Understanding the dynamic relationship between mucus-associated microbiota and host health is critical. However, studies predominantly using stool samples may not accurately represent these bacterial communities. Here, we investigated the mucus-associated microbiota in the gastrointestinal tract of mice and the terminal ileum of humans using different sample types: mucosal washes, brushes, scrapings, and intestinal contents in mice and biopsies, brushes and mucosal washes in humans. We used DNA quantification and 16S rRNA amplicon sequencing to evaluate the comparability of the information yielded from the different sample types under a controlled benchmark. In mice, mucosal washes and brushes had comparative bacterial DNA and host DNA contamination than scraping samples. Similarly, in humans, washes outperformed biopsies in bacterial DNA content. Read counts and microbiota alpha diversity remained remarkably similar in mice and between brushes and washes in humans. The composition of the microbiota varied based on the subsegment and sample type in mice and sample type in humans. We conclude that washes and brushes reduce host contamination without inducing substantial compositional bias when sampling mucosal microbiota. Our findings suggest that mucosal washes and brushes are a viable alternative to biopsies in humans and scrapings in mice, thereby improving the transferability of results across hosts. Our study highlights the importance of focusing on mucus-associated microbiota to better capture host-microbiome interactions at their closer interface.

The dynamics of microbial community changes in Korat chicken (KC) breast meat, an indigenous Thai crossbred, packed under traditional air-overwrapping (Con), vacuum packaging (VP), and modified atmosphere packaging (MAP) at 30 % CO2/70 % N2 were investigated, as well as their correlation with flavor attributes and acceptability during 12 days of chilled storage. Beta diversity and hierarchical clustering revealed that the microbial communities in VP and MAP were more similar than those in Con. The result suggested that packaging had a greater impact on microbial changes than storage time (p < 0.05). Alpha diversity demonstrated that both oxygen-depleting methods had lower microbial diversity and richness than Con. Two dominant phyla (Proteobacteria and Firmicutes) and nine dominant genera (e.g., Bacillus, Enterococcus) influenced meat flavor quality throughout storage time across packaging methods. The samples showed various rates of changes in flavor-related compounds, including pH, total volatile base nitrogen (TVB-N), thiobarbituric acid reactive substances (TBARS), inosine 5'-monophosphate (IMP), hypoxanthine (Hx), and volatile profiles. IMP and acids significantly enhanced flavor, showing a positive correlation with sensory scores (p < 0.05). In contrast, pH, TVB-N, TBARS, Hx, and aldehydes indicated meat deterioration-related undesirable traits. Proteobacteria, Bacillus, and Lactobacillus had positive correlations with desirable flavor compounds and sensory scores (p < 0.05). On the other hand, Firmicutes, Acinetobacter, and Brochothrix showed the opposite trend. Therefore, this study found that VP and MAP conditions regulated the microbial community, retaining meat flavor and acceptability throughout chilled storage for KC breast meat packaging. Moreover, it could reassure the packaging selection for the global poultry industry.

The intestinal microbiota of Penaeus vannamei is critical for its health and disease resistance, but imbalances can increase the risk of infections, especially by pathogenic Vibrio species. This study used the 2bRAD-M method to analyze the effects of dietary chitosan oligosaccharide (COS) supplementation on the gut microbiota of P. vannamei. Shrimp were fed diets with COS at 5‰ and 10‰ levels. Results showed that as COS concentration increased, beneficial microbial taxa (e.g., Bacteroidetes, Actinobacteria, and Campylobacter) significantly increased, while harmful bacteria decreased. For example, Vibrio parahemolyticus abundance dropped from 0.084 in controls to 0.033 in the 5‰ group, and Vibrio rotiforianus decreased from 0.216 in controls to 0.121 and 0.021 in the 5‰ and 10‰ groups, respectively. Photobacterium damselae also declined from 0.244 in controls to 0.049 and 0.094 in the 5‰ and 10‰ groups. These findings indicate that COS supplementation can enhance beneficial microbes and reduce harmful bacteria in P. vannamei intestines. This study highlights COS as a sustainable dietary intervention to improve shrimp health and reduce antibiotic use in aquaculture.

This study demonstrates that dietary chitosan oligosaccharide (COS) supplementation can effectively modulate the intestinal microbiota of Penaeus vannamei. At 5‰ and 10‰ levels, COS increased beneficial bacteria (e.g., Bacteroidetes and Actinobacteria) while reducing harmful pathogens like Vibrio parahaemolyticus and Vibrio rotiferianus. This shift enhances nutrient absorption, immune function, and disease resistance in shrimp. COS thus offers a sustainable alternative to antibiotics in aquaculture, promoting healthy growth and reducing environmental impact.

The human microbiome is a complex and dynamic community of microbes, thought to have symbiotic benefit to its host. Influences of the gut microbiome on brain microglia have been identified as a potential mechanism contributing to neurodegenerative diseases, such as Alzheimer's disease, motor neurone disease and Parkinson's disease (Boddy SL, Giovannelli I, Sassani M, et al. The gut microbiome: A key player in the complexity of amyotrophic lateral sclerosis (ALS). BMC Med. 2021;19(1):13). We hypothesize that population level differences in the gut microbiome will predict the incidence of Alzheimer's disease using machine learning methods. Cross-sectional analyses were performed in R, using two large, open-access microbiome datasets (n = 959 and n = 2012). Countries in these datasets were grouped based on Alzheimer's disease incidence and the gut microbiome profiles compared. In countries with a high incidence of Alzheimer's disease, there is a significantly lower diversity of the gut microbiome (P < 0.05). A permutational analysis of variance test (P < 0.05) revealed significant differences in the microbiome profile between countries with high versus low incidence of Alzheimer's disease with several contributing taxa identified: at a species level Escherichia coli, and at a genus level Haemophilus and Akkermansia were found to be reproducibly protective in both datasets. Additionally, using machine learning, we were able to predict the incidence of Alzheimer's disease within a country based on the microbiome profile (mean area under the curve 0.889 and 0.927). We conclude that differences in the microbiome can predict the varying incidence of Alzheimer's disease between countries. Our results support a key role of the gut microbiome in neurodegeneration at a population level.

This study evaluates for the first time the modifications in the microbial communities and sensory attributes caused by Self-Induced Anaerobiosis Fermentation (SIAF) compared to the Conventional processing of Coffea canephora var. Conilon. Microorganisms were identified through high-throughput sequencing of the 16S rRNA V3/V4 region for bacteria and the ITS region for fungi. Sensory attributes of roasted coffee were evaluated by Q-Graders. The relationship between microbial population, processing methods, and sensory attributes was investigated using principal component analysis. Before fermentation, 74 bacterial and 21 fungal species were identified in the natural coffee, whereas 44 bacterial and 15 fungal species were found in the pulped coffee. Torulaspora, Wickerhamomyces, and Meyerozyma exhibited more ITS region sequences, while Acetobacter, Enterobacter, and Lysinibacillus were predominant in the 16S region. In the natural coffee, Wickerhamomyces showed the highest relative abundance (45%) at 0 h. After 72 h, Meyerozyma (45%) and Torulaspora (75%) prevailed in Conventional processing and SIAF, respectively. In the pulped coffee, Torulaspora was the most abundant in the SIAF method, before (92%) and after (81%) fermentation, while Wickerhamomyces (39%) dominated after 72 h in the Conventional method. Enterobacteriaceae levels decreased, while Lactobacillaceae levels increased in SIAF natural coffee during the fermentation process. SIAF favored the presence of yeast and LAB while inhibiting mycotoxigenic fungi and Enterobacteriaceae. Torulaspora, Lactiplantibacillus, and Lactococcus showed the highest Pearson correlation coefficient with flavor (0.92), aftertaste (0.99), and bitterness/sweetness (0.89), respectively. Changes in coffee microbiota during SIAF improved sensory attributes, resulting in better-quality beverages.

This study investigated the effects of different non-starch polysaccharide (NSP) sources with NSP degrading enzymes (NSPases) and the influence on the mucosa-associated microbiota and intestinal immunity of nursery pigs, on growth performance and carcass traits at market weight.

One hundred and sixty newly weaned pigs at 7.0 ± 0.3 kg body weight (BW) were allotted in a 2 × 2 factorial with NSP sources and NSPases serving as factors. The 4 dietary treatments were: DDGS, corn distillers' dried grains with solubles as source of NSP; DDGS + NSPases (DDGS +), DDGS with xylanase at 0.01%, 3,000 U/kg of feed and β-mannanase at 0.05%, 400 U/kg of feed; SHWB, soybean hulls and wheat bran replacing corn DDGS as the source of NSP; SHWB with NSPases (SHWB +), SHWB with xylanase at 0.01%, 3,000 U/kg of feed and β-mannanase at 0.05%, 400 U/kg of feed. Pigs were fed for 37 d and housed in groups of 4 pigs per pen. At d 37, the median body weight pig in each pen was euthanized for sampling to analyze intestinal health parameters. Remaining pigs were fed a common diet for subsequent phases to evaluate the carryover effect on growth and carcass traits.

The SHWB decreased (P < 0.05) the relative abundance of Helicobacter, tended to increase (P = 0.074) the relative abundance of Lactobacillus, increased (P < 0.05) immunoglobulin G (IgG) in the jejunal mucosa, tended to increase (P = 0.096) the villus height (VH) in the jejunum, and tended to improve ADG (P = 0.099) and feed efficiency (P = 0.068) during phase 1 compared to DDGS treatment. Supplementation of NSPases increased (P < 0.05) Shannon index of diversity, increased the relative abundance of Streptococcus and Acinetobacter, and tended to increase (P = 0.082) dry matter digestibility. The BW of pigs fed SHWB was more uniform (P < 0.05) at the end of the 120 d study. Additionally, hot carcass weight of pigs fed SHWB tended to be more uniform (P = 0.089) than DDGS treatment.

Soybean hulls and wheat bran replacing DDGS in nursery diets improved uniformity of pigs at market weight, which might be attributed to beneficial modulation of the mucosa-associated microbiota and enhanced intestinal morphology during the nursery phase. Supplementation of NSPases had beneficial effects on the intestinal mucosa-associated microbiota, digestibility, and intestinal immunity in SHWB treatment, whereas no carryover effects were overserved at market weight.

Bacterial secondary metabolites are crucial bioactive compounds with significant therapeutic potential, playing key roles in ecological processes and the discovery of novel antimicrobial agents and natural products. Cenotes, as extreme environments, harbour untapped microbial diversity and hold an interesting potential as sources of novel secondary metabolites. While research has focused on the fauna and flora of cenotes, the study of their microbial communities and their biosynthetic capabilities remains limited. Advances in metagenomics and genome sequencing have greatly improved the capacity to explore these communities and their metabolites. In this study, we analysed the microbial diversity and biotechnological potential of micro-organisms inhabiting sediments from a coastal cenote. Metagenomic analyses revealed a rich diversity of bacterial and archaeal communities, containing several novel biosynthetic gene clusters (BGCs) linked to secondary metabolite production. Notably, polyketide synthase BGCs, including those encoding ladderanes and aryl-polyenes, were identified. Bioinformatics analyses of these pathways suggest the presence of compounds with potential industrial and pharmaceutical applications. These findings highlight the biotechnological value of cenotes as reservoirs of secondary metabolites. The study and conservation of these ecosystems are essential to facilitate the discovery of new bioactive compounds that could benefit various industries.

The chicken's gastrointestinal tract is home to complex and diverse microbial communities that can be manipulated to enhance health and productivity. Although polyphenols have recently attracted the attention of researchers due to their potent antioxidant capabilities, their impact on the gut microbiota remains largely unexplored. Hence, in this study, we conducted a comprehensive analysis of the effects of dietary supplementation with polyphenol-rich extract from shredded, steam-exploded pine particles (PSPP) on growth, meat quality, and gut microbial dynamics in broiler chickens. Supplementation of PSPP was found to significantly improve birds' FCR until the third week of the trial but only marginally affected meat quality. Based on metataxonomic analyses of the cecal microbiotas of broilers fed increasing concentrations of PSPP, dietary PSPP modulated the composition of the cecal microbiota of the birds with a concomitant increase of Bacteroidetes and a decrease in the Firmicutes population. Similar trends were observed for the proportions of Alistipes and Faecalibacterium at the genus level. Additionally, 43 unique bacterial species were detected in the cecal microbiome of birds fed with PSPP. However, microbial diversity did not vary significantly among treatment groups. A particularly interesting finding was the specialization observed in the microbiome of birds receiving PSPP supplementation. Microbial co-occurrence network analyses revealed substantial modifications in their network structure when compared to control birds. Families like Rikenellaceae and Eubacteriaceae were notably absent, and the number of microbial interactions was drastically lower in the PSPP-fed group. Microbial taxa modeling revealed that the impact of increasing dietary PSPP levels primarily affected genus-level taxa, showing a decreasing trend. Overall, this offers compelling evidence that continuous PSPP supplementation may not only alter the composition of intestinal microbes but also have a profound effect on the interactions among different microbial species. Conversely, PSPP had minimal effects on broilers' performance and meat quality.

Arterial hypertension is influenced by the intestinal microbiota and its metabolites, which play a crucial role in host health. Dietary peptides are multifunctional molecules with therapeutic potential for managing hypertension. This study aimed to evaluate the impact of incorporating enzymatically hydrolyzed poultry byproduct meal (EHPM-c) into extruded dry diets on the fecal microbiota and blood pressure parameters of elderly obese cats. Eighteen owners of neutered, clinically healthy male and female cats of various breeds were randomly assigned to two groups: control (30.8%, conventional poultry byproduct meal-CPM-c) and test (17.07%, CPM-c + 12.0% EHPM-c). Clinical values of systolic blood pressure, serum aldosterone concentrations, angiotensin-converting enzyme I activity, and fecal microbiota using 16S rRNA were measured. Data were processed using SAS software (PROC MIXED, PROC GLIMMIX, and PROC CORR; p < 0.05). Both groups exhibited high microbial alpha diversity, with no significant differences in beta diversity. Although the inclusion of 12.0% EHPM-c had no measurable effect on blood pressure, both diets promoted beneficial modulation of the fecal microbiota, improving intestinal health. These findings underscore the importance of diet in maintaining gut homeostasis in obese senior cats. While the inclusion of 12.0% EHPM-c did not significantly alter blood pressure parameters, the modulation of the fecal microbiota suggests a potential role in maintaining intestinal health. These results highlight the need for further studies to explore different inclusion levels and longer intervention periods.

Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications.IMPORTANCEAlthough soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction-less than 1%-can be cultured under specific media and cultivation conditions. This indicates that there are ample opportunities in harvesting the diverse environmental microorganisms if isolating and recovering these uncultured microorganisms are possible. This paper presents a new cultivation technique composed of isolating single-soil microorganism cell from an in situ soil microorganism community in microfluidic droplets and conducting in-droplet cultivation in media supplemented by soil extract or soil metabolites. This method enables the recovery of a broader diversity of the original microorganism community, laying the groundwork for a high-throughput phenotyping of these diverse microorganisms from their natural habitats.

All animals harbor microbiomes, which are obtained from the surrounding environment and are impacted by host behavior and life stage. To determine how two non-mutually exclusive drivers - physical environment and social organization - affect an organism's microbiome, we examined the bacterial communities within and around nests of harvester ants (Veromessor andrei). We collected soil and nest content samples from five different ant nests. We used 16S rRNA gene sequencing and calculated alpha and beta diversity to compare bacterial diversity and community composition across samples. To test the hypotheses that physical environment and/or social organization impact ant colonies' community of microbes we compared our samples across (i) sample types (ants, brood, seeds and reproductives (winged alates), and soil), (ii) soil inside and outside the nest, and (iii) soil from different chamber types. Interestingly, we found that both the environment and social organization impact the bacterial communities of the microbiome of V. andrei colonies. Soil from the five nests differed from one another in a way that mapped onto their geographical distance. Furthermore, soil from inside the nests resembled the surrounding soil, supporting the physical environment hypothesis. However, the bacterial communities associated with the contents within the nest chambers, i.e., ants, brood, seeds, and reproductives, differed from one another and from the surrounding soil, supporting the social organization hypotheses. This study highlights the importance of considering environmental and social factors in understanding microbiome dynamics.

Reducing crude protein (CP) in weaner pig diets lowers post-weaning diarrhoea risk but may impair growth performance. This study aimed to identify the beneficial effects of organic acid (OA)-preserved grain and butyric acid supplementation on gut health and growth in low-CP diets. At harvest, grain was divided into two batches: one dried at 65 °C, the other treated with a propionic acid. Ninety-six piglets (28 days old) were assigned to four treatments: (1) dried grain, (2) OA-preserved grain, (3) dried grain + 3% butyric acid, and (4) OA-preserved grain + 3% butyric acid. On day 8, microbial composition, inflammatory markers, volatile fatty acids, and intestinal morphology were assessed. The OA-preserved grain improved feed conversion ratio (p < 0.05) increased beneficial gut bacteria (p < 0.01), elevated caecal butyrate (p < 0.05), reduced jejunal CXCL8 expression (p < 0.05), and enhanced nutrient digestibility (p < 0.01). Butyric acid reduced feed intake (p < 0.05), improved nutrient digestibility (p < 0.01), decreased colonic Proteobacteria (p < 0.05), and increased colonic propionate and butyrate (p < 0.01). Combining OA-preserved grain with butyric acid elevated ileal Proteobacteria and Pasteurellaceae (p < 0.05). In conclusion, while OA-preserved grain improves feed efficiency, nutrient digestibility, and gut microbiota, supplementing butyric acid enhances nutrient digestibility but reduces feed intake, and their combination may disrupt the microbial balance.

The oral microbiome plays an important role in the development and progression of periodontal disease. The purpose of this study was to compare microbial profiles of oral cavities in good health, with gingivitis, and in a state of periodontitis, and to identify novel pathogens involved in periodontal diseases.

One hundred and two participants, including 33 healthy controls, 41 patients with gingivitis, and 28 patients with periodontitis, were included in this cross-sectional study. Salivary oral microbiomes were investigated using 16S rRNA metagenomic sequencing, and the microbial profiles of each group were compared using age- and sex-adjusted general linear models.

The abundance of amplicon sequence variants and Chao1 diversity were significantly elevated in the gingivitis and periodontitis groups relative to healthy controls (p = 0.046). Based on linear discriminant analysis (LDA) scores (>2), Tenericutes, Mollicutes, Mycoplasmatales, Mycoplasmataceae, Mycoplasma, Bacteroidaceae, and Phocaeicola were significantly enriched in the gingivitis group, and Synergistetes, Synergistia, Synergistales, Synergistaceae, Fretibacterium, Sinanaerobacter, and Filifactor were enriched in the periodontitis group. The relative abundances of Fretibacterium fastidiosum, Sinanaerobacter chloroacetimidivorans, and Filifactor alocis (q = 0.008, all bacteria) were highest in the periodontitis group and lowest in the control group. The relative abundance of Treponema denticola was significantly elevated in the periodontitis group compared to the other two groups (q = 0.024).

Oral microbiomes differed between groups. T. denticola, F. fastidiosum, S. chloroacetimidivorans and F. alocis were significantly more abundant in the periodontitis group than in the control group. Additionally, the abundance of T. denticola and F. fastidiosum in the periodontitis group was significantly different from that in the gingivitis group.

Turkey litter waste is lignocellulosic waste that can be sustainably used as an energy source through anaerobic digestion (AD). The 16S ribosomal RNA technique helps to unravel microbial diversity and predominant metabolic pathways. The assays were performed in 600-mL-glass bottles with 400 mL volume, for 60 days at 37 °C. The study evaluated the physicochemical parameters, the composition of the microbiota, and the functional inference in AD of different concentrations of turkey litter (T) using two inocula: granular inoculum (S) and commercial inoculum (B). The highest accumulated methane production (633 mL CH4·L-1) was observed in the test containing 25.5 g VS·L-1 of turkey litter with the addition of the two inocula (T3BS). In tests without inoculum (T3) and with commercial inoculum (T3B), there was an accumulation of acids and consequent inhibition of methane production 239 mL CH4·L-1 and 389 mL CH4·L-1, respectively. Bacteroidota, Firmicutes, and Actinobacteria were the main phyla identified. The presence of archaea Methanobacterium, Methanocorpusculum, and Methanolinea highlighted the hydrogenotrophic metabolic pathway in T3BS. Functional prediction showed enzymes involved in three metabolic pathways in turkey litter biodigestion: acetotrophic, hydrogenotrophic, and methylotrophic methanogenesis. The predominant hydrogenotrophic pathway can be observed by analyzing the microbiota, archaea involved in this specific pathway, genes involved, and relative acid consumption for T3S and T3BS samples with higher methane production. Molecular tools help to understand the main groups of microorganisms and metabolic pathways involved in turkey litter AD, such as the use of different inocula, allowing the development of strategies for the sustainable disposal of turkey litter.

The skin and gut microbiota are crucial to amphibians. Triadimefon (TF), a widely used triazole fungicide, controls crop diseases and regulates growth, with uncertain effects on amphibian microbiota. Contamination, typically involving mixed chemicals at low concentrations, including cadmium (Cd) and TF, may detrimentally affect amphibian growth, survival, and microbiota health in both the skin and gut, but few research has examined these consequences. This research examines the impact of Cd and TF on Rana dybowskii tadpoles, focusing on survival, body mass, and microbiome changes over 28 days across four groups: control, Cd, TF, and Cd + TF groups. Results showed significant reductions in survival and body mass in Cd and TF-treated groups, with the combination group being the most affected. Microbiota analysis revealed significant dysbiosis in both gut and skin microbiomes under pollutant stress, with a marked microbiota and a shift in dominant microbial communities. Function prediction analysis based on the microbiome composition highlighted significant differences across various biological pathways, including metabolism, immune system, environmental adaptation, and disease resistance. These alterations suggest that pollutant exposure compromises the tadpoles' ability to maintain homeostasis and resist pathogens. In conclusion, this study reveals the detrimental effects of Cd and TF on the survival, growth, and microbiomes of R. dybowskii tadpoles, indicating significant environmental and health risks.

Commercial livestock producers need to prioritize genetic progress for health and efficiency traits to address productivity, welfare, and environmental concerns but face challenges due to limited pedigree information in extensive multi-sire breeding scenarios. Utilizing pooled DNA for genotyping and integrating seminal microbiome information into genomic models could enhance predictions of male fertility traits, thus addressing complexities in reproductive performance and inbreeding effects. Using the Angus Australia database comprising genotypes and pedigree data for 78,555 animals, we simulated percentage of normal sperm (PNS) and prolificacy of sires, resulting in 713 sires and 27,557 progeny in the final dataset. Publicly available microbiome data from 45 bulls was used to simulate data for the 713 sires. By incorporating both genomic and microbiome information our models were able to explain a larger proportion of phenotypic variation in both PNS (0.94) and prolificacy (0.56) compared to models using a single data source (e.g., 0.36 and 0.41, respectively, using only genomic information). Additionally, models containing both genomic and microbiome data revealed larger phenotypic differences between animals in the top and bottom quartile of predictions, indicating potential for improved productivity and sustainability in livestock farming systems. Inbreeding depression was observed to affect fertility traits, which makes the incorporation of microbiome information on the prediction of fertility traits even more actionable. Crucially, our inferences demonstrate the potential of the semen microbiome to contribute to the improvement of fertility traits in cattle and pave the way for the development of targeted microbiome interventions to improve reproductive performance in livestock.

This study investigated whether organic acid (OA)-preserved grain could mitigate the negative effects of low crude protein (CP) diets on growth performance, intestinal health, and the coefficient of total tract digestibility (CATTD) of nutrients in weaned piglets. The grain was either conventionally dried or preserved post-harvest with 4 kg of OA per tonne. Ninety-six piglets (28 days old) were assigned to one of four diets in a 2 × 2 factorial design: (1) dried standard CP diet, (2) OA-preserved standard CP diet, (3) dried low CP diet, and (4) OA-preserved low CP diet. Standard and low CP diets contained 20% and 19% CP during the first 15 days, reduced to 19% and 17% CP from days 15-35 post-weaning. Faecal scores (FS) were assessed twice a day while microbial composition, inflammatory markers, colonic volatile fatty acid concentrations, and intestinal morphology were measured on the 8th day post-weaning. Performance metrics were measured over the 35-day experimental period. Low CP diets consistently reduced FS (p < 0.05) and increased colonic molar butyrate proportions (p < 0.01) but increased duodenal IL1B expression compared to standard CP diets (p < 0.05). The OA-preserved grain enhanced beneficial microbial populations (Lactobacillus, Roseburia) while lowering pro-inflammatory cytokines (IL1A, IL17) (p < 0.05). While dried grain with low CP diets reduced average daily gain (ADG), colonic short-chain fatty acids (SCFA) concentrations, and nitrogen digestibility, OA-preserved grain with low CP maintained these parameters and improved final body weight (p < 0.05). Overall, OA-preserved grain mitigated the performance decline associated with low CP diets by enhancing gut health and nutrient digestibility and reducing inflammation, thus presenting a promising alternative nutritional strategy for post-weaned piglets.

spinal cord injury (SCI) disrupts the gut microbiota, worsening the injury's impact. Fecal microbiota transplantation (FMT) is increasingly recognized as a promising strategy to improve neural function post-SCI, yet its precise mechanisms are still far from clear. The present study aims to elucidate how FMT influences motor function recovery and its underlying mechanisms utilizing a SCI mouse model.

Mice with SCI received FMT from healthy donors. We used 16 S rRNA amplicon sequencing to analyze the alterations of gut microbes. Pathological alterations in the spinal cord tissue, including neuronal survival, axonal regeneration, cell proliferation, and neuroinflammation, were assessed among experimental groups. Additionally, RNA sequencing (RNA-seq) was used to explore alterations in relevant signaling pathways.

Significant shifts in gut microbiota composition following SCI were observed through 16 S rRNA analysis. On day 7 post-SCI, the FMT group exhibited a significantly higher diversity of gut microbiota compared to the ABX group, with the composition in the FMT group more closely resembling that of healthy mice. FMT promoted neuronal survival and axonal regeneration, leading to notable improvements in motor function compared to control mice. Immunofluorescence staining showed increased neuronal survival, alleviated extracellular matrix (ECM) deposition, diminished glial scar formation, and reduced inflammation in FMT-treated mice. RNA-seq analysis indicated that FMT induced transcriptomic changes associated with material metabolism, ECM remodeling, and anti-inflammatory responses.

FMT restored gut microbiota balance in SCI mice, mitigated inflammation, and promoted ECM remodeling, establishing an optimal environment for neural recovery. These findings demonstrated that FMT may represent a valuable approach to enhance functional recovery following SCI.

In this study, we first verified the feasibility of using Antarctic krill as a raw material for quick-brewed fish sauce, and the results showed that the amino acid nitrogen (AAN)and total soluble nitrogen(TSN) in the fermented 30 days fish sauce met the national level fish sauce standards, but the histamine content exceeded the maximum limit value of histamine in fish sauce (400 mg/kg) set by the International Codex Alimentarius Commission (CAC) and the European Union (EU). On this basis, the correlation between physicochemical indexes and bacterial communities during the fermentation of fish sauce was investigated using high-throughput sequencing, culture method. The correlation analyses revealed the relationship between bacterial communities and the quality and safety of fish sauce, and these studies will be helpful for the development of Antarctic krill fish sauce. The results showed that Staphylococcus were positively correlated with the accumulation of histamine and TVB-N during fermentation. This may be due to the presence of genes encoding histidine decarboxylase in Staphylococcus. Virgibacillus was positively correlated with the accumulation of AAN during fermentation. It was also found that Virgibacillus dokdonensis had a high protease activity (153.22 U/mL) and Staphylococcus epidermidis was the most capable of producing histamine at 31.59 mg/kg. Therefore histamine can be reduced by adding bacteria that inhibit the growth of Staphylococcus or degrade histamine as a fermenter.

Prenatal and postpartum depression may be influenced by the composition of host associated microbiomes. As such, the objective of this study was to elucidate the relationship between the human gut or vaginal microbiomes in pregnancy with prenatal or postpartum depression.

140 female participants were recruited at their first prenatal visit and completed the Edinburgh Postnatal Depression Scale (EPDS) to screen for depression and anxiety, in addition the EPDS was completed one month postpartum. Vaginal and stool biospecimens were collected in the third trimester, analyzed using 16S rRNA gene sequencing, and assessed for alpha and beta diversity. Individual taxa differences and clustering using the k-medoids algorithm enabled community state type classification.

Participants with higher postpartum EPDS scores had higher species richness and lower abundance of L. crispatus in the vaginal microbiota compared to those with lower EPDS scores. Participants with a higher prenatal EPDS score had lower species richness of the gut microbiome. Participants with a vaginal community state type dominated by L. iners had the highest mean prenatal EPDS scores, whereas postpartum EPDS scores were similar regardless of prenatal vaginal state type.

Our small sample size and participant's self-report bias limits generalizability of results.

Depression in the prenatal and postpartum period is associated with the composition and diversity of the gut and vaginal microbiomes in the third trimester of pregnancy. These results provide a foundational understanding of the microbial relationships between maternal health and depression for identifying potential therapeutic treatments.

Previous research has shown that microbes play a role in immune-related diseases. Our study reveals that children with Henoch-Schönlein purpura nephritis have distinct and altered tongue coating microbiota, characterized by significant changes in species richness, diversity, and specific microbial compositions compared with healthy controls. Nevertheless, the particular involvement of tongue coating microbiota in Henoch-Schönlein Purpura remains unclear. A total of 26 children were enrolled, including 13 patients with HSP and 13 healthy children. Tongue coating samples were collected for DNA extraction and 16S rRNA gene sequencing. Alpha diversity indices, including ACE, Chao1, Shannon, and Simpson indices, revealed significantly lower richness and diversity of tongue coating microbiota in children with Henoch-Schönlein purpura compared to healthy controls. Beta diversity analysis demonstrated distinct clustering of microbial communities between HSP and healthy children, with significant compositional differences. 16S rRNA gene sequencing showed that the relative abundance of key genera, such as Veillonella and Prevotella, differed between the two groups. A random forest algorithm identified five genera as potential diagnostic biomarkers for HSP. Co-occurrence analysis revealed different hub microbes in HSP and healthy children. BugBase predicted an increased proportion of stress-tolerant bacteria in the HSP group compared to the healthy controls group. PICRUSt analysis indicated alterations in metabolic functions of tongue coating microbiota between HSP and healthy children, with 25 KEGG pathways exhibiting significant differences. Children with HSP exhibit marked differences in their tongue coating microbiota when contrasted with their healthy counterparts.

Understanding the link between prepregnancy nutritional status and gut microbiota during pregnancy may lead to novel maternal and child health interventions. We explored the association of prepregnancy body mass index (BMI) status with gut microbiota diversity and abundance during pregnancy.

A cross-sectional study was conducted on 90 pregnant women from primary health centers in Jakarta, Indonesia. Trained staff interviewed women on sociodemographic characteristics and nutrient intake, gathered data on prepregnancy BMI from antenatal records, and obtained fecal samples. Samples were analyzed for microbiota diversity indices [Shannon, Faith phylogenetic diversity (Faith PD), and Chao1] and abundance using 16S ribosome ribonucleic acid sequencing. Multivariate logistic regression was performed although adjusting for carbohydrate and protein intake, ethnicity, and education to determine the relationship between prepregnancy BMI and the alpha diversity index and the presence of the phylum Firmicutes and genera Prevotella and Blautia.

Pregnant women who were overweight or obese (BMI ≥23.0 kg/m2) before pregnancy had significantly lower odds of having gut microbiota diversity above the median of Shannon index [adjusted odds ratio (aOR): 0.4, 95% confidence interval (CI): 0.1, 0.9, P = 0.042], Faith PD (aOR: 0.2, 95% CI: 0.1, 0.8, P = 0.015), and Chao1 (aOR: 0.3, 95% CI: 0.1, 0.7, P = 0.006) compared with those who were neither overweight nor obese. Prepregnant women with overweight or obesity also had significantly lower odds of having levels above the median of the phylum Firmicutes (aOR: 0.38, 95% CI: 0.15, 0.98, P = 0.045) and genus Blautia (aOR: 0.32, 95% CI: 0.12, 0.85, P = 0.022) compared with women without overweight and obesity.

Prepregnancy overweight or obese status was associated with lower gut microbiota diversity and lower abundance of Firmicutes and Blautia among pregnant women in an urban community. These findings suggest that prepregnancy interventions to control BMI may improve gut flora and potentially benefit pregnant women.

Hydrophobic organic compounds (HOCs), such as pyrene, pose significant challenges for microbial-based remediation in soil due to limited substrate availability and the sustainability of augmented microbes. Research targets are to investigate the potential of biofilm-forming bacterial cells to enhance pyrene bioavailability and biodegradation in two different hydrocarbon-contaminated soil microcosms, employing microbiological, molecular, and chemical analysis validated through statistical tools. The microcosm augmented with strong biofilm bacterial consortia (A) significantly enhanced pyrene availability by 1-1.5% compared to the weak biofilm consortia (B) and mixed consortia (AB). Analysis of 16 S rDNA amplicons revealed notable differences in bacterial community composition between consortia A and B augmented soil, with Proteobacteria as the dominant phylum. Taxonomic composition of soil microbiome predicted enhanced xenobiotic biodegradative potential of strong biofilm consortia (A) up to 20 days, exhibiting a higher abundance of functional genes related to upstream degradative pathway of PAHs, such as naphthalene dioxygenase (nahAa), PAH dioxygenase subunit genes (nidA, nidB), extradiol dioxygenase (phdF) and aldehyde dehydrogenase (nidD). Our study highlights the significant role of biofilm-forming bacteria as "bioavailability enhancers," for high molecular weight PAHs like pyrene, in contaminated soils with their implications for designing future sustainable bioremediation programs.

The amylolytic susceptibility of starch-lipid complexes with different forms of crystallites has been studied extensively, but the fermentation properties of these complexes remain little understood. Hence, the in vitro fecal fermentation properties of starch-lipid complexes with VI-type and VII-type crystallites were investigated in the present study. Compared to VI-type complexes, fermentation of VII-type complexes caused more severe disruption to the crystallites and resulted in greater acid, reducing sugar, and short-chain fatty acids (SCFAs) production. Moreover, fermentation of VII-type complexes promoted a greater relative abundance of SCFAs-producing bacteria in the fecal microbiota than did VI-type complexes. Our results show that the more stable VII-type complexes are utilized more effectively than VI-type complexes, which can be attributed to the bacteria binding more readily to VII-type than to VI-type complexes. Therefore, VII-type complexes were considered to deliver better health benefits than VI-type complexes due to their greater potential for producing SCFAs and stimulating beneficial gut microbial activity in the colon.

To evaluate the associations between the quality of the diet and its components and microbial diversity and composition in peritoneal dialysis (PD) patients.

This cross-sectional study included PD patients for at least 3 months, aged 18-75 years and clinically stable. The Diet Quality Index (DQI), validated for the Brazilian population, is based on the energy density of 11 components ("sugar and sweets;" "beef, pork, and processed meat;" "refined grains and breads;" "animal fat;" "poultry, fish, and eggs;" "whole cereals, tubers, and roots;" "fruits"; "nonstarch vegetables;" "legumes and nuts;" "milk and dairy products;" and "vegetable oil"). A proportional score-based on the adequacy of the intake to Brazilian dietary guidelines-is calculated, and a final score ranged from 0 (worse) to 100 (better) is obtained. Fecal samples were collected at home, in a sterile material, kept refrigerated, and delivered to the clinic within 12 hours; α-diversity indices (Observed operational taxonomic units, Chao-1, Shannon's, Gini-Simpson's, Pielou eveness, and Faith phylogenetics) and microbial profile were determined by 16S ribosomal DNA with polymerase chain reaction-amplification and sequenced on an Illumina MiSeq platform.

Forty-three participants were included (53.5% men, 52.4 ± 14.1 years, body mass index: 25.9 ± 4.1 kg/m2, 30.2% had diabetes mellitus). DQI score was 50.5 (41.9-54.9). The lowest energy density was for the components "animal fat" and "whole cereals and breads, tubers, and roots," and the highest were for "refined grains and bread" and "beef, pork, and processed meat." Diversity indices and Enterorhabdus genus were directly associated with the energy density of the components "whole cereals and breads, tubers, and roots" and inversely with "refined grains and bread," after adjustments for age and diabetes.

Even low, the intake of whole cereals, tubers, and roots has the potential to positively influence the microbiota profile in PD patients.

Understanding microbial colonization on different membranes is critical for guided bone regeneration procedures such as socket preservation, as biofilm formation may affect healing and clinical outcomes. This randomized controlled clinical trial (RCT) investigates, for the first time, the microbiome of two different high-density polytetrafluoroethylene (d-PTFE) membranes that are used in socket preservation on a highly molecular level and in vivo.

This RCT enrolled 39 participants, with a total of 48 extraction sites, requiring subsequent implant placement. Sites were assigned to two groups, each receiving socket grafting with a composite bone graft (50% autogenous bone, 50% bovine xenograft) and covered by either a permamem® (group P) or a Cytoplast™ (group C). The membranes were removed after four weeks and analyzed using scanning electron microscopy (SEM) for bacterial adherence, qPCR for bacterial species quantification, and next-generation sequencing (NGS) for microbial diversity and composition assessment.

The four-week healing period was uneventful in both groups. The SEM analysis revealed multispecies biofilms on both membranes, with membranes from group C showing a denser extracellular matrix compared with membranes from group P. The qPCR analysis indicated a higher overall bacterial load on group C membranes. The NGS demonstrated significantly higher alpha diversity on group C membranes, while beta diversity indicated comparable microbiota compositions between the groups.

This study highlights the distinct microbial profiles of two d-PTFE membranes during the four-week socket preservation period. Therefore, the membrane type and design do, indeed, influence the biofilm composition and microbial diversity. These findings may have implications for healing outcomes and the risk of infection in the dental implant bed and should therefore be further explored.

The 16S rRNA metabarcoding, based on Next-Generation Sequencing (NGS), is used to assess microbial biodiversity in various matrices, including food. The process involves a "dry-lab" phase where NGS data are processed through bioinformatic pipelines, which finally rely on taxonomic unit assignment against reference databases to assign them at order, genus, and species levels. Today, several public genomic reference databases are available for the taxonomic assignment of the 16S rRNA sequences. In this study, 42 insect-based food products were chosen as food models to find out how reference database choice could affect the microbiome results in food matrices. At the same time, this study aims to evaluate the most suitable reference database to assess the microbial composition of these still poorly investigated products. The V3-V4 region was sequenced by Illumina technology, and the R package "DADA2" was used for the bioinformatic analysis. After a bibliographic search, three public databases (SILVA, RDP, NCBI RefSeq) were compared based on amplicon sequence variant (ASV) assignment percentages at different taxonomic levels and diversity indices. SILVA assigned a significantly higher percentage of ASVs to the family and genus levels compared to RefSeq and RDP. However, no significant differences were noted in microbial composition between the databases according to α and β diversity results. A total of 121 genera were identified, with 56.2% detected by all three databases, though some taxa were identified only by one or two. The study highlights the importance of using updated reference databases for accurate microbiome characterization, contributing to the optimization of metabarcoding data analysis in food microbiota studies, including novel foods.

Paddy fields are a major anthropogenic source of global methane (CH4) emissions, a powerful greenhouse gas (GHG). This study aimed at gaining insights of different organic and inorganic conductive materials (CMs) - biochar, fungal melanin, and magnetite - to mitigate CH4 emissions, and on their influence on key microbial populations, mimicking the postharvest season throughout the degradation of rice straw in microcosms under anaerobic conditions encompassing postharvest paddy rice soils from the Ebro Delta, Spain. Results showed that fungal melanin was the most effective CM, significantly reducing CH4 emissions by 29 %, while biochar amendment also reduced emissions by 10 %. Magnetite slightly increased CH4 production (3 %), but this result was non-significant compared to unamended control microcosms. All treatments (with and without CM) displayed the acetoclastic methanogenesis pathway according to isotopic signature of δ13C-CH4, δ13C-CO2 and δ2H-CH4. In the presence of CMs, the archaeal populations showed a major abundance of Methanobacteria, Methanosarcina, and Bathyarchaeia. Furthermore, linear discriminant analysis effect size (LefSe) revealed specific positive linkages between fungal melanin and electroactive bacteria like Geobacter, biochar with Clostridia, and magnetite with Thiobacillus, and specifically related with archaea, particularly Bathyarchaeia. Biochar may diversify volatile fatty acids (VFA) utilization leading to a final mitigation of cumulative CH4 emissions through complex microbial interactions in the later stages of incubation. In contrast, fungal melanin increased VFA production, while delaying CH4 production, and may have diverted the electron flow towards melanin quinone reduction, suppressing methanogenesis by oxidizing organic compounds. These results suggest that CMs might facilitate specific potential direct interspecies electron transfer (DIET) between syntrophic electroactive bacteria (i.e. Geobacter, Clostridia) and electroactive methanogens such as Methanosarcina and Methanobacteria, but also with alternative microbial populations with the potential for hampering methanogenesis in a certain extent.

Palm trees (Arecaceae) are among the most popular ornamental plants worldwide. Despite extensive research on the fungi associated with Arecaceae, the diversity and ecological dynamics of fungi affecting ornamental palms remain poorly studied, although they have significant impact on palm health and economic value. Furthermore, while research on palm fungal diversity has traditionally focused on tropical assemblages, ornamental palms in temperate climates offer a unique opportunity to explore the diversity of palm fungi in non-native habitats. The present study conducted a preliminary assessment of the diversity and ecology of potential phytopathogenic fungi associated with foliar lesions on various ornamental palm host species in Portugal, combining morphological examination, PCR-based genomic fingerprinting, and biodiversity data analysis. The examination of 134 foliar lesions sampled from 100 palm trees resulted in a collection of 2064 palm leaf spotting fungi (PLSF), representing a diverse fungal assemblage of 320 molecular operational taxonomic units (MOTUs) across 97 genera. The overall fungal community composition revealed a distinct assemblage dominated by Neosetophoma, Alternaria, Phoma, and Cladosporium, with a profusion of infrequent and rare taxa consistent with a logseries distribution. Significantly positive co-occurrence (CO) patterns among prevalent and uncommon taxa suggest potential synergistic interactions enhancing fungal colonisation, persistence, and pathogenicity. The taxonomic structures of the PLSF contrasted markedly from tropical palm fungi, especially in the prevalence of pleosporalean coelomycetes of the Didymellaceae and Phaeosphaeriaceae, including recently introduced or not previously documented genera on Arecaceae. This novel assemblage suggests that climatic constraints shape the structure of palm fungal communities, resulting in distinctive temperate and tropical assemblages. In addition, the fungal assemblages varied significantly across palm host species, with temperate-native palms hosting more diverse, coelomycete-enriched communities. The present findings highlight foliar lesions as hyperdiverse microhabitats harbouring fungal communities with intricate interactions and a complex interplay of climatic, host, and ecological factors. With climate change altering environmental conditions, the identification of fungi thriving in or inhabiting these microhabitats becomes crucial for predicting shifts in pathogen dynamics and mitigating future fungal disease outbreaks. Understanding these complex ecological dynamics is essential for identifying potential phytopathogenic threats and developing effective management strategies for the health and sustainability of ornamental plants.

Studies of microbial communities vary widely in terms of analysis methods. In this growing field, the wide variety of diversity measures and lack of consistency make it harder to compare different studies. Most existing alpha diversity metrics are inherited from other disciplines and their assumptions are not always directly meaningful or true for microbiome data. Many existing microbiome studies apply one or some alpha diversity metrics with no fundamentals but also an unclear results interpretation. This work focuses on a theoretical, empirical, and comparative analysis of 19 frequently and less-frequently used microbial alpha diversity metrics grouped into 4 proposed categories, including key features of every analyzed metric with their mathematical assumptions, to provide a deeper understanding of the existing metrics and a practical implementation guide for future studies. Key metrics that should be required in microbiome analysis include richness, phylogenetic diversity, entropy, dominance of a few microbes over others, and an estimate of unobserved microbes. Collectively, these metrics contribute to a comprehensive set of analyses characterizing samples, allowing the determination of key aspects that might be otherwise obscured by partial or biased information. These guidelines enable further detailed analysis by each author according to their specific interests and clinical trials. Several practical examples are provided to illustrate how these recommendations improve the quality and depth of information obtained, facilitating better interpretation when working with microbiome data. These guidelines can be applied to both existing and future research studies, enhancing the standardization, consistency, and robustness of the analyses conducted. This approach aims to improve the capture of biological diversity, leading to better interpretations and insights.

Plant litter is an important input source of carbon and nitrogen in soil. While microplastics (MPs) and plant litter are ubiquitously present in soil, their combined impact on soil biogeochemical processes remains poorly understood. To address this gap, we examined the soil changes resulting from the coexistence of plant litter (Alfalfa) and polyethylene microplastics (PE). The soil changes included physicochemical properties, composition of soil dissolved organic matter, and structure of the soil microbial community. The results showed that the addition of polyethylene (PE) inhibited the degradation of humus-like substances and decreased the quantity of humic acid-like compounds in soil dissolved organic matter (DOM). PE negatively impacted plant litter decomposition, disrupted soil organic carbon (SOC) breakdown, interfered with the nitrogen cycle, and significantly altered microbial community structures during the process. By day 35, SOC and total nitrogen (TN) levels were reduced by 39.8% and 10.1%, respectively, in the presence of PE. Furthermore, PE significantly decreased the abundance of nitrogen-fixing microbes, including Streptomyces (43.1%) and Bacillus (45.9%), which play key roles in nitrate reduction to ammonium. This study highlights the environmental effects of MPs on plant litter decomposition and their potential implications for soil biogeochemical processes.

Dietary intake has been suggested to be associated with the oral microbiome, but no study has examined the association between overall diet quality and the oral microbiome.

This study aimed to investigate the cross-sectional association between the Healthy Eating Index-2020 (HEI-2020) and the diversity and composition of the oral microbiome among participants in the Buffalo Osteoporosis and Periodontal Disease (OsteoPerio) Study.

In 1175 postmenopausal women (mean age: 67 ± 7.0 y), we estimated the HEI-2020 scores for each woman from a food frequency questionnaire administered from 1997 to 2000. Bacterial DNA was extracted from subgingival plaque samples and analyzed using 16S ribosomal RNA sequencing. The alpha-diversity (within-sample diversity) and β-diversity (between-sample diversity) across HEI-2020 quartiles were examined using analysis of covariance and permutational multivariate analysis of variance, respectively. The associations between the HEI-2020 score and the relative abundance of microbial taxa were examined by linear regression models. The analyses were further conducted for individual components of the HEI-2020.

No statistically significant associations were observed between the HEI-2020 scores and alpha- or beta-diversity. However, greater consumption of seafood, plant proteins, and total protein and lower consumption of added sugars were positively associated with alpha-diversity. After we applied a false detection rate (FDR) correction, higher HEI-2020 scores were significantly associated with decreased abundance of Lautropia, Streptococcus gordonii, Cardiobacterium valvarum, and Cardiobacterium hominis, and increased abundance of Selenomonas sp. oral taxon 133 and Selenomonas dianae (FDR-adjusted P values < 0.10). Additionally, 28 other taxa were identified as being associated with HEI-2020 components.

Although the HEI-2020 was associated with the composition, but not the diversity, of the oral microbiome, individual HEI-2020 components were associated with both its diversity and composition. Specific dietary components may have more impact on the diversity and composition of oral microbiome than overall diet quality assessed by the HEI-2020.

Effective microorganisms pose a great potential in wastewater treatment. In the present study, effective microorganisms' formulations were developed using different organic substrates that support the growth of more beneficial microorganisms for sewage treatment. Based on the metagenomic analysis and biochemical profile information, the fish waste-based effective microorganisms' formulation was identified as the effective formulation. Metagenomic analysis showed that fish-based effective microorganisms' formulation had the Lactobacillus and Acetobacter groups of bacteria. The dominant groups were Lactobacillus pontis (64.85%), Acetobacter aceti (8.92%), and Lactobacillus reuteri (8.98%). The developed fish waste-based effective microorganisms' formulation was used to treat the sewage water with different concentrations. Effective microorganisms' formulation at 3% showed appreciable results. It recorded a significant reduction in BOD from 389.2 to 117.9 mg L-1 and COD from 820.5 to 257.1 mg L-1 in 96 h. It also significantly decreased the concentration of ammoniacal and nitrate nitrogen, phosphorus, sulphate, and coliforms. Besides, the effective microorganisms' formulation ensured the reduced level of odour from sewage water. Therefore, we can effectively use the effective microorganisms' formulation for sewage water treatment and recycling.

Species host diverse microbial communities that can impact their digestion and health, which has led to much interest in understanding the factors that influence their microbiota. We studied the developmental, environmental, and social factors that influence the microbiota of nestling barn owls (Tyto alba) through a partial cross-fostering experiment that manipulated the social and nest environment of the nestlings. We then examined the nestling microbiota before and three weeks after the exchange of nestlings between nests, along with the microbiota of the adults at the nest and nestlings in unmanipulated nests.

We found that nestlings had higher bacterial diversity and different bacterial communities than adults. The microbiota of nestlings was more like that of their mothers than their fathers, but the similarity to the father tended to increase with the amount of time the father was in close proximity to the nest, as measured from movement data. Cross-fostered offspring had higher bacterial diversity and greater changes in bacterial community composition over time than control offspring. Cross-fostering led the microbiota of the nestlings in the experiment to converge on similar bacterial communities. The microbiota of nestling owls therefore rapidly changed along with alterations to their social and nest environments.

These results highlight the dynamic nature of the microbiota during early development and that social interactions can shape microbial communities.

This article aims to explore the role of the human gut microbiota (GM) in the pathogenesis of neurological, psychiatric, and neurodevelopmental disorders, highlighting its influence on health and disease, and investigating potential therapeutic strategies targeting GM modulation.

A comprehensive analysis of the gut microbiota's composition and its interaction with the human body, particularly, its role in neurological and psychiatric conditions, is provided. The review discusses factors influencing GM composition, including birth mode, breastfeeding, diet, medications, and geography. Additionally, it examines the GM's functions, such as nutrient absorption, immune regulation, and pathogen defense, alongside its interactions with the nervous system through the gut-brain axis, neurotransmitters, and short-chain fatty acids (SCFAs).

Alterations in the GM are linked to various disorders, including Parkinson's disease, multiple sclerosis, depression, schizophrenia, ADHD, and autism. The GM influences cognitive functions, stress responses, and mood regulation. Antibiotic use disrupts GM diversity, increasing the risk of metabolic disorders, obesity, and allergic diseases. Emerging therapies such as probiotics, prebiotics, and microbiota transplantation show promise in modulating the GM and alleviating symptoms of neurological and psychiatric conditions.

The modulation of the GM represents a promising approach for personalized treatment strategies. Further research is needed to better understand the underlying mechanisms and to develop targeted therapies aimed at restoring GM balance for improved clinical outcomes.

The development of antibody drugs through animal immunization typically requires the humanization of host antibodies to address concerns about immunogenicity in humans. However, employing an animal model capable of producing human antibodies presents the opportunity to develop antibody drugs without the need for humanization. Despite the ratio of human immunoglobulin (Ig) κ to Igλ usage being approximately 60%:40%, the majority of approved antibody therapeutics are kappa antibodies, and the development of lambda antibodies as therapeutic agents has lagged behind. Therefore, in this study, we developed mice carrying the IGH and IGL loci (IGHL), which can produce human lambda antibodies, using mouse artificial chromosome (MAC) vectors. We demonstrated that IGHL mice consistently retain the human lambda antibody locus integrated on the MAC across generations and can be induced to produce specific antibodies upon antigen stimulation. These findings provide a promising platform for advancing lambda antibody drugs, which have historically been neglected.

Pollen is a crucial source of nutrients and energy for pollinators. It also provides a unique habitat and resource for microbiota. Previous research on the microbiome of pollen has largely focused on angiosperm systems, with limited research into coniferous gymnosperms. This study characterises the pollen microbiome and metabolome associated with one of the world's most widely grown tree species, Pinus radiata. Trees were sampled from locations across Canterbury, New Zealand. Repeated collections were undertaken in 2020 and 2021.

Metabolomic analysis revealed the main compounds present on P. radiata pollen to be amino acids (principally proline), and carbohydrates (fructose, glucose, and sucrose). Although phenolic compounds such as ρ-coumaric acid and catechin, and terpenoids such as dehydroabietic acid, were present at low concentrations, their strong bioactive natures mean they may be important in ecological filtering of microbiome communities on pollen. The P. radiata pollen microbiome was richer in fungal taxa compared with bacteria, which differs from many angiosperm species. Geographic range and annual variation were evaluated as drivers of microbiome assembly. Neither sampling location (geographic range) nor annual variation significantly influenced the fungal community which exhibited remarkable conservation across samples. However, some bacterial taxa exhibited sensitivity to geographic distances and yearly variations, suggesting a secondary role of these factors for some taxa. A core microbiome was identified in P. radiata pollen, characterized by a consistent presence of specific fungal and bacterial taxa across samples. While the dominant phyla, Proteobacteria and Ascomycota, align with findings from other pollen microbiome studies, unique core members were unidentified at genus level.

This tree species-specific microbiome assembly emphasizes the crucial role of the host plant in shaping the pollen microbiome. These findings contribute to a deeper understanding of pollen microbiomes in gymnosperms, shedding light on the need to look further at their ecological and functional roles.

Clinical studies strongly suggest the importance of diet quality on cognition in youth populations (15-24 years). The Mediterranean diet (MeDi) has been shown to improve cognition in contrast to the commonly consumed Western diet (WD). The gut microbiota may serve as a mechanism for diet-induced changes in cognition. Ten-week-old male Sprague Dawley rats were assigned a MeDi or WD (n=10/group) for 14 weeks. Prior to neurobehavior assessments, microbiota community composition was assessed. At the genus level, the relative abundance of four bacteria increased with the MeDi and five decreased compared to the WD. Rats in the MeDi group demonstrated cognitive flexibility and improvement in reference and working memory relative to the WD group. At the end of the study, serum cytokines were increased, and low-density lipoproteins were decreased in the MeDi group. Markers for neuroinflammation, blood-brain barrier, glial cells, and synaptic plasticity in brain regions did not differ between groups. Overall, the MeDi modulated gut microbiota, cognitive function, and serum lipid and cytokines but not gene expression in the brain compared to the WD. Further studies are needed to determine causality between diet-modulated gut microbiota, cognitive function, and immune function.

Afforestation exerts a profound impact on soil fungal communities, with the nature and extent of these changes significantly influenced by the specific tree species selected. While extensive research has addressed the aboveground ecological outcomes of afforestation, the nuanced interactions between tree species and soil fungal dynamics remain underexplored. This study investigated the effects of afforestation with Caragana microphylla (CMI), Populus simonii (PSI), and Pinus sylvestris var. mongolica (PSY) on soil fungal diversity, functional guilds, and co-occurrence networks, drawing comparisons with neighboring grasslands. Our findings reveal a significant increase in soil fungal Chao1 richness following afforestation, though the degree of enhancement varied across tree species. Specifically, CMI and PSI forests showed notable increases in fungal richness, whereas the response in PSY forests was comparatively modest. Saprotrophic fungal groups, integral to organic matter decomposition, showed a substantial increase across all afforested sites, with CMI forests exhibiting an impressive 205.58% rise. Conversely, pathogenic fungi, which can negatively impact plant health, demonstrated a marked decrease within plantation forests. Symbiotic groups, particularly ectomycorrhizal fungi, were notably enriched solely in PSI forests. Co-occurrence network analysis further indicated that afforestation alters fungal network complexity: CMI forests displayed increased network interactions, while PSI and PSY forests exhibited a reduction in network connectivity. Soil bulk density and organic carbon content emerged as key factors influencing network complexity, whereas tree species identity played a crucial role in shaping soil fungal community composition. Collectively, these results emphasize the importance of adopting a species-specific strategy for afforestation to optimize soil fungal diversity and network structure, ultimately enhancing the ecological resilience and sustainability of forest plantation ecosystems.

This study used hot-air oven drying with Bacillus subtilis KC3 inoculation to improve shrimp paste production. The fermentation rate, quality characteristics, as well as microbial profiles, were compared to those produced using sun-drying with/without inoculation. B. subtilis inoculation increased the degree of hydrolysis of shrimp paste (22.3-32.1 %) during fermentation, compared to those without inoculation (12.7-25.4 %), regardless of different drying methods (p < 0.05). The result corresponded to the faster development of shrimp paste characteristics, particularly color and browning intensity of inoculated samples when fermented for the same duration. More abundant halophilic, proteolytic, and lipolytic bacteria (p < 0.05) were also obtained in inoculated samples, confirming accelerated fermentation. Interestingly, there was no difference in proximate composition, pH, and aw among samples (p > 0.05), which were still in the range regulated by the product's standard. However, the protein and lipid degradation products such as nitrogen contents, 5'-nucleotides, free fatty acids or TBARS values, varied among samples, potentially influencing the release of desirable flavor precursors to a certain extent. The inoculation increased microbial richness and evenness/uniformity, according to next-generation sequencing analysis on microbiota profiles. Pearson's correlation also revealed that these microbiota profiles were correlated with several desirable quality characteristics to varying degrees. Thus, combining the inoculation with B. subtilis KC3 can enhance shrimp paste fermentation and quality when produced using an alternative hot-air oven while maintaining quality characteristics. The findings suggested the possibility of achieving a more efficient and consistent production process for shrimp paste.

Studies have shown correlations between gut microbiota and neurocognitive function, but little was known about the early postnatal gut microbiota and intraventricular hemorrhage (IVH). We aimed to explore the characteristics of gut microbiota in premature infants and their relationship with IVH, further exploring potential therapeutic targets.

Premature infants delivered at Peking University First Hospital from February 2023 to August 2023 were recruited as a cohort. Feces samples were collected on postnatal days 1, 3, and 5. Premature infants were divided into normal, mild IVH, and severe IVH groups based on cranial ultrasound. 16S rRNA amplicon sequencing technology was used to determine the fecal microbiota, and the results were analyzed.

Thirty-eight premature infants were enrolled. There was a significant difference in alpha and beta diversity among the three groups. The relative abundance of E. coli and A. muciniphila was different among the three groups. Further random forest analysis indicated that S. lutetiensis, L. mirabilis, and N. macacae can effectively distinguish premature infants with IVH. Finally, the phylogenetic investigation of communities by reconstruction of unobserved states2 (PICRUSt2) functional gene analysis predicted significant differences in energy metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, and membrane transport between normal and severe IVH groups.

The gut microbiota in the early postnatal period of premature infants is closely associated with the IVH status. As age increases, the differences in gut microbiota of premature infants with different degrees of IVH continue to increase, and the trend of changes with severity of IVH becomes more and more obvious. E. coli, A. muciniphila, S. lutetiensis, L. mirabilis, N. macacae, G. haemolysans, and S. oralis can effectively distinguish between IVH infants and normal premature infants. The results indicate that gut microbiota is expected to provide effective therapeutic targets for the diagnosis and treatment of IVH.