gut microbiota, and exploring the impact of nutritional patterns on gut microbiota changes can help protect gut health. However, few studies have focused on the dietary impact on the gut microbiota over an experimental timeframe. In this study, 16S rRNA gene sequencing was employed to investigate the gut microbiota of mice under different dietary patterns, including AIN-93G diet (Control), high protein diet (HPD), high fiber diet (HFD), and switch diet (Switch). The alpha diversity of the HPD group significantly decreased, but HFD can restore this decline. During HPD, some genera were significantly upregulated (e.g., Feacalibaculum) and downregulated (e.g., Parabacteroides). However, after receiving HFD, other genera were upregulated (e.g., Akkermansia) and downregulated (e.g., Lactobacillus). In addition, the interaction between pathogenic bacteria was more pronounced during HPD, while the main effect was probiotics during HFD. In conclusion, the plasticity exhibited by the gut microbiota was subject to dietary influences, wherein disparate dietary regimens hold pivotal significance in upholding the well-being of the host. Therefore, our findings provide new ideas and references for the relationship between diets and gut microbiota.
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Affiliation(s)
- Siqi Yao
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha 410008, China;
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Yiming Zhao
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha 410078, China; (H.C.); (J.H.)
| | - Ruizheng Sun
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Liyu Chen
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha 410078, China; (H.C.); (J.H.)
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China; (Y.Z.); (R.S.); (L.C.)
| | - Shuijiao Chen
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha 410008, China;
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital of Central South University, Changsha 410008, China
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26
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Yin Y, Liao Y, Li J, Pei Z, Wang L, Shi Y, Peng H, Tan Y, Li C, Bai H, Ma C, Gong Y, Wei T, Peng H. Lactobacillus plantarum GX17 benefits growth performance and improves functions of intestinal barrier/intestinal flora among yellow-feathered broilers. Front Immunol 2023; 14:1195382. [PMID: 37465686 PMCID: PMC10351386 DOI: 10.3389/fimmu.2023.1195382] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023] Open
Abstract
Lactobacillus plantarum has recently been found to be a natural source feed additive bacteria with great advantages in food safety and animal welfare. Discovering novel strains with commercial application potentiation could benefit the local poultry industry, and in particular support Chinese farmers. In this study, we tested a recently isolated novel strain of Lactobacillus plantarum GX17 as a feed additive on the growth performance and intestinal barrier functions of 1-day-old Chinese yellow-feather chicks. As good as other commercial probiotics, feeding with Lactobacillus plantarum GX17 showed significant improvements in humoral immune responses and enhanced the immune effect after vaccination for either the Newcastle disease vaccine or the avian influenza vaccine. This study also found that feeding with Lactobacillus plantarum GX17 improved the feed-to-weight ratio and caused a significant increase of the villus length to crypt depth ratio. Furthermore, Lactobacillus plantarum GX17 significantly up-regulated the mRNA expression of CLDN, MUC2, and TLR2, all of which are jejunum-associated barrier genes, indicating an improvement of the intestinal barrier functions by enhancing the tight junction between epithelia cells. These results are comparable to the effects of feeding the commercial complex probiotics that improve the expression levels of CLDN, ocludin, MUC2, TLR2, and TLR4. In terms of maintaining intestinal health, commercial complex probiotics increased the relative abundance of Parabacteroides and Romboutsia, while Lactobacillus plantarum GX17 increased the relative abundance of Pseudoflavonifractor. Our data suggest that Lactobacillus plantarum GX17 could enhance the intestinal absorption of nutrients and therefore improve the growth performance of Chinese yellow-feather chicks. In conclusion, compared with the commercial complex probiotics, Lactobacillus plantarum GX17 has more positive effects on the growth performance and intestinal barrier function of yellow-feather chickens, and can be used as a feed additive.
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Affiliation(s)
- Yangyan Yin
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
- Institute of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yuying Liao
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Jun Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Zhe Pei
- Virginia Tech, Department of Engineering, Blacksburg, New York, NY, United States
| | - Leping Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
- Institute of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yan Shi
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
- Institute of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hongyan Peng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
- Institute of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yizhou Tan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
- Institute of Animal Science and Technology, Guangxi University, Nanning, China
| | - Changting Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Huili Bai
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Chunxia Ma
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
| | - Yu Gong
- Guizhou Provincial Livestock and Poultry Genetic Resources Management Station, Guiyang, China
| | - Tianchao Wei
- Institute of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hao Peng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of China(Guangxi)-Association of Southeast Asian Nations (ASEAN) Cross-border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, China
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Sciarra F, Franceschini E, Campolo F, Venneri MA. The Diagnostic Potential of the Human Blood Microbiome: Are We Dreaming or Awake? Int J Mol Sci 2023; 24:10422. [PMID: 37445600 DOI: 10.3390/ijms241310422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Human blood has historically been considered a sterile environment. Recently, a thriving microbiome dominated by Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes phyla was detected in healthy blood. The localization of these microbes is restricted to some blood cell populations, particularly the peripheral blood mononuclear cells and erythrocytes. It was hypothesized that the blood microbiome originates from the skin-oral-gut axis. In addition, many studies have evaluated the potential of blood microbiome dysbiosis as a prognostic marker in cardiovascular diseases, cirrhosis, severe liver fibrosis, severe acute pancreatitis, type 2 diabetes, and chronic kidney diseases. The present review aims to summarize current findings and most recent evidence in the field.
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Affiliation(s)
- Francesca Sciarra
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Edoardo Franceschini
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Federica Campolo
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Mary Anna Venneri
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
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28
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Saha S, Xiong JQ, Patil SM, Ha GS, Hoh JK, Park HK, Chung W, Chang SW, Khan MA, Park HB, Jeon BH. Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131200. [PMID: 36958158 DOI: 10.1016/j.jhazmat.2023.131200] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/04/2023] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
The preeminence of sulfonamide drug resistance genes in food waste (FW) and the increased utilization of high-strength organic FW in anaerobic digestion (AD) to enhance methane production have raised severe public health concerns in wastewater treatment plants worldwide. In this regard, the dissemination patterns of different sulfonamide resistance genes (sul1 and sul2) and their impact on the digester core microbiota during AD of FW leachate (FWL) were evaluated. The presence of various sulfonamide antibiotics (SAs) in FWL digesters improved the final methane yield by 37 % during AD compared with FWL digesters without SAs. Microbial population shifts towards hydrolytic, acidogenic, and acetogenic bacteria in the phyla Actinobacteriota, Bacteroidota, Chloroflexi, Firmicutes, Proteobacteria, and Synergistota occurred due to SA induced substrate digestion and absorption through active transport; butanoate, propanoate, and pyruvate metabolism; glycolysis; gluconeogenesis; the citrate cycle; and pentose phosphate pathway. The initial dominance of Methanosaeta (89-96 %) declined to 47-53 % as AD progressed and shifted towards Methanosarcina (40 %) in digesters with the highest SA concentrations at the end of AD. Dissemination of sul1 depended on class 1 integron gene (intl1)-based horizontal gene transfer to pathogenic members of Chloroflexi, Firmicutes, and Patescibacteria, whereas sul2 was transmitted to Synergistota independent of intl1. Low susceptibility and ability to utilize SAs during methanogenesis shielded methanogenic archaea against selection pressure, thus preventing them from interacting with sul or intl1 genes, thereby minimizing the risk of antibiotic resistance development. The observed emergence of cationic antimicrobial peptide, vancomycin, and β-lactam resistance in the core microbiota during AD of FWL in the presence of SAs suggests that multidrug resistance caused by bacterial transformation could lead to an increase in the environmental resistome through wastewater sludge treatment.
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Affiliation(s)
- Shouvik Saha
- Natural Resources Research Institute, University of Minnesota Duluth, Duluth, MN 55812, USA; Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, the Republic of Korea
| | - Jiu-Qiang Xiong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong, China
| | - Swapnil M Patil
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, the Republic of Korea
| | - Geon-Soo Ha
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, the Republic of Korea
| | - Jeong-Kyu Hoh
- Department of Obstetrics and Gynecology, College of Medicine, Hanyang University, Seoul 04763, the Republic of Korea
| | - Hyun-Kyung Park
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul 04763, the Republic of Korea
| | - Woojin Chung
- Department of Environmental Energy Engineering, Kyonggi University, Suwon 16227, the Republic of Korea
| | - Soon Woong Chang
- Department of Environmental Energy Engineering, Kyonggi University, Suwon 16227, the Republic of Korea
| | - Moonis Ali Khan
- Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ho Bum Park
- Department of Energy Engineering, Hanyang University, Seoul 04763, the Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, the Republic of Korea.
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29
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Segota I, Watrous JD, Kantz ED, Nallamshetty S, Tiwari S, Cheng S, Jain M, Long T. Reconstructing the landscape of gut microbial species across 29,000 diverse individuals. Nucleic Acids Res 2023; 51:4178-4190. [PMID: 37070603 PMCID: PMC10201371 DOI: 10.1093/nar/gkad249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
The human gut microbiome has been linked to health and disease. Investigation of the human microbiome has largely employed 16S amplicon sequencing, with limited ability to distinguish microbes at the species level. Herein, we describe the development of Reference-based Exact Mapping (RExMap) of microbial amplicon variants that enables mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures ∼75% of microbial species identified by whole-genome shotgun sequencing, despite hundreds-fold less sequencing depth. RExMap re-analysis of existing 16S data from 29,349 individuals across 16 regions from around the world reveals a detailed landscape of gut microbial species across populations and geography. Moreover, RExMap identifies a core set of fifteen gut microbes shared by humans. Core microbes are established soon after birth and closely associate with BMI across multiple independent studies. RExMap and the human microbiome dataset are presented as resources with which to explore the role of the human microbiome.
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Affiliation(s)
- Igor Segota
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeramie D Watrous
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Edward D Kantz
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Saumya Tiwari
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Cheng
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mohit Jain
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tao Long
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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30
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Ouyang J, Li Y, Wu Y, Tang H, Zheng S, Xiong Y, Wang L, Wang C, Luo K, Gao Y, Yan X, Chen H. Microbial diversity and community composition of fecal microbiota in dual-purpose and egg type ducks. Front Microbiol 2023; 14:1092100. [PMID: 37065156 PMCID: PMC10102352 DOI: 10.3389/fmicb.2023.1092100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
IntroductionDucks are important agricultural animals, which can be divided into egg and dual-purpose type ducks according to economic use. The gut microbiota of ducks plays an important role in their metabolism, immune regulation, and health maintenance.MethodsHere, we use 16S rDNA V4 hypervariable amplicon sequencing to investigate the compositions and community structures of fecal microbiota between egg (five breeds, 96 individuals) and dual-purpose type ducks (four breeds, 73 individuals) that were reared under the same conditions.ResultsThe alpha diversity of fecal microflora in egg type ducks was significantly higher than that in dual-type ducks. In contrast, there is no significant difference in the fecal microbial community richness between the two groups. MetaStat analysis showed that the abundance of Peptostreptococcaceae, Streptococcaceae, Lactobacillus, Romboutsia, and Campylobacter were significantly different between the two groups. The biomarkers associated with the egg and dual-purpose type ducks were identified using LEfSe analysis and IndVal index. Function prediction of the gut microbiota indicated significant differences between the two groups. The functions of environmental information processing, carbohydrate metabolism, lipid metabolism, xenobiotic biodegradation and metabolism, and metabolism of terpenoids and polyketides were more abundant in egg type ducks. Conversely, the genetic information processing, nucleotide metabolism, biosynthesis of amino acids and secondary metabolites, glycan biosynthesis and metabolism, fatty acid elongation, and insulin resistance were significantly enriched in dual-purpose type ducks.DiscussionThis study explored the structure and diversity of the gut microbiota of ducks from different economic-use groups, and provides a reference for improving duck performance by using related probiotics in production.
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31
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Najafi F, Fernández-Rodríguez D, Parvizi J. Sterile Setup Table in the Operating Room Is Not So Sterile. J Arthroplasty 2023; 38:562-566.e3. [PMID: 36154865 DOI: 10.1016/j.arth.2022.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND One of the important factors for surgical site infection prevention is the implementation of an ultraclean operating room. This study was designed to evaluate back-table sterility during total joint arthroplasty. METHODS This prospective study includes 52 patients undergoing primary total joint arthroplasty between November 2021 and January 2022. A total of 4 swabs (2 air swabs and 2 table swabs) were obtained for each case, at the conclusion of surgery and prior to the takedown of drapes. One swab from each set was sent for culture, and the other was sent for next-generation sequencing (NGS) analysis. RESULTS Among 104 back-table swabs, a total of 13 (12.5%) organisms were isolated. Of these, 7 organisms were isolated by culture and 6 by NGS. No microorganisms were isolated by both culture and NGS from back-table swabs. Among 104 air swabs, a total of 11 (10.6%) organisms were isolated. Of these, 6 microorganisms were isolated by culture and 5 by NGS. In 4 of the 104 swabs, both culture- and NGS-isolated organisms were from air swabs. Of the 104 (12.5%) back-table and air swabs, 13 were culture positive. While more than 1 pathogen was identified in 2 air swabs, all back-table swabs were monomicrobial by culture. Pathogens were identified from 11 of 104 (10.6%) swabs by NGS, while more than 1 pathogen was identified in 4 swabs (2 air and 2 back table). CONCLUSION The findings of this study raise an important issue that the surgical field including the sterile table setup for instruments is not "sterile" and can harbor pathogens.
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Affiliation(s)
- Farideh Najafi
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Javad Parvizi
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, Pennsylvania
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Response of Intestinal Microbiota of Tiger Puffer ( Takifugu rubripes) to the Fish Oil Finishing Strategy. Microorganisms 2023; 11:microorganisms11010208. [PMID: 36677500 PMCID: PMC9862291 DOI: 10.3390/microorganisms11010208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The fish oil finishing (FOF) strategy, that is, re-feeding fish with fish oil (FO)-based diet after a certain period of feeding with alternative lipid source-based diets. On tiger puffer, the present study investigated the response of intestinal microbiota to FOF. Fish were fed four diets based on FO, soybean oil, palm oil and beef tallow as lipid sources, respectively, firstly for 50 days (growing-out period), and then fed the FO-based diet for 30 more days (FOF period). The results showed that dietary terrestrially sourced oils impaired the intestinal function in the growing-out period. However, the activities of amylase, trypsin and anti-oxidative enzymes (SOD, CAT, T-AOC), as well as gene expression of inflammatory cytokines (IL-1β, TNF-α, TGF-β) and tight junction protein (Claudin4, Claudin7, Claudin18, JAM, ZO-1) in the intestine were significantly recovered by FOF. The 16S rDNA sequencing analysis showed that FOF improved the similarity of bacterial community among the groups. The MetaStat analysis confirmed that FOF regulated the abundance of butyric acid-producing bacteria (Lachnospiraceae, Eubacterium, Butyricicoccus, Clostridium and Roseburia) and bacteria related to digestion and absorption (Sphingomonas, Romboutsia and Brevibacillus). In conclusion, FOF can recover the intestine function. The intestinal microbiota probably participated in and played a key role in the recovery process.
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33
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Morshed SM, Chen YY, Lin CH, Chen YP, Lee TH. Freshwater transfer affected intestinal microbiota with correlation to cytokine gene expression in Asian sea bass. Front Microbiol 2023; 14:1097954. [PMID: 37089546 PMCID: PMC10117908 DOI: 10.3389/fmicb.2023.1097954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
As a catadromous fish, Asian sea bass (Lates calcarifer) juveniles migrate from seawater (SW) to freshwater (FW) for growth and development. During migration, they undergo physiological changes to acclimate to environmental salinity. Thus, it is crucial to understand how SW-to-FW migration affects the gut microbiota of catadromous fish. To the best of our knowledge, no study has revealed the effects of transfer to hypotonic environments on a catadromous fish microbiota. In this study, we aimed to determine the effects of FW transfer on the microbiota and cytokine gene expression in the intestines of juvenile catadromous Asian sea bass. The relationship between the water and the gut microbiota of this euryhaline species was also examined. We found that FW transfer affected both mucosa- and digesta-associated microbiota of Asian sea bass. Plesiomonas and Cetobacterium were dominant in both the mucosa- and digesta-associated microbiota of FW-acclimated sea bass. The pathogenic genera Vibrio, Staphylococcus, and Acinetobacter were dominant in the SW group. Although dominant fish microbes were present in the water, fish had their own unique microbes. Vitamin B6 metabolism was highly expressed in the FW fish microbiota, whereas arginine, proline, and lipid metabolism were highly expressed in the SW fish microbiota. Additionally, the correlation between cytokine gene expression and microbiota was found to be affected by FW transfer. Taken together, our results demonstrated that FW transfer altered the composition and functions of mucosa- and digesta-associated microbiota of catadromous Asian sea bass intestines, which correlated with cytokine gene expression.
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Affiliation(s)
- Syed Monzur Morshed
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Yi Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Hao Lin
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Yen-Po Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Yen-Po Chen,
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Tsung-Han Lee,
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Shang Z, Wang Y, An M, Chen X, Kulyar MFEA, Tan Z, Liu S, Li K. The successional trajectory of bacterial and fungal communities in soil are fabricated by yaks’ excrement contamination in plateau, China. Front Microbiol 2022; 13:1016852. [DOI: 10.3389/fmicb.2022.1016852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
The soil microbiome is crucial in determining contemporary realistic conditions for future terrestrial ecological and evolutionary development. However, the precise mechanism between the fecal deposition in livestock grazing and changes in the soil microbiome remains unknown. This is the first in-depth study of bacterial and fungal taxonomic changes of excrement contaminated soils in the plateau (>3,500 m). This suggests the functional shifts towards a harmful-dominated soil microbiome. According to our findings, excrement contamination significantly reduced the soil bacterial and fungal diversity and richness. Furthermore, a continuous decrease in the relative abundance of microorganisms was associated with nutrient cycling, soil pollution purification, and root-soil stability with the increasing degree of excrement contamination. In comparison, soil pathogens were found to have the opposite trend in the scenario, further deteriorating normal soil function and system resilience. Such colonization and succession of the microbiome might provide an important potential theoretical instruction for microbiome-based soil health protection measures in the plateau of China.
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Comparative study between the effects of aged and fresh Chinese baijiu on gut microbiota and host metabolism. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Dekkers KF, Sayols-Baixeras S, Baldanzi G, Nowak C, Hammar U, Nguyen D, Varotsis G, Brunkwall L, Nielsen N, Eklund AC, Bak Holm J, Nielsen HB, Ottosson F, Lin YT, Ahmad S, Lind L, Sundström J, Engström G, Smith JG, Ärnlöv J, Orho-Melander M, Fall T. An online atlas of human plasma metabolite signatures of gut microbiome composition. Nat Commun 2022; 13:5370. [PMID: 36151114 PMCID: PMC9508139 DOI: 10.1038/s41467-022-33050-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/26/2022] [Indexed: 11/27/2022] Open
Abstract
Human gut microbiota produce a variety of molecules, some of which enter the bloodstream and impact health. Conversely, dietary or pharmacological compounds may affect the microbiota before entering the circulation. Characterization of these interactions is an important step towards understanding the effects of the gut microbiota on health. In this cross-sectional study, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for a detailed characterization of the gut microbiota and plasma metabolome, respectively, of 8583 participants invited at age 50 to 64 from the population-based Swedish CArdioPulmonary bioImage Study. Here, we find that the gut microbiota explain up to 58% of the variance of individual plasma metabolites and we present 997 associations between alpha diversity and plasma metabolites and 546,819 associations between specific gut metagenomic species and plasma metabolites in an online atlas (https://gutsyatlas.serve.scilifelab.se/). We exemplify the potential of this resource by presenting novel associations between dietary factors and oral medication with the gut microbiome, and microbial species strongly associated with the uremic toxin p-cresol sulfate. This resource can be used as the basis for targeted studies of perturbation of specific metabolites and for identification of candidate plasma biomarkers of gut microbiota composition. Here, Dekkers et al. characterize associations of 1528 gut metagenomic species with the plasma metabolome in 8583 participants of the SCAPIS Study, and find that gut microbiota explain up to 58% of the variance of individual plasma metabolites.
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Affiliation(s)
- Koen F Dekkers
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sergi Sayols-Baixeras
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,CIBER Cardiovascular diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Gabriel Baldanzi
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christoph Nowak
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Science and Society, Karolinska Institute, Huddinge, Sweden
| | - Ulf Hammar
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Diem Nguyen
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Georgios Varotsis
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | | | | | - Filip Ottosson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Yi-Ting Lin
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Shafqat Ahmad
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Johan Sundström
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden.,The George Institute for Global Health, University of New South Wales, Sydney, Australia
| | - Gunnar Engström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - J Gustav Smith
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden.,Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
| | - Johan Ärnlöv
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Science and Society, Karolinska Institute, Huddinge, Sweden.,School of Health and Social Studies, Dalarna University, Falun, Sweden
| | | | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Tagg AS, Sperlea T, Labrenz M, Harrison JP, Ojeda JJ, Sapp M. Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth. Microorganisms 2022; 10:microorganisms10091775. [PMID: 36144377 PMCID: PMC9506493 DOI: 10.3390/microorganisms10091775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces.
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Affiliation(s)
- Alexander S. Tagg
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, UK
- Correspondence:
| | - Theodor Sperlea
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
| | - Matthias Labrenz
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
| | - Jesse P. Harrison
- CSC—IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Jesús J. Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, UK
| | - Melanie Sapp
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany
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Wang X, Chen Z, Qiao S, Zhu Q, Zuo Z, Guo B. Analysis of Alterations of the Gut Microbiota in Moderate to Severe Psoriasis Patients Using 16S rRNA Gene Sequencing. Indian J Dermatol 2022; 67:495-503. [PMID: 36865841 PMCID: PMC9971763 DOI: 10.4103/ijd.ijd_297_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Background Psoriasis is an inflammatory skin disease. The correlation between intestinal microbiota and immune-mediated diseases makes scientists pay attention to the pathogenic role of microbiota. Objective The aim of this study was to identify the gut microbial composition of patients with psoriasis. Methods 16S rRNA gene sequencing method was used to analyse the faecal samples which was collected from 28 moderately severe psoriasis patients and 21 healthy controls and was followed by the analysing of informatics methods. Results No visible differences can be observed in the diversity of gut microbiota between the psoriasis and the healthy patients, but the composition of the gut microbiota illustrate significant distinction between these two groups. At the phylum level, compared to the healthy control group, the psoriasis group shows higher relative abundance of Bacteroidetes and lower relative abundance of Proteobacteria (P < 0.05). At the genus level, unidentified_Enterobacteriaceae, unidentified_Lachnospiraceae, Romboutsia, Subdoligranulum, unidentified_Erysipelotrichaceae, Dorea were relatively less abundant in psoriasis patients, whereas Lactobacillus, Dialister were relatively more abundant in psoriasis group (all P < 0.05). LefSe analysis (linear discriminant analysis effect size) indicated that Negativicutes and Bacteroidia were potential biomarkers for psoriasis. Conclusion This study identified the intestinal microecological environment of patients with psoriasis and healthy people, proving that psoriasis patients have a remarkably disturbed microbiome, and found several biomarkers of intestinal microorganisms in patients with psoriasis.
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Affiliation(s)
- Xiaomeng Wang
- From the Department of Dermatology, The Third Affiliated Hospital of Anhui Medical University, The First People's Hospital of Hefei, Hefei, Anhui, China
| | - Zheng Chen
- From the Department of Dermatology, The Third Affiliated Hospital of Anhui Medical University, The First People's Hospital of Hefei, Hefei, Anhui, China
| | - Song Qiao
- From the Department of Dermatology, The Third Affiliated Hospital of Anhui Medical University, The First People's Hospital of Hefei, Hefei, Anhui, China
| | - Qiming Zhu
- From the Department of Dermatology, The Third Affiliated Hospital of Anhui Medical University, The First People's Hospital of Hefei, Hefei, Anhui, China
| | - Zongbao Zuo
- Department of Plastic Surgery, The Second People's Hospital of Anhui Province, Hefei, Anhui, China
| | - Birong Guo
- From the Department of Dermatology, The Third Affiliated Hospital of Anhui Medical University, The First People's Hospital of Hefei, Hefei, Anhui, China
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Chehade SB, Green GBH, Graham CD, Chakraborti A, Vashai B, Moon A, Williams MB, Vickers B, Berryhill T, Van Der Pol W, Wilson L, Powell ML, Smith DL, Barnes S, Morrow C, Mukhtar MS, Kennedy GD, Bibb JA, Watts SA. A modified standard American diet induces physiological parameters associated with metabolic syndrome in C57BL/6J mice. Front Nutr 2022; 9:929446. [PMID: 36105576 PMCID: PMC9464921 DOI: 10.3389/fnut.2022.929446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/26/2022] [Indexed: 01/09/2023] Open
Abstract
Investigations into the causative role that western dietary patterns have on obesity and disease pathogenesis have speculated that quality and quantity of dietary fats and/or carbohydrates have a predictive role in the development of these disorders. Standard reference diets such as the AIN-93 rodent diet have historically been used to promote animal health and reduce variation of results across experiments, rather than model modern human dietary habits or nutrition-related pathologies. In rodents high-fat diets (HFDs) became a classic tool to investigate diet-induced obesity (DIO). These murine diets often relied on a single fat source with the most DIO consistent HFDs containing levels of fat up to 45-60% (kcal), higher than the reported human intake of 33-35% (kcal). More recently, researchers are formulating experimental animal (pre-clinical) diets that reflect mean human macro- and micronutrient consumption levels described by the National Health and Nutrition Examination Survey (NHANES). These diets attempt to integrate relevant ingredient sources and levels of nutrients; however, they most often fail to include high-fructose corn syrup (HFCS) as a source of dietary carbohydrate. We have formulated a modified Standard American Diet (mSAD) that incorporates relevant levels and sources of nutrient classes, including dietary HFCS, to assess the basal physiologies associated with mSAD consumption. Mice proffered the mSAD for 15 weeks displayed a phenotype consistent with metabolic syndrome, exhibiting increased adiposity, fasting hyperglycemia with impaired glucose and insulin tolerance. Metabolic alterations were evidenced at the tissue level as crown-like structures (CLS) in adipose tissue and fatty acid deposition in the liver, and targeted 16S rRNA metagenomics revealed microbial compositional shifts between dietary groups. This study suggests diet quality significantly affects metabolic homeostasis, emphasizing the importance of developing relevant pre-clinical diets to investigate chronic diseases highly impacted by western dietary consumption patterns.
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Affiliation(s)
- Sophie B. Chehade
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - George B. H. Green
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Christopher D. Graham
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ayanabha Chakraborti
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bijal Vashai
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Amber Moon
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Michael B. Williams
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Benjamin Vickers
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Taylor Berryhill
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - William Van Der Pol
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Landon Wilson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mickie L. Powell
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Daniel L. Smith
- Department of Nutrition Sciences, Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Stephen Barnes
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Casey Morrow
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gregory D. Kennedy
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - James A. Bibb
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Stephen A. Watts
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
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Evaluation of Prebiotics through an In Vitro Gastrointestinal Digestion and Fecal Fermentation Experiment: Further Idea on the Implementation of Machine Learning Technique. Foods 2022; 11:foods11162490. [PMID: 36010490 PMCID: PMC9407061 DOI: 10.3390/foods11162490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Prebiotics are non-digestible food ingredients that promote the growth of beneficial gut microorganisms and foster their activities. The performance of prebiotics has often been tested in mouse models in which the gut ecology differs from that of humans. In this study, we instead performed an in vitro gastrointestinal digestion and fecal fermentation experiment to evaluate the efficiency of eight different prebiotics. Feces obtained from 11 different individuals were used to ferment digested prebiotics. The total DNA from each sample was extracted and sequenced through Illumina MiSeq for microbial community analysis. The amount of short-chain fatty acids was assessed through gas chromatography. We found links between community shifts and the increased amount of short-chain fatty acids after prebiotics treatment. The results from differential abundance analysis showed increases in beneficial gut microorganisms, such as Bifidobacterium, Faeclibacterium, and Agathobacter, after prebiotics treatment. We were also able to construct well-performing machine-learning models that could predict the amount of short-chain fatty acids based on the gut microbial community structure. Finally, we provide an idea for further implementation of machine-learning techniques to find customized prebiotics.
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Zhao C, Liu L, Gao L, Bai L. A comprehensive comparison of fecal microbiota in three ecological bird groups of raptors, waders, and waterfowl. Front Microbiol 2022; 13:919111. [PMID: 36003944 PMCID: PMC9393522 DOI: 10.3389/fmicb.2022.919111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota plays a vital role in maintaining the health and immunity of wild birds. However, less is known about the comparison of fecal microbiota between different ecological groups of wild birds, particularly in the Yellow River National Wetland in Baotou, China, an important transit point for birds migrating all over the East Asia-Australian and Central Asian flyways. In this study, we characterized the fecal microbiota and potential microbial function in nine bird species of raptors, waders, and waterfowl using 16S rRNA gene amplicon sequencing to reveal the microbiota differences and interaction patterns. The results indicated that there was no significant difference in α-diversity, but a significant difference in β-diversity between the three groups of birds. The fecal bacterial microbiota was dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes in all groups of birds. Furthermore, we identified five bacterial genera that were significantly higher in raptors, five genera that were significantly higher in waders, and two genera that were more abundant in waterfowl. The bacterial co-occurrence network results revealed 15 and 26 key genera in raptors and waterfowls, respectively. The microbial network in waterfowl exhibited a stronger correlation pattern than that in raptors. PICRUSt2 predictions indicated that fecal bacterial function was significantly enriched in the antibiotic biosynthesis pathway in all three groups. Metabolic pathways related to cell motility (bacterial chemotaxis and flagellar assembly) were significantly more abundant in raptors than in waders, whereas waders were enriched in lipid metabolism (synthesis and degradation of ketone bodies and fatty acid biosynthesis). The fecal microbiota in waterfowl harbored more abundant vitamin B6 metabolism, RNA polymerase, and tyrosine and tryptophan biosynthesis. This comparative study revealed the microbial community structure, microbial co-occurrence patterns, and potential functions, providing a better understanding of the ecology and conservation of wild birds. Future studies may focus on unraveling metagenomic functions and dynamics along with the migration routine or different seasons by metagenomics or metatranscriptomics.
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Guan Y, Jia J, Fan X, Li K, Wang Z. Anthropogenic impacts on antibiotic resistance genes and their hosts from pristine to urban river using metagenomic and binning approaches. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 249:106221. [PMID: 35709638 DOI: 10.1016/j.aquatox.2022.106221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Driven by anthropogenic pressure, Antibiotic resistance genes (ARGs) could transfer from the environmental resistome into human commensals or even pathogens. The transport of ARGs through aquatic ecosystems is crucial and has attracted attention. Here, we employed metagenomic and binning to compare ARGs profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their hosts between pristine and anthropogenic influenced rivers and explore the ecological mechanisms underlying the dissemination of ARGs induced by anthropogenic activities. The significantly increased relative abundance of macrolide-lincosamide-streptogramins, vancomycin, β-lactam and sulfonamide resistance genes along the environmental gradient from pristine to polluted sediments implied that anthropogenic impact aided the emergence and dissemination of certain ARGs. At the lower reach of the Ba River, the higher ratios for contigs carrying more than one ARG suggested that anthropogenic pollution favored the co-occurrence of multiple ARGs. Anthropogenic pressures also increased the relative abundance of advantaged hosts, including Chloroflexi, Firmicutes and Euryarchaeota. At the lower reach of Ba River, Romboutsia timonensis carrying multiple ARGs and ICEs were successfully recovered, posing a serious threat to human health by affecting the metabolism of gut microbiomes. And Methanothrix soehngenii affiliated to archaea carrying multiple ARGs, MRGs and ICEs were also recovered from the lower Ba River. The partial least squares path modeling revealed that MGEs were the most predominant factors inducing the ARG profiles, and the antibiotic resistance could be enriched by co-transfer with MRGs. Furthermore, environmental factors could impact the ARG profiles indirectly by first influencing the ARGs' hosts.
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Affiliation(s)
- Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiqi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs. Commun Biol 2022; 5:770. [PMID: 35908086 PMCID: PMC9338936 DOI: 10.1038/s42003-022-03679-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/07/2022] [Indexed: 12/25/2022] Open
Abstract
Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0–30%). Fish gut microbiomes were significantly more variable at degraded reefs, a pattern driven by changes in the relative abundance of the most common taxa potentially associated with stress. We also demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which may suggest a less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions may be vulnerable to severe coral degradation. The gut microbiome composition of the coral-feeding butterflyfish across Caribbean reefs is more variable at degraded reefs. These microbiomes have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria.
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Haryono MAS, Law YY, Arumugam K, Liew LCW, Nguyen TQN, Drautz-Moses DI, Schuster SC, Wuertz S, Williams RBH. Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling. Front Microbiol 2022; 13:869135. [PMID: 35756038 PMCID: PMC9230771 DOI: 10.3389/fmicb.2022.869135] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/05/2022] [Indexed: 01/23/2023] Open
Abstract
The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.
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Affiliation(s)
- Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Ying Yu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Larry C-W Liew
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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Liu J, Ding L, Zhai X, Wang D, Xiao C, Hui X, Sun T, Yu M, Zhang Q, Li M, Xiao X. Maternal Dietary Betaine Prevents High-Fat Diet-Induced Metabolic Disorders and Gut Microbiota Alterations in Mouse Dams and Offspring From Young to Adult. Front Microbiol 2022; 13:809642. [PMID: 35479641 PMCID: PMC9037091 DOI: 10.3389/fmicb.2022.809642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/24/2022] [Indexed: 12/20/2022] Open
Abstract
Early life is a critical window for preventing the intergenerational transmission of metabolic diseases. Betaine has been proven to play a role in improving glucose and lipid metabolism disorders in animal models. However, whether maternal betaine supplementation plays a role in regulating gut microbiota in both dams and offspring remains unclear. In this study, C57BL/6 female mice were fed with control diet (Ctr), high-fat diet (HF), and high-fat with betaine supplementation (0.3% betaine in the diet, HFB) from 3 weeks prior to mating and lasted throughout pregnancy and lactation. After weaning, the offspring got free access to normal chow diet until 20 weeks of age. We found that maternal dietary betaine supplementation significantly improved glucose and insulin resistance, as well as reduced free fatty acid (FFA) concentration in dams and offspring from young to adult. When compared to the HF group, Intestinimonas and Acetatifactor were reduced by betaine supplementation in dams; Desulfovibrio was reduced in 4-week-old offspring of the HFB group; and Lachnoclostridium was enriched in 20-week-old offspring of the HFB group. Moreover, the persistent elevated genus Romboutsia in both dams and offspring in the HFB group was reported for the first time. Overall, maternal betaine could dramatically alleviate the detrimental effects of maternal overnutrition on metabolism in both dams and offspring. The persistent alterations in gut microbiota might play critical roles in uncovering the intergenerational metabolic benefits of maternal betaine, which highlights evidence for combating generational metabolic diseases.
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Affiliation(s)
- Jieying Liu
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Lu Ding
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiao Zhai
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Dongmei Wang
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Cheng Xiao
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangyi Hui
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianshu Sun
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Miao Yu
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qian Zhang
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Li
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinhua Xiao
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Wang L, Zhang Y, Guo X, Gong L, Dong B. Beneficial Alteration in Growth Performance, Immune Status, and Intestinal Microbiota by Supplementation of Activated Charcoal-Herb Extractum Complex in Broilers. Front Microbiol 2022; 13:856634. [PMID: 35495714 PMCID: PMC9051449 DOI: 10.3389/fmicb.2022.856634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/21/2022] [Indexed: 12/11/2022] Open
Abstract
This study aimed to examine the effects of activated charcoal-herb extractum complex (CHC) on the growth performance of broilers, inflammatory status, microbiota, and their relationships. A total of 864 1-day-old Arbor Acres male broilers (41.83 ± 0.64 g) were distributed to eight dietary treatments with six replicates (18 birds per replicate), which were a corn-soybean meal-based diet (NCON); basal diets supplemented with 250, 500, 750, or 1,000 mg/kg CHC, and three positive controls; basal diets supplemented with 200 mg/kg antibacterial peptide (AMP), 200 mg/kg calsporin (Probio) or 500 mg/kg montmorillonite. The study period was 42 days including the starter (day 0-21) and grower (day 22-42) phases. Compared with the NCON group, CHC supplementation (optimal dose of 500 mg/kg) increased (p < 0.05) growth performance and tended to increase feed conversion rate in broilers. CHC (optimal dose of 500 mg/kg) decreased the level of the interleukin-1β (IL-1β) and interferon-γ (IFN-γ) in serum and improved the levels of immunoglobulins A (IgA) and immunoglobulins A (IgM) in serum, and secretory immunoglobulin A (SIgA) in the mucosa of duodenum and jejunum (p < 0.05). In the ileum, CHC supplementation decreased community abundance represented by lower Sobs, Chao 1, Ace, and Shannon compared with NCON (p < 0.05). At the phylum level, CHC supplementation increased the abundance of Firmicutes, while decreasing the abundance of Bacteroidetes in ileum and cecum (p < 0.05). At the genus level, compared with the NCON group, CHC markedly reduced (p < 0.05) the abundances of pathogenic bacteria Alistipes in the ileum, which were negatively associated with the levels of SIgA and IL-1β in ileum mucosa. In conclusion, CHC had beneficial effects on growth performance, immune status, and intestinal microbiota composition. CHC had dual functions of absorption like clays and antibacterial like antibacterial peptides.
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Affiliation(s)
| | | | | | | | - Bing Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Xiang L, Ying Z, Xue M, Xiaoxian P, Xiaorong L, Chunyang L, Yu W, Mingcheng L, Binxian L. A novel Lactobacillus bulgaricus isolate can maintain the intestinal health, improve the growth performance and reduce the colonization of E. coli O157:H7 in broilers. Br Poult Sci 2022; 63:621-632. [PMID: 35383527 DOI: 10.1080/00071668.2022.2062220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. This study aimed at the effects of a novel Lactobacillus bulgaricus (L. bulgaricus) strain and Enterohemorrhagic Escherichia coli (E. coli) O157: H7 on intestinal flora and growth performance of broilers, and the protective effect of L. bulgaricus on broilers in challenged experiment by E. coli O157: H7.2. In vitro bacteriostatic test showed that the cell-free supernatant (CFS) of L. bulgaricus isolate had obvious inhibitory effect on E. coli O157: H7.3. Eighty 1-day-old male broilers were randomly assigned into 4 treatment groups with 4 replicate per treatment. All group received basic diet in addition to the specific treatments: NC group, gavage with normal saline; In LBP group, gavage with L. bulgaricus isolate (1×109 CFU/mL) during the whole process, and challenged with E. coli O157: H7 (3×109 CFU/mL); EC group, gavage with E. coli O157: H7 (3×109 CFU/mL); LB Group, gavage with L. bulgaricus isolate. At the age of 21 days, broilers were weighed and feed conversion ratio (FCR) was calculated. Cecum and cecal contents, ileum and feces samples were taken after slaughter.4. The challenge of E. coli O157: H7 resulted in an increase in TLR-4, NF-κB and IL-8 mRNA in cecal tissue, a decrease in Villus: crypt ratio in ileum, a decrease in overall diversity of intestinal microflora and a poor FCR.5. The L. bulgaricus isolate decreased the mRNA expression of TLR-4, NF-κB and IL-8 induced by E. coli O157: H7, reduced the content of E. coli O157: H7 in the cecum of broilers, increased the Villus: crypt ratio, increased the abundance of beneficial bacteria and overall diversity of intestinal microflora, made good FCR.6. The L. bulgaricus isolate can maintain the intestinal health, improve the growth performance of broilers and reduce the colonization of E. coli O157:H7 in the cecum.
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Affiliation(s)
- Li Xiang
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Zhang Ying
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Meng Xue
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Pei Xiaoxian
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Liu Xiaorong
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Lan Chunyang
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Wang Yu
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Li Mingcheng
- School of Laboratory Medicine, Beihua University, Jilin, Jilin 132013, China
| | - Li Binxian
- Dept. of Clinical Microbiology, Associated Hospital, Beihua University, Jilin, Jilin 132013, China
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48
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Abstract
Prior study has demonstrated that gut microbiota at the genus level is significantly altered in patients with growth hormone (GH)-secreting pituitary adenoma (GHPA). Yet, no studies exist describing the state of gut microbiota at species level in GHPA. We performed a study using 16S rRNA amplicon sequencing in a cohort of patients with GH-secreting pituitary adenoma (GHPA, n = 28) and healthy controls (n = 67). Among them, 9 patients and 10 healthy controls were randomly chosen and enrolled in metagenomics shotgun sequencing, generating 280,426,512 reads after aligning to NCBI GenBank DataBase to acquire taxa information at the species level. Weighted UniFrac analysis revealed that microbial diversity was notably decreased in patients with GHPA, consistent with a previous study. With 16S rRNA sequencing, after correction for false-discovery rate (FDR), rank-sum test at the genus level revealed that the relative abundance of Oscillibacter and Enterobacter was remarkably increased in patients and Blautia and Romboutsia genera predominated in the controls, augmented by additional LEfSe (linear discriminant analysis effect size) analysis. As for further comparison at the species level with metagenomics sequencing, rank-sum test together with LEfSe analysis confirmed the enrichment of Alistipes shahii and Odoribacter splanchnicus in the patient group. Notably, LEfSe analysis with metagenomics also demonstrated that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND, derived from Enterobacter, were both significantly enriched in patients. Functional analysis showed that amino acid metabolism pathway was remarkably enriched in GHPA, while carbohydrate metabolism pathway was notably enriched in controls. Further, significant positive correlations were observed between Enterobacter and baseline insulin-like growth factor 1 (IGF-1), indicating that Enterobacter may be strongly associated with GH/IGF-1 axis in GHPA. Our data extend our insight into the GHPA microbiome, which may shed further light on GHPA pathogenesis and facilitate the exploration of novel therapeutic targets based on microbiota manipulation. IMPORTANCE Dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extraintestinal diseases. Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of GH and IGF-1, causing increased morbidity and mortality. Researches have reported that the GH/IGF-1 axis exerts its own influence on the intestinal microflora. Here, the results showed that compared with healthy controls, GHPA patients not only decreased the alpha diversity of the intestinal flora but also significantly changed their beta diversity. Further, metagenomics shotgun sequencing in the present study exhibited that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND were enriched in patients. Also, we were pleasantly surprised to find that the Enterobacter genus was strongly positively correlated with baseline IGF-1 levels. Collectively, our work provides the first glimpse of the dysbiosis of the gut microbiota at species level, providing a better understanding of the pathophysiological process of GHPA.
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49
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Zhou GW, Zheng F, Fan XT, Li MJ, Sun QY, Zhu YG, Yang XR. Host age increased conjugal plasmid transfer in gut microbiota of the soil invertebrate Caenorhabditis elegans. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127525. [PMID: 34879519 DOI: 10.1016/j.jhazmat.2021.127525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/03/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Plasmid conjugation contributes greatly to the spread of antibiotic resistance genes (ARGs) in soils. However, the spread potential in the gut of soil fauna remains poorly studied, and little was known about the impact of host age on ARGs dissemination in the gut microbiota of soil animals. Here, the typical nematode-Caenorhabditis elegans was employed as the model soil animal, aiming to investigate transfer of broad-host-range IncP-1ɛ from Escherichia coli MG1655 to gut microbiota within 6 days under varied temperature gradients (15, 20 and 25 °C) using qPCR combined with plate screening. Results showed that conjugation rates increased with incubation time and rising temperature in the gut of C. elegans, sharing a similar trend with abundances of plasmid conjugation relevant genes such as trbBp (mating pair formation) and trfAp (plasmid replication). Incubation time and temperature significantly shaped the gut microbial community of C. elegans. Core microbiota in the gut of C. elegans, including Enterobacteriaceae, Lactobacillaceae and Leuconostocaceae, constituted a large part of transconjugal pool for plasmid IncP-1ɛ. Our results highlight an important sink of gut microbiota for ARGs dissemination and upregulation of ARGs transfer in the gut microbiota with host age, further potentially stimulating evolution of ARGs in terrestrial environments.
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Affiliation(s)
- Guo-Wei Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Fei Zheng
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; School of Life Sciences, Hebei University, Baoding 071002, China
| | - Xiao-Ting Fan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming-Jun Li
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Qing-Ye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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50
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Thuy-Boun PS, Wang AY, Crissien-Martinez A, Xu JH, Chatterjee S, Stupp GS, Su AI, Coyle WJ, Wolan DW. Quantitative metaproteomics and activity-based protein profiling of patient fecal microbiome identifies host and microbial serine-type endopeptidase activity associated with ulcerative colitis. Mol Cell Proteomics 2022; 21:100197. [PMID: 35033677 PMCID: PMC8941213 DOI: 10.1016/j.mcpro.2022.100197] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.
Identified 176 significantly altered protein groups between healthy and UC patients. Serine-type endopeptidase activity is overrepresented in UC patients. Fluorophosphonate ABPP shows that endopeptidases are active in fecal samples. ABPP enrichment helps identify additional putative serine hydrolases in samples. De novo sequencing used to estimate number of MS2 spectra unidentified by ComPIL.
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Affiliation(s)
- Peter S Thuy-Boun
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Ana Y Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Janice H Xu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Sandip Chatterjee
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Gregory S Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Walter J Coyle
- Scripps Clinic Gastroenterology Division, La Jolla, CA 92037
| | - Dennis W Wolan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.
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