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Pan M, O'Flaherty S, Hibberd A, Gerdes S, Morovic W, Barrangou R. The curated Lactobacillus acidophilus NCFM genome provides insights into strain specificity and microevolution. BMC Genomics 2025; 26:1. [PMID: 39754036 PMCID: PMC11697832 DOI: 10.1186/s12864-024-11177-2] [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: 06/17/2024] [Accepted: 12/20/2024] [Indexed: 01/07/2025] Open
Abstract
BACKGROUND The advent of next generation sequencing technologies has enabled a surge in the number of whole genome sequences in public databases, and our understanding of the composition and evolution of bacterial genomes. Besides model organisms and pathogens, some attention has been dedicated to industrial bacteria, notably members of the Lactobacillaceae family that are commonly studied and formulated as probiotic bacteria. Of particular interest is Lactobacillus acidophilus NCFM, an extensively studied strain that has been widely commercialized for decades and is being used for the delivery of vaccines and therapeutics. RESULTS Here, we revisit the L. acidophilus genome, which was sequenced twenty years ago, and determined the core and pan genomes of 114 publicly available L. acidophilus strains, spanning commercial isolates, academic strains and clones from the scientific literature. Results indicate a predictable high level of homogeneity within the species, but also reveal surprising mis-assemblies. Furthermore, by investigating twenty one available L. acidophilus NCFM-derived variants, we document overall genomic stability, with no observed genomic re-arrangement or inversions. CONCLUSION This study provides a comparative analysis of the currently available genomes for L. acidophilus and examines microevolution patterns for several strains derived from L. acidophilus NCFM, which revealed no to very few SNPs with strains sequenced at different points in time using different sequencing technologies and platforms. This re-affirms its suitability for industrial deployment as a probiotic and its use as an engineering chassis and delivery modality for novel biotherapeutics.
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Affiliation(s)
- Meichen Pan
- Department of Food, Bioprocessing, & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Sarah O'Flaherty
- Department of Food, Bioprocessing, & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | | | | | | | - Rodolphe Barrangou
- Department of Food, Bioprocessing, & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
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2
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Beattie RE. Probiotics for oral health: a critical evaluation of bacterial strains. Front Microbiol 2024; 15:1430810. [PMID: 38979537 PMCID: PMC11228166 DOI: 10.3389/fmicb.2024.1430810] [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: 05/10/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024] Open
Abstract
Oral health is critical for total body health and well-being; however, little improvement in oral health status has occurred in the U.S. over the past 20 years. Tooth decay and gum disease remain highly prevalent, with more than 90% and 50% of adults suffering from these conditions, respectively. To combat this lack of improvement, alternative approaches to dental care are now being suggested. One such alternative therapy is probiotics for oral care. In the oral cavity, probiotic strains have been shown to reduce levels of oral pathogens, inhibit the formation of dental caries, and reduce the levels of bacteria that cause halitosis. However, as the oral care probiotic market expands, many products contain bacterial species and strains with no documented health benefits leading to confusion and mistrust among consumers and clinicians. This confusion is enhanced by the regulatory status of probiotic products which puts the onus of safety and efficacy on the manufacturer rather than a central regulatory body. The overarching goal of this review is to provide consumers and clinicians with documented evidence supporting (or refuting) the health benefits of oral care probiotics marketed for sale in the United States. This includes defining what constitutes an oral care probiotic product and a strain level analysis of candidate probiotics from the genera Streptococcus, Lactobacillus, Bifidobacterium, and Bacillus. Additionally, prebiotics and postbiotics will be discussed. Finally, a set of considerations for consumers and clinicians is provided to empower probiotic product decision making. Together, this review will improve understanding of oral care probiotics marketed in the US for dental professionals and consumers.
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3
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Huuskonen L, Anglenius H, Ahonen I, Tiihonen K. Effects of Bacterial Lysates and Metabolites on Collagen Homeostasis in TNF-α-Challenged Human Dermal Fibroblasts. Microorganisms 2023; 11:1465. [PMID: 37374969 DOI: 10.3390/microorganisms11061465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
During skin aging, the production of extracellular matrix (ECM) proteins, such as type I collagen, decreases and the synthesis of ECM-degrading matrix metalloproteinases (MMPs) rises, leading to an imbalance in homeostasis and to wrinkle formation. In this study, we examined the effects of bacterial lysates and metabolites from three bifidobacteria and five lactobacilli on collagen homeostasis in human dermal fibroblasts during challenge with tumor necrosis factor alpha (TNF-α), modeling an inflammatory condition that damages the skin's structure. Antiaging properties were measured, based on fibroblast cell viability and confluence, amount of type I pro-collagen, ratio of MMP-1 to type I pro-collagen, cytokines, and growth factors. The TNF-α challenge increased the MMP-1/type I pro-collagen ratio and levels of proinflammatory cytokines, as expected. With the probiotics, differences were clearly dependent on bacterial species, strain, and form. In general, the lysates elicited less pronounced responses in the biomarkers. Of all strains, the Bifidobacterium animalis ssp. lactis strains Bl-04 and B420 best maintained type I pro-collagen production and the MMP-1/collagen type I ratio under no-challenge and challenge conditions. Metabolites that were produced by bifidobacteria, but not their lysates, reduced several proinflammatory cytokines (IL-6, IL-8, and TNF-α) during the challenge, whereas those from lactobacilli did not. These results indicate that B. animalis ssp. lactis-produced metabolites, especially those of strains Bl-04 and B420, could support collagen homeostasis in the skin.
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Affiliation(s)
- Laura Huuskonen
- IFF Health and Biosciences, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | - Heli Anglenius
- IFF Health and Biosciences, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | | | - Kirsti Tiihonen
- IFF Health and Biosciences, Sokeritehtaantie 20, 02460 Kantvik, Finland
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4
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Novel Insights into the Molecular Mechanisms Underlying Robustness and Stability in Probiotic Bifidobacteria. Appl Environ Microbiol 2023; 89:e0008223. [PMID: 36802222 PMCID: PMC10057886 DOI: 10.1128/aem.00082-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Some probiotic bifidobacteria are highly robust and shelf-stable, whereas others are difficult to produce, due to their sensitivity to stressors. This limits their potential use as probiotics. Here, we investigate the molecular mechanisms underlying the variability in stress physiologies of Bifidobacterium animalis subsp. lactis BB-12 and Bifidobacterium longum subsp. longum BB-46, by applying a combination of classical physiological characterization and transcriptome profiling. The growth behavior, metabolite production, and global gene expression profiles differed considerably between the strains. BB-12 consistently showed higher expression levels of multiple stress-associated genes, compared to BB-46. This difference, besides higher cell surface hydrophobicity and a lower ratio of unsaturated to saturated fatty acids in the cell membrane of BB-12, should contribute to its higher robustness and stability. In BB-46, the expression of genes related to DNA repair and fatty acid biosynthesis was higher in the stationary than in the exponential phase, which was associated with enhanced stability of BB-46 cells harvested in the stationary phase. The results presented herein highlight important genomic and physiological features contributing to the stability and robustness of the studied Bifidobacterium strains. IMPORTANCE Probiotics are industrially and clinically important microorganisms. To exert their health-promoting effects, probiotic microorganisms must be administered at high counts, while maintaining their viability at the time of consumption. In addition, intestinal survival and bioactivity are important criteria for probiotics. Although bifidobacteria are among the most well-documented probiotics, the industrial-scale production and commercialization of some Bifidobacterium strains is challenged by their high sensitivity to environmental stressors encountered during manufacturing and storage. Through a comprehensive comparison of the metabolic and physiological characteristics of 2 Bifidobacterium strains, we identify key biological markers that can serve as indicators for robustness and stability in bifidobacteria.
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5
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Abstract
Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics. By definition, probiotic cells need to be viable despite being exposed to several stressors in the course of their production, storage, and administration. Examples of common stressors encountered by probiotic bifidobacteria include oxygen, acid, and bile salts. As bifidobacteria are highly heterogenous in terms of their tolerance to these stressors, poor stability and/or robustness can hamper the industrial-scale production and commercialization of many strains. Therefore, interest in the stress physiology of bifidobacteria has intensified in recent decades, and many studies have been established to obtain insights into the molecular mechanisms underlying their stability and robustness. By complementing traditional methodologies, omics technologies have opened new avenues for enhancing the understanding of the defense mechanisms of bifidobacteria against stress. In this review, we summarize and evaluate the current knowledge on the multilayered responses of bifidobacteria to stressors, including the most recent insights and hypotheses. We address the prevailing stressors that may affect the cell viability during production and use as probiotics. Besides phenotypic effects, molecular mechanisms that have been found to underlie the stress response are described. We further discuss strategies that can be applied to improve the stability of probiotic bifidobacteria and highlight knowledge gaps that should be addressed in future studies.
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Affiliation(s)
- Marie Schöpping
- Systems Biology, Discovery, Chr. Hansen A/S, Hørsholm, Denmark
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ahmad A. Zeidan
- Systems Biology, Discovery, Chr. Hansen A/S, Hørsholm, Denmark
| | - Carl Johan Franzén
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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6
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Detection and identification of Lactobacillus acidophilus species and its commercial probiotic strains using CRISPR loci-based amplicon analysis. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium. Proc Natl Acad Sci U S A 2022; 119:e2205068119. [PMID: 35857876 PMCID: PMC9335239 DOI: 10.1073/pnas.2205068119] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Bifidobacterium is a commensal bacterial genus ubiquitous in the human gastrointestinal tract, which is associated with a range of health benefits. The advent of CRISPR-based genome editing technologies provides opportunities to investigate the genetics of important bacteria and transcend the lack of genetic tools in bifidobacteria to study the basis for their health-promoting attributes. Here, we repurpose the endogenous type I-G CRISPR-Cas system and adopt an exogenous CRISPR base editor for genome engineering in B. animalis subsp. lactis, demonstrating that both genomic and epigenetic contexts drive editing outcomes across strains. We reprogrammed the endogenous type I-G system to screen for naturally occurring large deletions up to 27 kb and to generate a 500-bp deletion in tetW to abolish tetracycline resistance. A CRISPR-cytosine base editor was optimized to install C•G-to-T•A amber mutations to resensitize multiple B. lactis strains to tetracycline. Remarkably, we uncovered epigenetic patterns that are distributed unevenly among B. lactis strains, despite their genomic homogeneity, that may contribute to editing efficiency variability. Insights were also expanded to Bifidobacterium longum subsp. infantis to emphasize the broad relevance of these findings. This study highlights the need to develop individualized CRISPR-based genome engineering approaches for distinct bacterial strains and opens avenues for engineering of next generation probiotics.
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8
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Cheng J, Laitila A, Ouwehand AC. Bifidobacterium animalis subsp. lactis HN019 Effects on Gut Health: A Review. Front Nutr 2022; 8:790561. [PMID: 34970580 PMCID: PMC8712437 DOI: 10.3389/fnut.2021.790561] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/22/2021] [Indexed: 12/19/2022] Open
Abstract
Optimal gut motility is central to bowel function and gut health. The link between the gut dysmotility related disorders and dysfunctional-intestinal barriers has led to a hypothesis that certain probiotics could help in normalizing gut motility and maintain gut health. This review investigates the roles of Bifidobacterium animalis subsp. lactis HN019 (B. lactis HN019™) on gut health, and its mechanisms of action in various pre-clinical and clinical studies. Research supports the hypothesis that B. lactis HN019™ has a beneficial role in maintaining intestinal barrier function during gastrointestinal infections by competing and excluding potential pathogens via different mechanisms; maintaining normal tight junction function in vitro; and regulating host immune defense toward pathogens in both in vitro and human studies. This has been observed to lead to reduced incidence of diarrhea. Interestingly, B. lactis HN019™ also supports normal physiological function in immunosenescent elderly and competes and excludes potential pathogens. Furthermore, B. lactis HN019™ reduced intestinal transit time and increased bowel movement frequency in functional constipation, potentially by modulating gut–brain–microbiota axis, mainly via serotonin signaling pathway, through short chain fatty acids derived from microbial fermentation. B. lactis HN019™ is thus a probiotic that can contribute to relieving gut dysmotility related disorders.
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Affiliation(s)
- Jing Cheng
- International Flavors & Fragrances Inc., Global Health and Nutrition Science, Danisco Sweeteners Oy, Kantvik, Finland
| | - Arja Laitila
- International Flavors & Fragrances Inc., Global Health and Nutrition Science, Danisco Sweeteners Oy, Kantvik, Finland
| | - Arthur C Ouwehand
- International Flavors & Fragrances Inc., Global Health and Nutrition Science, Danisco Sweeteners Oy, Kantvik, Finland
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9
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Zhou Z, He N, Han Q, Liu S, Xue R, Hao J, Li S. Characterization and Application of a New β-Galactosidase Gal42 From Marine Bacterium Bacillus sp. BY02. Front Microbiol 2021; 12:742300. [PMID: 34759900 PMCID: PMC8573354 DOI: 10.3389/fmicb.2021.742300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/16/2021] [Indexed: 12/04/2022] Open
Abstract
β-Galactosidase plays an important role in medicine and dairy industry. In this study, a new glycoside hydrolase family 42 (GH42) β-galactosidase-encoding gene, gal42, was cloned from a newly isolated marine bacterium Bacillus sp. BY02 and expressed in Escherichia coli. Structural characterization indicated that the encoding β-galactosidase, Gal42, is a homotrimer in solution, and homology modeling indicated that it retains the zinc binding sites of the Cys cluster. The reaction activity of Gal42 was significantly increased by Zn2+ (229.6%) and other divalent metal ions (Mn2+, Mg2+, and Co2+), while its activity was inhibited by EDTA (53.9%). Meanwhile, the thermo-stability of the Gal42 was also significantly enhanced by 5 and 10 mM of zinc ion supplement, which suggested that the “Cys-Zn” motif played important roles in both structural stability and catalytic function. Furthermore, Gal42 showed effective lactose hydrolysis activity, which makes the enzyme hydrolyze the lactose in milk effectively. These properties make Gal42 a potential candidate in food technology.
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Affiliation(s)
- Zihan Zhou
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ningning He
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Qi Han
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Songshen Liu
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ruikun Xue
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Jianhua Hao
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Jiangsu Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resource, Lianyungang, China
| | - Shangyong Li
- School of Basic Medicine, Qingdao University, Qingdao, China
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10
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Genome of Bifidobacterium longum NCIM 5672 provides insights into its acid-tolerance mechanism and probiotic properties. Arch Microbiol 2021; 203:6109-6118. [PMID: 34553262 DOI: 10.1007/s00203-021-02573-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 01/02/2023]
Abstract
Bifidobacterium longum NCIM 5672 is a probiotic strain isolated from the Indian infant feces. The probiotic efficacy of Bifidobacteria is majorly affected by its acid tolerance. This study determined the probiotic properties and acid-tolerance mechanism of B. longum NCIM 5672 using whole-genome sequencing. The genome annotation is carried out using the RAST web server and NCBI PGAAP. The draft genome sequence of this strain, assembled in 63 contigs, consists of 22,46,978 base pairs, 1900 coding sequences and a GC content of 59.6%. The genome annotation revealed that seven candidate genes might be involved in regulating the acid tolerance of B. longum NCIM 5672. Furthermore, the presence of genes associated with immunomodulation and cell adhesion support the probiotic background of the strain. The analysis of candidate acid- tolerance-associated genes revealed three genes, argC, argH, and dapA, may play an essential role in high acid tolerance in B. longum NCIM 5672. The results of RT-qPCR supported this conclusion. Altogether, the results presented here supply an effective way to select acid-resistant strains for the food industry and provide new strategies to enhance this species' industrial applications and health-promoting properties.
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11
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Ambrogi V, Bottacini F, Cao L, Kuipers B, Schoterman M, van Sinderen D. Galacto-oligosaccharides as infant prebiotics: production, application, bioactive activities and future perspectives. Crit Rev Food Sci Nutr 2021; 63:753-766. [PMID: 34477457 DOI: 10.1080/10408398.2021.1953437] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Galacto-oligosaccharides (GOS) are non-digestible oligosaccharides characterized by a mix of structures that vary in their degree of polymerization (DP) and glycosidic linkage between the galactose moieties or between galactose and glucose. They have enjoyed extensive scientific scrutiny, and their health-promoting effects are supported by a large number of scientific and clinical studies. A variety of GOS-associated health-promoting effects have been reported, such as growth promotion of beneficial bacteria, in particular bifidobacteria and lactobacilli, inhibition of pathogen adhesion and improvement of gut barrier function. GOS have attracted significant interest from food industries for their versatility as a bioactive ingredient and in particular as a functional component of infant formulations. These oligosaccharides are produced in a kinetically-controlled reaction involving lactose transgalactosylation, being catalyzed by particular β-galactosidases of bacterial or fungal origin. Despite the well-established technology applied for GOS production, this process may still meet with technological challenges when employed at an industrial scale. The current review will cover relevant scientific literature on the beneficial physiological properties of GOS as a prebiotic for the infant gut microbiota, details of GOS structures, the associated reaction mechanism of β-galactosidase, and its (large-scale) production.
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Affiliation(s)
- Valentina Ambrogi
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Linqiu Cao
- FrieslandCampina, Amersfoort, The Netherlands
| | - Bas Kuipers
- FrieslandCampina, Amersfoort, The Netherlands
| | | | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
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12
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Dang TD, Yong CC, Rheem S, Oh S. Optimizing the composition of the medium for the viable cells of Bifidobacterium animalis subsp. lactis JNU306 using response surface methodology. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 63:603-613. [PMID: 34189508 PMCID: PMC8204007 DOI: 10.5187/jast.2021.e43] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/03/2022]
Abstract
This research improved the growth potential of Bifidobacterium
animalis subsp lactis strain JNU306, a commercial medium that is
appropriate for large-scale production, in yeast extract, soy peptone, glucose,
L-cysteine, and ferrous sulfate. Response surface methodology (RSM) was used to
optimize the components of this medium, using a central composite design and
subsequent analyses. A second-order polynomial regression model, which was
fitted to the data at first, significantly lacked fitness. Thus, through further
analyses, the model with linear and quadratic terms plus two-way, three-way, and
four-way interactions was selected as the final model. Through this model, the
optimized medium composition was found as 2.8791% yeast extract, 2.8030% peptone
soy, 0.6196% glucose, 0.2823% L-cysteine, and 0.0055% ferrous sulfate, w/v. This
optimized medium ensured that the maximum biomass was no lower than the biomass
from the commonly used blood-liver (BL) medium. The application of RSM improved
the biomass production of this strain in a more cost-effective way by creating
an optimum medium. This result shows that B. animalis subsp
lactis JNU306 may be used as a commercial starter culture
in manufacturing probiotics, including dairy products.
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Affiliation(s)
- Thi Duyen Dang
- Department of Animal Science, Chonnam National University, Gwangju 61186, Korea.,Western Highlands Agriculture and Forestry Science Institute, Buon Ma Thuot, Dak Lak Province 63161, Viet Nam
| | - Cheng Chung Yong
- Department of Animal Science, Chonnam National University, Gwangju 61186, Korea
| | - Sungsue Rheem
- Graduate School of Public Administration, Korea University, Sejong 30019, Korea
| | - Sejong Oh
- Department of Animal Science, Chonnam National University, Gwangju 61186, Korea
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13
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Engevik MA, Danhof HA, Hall A, Engevik KA, Horvath TD, Haidacher SJ, Hoch KM, Endres BT, Bajaj M, Garey KW, Britton RA, Spinler JK, Haag AM, Versalovic J. The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal. BMC Microbiol 2021; 21:154. [PMID: 34030655 PMCID: PMC8145834 DOI: 10.1186/s12866-021-02166-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/30/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Bifidobacteria are commensal microbes of the mammalian gastrointestinal tract. In this study, we aimed to identify the intestinal colonization mechanisms and key metabolic pathways implemented by Bifidobacterium dentium. RESULTS B. dentium displayed acid resistance, with high viability over a pH range from 4 to 7; findings that correlated to the expression of Na+/H+ antiporters within the B. dentium genome. B. dentium was found to adhere to human MUC2+ mucus and harbor mucin-binding proteins. Using microbial phenotyping microarrays and fully-defined media, we demonstrated that in the absence of glucose, B. dentium could metabolize a variety of nutrient sources. Many of these nutrient sources were plant-based, suggesting that B. dentium can consume dietary substances. In contrast to other bifidobacteria, B. dentium was largely unable to grow on compounds found in human mucus; a finding that was supported by its glycosyl hydrolase (GH) profile. Of the proteins identified in B. dentium by proteomic analysis, a large cohort of proteins were associated with diverse metabolic pathways, indicating metabolic plasticity which supports colonization of the dynamic gastrointestinal environment. CONCLUSIONS Taken together, we conclude that B. dentium is well adapted for commensalism in the gastrointestinal tract.
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Affiliation(s)
- Melinda A Engevik
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA.
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
- Department of Regernative Medicine & Cell Biology, Medical University of South Carolina, SC, Charleston, USA.
| | - Heather A Danhof
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anne Hall
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Kristen A Engevik
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Thomas D Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Sigmund J Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Kathleen M Hoch
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Bradley T Endres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Meghna Bajaj
- Department of Chemistry and Physics, and Department of Biotechnology, Alcorn State University, Lorman, MS, 39096, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Robert A Britton
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer K Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Anthony M Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
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14
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Luo Y, Xiao Y, Zhao J, Zhang H, Chen W, Zhai Q. The role of mucin and oligosaccharides via cross-feeding activities by Bifidobacterium: A review. Int J Biol Macromol 2020; 167:1329-1337. [PMID: 33202267 DOI: 10.1016/j.ijbiomac.2020.11.087] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
Bifidobacteria are one genus of low-abundance gut commensals that are often associated with host health-promoting effects. Bifidobacteria can degrade various dietary fibers (i.e., galactooligosaccharides, fructooligosaccharides, inulin), and are reported as one of the few gut-dwelling microbes that can utilize host-derived carbohydrates (mucin and human milk oligosaccharides). Previous studies have noted that the superior carbohydrate-metabolizing abilities of bifidobacteria facilitate the intestinal colonization of this genus and also benefit other gut symbionts, in particular butyrate-producing bacteria, via cooperative metabolic interactions. Given that such cross-feeding activities of bifidobacteria on mucin and oligosaccharides have not been systematically summarized, here we review the carbohydrate-degrading capabilities of various bifidobacterial strains that were identified in vitro experiments, the core enzymes involved in the degradation mechanisms, and social behavior between bifidobacteria and other intestinal microbes, as well as among species-specific bifidobacterial strains. The purpose of this review is to enhance our understanding of the interactions of prebiotics and probiotics, which sheds new light on the future use of oligosaccharides and bifidobacteria for nutritional intervention or clinical application.
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Affiliation(s)
- Yanhong Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China; Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
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15
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Zhong C, Ukowitz C, Domig KJ, Nidetzky B. Short-Chain Cello-oligosaccharides: Intensification and Scale-up of Their Enzymatic Production and Selective Growth Promotion among Probiotic Bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8557-8567. [PMID: 32687709 PMCID: PMC7458430 DOI: 10.1021/acs.jafc.0c02660] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Short-chain cello-oligosaccharides (COS; degree of polymerization, DP ≤ 6) are promising water-soluble dietary fibers. An efficient approach to their bottom-up synthesis is from sucrose and glucose using glycoside phosphorylases. Here, we show the intensification and scale up (20 mL; gram scale) of COS production to 93 g/L product and in 82 mol % yield from sucrose (0.5 M). The COS were comprised of DP 3 (33 wt %), DP 4 (34 wt %), DP 5 (24 wt %), and DP 6 (9 wt %) and involved minimal loss (≤10 mol %) to insoluble fractions. After isolation (≥95% purity; ≥90% yield), the COS were examined for growth promotion of probiotic strains. Benchmarked against inulin, trans-galacto-oligosaccharides, and cellobiose, COS showed up to 4.1-fold stimulation of cell density for Clostridium butyricum, Lactococcus lactis subsp. lactis, Lactobacillus paracasei subsp. paracasei, and Lactobacillus rhamnosus but were less efficient with Bifidobacterium sp. This study shows the COS as selectively functional carbohydrates with prebiotic potential and demonstrates their efficient enzymatic production.
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Affiliation(s)
- Chao Zhong
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Graz 8010, Austria
| | - Christina Ukowitz
- Institute
of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences
(BOKU), Vienna 1190, Austria
| | - Konrad J. Domig
- Institute
of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences
(BOKU), Vienna 1190, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Graz 8010, Austria
- Austrian
Centre of Industrial Biotechnology (acib), Graz 8010, Austria
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16
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Wong CB, Odamaki T, Xiao JZ. Insights into the reason of Human-Residential Bifidobacteria (HRB) being the natural inhabitants of the human gut and their potential health-promoting benefits. FEMS Microbiol Rev 2020; 44:369-385. [PMID: 32319522 PMCID: PMC7326374 DOI: 10.1093/femsre/fuaa010] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Members of Bifidobacterium are among the first microbes to colonise the human gut, and certain species are recognised as the natural resident of human gut microbiota. Their presence in the human gut has been associated with health-promoting benefits and reduced abundance of this genus is linked with several diseases. Bifidobacterial species are assumed to have coevolved with their hosts and include members that are naturally present in the human gut, thus recognised as Human-Residential Bifidobacteria (HRB). The physiological functions of these bacteria and the reasons why they occur in and how they adapt to the human gut are of immense significance. In this review, we provide an overview of the biology of bifidobacteria as members of the human gut microbiota and address factors that contribute to the preponderance of HRB in the human gut. We highlight some of the important genetic attributes and core physiological traits of these bacteria that may explain their adaptive advantages, ecological fitness, and competitiveness in the human gut. This review will help to widen our understanding of one of the most important human commensal bacteria and shed light on the practical consideration for selecting bifidobacterial strains as human probiotics.
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Affiliation(s)
- Chyn Boon Wong
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
| | - Jin-zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
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17
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Tsukimi T, Watabe T, Tanaka K, Sato MP, Suzuki H, Tomita M, Fukuda S. Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals. J Genomics 2020; 8:37-42. [PMID: 32328204 PMCID: PMC7171383 DOI: 10.7150/jgen.38516] [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: 07/17/2019] [Accepted: 11/20/2019] [Indexed: 11/05/2022] Open
Abstract
Bifidobacterium species are well recognized as probiotics and colonized in various parts of the human body. Here, we report the draft genome sequences of Bifidobacterium animalis isolated from two healthy Japanese volunteers, one of which was sampled twice before and after a 10-year interval. A core genome phylogeny analysis indicated that the strains isolated from the same volunteer were closely related. This paper is the first report of multiple draft genome sequences of B. animalis independently isolated from the same individual and provides insight into the probiotic potential of a member of this species.
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Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Tsubasa Watabe
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Kazuki Tanaka
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Mitsuhiko P Sato
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka 812-8582, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Faculty of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,Faculty of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, 3-25-13 Tonomachi, Kawasaki, Kanagawa 210-0821, Japan.,Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Metabologenomics, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
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18
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Mora D, Filardi R, Arioli S, Boeren S, Aalvink S, de Vos WM. Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3. Microb Biotechnol 2019; 12:1371-1386. [PMID: 31402586 PMCID: PMC6801179 DOI: 10.1111/1751-7915.13476] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/17/2022] Open
Abstract
The growing commercial interest in multi-strain formulations marketed as probiotics has not been accompanied by an equal increase in the evaluation of quality levels of these biotechnological products. The multi-strain product VSL#3 was used as a model to setup a microbiological characterization that could be extended to other formulations with high complexity. Shotgun metagenomics by deep Illumina sequencing was applied to DNA isolated from the commercial VSL#3 product to confirm strains identity safety and composition. Single-cell analysis was used to evaluate the cell viability, and β-galactosidase and urease activity have been used as marker to monitor the reproducibility of the production process. Similarly, these lots were characterized in detail by a metaproteomics approach for which a robust protein extraction protocol was combined with advanced mass spectrometry. The results identified over 1600 protein groups belonging to all strains present in the VSL#3 formulation. Of interest, only 3.2 % proteins showed significant differences mainly related to small variations in strain abundance. The protocols developed in this study addressed several quality criteria that are relevant for marketed multi-strain products and these represent the first efforts to define the quality of complex probiotic formulations such as VSL#3.
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Affiliation(s)
- Diego Mora
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Rossella Filardi
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Stefania Arioli
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Sjef Boeren
- Laboratory of BiochemistryWageningen UniversityWageningenThe Netherlands
| | - Steven Aalvink
- Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
| | - Willem M. de Vos
- Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
- Human Microbiome Research Program Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
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19
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20
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Gao D, Chang K, Ding G, Wu H, Chen Y, Jia M, Liu X, Wang S, Jin Y, Pan H, Li H. Genomic insights into a robust gamma-aminobutyric acid-producer Lactobacillus brevis CD0817. AMB Express 2019; 9:72. [PMID: 31127390 PMCID: PMC6534642 DOI: 10.1186/s13568-019-0799-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/16/2019] [Indexed: 01/22/2023] Open
Abstract
Lactobacillus brevis CD0817, a strain isolated from a healthy adult gut, was currently the most efficient lactic acid bacterial cell factory for gamma-aminobutyric acid. In this study, the complete genome sequence of CD0817 was determined and compared with some related L. brevis genomes. The CD0817 genome consists of one 2,990,570-bp chromosome and four plasmids. The comparative genomic and phylogenetic analysis revealed that L. brevis CD0817 was not very conserved with low GABA-producing L. brevis strains. A significant divergence was that CD0817 harbors only the gadCA operon whereas the low GABA-producing L. brevis strains contain the operon and gadB. The gadB seemed to only marginally contribute to the accumulation of GABA. The high GABA production ability of CD0817 may be associated with its extraordinary genome.
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21
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Segawa T, Fukuchi S, Bodington D, Tsuchida S, Mbehang Nguema PP, Mori H, Ushida K. Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior. Microorganisms 2019; 7:microorganisms7040099. [PMID: 30987363 PMCID: PMC6518056 DOI: 10.3390/microorganisms7040099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 01/18/2023] Open
Abstract
Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan.
| | - Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan.
| | - Dylan Bodington
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
| | - Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
| | | | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
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22
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Dissecting the Evolutionary Development of the Species Bifidobacterium animalis through Comparative Genomics Analyses. Appl Environ Microbiol 2019; 85:AEM.02806-18. [PMID: 30709821 DOI: 10.1128/aem.02806-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
Bifidobacteria are members of the gut microbiota of animals, including mammals, birds, and social insects. In this study, we analyzed and determined the pangenome of Bifidobacterium animalis species, encompassing B. animalis subsp. animalis and the B. animalis subsp. lactis taxon, which is one of the most intensely exploited probiotic bifidobacterial species. In order to reveal differences within the B. animalis species, detailed comparative genomics and phylogenomics analyses were performed, indicating that these two subspecies recently arose through divergent evolutionary events. A subspecies-specific core genome was identified for both B. animalis subspecies, revealing the existence of subspecies-defining genes involved in carbohydrate metabolism. Notably, these in silico analyses coupled with carbohydrate profiling assays suggest genetic adaptations toward a distinct glycan milieu for each member of the B. animalis subspecies, resulting in a divergent evolutionary development of the two subspecies.IMPORTANCE The majority of characterized B. animalis strains have been isolated from human fecal samples. In order to explore genome variability within this species, we isolated 15 novel strains from the gastrointestinal tracts of different animals, including mammals and birds. The present study allowed us to reconstruct the pangenome of this taxon, including the genome contents of 56 B. animalis strains. Through careful assessment of subspecies-specific core genes of the B. animalis subsp. animalis/lactis taxon, we identified genes encoding enzymes involved in carbohydrate transport and metabolism, while unveiling specific gene acquisition and loss events that caused the evolutionary emergence of these two subspecies.
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23
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Fenster K, Freeburg B, Hollard C, Wong C, Rønhave Laursen R, Ouwehand AC. The Production and Delivery of Probiotics: A Review of a Practical Approach. Microorganisms 2019; 7:E83. [PMID: 30884906 PMCID: PMC6463069 DOI: 10.3390/microorganisms7030083] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 01/13/2023] Open
Abstract
To successfully deliver probiotic benefits to the consumer, several criteria must be met. Here, we discuss the often-forgotten challenges in manufacturing the strains and incorporating them in consumer products that provide the required dose at the end of shelf life. For manufacturing, an intricate production process is required that ensures both high yield and stability and must also be able to meet requirements such as the absence of specific allergens, which precludes some obvious culture media ingredients. Reproducibility is important to ensure constant high performance and quality. To ensure this, quality control throughout the whole production process, from raw materials to the final product, is essential, as is the documentation of this quality control. Consumer product formulation requires extensive skill and experience. Traditionally, probiotic lactic acid bacteria and bifidobacteria have been incorporated in fermented dairy products, with limited shelf life and refrigerated storage. Currently, probiotics may be incorporated in dietary supplements and other "dry" food matrices which are expected to have up to 24 months of stability at ambient temperature and humidity. With the right choice of production process, product formulation, and strains, high-quality probiotics can be successfully included in a wide variety of delivery formats to suit consumer requirements.
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Affiliation(s)
- Kurt Fenster
- DuPont Nutrition and Health, Madison, WI 53716, USA.
| | | | - Chris Hollard
- DuPont Nutrition and Health, Madison, WI 53716, USA.
| | - Connie Wong
- DuPont Nutrition and Health, Madison, WI 53716, USA.
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24
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Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS, Makharia GK. Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls. Front Microbiol 2019; 10:164. [PMID: 30800106 PMCID: PMC6376745 DOI: 10.3389/fmicb.2019.00164] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022] Open
Abstract
Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.
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Affiliation(s)
- Rahul Bodkhe
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Sudarshan A Shetty
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Dhiraj P Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Anil K Verma
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Khushbo Bhatia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Asha Mishra
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Gurvinder Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Pranav Pande
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | | | | | | | - Vineet Ahuja
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
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25
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Dimidi E, Zdanaviciene A, Christodoulides S, Taheri S, Louis P, Duncan PI, Emami N, Crabbé R, De Castro CA, McLean P, Bergonzelli GE, Whelan K, Mark Scott S. Randomised clinical trial: Bifidobacterium lactis NCC2818 probiotic vs placebo, and impact on gut transit time, symptoms, and gut microbiology in chronic constipation. Aliment Pharmacol Ther 2019; 49:251-264. [PMID: 30585341 DOI: 10.1111/apt.15073] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/15/2018] [Accepted: 11/03/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Constipation is a prevalent gastrointestinal disorder. Patient dissatisfaction with prescribed medications is common, and there is need for alternative management strategies. Evidence shows that Bifidobacterium species may be beneficial in constipation. AIM To investigate changes in physiological and clinical measures of gut function in patients with chronic constipation following the consumption of Bifidobacterium lactis NCC2818, compared to placebo. METHODS Participants were randomised to a 4-week supplementation with B. lactis NCC2818 (1.5 x 1010 CFU/d) or placebo. Gut transit time was measured using a radio-opaque marker, while symptoms and quality of life were assessed using validated questionnaires. Gut microbiota composition was assessed using quantitative polymerase chain reaction. Analysis of covariance was used for normally distributed variables, and Mann-Whitney test for non-normally distributed variables. RESULTS Seventy-five participants were randomised. There was no significant difference between the probiotic and placebo groups in gut transit time change from baseline to week 2 (-11.7 hours, SD 33.0 hours vs -12.9 hours, SD 33.6 hours; P = 0.863) or to week 4 (-20.4 hours, SD 32.5 h vs -8.7 hours, SD 33.8 hours; P = 0.103). There were also no improvements in stool output, symptoms, or quality of life. No differences were found in Bifidobacterium concentrations between the probiotic and placebo groups at week 4 (9.5 log10 /g dry faeces, SD 0.3 vs 9.4 log10 /g, SD 1.0; P = 0.509). CONCLUSIONS Bifidobacterium lactis NCC2818 was not effective in the management of mild chronic constipation. This study highlights the importance of further studies and their publication to better understand the strain-specific effects of probiotics.
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Affiliation(s)
- Eirini Dimidi
- Department of Nutritional Sciences, King's College London, London, UK
| | | | - Stephanos Christodoulides
- Department of Nutritional Sciences, King's College London, London, UK.,Blizard Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Shiva Taheri
- Blizard Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Petra Louis
- Microbiology Group, Gut Health Theme, The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Peter I Duncan
- Department of Gastrointestinal Health, Nestlé Research, Lausanne, Switzerland
| | - Nashmil Emami
- Clinical Development Unit, Nestlé Research, Lausanne, Switzerland
| | - Rafael Crabbé
- Clinical Development Unit, Nestlé Research, Lausanne, Switzerland
| | | | - Peter McLean
- Department of Gastrointestinal Health, Nestlé Research, Lausanne, Switzerland
| | | | - Kevin Whelan
- Department of Nutritional Sciences, King's College London, London, UK
| | - S Mark Scott
- Blizard Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
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26
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Taylor AJ, Stasiewicz MJ. CRISPR-Based Subtyping Using Whole Genome Sequence Data Does Not Improve Differentiation of Persistent and Sporadic Listeria monocytogenes Strains. J Food Sci 2019; 84:319-326. [PMID: 30620778 DOI: 10.1111/1750-3841.14426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Abstract
The foodborne pathogen Listeria monocytogenes can persist in food-associated environments for long periods. To identify persistent strains, the subtyping method pulsed-field gel electrophoresis (PFGE) is being replaced by whole genome sequence (WGS)-based subtyping. It was hypothesized that analyzing specific mobile genetic elements, CRISPR (Clustered Regularly Interspaced Short Palindromic Short Repeat) spacer arrays, extracted from WGS data, could differentiate persistent and sporadic isolates within WGS-based clades. To test this hypothesis, 175 L. monocytogenes isolates, previously recovered from retail delis, were analyzed for CRISPR spacers using CRISPRFinder. These isolates represent 23 phylogenetic clades defined by WGS-based single nucleotide polymorphisms and closely related sporadic isolates. In 174/175 (99.4%) of isolates, at least one array with one spacer was identified. Numbers of spacers in a single array ranged from 1 to 28 spacers. Isolates were grouped into 13 spacer patterns (SPs) based on observed variability in the presence or absence of whole spacers. SP variation was consistent with WGS-based clades forming patterns of (i) one SP to one clade, (ii) one SP across many clades, (iii) many SPs within one clade, and (iv) many SPs across many clades. Unfortunately, SPs did not appear to differentiate persistent from sporadic isolates within any WGS-based clade. Overall, these data show that (i) CRISPR arrays are common in WGS data for these food-associated L. monocytogenes and (ii) CRISPR subtyping cannot improve the identification of persistent or sporadic isolates from retail delis. PRACTICAL APPLICATION: CRISPR spacer arrays are present in L. monocytogenes isolates and CRISPR spacer patterns are consistent with previous subtyping methods. These mobile genetic artifacts cannot improve the differentiation between persistent and sporadic L. monocytogenes isolates, used in this study. While CRISPR-based subtyping has been useful for other pathogens, it is not useful in understanding persistence in L. monocytogenes. Thus, the food safety community might be able to use CRISPRs in other areas, but CRISPRs do not seem likely to improve the differentiation of persistence in L. monocytogenes isolates from retail delis.
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Affiliation(s)
- Alexander J Taylor
- Dept. of Food Science and Human Nutrition, Coll. of Agricultural, Consumer, and Environmental Sciences, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew J Stasiewicz
- Dept. of Food Science and Human Nutrition, Coll. of Agricultural, Consumer, and Environmental Sciences, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Leboš-Pavunc A, Penava L, Ranilović J, Novak J, Banić M, Butorac K, Petrović E, Mihaljević-Herman V, Bendelja K, Savić-Mlakar A, Durgo K, Kos B, Šušković J. Influence of Dehydrated Wheat/Rice Cereal Matrices on Probiotic Activity of Bifidobacterium animalis ssp. lactis BB-12® §. Food Technol Biotechnol 2019; 57:147-158. [PMID: 31537964 PMCID: PMC6718970 DOI: 10.17113/ftb.57.02.19.6142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Three novel dehydrated wheat/rice cereal functional products with an addition of well documented probiotic Bifidobacterium animalis ssp. lactis BB-12® (BB-12®) were developed in Podravka factory for the infants older than 4 months: instant rice cereal, instant rice cereal with fruits and instant wheat cereal with vanilla. Notably, the number of viable BB-12® cells in each of the novel products was higher than the required minimal number of probiotic cells per gram of product (106 CFU/g) during the storage period of 106 weeks. Therefore, BB-12® strain recovery and genome stability were evaluated by strain-specific polimerase chain reaction and amplified fragment length polymorphism fingerprinting analysis. Further aim was to evaluate the influence of these three different cereal food matrices on specific probiotic properties of BB-12® strain in vitro. Applied food matrices positively influenced the survival in the simulated conditions of the gastrointestinal tract and antagonistic activity against undesirable microorganisms, while no influence on auto- and coaggregation ability of B. animalis ssp. lactis BB-12® was observed. Adhesion to extracellular matrix proteins and intestinal epithelial Caco-2 cells together with antibacterial activity emphasized competitive pathogen exclusion from Caco-2 cells by probiotic strain BB-12®.
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Affiliation(s)
- Andreja Leboš-Pavunc
- University of Zagreb, Faculty of Food Technology and Biotechnology, Laboratory of Antibiotic, Enzyme, Probiotic and Starter Culture Technologies, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Lenkica Penava
- Belupo, Pharmaceuticals & Cosmetics Inc., Nutraceuticals, Business Development and Registration, I. Savica 36, 10000 Zagreb, Croatia
| | - Jasmina Ranilović
- Podravka, Research and Development, Ante Starčevića 32, 48000 Koprivnica, Croatia
| | - Jasna Novak
- University of Zagreb, Faculty of Food Technology and Biotechnology, Laboratory of Antibiotic, Enzyme, Probiotic and Starter Culture Technologies, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Martina Banić
- University of Zagreb, Faculty of Food Technology and Biotechnology, Laboratory of Antibiotic, Enzyme, Probiotic and Starter Culture Technologies, Pierottijeva 6, 10000 Zagreb, Croatia.,University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Rockefellerova 10, 10000 Zagreb, Croatia
| | - Katarina Butorac
- University of Zagreb, Faculty of Food Technology and Biotechnology, Laboratory of Antibiotic, Enzyme, Probiotic and Starter Culture Technologies, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Emilija Petrović
- Podravka, Research and Development, Ante Starčevića 32, 48000 Koprivnica, Croatia
| | | | - Krešo Bendelja
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Rockefellerova 10, 10000 Zagreb, Croatia
| | - Ana Savić-Mlakar
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Rockefellerova 10, 10000 Zagreb, Croatia
| | - Ksenija Durgo
- University of Zagreb, Faculty of Food Technology and Biotechnology, Laboratory for Biology and Microbial Genetics, Pierottijeva 6, 10000 Zagreb, Croatia.,Podravka, Research and Development, Ante Starčevića 32, 48000 Koprivnica, Croatia
| | - Blaženka Kos
- University of Zagreb, Faculty of Food Technology and Biotechnology, Laboratory of Antibiotic, Enzyme, Probiotic and Starter Culture Technologies, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jagoda Šušković
- University of Zagreb, Faculty of Food Technology and Biotechnology, Laboratory of Antibiotic, Enzyme, Probiotic and Starter Culture Technologies, Pierottijeva 6, 10000 Zagreb, Croatia
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Morovic W, Roos P, Zabel B, Hidalgo-Cantabrana C, Kiefer A, Barrangou R. Transcriptional and Functional Analysis of Bifidobacterium animalis subsp. lactis Exposure to Tetracycline. Appl Environ Microbiol 2018; 84:e01999-18. [PMID: 30266728 PMCID: PMC6238047 DOI: 10.1128/aem.01999-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/25/2018] [Indexed: 12/11/2022] Open
Abstract
Commercial probiotic bacteria must be tested for acquired antibiotic resistance elements to avoid potential transfer to pathogens. The European Food Safety Authority recommends testing resistance using microdilution culture techniques previously used to establish inhibitory thresholds for the Bifidobacterium genus. Many Bifidobacterium animalis subsp. lactis strains exhibit increased resistance to tetracycline, historically attributed to the ribosomal protection gene tet(W). However, some strains that harbor genetically identical tet(W) genes show various inhibition levels, suggesting that other genetic elements also contribute to observed differences. Here, we adapted several molecular assays to confirm the inhibition of B. animalis subsp. lactis strains Bl-04 and HN019 and employed RNA sequencing to assess the transcriptional differences related to genomic polymorphisms. We detected specific stress responses to the antibiotic by correlating ATP concentration to number of viable genome copies from droplet digital PCR and found that the bacteria were still metabolically active in high drug concentrations. Transcriptional analyses revealed that several polymorphic regions, particularly a novel multidrug efflux transporter, were differentially expressed between the strains in each experimental condition, likely having phenotypic effects. We also found that the tet(W) gene was upregulated only during subinhibitory tetracycline concentrations, while two novel tetracycline resistance genes were upregulated at high concentrations. Furthermore, many genes involved in amino acid metabolism and transporter function were upregulated, while genes for complex carbohydrate utilization, protein metabolism, and clustered regularly interspaced short palindromic repeat(s) (CRISPR)-Cas systems were downregulated. These results provide high-throughput means for assessing antibiotic resistances of two highly related probiotic strains and determine the genetic network that contributes to the global tetracycline response.IMPORTANCEBifidobacterium animalis subsp. lactis is widely used in human food and dietary supplements. Although well documented to be safe, B. animalis subsp. lactis strains must not contain transferable antibiotic resistance elements. Many B. animalis subsp. lactis strains have different resistance measurements despite being genetically similar, and the reasons for this are not well understood. In the current study, we sought to examine how genomic differences between two closely related industrial B. animalis subsp. lactis strains contribute to different resistance levels. This will lead to a better understanding of resistance, identify future targets for analysis of transferability, and expand our understanding of tetracycline resistance in bacteria.
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Affiliation(s)
- Wesley Morovic
- Genomics & Microbiome Science, DuPont Nutrition & Health, Madison, Wisconsin, USA
| | - Paige Roos
- Genomics Laboratory, DuPont Pioneer, Johnston, Iowa, USA
| | - Bryan Zabel
- Genomics & Microbiome Science, DuPont Nutrition & Health, Madison, Wisconsin, USA
| | - Claudio Hidalgo-Cantabrana
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Anthony Kiefer
- Probiotic Development, DuPont Nutrition & Health, Madison, Wisconsin, USA
| | - Rodolphe Barrangou
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
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29
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Liu Y, Chen W, Yu Y, Zhang Q, Qu Q, Duan W, Zhao Y, Weng S, Zhao G, Dou T. Identification and characterisation of bifidobacteria in infant formula milk powder obtained from the Chinese market. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Hansen SJZ, Morovic W, DeMeules M, Stahl B, Sindelar CW. Absolute Enumeration of Probiotic Strains Lactobacillus acidophilus NCFM ® and Bifidobacterium animalis subsp. lactis Bl-04 ® via Chip-Based Digital PCR. Front Microbiol 2018; 9:704. [PMID: 29696008 PMCID: PMC5904286 DOI: 10.3389/fmicb.2018.00704] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/27/2018] [Indexed: 12/16/2022] Open
Abstract
The current standard for enumeration of probiotics to obtain colony forming units by plate counts has several drawbacks: long time to results, high variability and the inability to discern between bacterial strains. Accurate probiotic cell counts are important to confirm the delivery of a clinically documented dose for its associated health benefits. A method is described using chip-based digital PCR (cdPCR) to enumerate Bifidobacterium animalis subsp. lactis Bl-04 and Lactobacillus acidophilus NCFM both as single strains and in combination. Primers and probes were designed to differentiate the target strains against other strains of the same species using known single copy, genetic differences. The assay was optimized to include propidium monoazide pre-treatment to prevent amplification of DNA associated with dead probiotic cells as well as liberation of DNA from cells with intact membranes using bead beating. The resulting assay was able to successfully enumerate each strain whether alone or in multiplex. The cdPCR method had a 4 and 5% relative standard deviation (RSD) for Bl-04 and NCFM, respectively, making it more precise than plate counts with an industry accepted RSD of 15%. cdPCR has the potential to replace traditional plate counts because of its precision, strain specificity and the ability to obtain results in a matter of hours.
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Affiliation(s)
- Sarah J Z Hansen
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
| | - Wesley Morovic
- Genomics and Microbiome Sciences, DuPont Nutrition & Health, Madison, WI, United States
| | - Martha DeMeules
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
| | - Buffy Stahl
- Genomics and Microbiome Sciences, DuPont Nutrition & Health, Madison, WI, United States
| | - Connie W Sindelar
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
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31
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Douillard FP, Mora D, Eijlander RT, Wels M, de Vos WM. Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3. PLoS One 2018; 13:e0192452. [PMID: 29451876 PMCID: PMC5815585 DOI: 10.1371/journal.pone.0192452] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/23/2018] [Indexed: 02/07/2023] Open
Abstract
Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials. Phylogenetic and genomic data analysis allowed us to identify the 7 species present in the VSL#3 product as specified by the manufacturer. The 8 strains present belong to the species Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus helveticus, Bifidobacterium breve and B. animalis subsp. lactis (two distinct strains). Comparative genomics revealed that the draft genomes of the S. thermophilus and L. helveticus strains were predicted to encode most of the defence systems such as restriction modification and CRISPR-Cas systems. Genes associated with a variety of potential probiotic functions were also identified. Thus, in the three Bifidobacterium spp., gene clusters were predicted to encode tight adherence pili, known to promote bacteria-host interaction and intestinal barrier integrity, and to impact host cell development. Various repertoires of putative signalling proteins were predicted to be encoded by the genomes of the Lactobacillus spp., i.e. surface layer proteins, LPXTG-containing proteins, or sortase-dependent pili that may interact with the intestinal mucosa and dendritic cells. Taken altogether, the individual genomic characterization of the strains present in the VSL#3 product confirmed the product specifications, determined its coding capacity as well as identified potential probiotic functions.
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Affiliation(s)
- François P. Douillard
- Research Program Unit Immunobiology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Diego Mora
- Department of Food, Environmental, and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | | | - Willem M. de Vos
- Research Program Unit Immunobiology, Medicum, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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32
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Viborg AH, Katayama T, Arakawa T, Abou Hachem M, Lo Leggio L, Kitaoka M, Svensson B, Fushinobu S. Discovery of α-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42. J Biol Chem 2017; 292:21092-21101. [PMID: 29061847 DOI: 10.1074/jbc.m117.792598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 10/18/2017] [Indexed: 12/30/2022] Open
Abstract
Enzymes of the glycoside hydrolase family 42 (GH42) are widespread in bacteria of the human gut microbiome and play fundamental roles in the decomposition of both milk and plant oligosaccharides. All GH42 enzymes characterized so far have β-galactosidase activity. Here, we report the existence of a GH42 subfamily that is exclusively specific for α-l-arabinopyranoside and describe the first representative of this subfamily. We found that this enzyme (BlArap42B) from a probiotic Bifidobacterium species cannot hydrolyze β-galactosides. However, BlArap42B effectively hydrolyzed paeonolide and ginsenoside Rb2, plant glycosides containing an aromatic aglycone conjugated to α-l-arabinopyranosyl-(1,6)-β-d-glucopyranoside. Paeonolide, a natural glycoside from the roots of the plant genus Paeonia, is not hydrolyzed by classical GH42 β-galactosidases. X-ray crystallography revealed a unique Trp345-X12-Trp358 sequence motif at the BlArap42B active site, as compared with a Phe-X12-His motif in classical GH42 β-galactosidases. This analysis also indicated that the C6 position of galactose is blocked by the aromatic side chains, hence allowing accommodation only of Arap lacking this carbon. Automated docking of paeonolide revealed that it can fit into the BlArap42B active site. The Glcp moiety of paeonolide stacks onto the aromatic ring of the Trp252 at subsite +1 and C4-OH is hydrogen bonded with Asp249 Moreover, the aglycone stacks against Phe421 from the neighboring monomer in the BlArap42B trimer, forming a proposed subsite +2. These results further support the notion that evolution of metabolic specialization can be tracked at the structural level in key enzymes facilitating degradation of specific glycans in an ecological niche.
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Affiliation(s)
- Alexander Holm Viborg
- From the Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan.,the Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2400 Kgs. Lyngby, Denmark
| | - Takane Katayama
- the Graduate School of Biostudies, Kyoto University, Koyoto 606-8502, Japan.,the Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa 921-8836, Japan
| | - Takatoshi Arakawa
- From the Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Maher Abou Hachem
- the Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2400 Kgs. Lyngby, Denmark
| | - Leila Lo Leggio
- the Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark, and
| | - Motomitsu Kitaoka
- the Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
| | - Birte Svensson
- the Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2400 Kgs. Lyngby, Denmark
| | - Shinya Fushinobu
- From the Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan,
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33
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Charnchai P, Jantama SS, Jantama K. Genome analysis of food-processing stressful-resistant probiotic Bifidobacterium animalis subsp. lactis BF052, and its potential application in fermented soymilk. FEMS Microbiol Lett 2017; 364:4084568. [PMID: 28911187 DOI: 10.1093/femsle/fnx180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/16/2017] [Indexed: 01/13/2023] Open
Abstract
In this study, Bifidobacterium animalis subsp. lactis BF052 was demonstrated the growth capability in soymilk and could be thus supplemented as a probiotic starter that employed soymilk as one of its food vehicles. The complete genome sequence of BF052 was therefore determined to understand the genetic basis of BF052 as a technological and functional probiotic starter. The whole genome sequence of BF052 consists of a circular genome of 1938 624 bp with a G+C content of 60.50%. This research highlights relevant genes involving in its adaptive responses to industrial and/or environmental stresses and utilization of α-galacto-oligosaccharides in BF052 strain compared with other representative bifidobacterial genomes.
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Affiliation(s)
- Pattra Charnchai
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree, Muang, Nakhon Ratchasima 30000, Thailand
| | - Sirima Suvarnakuta Jantama
- Division of Biopharmacy, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Sathonlamark Road, Warin chamrap, Ubon Ratchathani 34190, Thailand
| | - Kaemwich Jantama
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree, Muang, Nakhon Ratchasima 30000, Thailand
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34
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Sun Y, Zhu DQ, Zhang QX, Pang XH, Sun SR, Liu F, Li AL, Meng XC. The Expression of GroEL Protein Amplified fromBifidobacterium animalissubsp.lactisKLDS 2.0603 and its Role in Competitive Adhesion to Caco-2. FOOD BIOTECHNOL 2016. [DOI: 10.1080/08905436.2016.1244769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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35
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Morovic W, Hibberd AA, Zabel B, Barrangou R, Stahl B. Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases. Front Microbiol 2016; 7:1747. [PMID: 27857709 PMCID: PMC5093124 DOI: 10.3389/fmicb.2016.01747] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
Recent advances in microbiome research have brought renewed focus on beneficial bacteria, many of which are available in food and dietary supplements. Although probiotics have historically been defined as microorganisms that convey health benefits when ingested in sufficient viable amounts, this description now includes the stipulation “well defined strains,” encompassing definitive taxonomy for consumer consideration and regulatory oversight. Here, we evaluated 52 commercial dietary supplements covering a range of labeled species using plate counting and targeted genotyping. Strain identities were assessed using methods recently published by the United States Pharmacopeial Convention. We also determined the relative abundance of individual bacteria by high-throughput sequencing (HTS) of the 16S rRNA sequence using paired-end 2 × 250 bp Illumina MiSeq technology. Using these methods, we tested the hypothesis that products do contain the quantitative and qualitative list of labeled microbial species. We found that 17 samples (33%) were below label claim for CFU prior to their expiration dates. A multiplexed-PCR scheme showed that only 30/52 (58%) of the products contained a correctly labeled classification, with issues encompassing incorrect taxonomy, missing species, and un-labeled species. The HTS revealed that many blended products consisted predominantly of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis. These results highlight the need for reliable methods to determine the correct taxonomy and quantify the relative amounts of mixed microbial populations in commercial probiotic products.
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Affiliation(s)
- Wesley Morovic
- Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA
| | - Ashley A Hibberd
- Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA
| | - Bryan Zabel
- Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University Raleigh, NC, USA
| | - Buffy Stahl
- Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA
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36
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Kwak MJ, Kwon SK, Yoon JK, Song JY, Seo JG, Chung MJ, Kim JF. Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function. Syst Appl Microbiol 2016; 39:429-439. [PMID: 27524178 DOI: 10.1016/j.syapm.2016.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 01/11/2023]
Abstract
Bifidobacteria, often associated with the gastrointestinal tract of animals, are well known for their roles as probiotics. Among the dozens of Bifidobacterium species, Bifidobacterium bifidum, B. breve, and B. longum are the ones most frequently isolated from the feces of infants and known to help the digestion of human milk oligosaccharides. To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species. Results show that a major evolutionary event leading to the clade of the infant-adapted species is linked to carbohydrate metabolism, but it is not the only factor responsible for the adaptation of bifidobacteria to the gut. The genome of B. longum subsp. infantis, a typical bifidobacterium in the gut of breast-fed infants, encodes proteins associated with several kinds of species-specific metabolic pathways, including urea metabolism and biosynthesis of riboflavin and lantibiotics. Our results demonstrate that these metabolic features, which are associated with the probiotic function of bifidobacteria, are species-specific and highly correlate with their phylogeny.
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Affiliation(s)
- Min-Jung Kwak
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jae-Kyung Yoon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jae-Gu Seo
- R&D Center, Cell Biotech Co., Ltd., 50, Aegibong-ro 409 beon-gil, Wolgot-myeon, Gimpo-si, Gyeonggi-do 10003, Republic of Korea
| | - Myung Jun Chung
- R&D Center, Cell Biotech Co., Ltd., 50, Aegibong-ro 409 beon-gil, Wolgot-myeon, Gimpo-si, Gyeonggi-do 10003, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seoul 03722, Republic of Korea.
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37
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O'Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Front Microbiol 2016; 7:925. [PMID: 27379055 PMCID: PMC4908950 DOI: 10.3389/fmicb.2016.00925] [Citation(s) in RCA: 554] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022] Open
Abstract
Members of the genus Bifidobacterium are among the first microbes to colonize the human gastrointestinal tract and are believed to exert positive health benefits on their host. Due to their purported health-promoting properties, bifidobacteria have been incorporated into many functional foods as active ingredients. Bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract, such as the human oral cavity, the insect gut and sewage. To be able to survive in these particular ecological niches, bifidobacteria must possess specific adaptations to be competitive. Determination of genome sequences has revealed genetic attributes that may explain bifidobacterial ecological fitness, such as metabolic abilities, evasion of the host adaptive immune system and colonization of the host through specific appendages. However, genetic modification is crucial toward fully elucidating the mechanisms by which bifidobacteria exert their adaptive abilities and beneficial properties. In this review we provide an up to date summary of the general features of bifidobacteria, whilst paying particular attention to the metabolic abilities of this species. We also describe methods that have allowed successful genetic manipulation of bifidobacteria.
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Affiliation(s)
- Amy O'Callaghan
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
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Nyanzi R, Jooste PJ, Eloff JN. Multi-Loci Gene Sequencing and Identification of Bifidobacteria Strains Isolated from Dairy and Pharmaceutical Sources in South Africa. FOOD BIOTECHNOL 2016. [DOI: 10.1080/08905436.2015.1132228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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39
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Abstract
Bacteria occur ubiquitously in nature and are broadly relevant throughout the food supply chain, with diverse and variable tolerance levels depending on their origin, biological role, and impact on the quality and safety of the product as well as on the health of the consumer. With increasing knowledge of and accessibility to the microbial composition of our environments, food supply, and host-associated microbiota, our understanding of and appreciation for the ratio of beneficial to undesirable bacteria are rapidly evolving. Therefore, there is a need for tools and technologies that allow definite, accurate, and high-resolution identification and typing of various groups of bacteria that include beneficial microbes such as starter cultures and probiotics, innocuous commensals, and undesirable pathogens and spoilage organisms. During the transition from the current molecular biology-based PFGE (pulsed-field gel electrophoresis) gold standard to the increasingly accessible omics-level whole-genome sequencing (WGS) N-gen standard, high-resolution technologies such as CRISPR-based genotyping constitute practical and powerful alternatives that provide valuable insights into genome microevolution and evolutionary trajectories. Indeed, several studies have shown potential for CRISPR-based typing of industrial starter cultures, health-promoting probiotic strains, animal commensal species, and problematic pathogens. Emerging CRISPR-based typing methods open new avenues for high-resolution typing of a broad range of bacteria and constitute a practical means for rapid tracking of a diversity of food-associated microbes.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695; .,Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802;
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40
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Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment. Appl Environ Microbiol 2015; 82:980-991. [PMID: 26590291 DOI: 10.1128/aem.03500-15] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bifidobacteria represent one of the dominant microbial groups that occur in the gut of various animals, being particularly prevalent during the suckling period of humans and other mammals. Their ability to compete with other gut bacteria is largely attributed to their saccharolytic features. Comparative and functional genomic as well as transcriptomic analyses have revealed the genetic background that underpins the overall saccharolytic phenotype for each of the 47 bifidobacterial (sub)species representing the genus Bifidobacterium, while also generating insightful information regarding carbohydrate resource sharing and cross-feeding among bifidobacteria. The abundance of bifidobacterial saccharolytic features in human microbiomes supports the notion that metabolic accessibility to dietary and/or host-derived glycans is a potent evolutionary force that has shaped the bifidobacterial genome.
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Morrill J, Kulcinskaja E, Sulewska AM, Lahtinen S, Stålbrand H, Svensson B, Abou Hachem M. The GH5 1,4-β-mannanase from Bifidobacterium animalis subsp. lactis Bl-04 possesses a low-affinity mannan-binding module and highlights the diversity of mannanolytic enzymes. BMC BIOCHEMISTRY 2015; 16:26. [PMID: 26558435 PMCID: PMC4642672 DOI: 10.1186/s12858-015-0055-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/29/2015] [Indexed: 12/18/2022]
Abstract
Background β-Mannans are abundant and diverse plant structural and storage polysaccharides. Certain human gut microbiota members including health-promoting Bifidobacterium spp. catabolize dietary mannans. Little insight is available on the enzymology of mannan deconstruction in the gut ecological niche. Here, we report the biochemical properties of the first family 5 subfamily 8 glycoside hydrolase (GH5_8) mannanase from the probiotic bacterium Bifidobacterium animalis subsp. lactis Bl-04 (BlMan5_8). Results BlMan5_8 possesses a novel low affinity carbohydrate binding module (CBM) specific for soluble mannan and displays the highest catalytic efficiency reported to date for a GH5 mannanase owing to a very high kcat (1828 ± 87 s-1) and a low Km (1.58 ± 0.23 g · L-1) using locust bean galactomannan as substrate. The novel CBM of BlMan5_8 mediates increased binding to soluble mannan based on affinity electrophoresis. Surface plasmon resonance analysis confirmed the binding of the CBM10 to manno-oligosaccharides, albeit with slightly lower affinity than the catalytic module of the enzyme. This is the first example of a low-affinity mannan-specific CBM, which forms a subfamily of CBM10 together with close homologs present only in mannanases. Members of this new subfamily lack an aromatic residue mediating binding to insoluble cellulose in canonical CBM10 members consistent with the observed low mannan affinity. Conclusion BlMan5_8 is evolved for efficient deconstruction of soluble mannans, which is reflected by an exceptionally low Km and the presence of an atypical low affinity CBM, which increases binding to specifically to soluble mannan while causing minimal decrease in catalytic efficiency as opposed to enzymes with canonical mannan binding modules. These features highlight fine tuning of catalytic and binding properties to support specialization towards a preferred substrate, which is likely to confer an advantage in the adaptation to competitive ecological niches. Electronic supplementary material The online version of this article (doi:10.1186/s12858-015-0055-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johan Morrill
- Department of Biochemistry and Structural Biology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-221 00, Lund, Sweden
| | - Evelina Kulcinskaja
- Department of Biochemistry and Structural Biology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-221 00, Lund, Sweden
| | - Anna Maria Sulewska
- Enzyme and Protein Chemistry (EPC), Department of Systems Biology, Technical University of Denmark (DTU), Søltofts Plads, building 224, DK-2800, Kgs Lyngby, Denmark.,Current address: Biochemistry and Bioprocessing, Department of Food Science, University of Copenhagen, Rolighedsvej 30, DK-1958, Fredriksberg C, Denmark
| | - Sampo Lahtinen
- Active Nutrition, DuPont Nutrition & Health, Sokeritehtaantie 20, 02460, Kantvik, Finland
| | - Henrik Stålbrand
- Department of Biochemistry and Structural Biology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-221 00, Lund, Sweden
| | - Birte Svensson
- Enzyme and Protein Chemistry (EPC), Department of Systems Biology, Technical University of Denmark (DTU), Søltofts Plads, building 224, DK-2800, Kgs Lyngby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry (EPC), Department of Systems Biology, Technical University of Denmark (DTU), Søltofts Plads, building 224, DK-2800, Kgs Lyngby, Denmark.
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42
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Abstract
Bacterial adaptive immunity hinges on CRISPR-Cas systems that provide DNA-encoded, RNA-mediated targeting of exogenous nucleic acids. A plethora of CRISPR molecular machines occur broadly in prokaryotic genomes, with a diversity of Cas nucleases that can be repurposed for various applications.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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43
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Oberg TS, Ward RE, Steele JL, Broadbent JR. Transcriptome analysis of Bifidobacterium longum strains that show a differential response to hydrogen peroxide stress. J Biotechnol 2015; 212:58-64. [PMID: 26299205 DOI: 10.1016/j.jbiotec.2015.06.405] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 06/16/2015] [Accepted: 06/19/2015] [Indexed: 01/02/2023]
Abstract
Consumer and commercial interest in foods containing probiotic bifidobacteria is increasing. However, because bifidobacteria are anaerobic, oxidative stress can diminish cell viability during production and storage of bioactive foods. We previously found Bifidobacterium longum strain NCC2705 had significantly greater intrinsic and inducible resistance to hydrogen peroxide (H2O2) than strain D2957. Here, we explored the basis for these differences by examining the transcriptional responses of both strains to sub-lethal H2O2 exposure for 5- or 60-min. Strain NCC2705 had 288 genes that were differentially expressed after the 5-min treatment and 114 differentially expressed genes after the 60-min treatment. In contrast, strain D2957 had only 21 and 90 differentially expressed genes after the 5- and 60-min treatments, respectively. Both strains showed up-regulation of genes coding enzymes implicated in oxidative stress resistance, such as thioredoxin, thioredoxin reductase, peroxiredoxin, ferredoxin, glutaredoxin, and anaerobic ribonucleotide reductase, but induction levels were typically highest in NCC2705. Compared to D2957, NCC2705 also had more up-regulated genes involved in transcriptional regulation and more down-regulated genes involved in sugar transport and metabolism. These results provide a greater understanding of the molecular basis for oxidative stress resistance in B. longum and the factors that contribute to strain-to-strain variability in survival in bioactive food products.
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Affiliation(s)
- Taylor S Oberg
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA.
| | - Robert E Ward
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA
| | - James L Steele
- Department of Food Science, University of Wisconsin, 1605 Linden Drive, Madison, WI 53706-1565, USA
| | - Jeff R Broadbent
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA
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44
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Ghali I, Shinkai T, Mitsumori M. Mining of luxS genes from rumen microbial consortia by metagenomic and metatranscriptomic approaches. Anim Sci J 2015; 87:666-73. [PMID: 26277986 DOI: 10.1111/asj.12476] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/27/2015] [Indexed: 11/27/2022]
Abstract
Although rumen bacterial communities vary depending on many factors such as diet, age and physiological conditions, a core microbiota exists within the rumen. In many natural environments, some bacteria use a quorum-sensing (QS) system to regulate their physiological activities. However, very limited information is available about QS systems in rumen. To investigate the autoinducer 2 (AI-2)-mediated QS system in rumen, we detected genes (luxS) encoding the AI-2 synthase (LuxS), from three datasets embedded in metagenomics RAST server (MG-RAST) and from a metatranscriptome dataset. We collected 135 luxS genes from the metagenomic datasets, which were presumed to originate from Bacteroidetes, Firmicutes, Fusobacteria and Actinobacteria, and 34 luxS genes from the metatranscriptome dataset, which probably originated from Bacteroidetes, Firmicutes and Spirochaetes. Because the essential amino acids for LuxS activity were conserved in the LuxS homologues predicted from luxS gene sequences from both datasets, the LuxS homologues probably function in the rumen. Since the largest number of sequences of luxS genes were collected from the genera Prevotella, Ruminococcus and Eubacterium, which include many fibrolytic bacteria and constituent members of biofilm on feed particles, an AI-2-mediated QS system is likely involved in biofilm formation and fibrolytic activity in the rumen.
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Affiliation(s)
- Ines Ghali
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takumi Shinkai
- NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Makoto Mitsumori
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
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45
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Briner AE, Lugli GA, Milani C, Duranti S, Turroni F, Gueimonde M, Margolles A, van Sinderen D, Ventura M, Barrangou R. Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium. PLoS One 2015; 10:e0133661. [PMID: 26230606 PMCID: PMC4521832 DOI: 10.1371/journal.pone.0133661] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/30/2015] [Indexed: 12/11/2022] Open
Abstract
CRISPR-Cas systems constitute adaptive immune systems for antiviral defense in bacteria. We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools.
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Affiliation(s)
- Alexandra E. Briner
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Francesca Turroni
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland
| | - Miguel Gueimonde
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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46
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Tanaka Y, Takami K, Nishijima T, Aoki R, Mawatari T, Ikeda T. Short- and long-term dynamics in the intestinal microbiota following ingestion of Bifidobacterium animalis subsp. lactis GCL2505. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2015; 34:77-85. [PMID: 26594607 PMCID: PMC4639512 DOI: 10.12938/bmfh.2015-001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/10/2015] [Indexed: 12/13/2022]
Abstract
Bifidobacterium animalis subsp. lactis GCL2505 (B. lactis
GCL2505) is able to survive passage through the intestines and proliferate. The daily dynamics of the
intestinal bifidobacteria following ingestion of probiotics are not yet clear. Moreover, the effects of
long-term ingestion of probiotics on the intestinal microbiota have not been well studied. Two experiments
were performed in the present study. In Experiment 1, 53 healthy female volunteers received B.
lactis GCL2505; B. bifidum GCL2080, which can survive but not proliferate in the
intestine; or yogurt fermented with Lactobacillus delbrueckii subsp.
bulgaricus and Streptococcus thermophilus for 2 weeks, and the daily
dynamics of intestinal bifidobacteria were investigated. The number of fecal bifidobacteria significantly
increased on day 1, and this was maintained until day 14 in the B. lactis GCL2505 ingestion
group. However, no significant change in the number of fecal bifidobacteria was observed in the other groups
throughout the ingestion period. In Experiment 2, 38 constipated volunteers received either B.
lactis GCL2505 or a placebo for 8 weeks. Both the number of fecal bifidobacteria and the frequency
of defecation significantly increased throughout the ingestion period in the B. lactis
GCL2505 ingestion group. These results suggested that the proliferation of ingested bifidobacteria within the
intestine contributed to a rapid increase in the amount of intestinal bifidobacteria and subsequent
maintenance of these levels. Moreover, B. lactis GCL2505 improved the intestinal microbiota
more effectively than non-proliferating bifidobacteria and lactic acid bacteria.
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Affiliation(s)
- Yoshiyuki Tanaka
- Institute of Health Science, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan ; R&D Division, Glico Dairy Products Co., Ltd., 2-14-1 Musashino, Akishima-shi, Tokyo 196-0021, Japan
| | - Kazuyo Takami
- R&D Division, Glico Dairy Products Co., Ltd., 2-14-1 Musashino, Akishima-shi, Tokyo 196-0021, Japan
| | - Tomohiko Nishijima
- R&D Division, Glico Dairy Products Co., Ltd., 2-14-1 Musashino, Akishima-shi, Tokyo 196-0021, Japan
| | - Ryo Aoki
- Institute of Health Science, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan ; R&D Division, Glico Dairy Products Co., Ltd., 2-14-1 Musashino, Akishima-shi, Tokyo 196-0021, Japan
| | - Takashi Mawatari
- Institute of Health Science, Ezaki Glico Co., Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan ; R&D Division, Glico Dairy Products Co., Ltd., 2-14-1 Musashino, Akishima-shi, Tokyo 196-0021, Japan
| | - Takayuki Ikeda
- Faculty of Human Life Science, Fuji Women's University, 4-5 Hanakawaminami, Ishikari-shi, Hokkaido 061-3204, Japan
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47
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Rouli L, Merhej V, Fournier PE, Raoult D. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect 2015; 7:72-85. [PMID: 26442149 PMCID: PMC4552756 DOI: 10.1016/j.nmni.2015.06.005] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 01/18/2023] Open
Abstract
The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position.
Pangenome is a new way of studying pathogenic bacteria. Pangenome can be used as a taxonomic tool. This review describes pangenome in the world of pathogenic bacteria.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - V Merhej
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - P-E Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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48
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Abstract
Since health benefits conferred by probiotics are strain-specific, identification to the strain level is mandatory to allow the monitoring of the presence and the abundance of specific probiotic in a product or in a gastrointestinal tract. Compared to standard plate counts, the reduced duration of the assays and higher specificity makes PCR-based methods (standard PCR and quantitative PCR) very appropriate for detection or quantification of probiotics. Development of strain-specific assay consists of 4 main stages: (1) strain-specific marker identification; (2) construction of potential strain-specific primers; (3) validation on DNA from pure cultures of target and related strains; and (4) validation on spiked samples. The most important and also the most challenging step is the identification of strain-specific sequences, which can be subsequently targeted by specific primers or probes. Such regions can be identified on sequences derived from 16S-23S internally transcribed spacers, randomly amplified polymorphic DNA, representational difference analysis and suppression subtractive hybridisation. Already known phenotypic or genotypic characteristics of the target strain can also be used to develop the strain-specific assay. However, the initial stage of strain-specific assay development can be replaced by comparative genomics analysis of target genome with related genomes in public databases. Advances in whole genome sequencing (WGS) have resulted in a cost reduction for bacterial genome sequencing and consequently have made this approach available to most laboratories. In the present paper I reviewed the available literature on PCR and qPCR assays developed for detection of a specific probiotic strain and discussed future WGS and comparative genomics-based approaches.
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Affiliation(s)
- P Treven
- 1 University of Ljubljana, Biotechnical Faculty, Institute of Dairy Science and Probiotics, Groblje 3, 1230 Domžale, Slovenia
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49
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Zhu DQ, Liu F, Sun Y, Yang LM, Xin L, Meng XC. Genome-wide identification of small RNAs in Bifidobacterium animalis subsp. lactis KLDS 2.0603 and their regulation role in the adaption to gastrointestinal environment. PLoS One 2015; 10:e0117373. [PMID: 25706951 PMCID: PMC4338058 DOI: 10.1371/journal.pone.0117373] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/21/2014] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVE Bifidobacteria are one of the predominant bacterial species in the human gastrointestinal tract (GIT) and play a vital role in the host's health by acting as probiotics. However, how they regulate themselves to adapt to GIT of their host remains unknown. METHODS Eighteen bifidobacterial strains were used to analyze their adaptive capacities towards simulated GIT environment. The strain with highest survival rate and adhesion ability was selected for comparative genome as well as transcriptomic analysis. RESULTS The Bifidobacterium animalis subsp. lactis KLDS 2.0603 strain was demonstrated to have the highest survival rate and adhesion ability in simulated GIT treatments. The comparative genome analysis revealed that the KLDS 2.0603 has most similar whole genome sequence compared with BB-12 strain. Eleven intergenic sRNAs were identified after genomes prediction and transcriptomic analysis of KLDS 2.0603. Transcriptomic analysis also showed that genes (mainly sRNAs targeted genes) and sRNAs were differentially expressed in different stress conditions, suggesting that sRNAs might play a crucial role in regulating genes involved in the stress resistance of this strain towards environmental changes. CONCLUSIONS This study first provided deep and comprehensive insights into the regulation of KLDS 2.0603 strain at transcription and post-transcription level towards environmental.
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Affiliation(s)
- De-Quan Zhu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, People’s Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, People’s Republic of China
- College of Life Science, Jiamusi University, Jiamusi, People’s Republic of China
| | - Fei Liu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, People’s Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Yu Sun
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, People’s Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Li-Mei Yang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, People’s Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Li Xin
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, People’s Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Xiang-Chen Meng
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, People’s Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, People’s Republic of China
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50
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Glanville J, King S, Guarner F, Hill C, Sanders ME. A review of the systematic review process and its applicability for use in evaluating evidence for health claims on probiotic foods in the European Union. Nutr J 2015; 14:16. [PMID: 25889449 PMCID: PMC4334596 DOI: 10.1186/s12937-015-0004-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/26/2015] [Indexed: 02/07/2023] Open
Abstract
This paper addresses the use of systematic review and meta-analysis to evaluate the strength of evidence for health benefits of probiotic foods, especially relating to health claim substantiation in the European Union. A systematic review is a protocol-driven, transparent and replicable approach, widely accepted in a number of scientific fields, and used by many policy-setting organizations to evaluate the strength of evidence to answer a focused research question. Many systematic reviews have been published on the broad category of probiotics for many different outcomes. Some of these reviews have been criticized for including poor quality studies, pooling heterogeneous study results, and not considering publication bias. Well-designed and -conducted systematic reviews should address such issues. Systematic reviews of probiotics have an additional challenge - rarely addressed in published reviews - in that there must be a scientifically sound basis for combining evidence on different strains, species or genera. The European Food Safety Authority (EFSA) is increasingly adopting the systematic review methodology. It remains to be seen how health claims supported by systematic reviews are evaluated within the EFSA approval process. The EFSA Panel on Dietetic Products, Nutrition and Allergies deems randomized trials to be the best approach to generating evidence about the effects of foods on health outcomes. They also acknowledge that systematic reviews (with or without meta-analyses) are the best approach to assess the totality of the evidence. It is reasonable to use these well-established methods to assess objectively the strength of evidence for a probiotic health claim. Use of the methods to combine results on more than a single strain or defined blend of strains will require a rationale that the different probiotics are substantively similar, either in identity or in their mode of action.
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Affiliation(s)
| | - Sarah King
- York Health Economics Consortium LTD, York, UK.
| | | | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
| | - Mary Ellen Sanders
- Dairy & Food Culture Technologies, 7119 S. Glencoe Ct., Centennial, CO, 80122, USA.
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