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Xiao M, Zhang C, Duan H, Narbad A, Zhao J, Chen W, Zhai Q, Yu L, Tian F. Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health. NPJ Biofilms Microbiomes 2024; 10:47. [PMID: 38898089 PMCID: PMC11186840 DOI: 10.1038/s41522-024-00524-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
Throughout the life span of a host, bifidobacteria have shown superior colonization and glycan abilities. Complex glycans, such as human milk oligosaccharides and plant glycans, that reach the colon are directly internalized by the transport system of bifidobacteria, cleaved into simple structures by extracellular glycosyl hydrolase, and transported to cells for fermentation. The glycan utilization of bifidobacteria introduces cross-feeding activities between bifidobacterial strains and other microbiota, which are influenced by host nutrition and regulate gut homeostasis. This review discusses bifidobacterial glycan utilization strategies, focusing on the cross-feeding involved in bifidobacteria and its potential health benefits. Furthermore, the impact of cross-feeding on the gut trophic niche of bifidobacteria and host health is also highlighted. This review provides novel insights into the interactions between microbe-microbe and host-microbe.
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Affiliation(s)
- Meifang Xiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chuan Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Hui Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park Colney, Norwich, Norfolk, NR4 7UA, UK
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. 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
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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Lordan C, Roche AK, Delsing D, Nauta A, Groeneveld A, MacSharry J, Cotter PD, van Sinderen D. Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond. Microbiol Mol Biol Rev 2024; 88:e0009423. [PMID: 38206006 PMCID: PMC10966949 DOI: 10.1128/mmbr.00094-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
SUMMARYHuman milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing neonate. Certain bifidobacterial species, being among the earliest gut colonizers of breast-fed infants, have an adapted functional capacity to metabolize various HMO structures. This ability is typically observed in infant-associated bifidobacteria, as opposed to bifidobacteria associated with a mature microbiota. In recent years, information has been gleaned regarding how these infant-associated bifidobacteria as well as certain other taxa are able to assimilate HMOs, including the mechanistic strategies enabling their acquisition and consumption. Additionally, complex metabolic interactions occur between microbes facilitated by HMOs, including the utilization of breakdown products released from HMO degradation. Interest in HMO-mediated changes in microbial composition and function has been the focal point of numerous studies, in recent times fueled by the availability of individual biosynthetic HMOs, some of which are now commonly included in infant formula. In this review, we outline the main HMO assimilatory and catabolic strategies employed by infant-associated bifidobacteria, discuss other taxa that exhibit breast milk glycan degradation capacity, and cover HMO-supported cross-feeding interactions and related metabolites that have been described thus far.
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Affiliation(s)
- Cathy Lordan
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
| | - Aoife K. Roche
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Arjen Nauta
- FrieslandCampina, Amersfoort, the Netherlands
| | | | - John MacSharry
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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Chang KC, Nagarajan N, Gan YH. Short-chain fatty acids of various lengths differentially inhibit Klebsiella pneumoniae and Enterobacteriaceae species. mSphere 2024; 9:e0078123. [PMID: 38305176 PMCID: PMC10900885 DOI: 10.1128/msphere.00781-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
The gut microbiota is inextricably linked to human health and disease. It can confer colonization resistance against invading pathogens either through niche occupation and nutrient competition or via its secreted metabolites. Short-chain fatty acids (SCFA) are the primary metabolites in the gut as a result of dietary fiber fermentation by the gut microbiota. In this work, we demonstrate that the interaction of single-species gut commensals on solid media is insufficient for pathogen inhibition, but supernatants from monocultures of these commensal bacteria enriched in acetate confer inhibition against anaerobic growth of the enteric pathogen Klebsiella pneumoniae. The three primary SCFAs (acetate, propionate, and butyrate) strongly inhibit the intestinal commensal Escherichia coli Nissle as well as a panel of enteric pathogens besides K. pneumoniae at physiological pH of the cecum and ascending colon. This inhibition was significantly milder on anaerobic gut commensals Bacteroides thetaiotaomicron and Bifidobacterium adolescentis previously demonstrated to be associated with microbiota recovery after antibiotic-induced dysbiosis. We describe a general suppression of bacterial membrane potential by these SCFAs at physiological cecum and ascending colonic pH. Furthermore, the strength of bacterial inhibition increases with increasing alkyl chain length. Overall, the insights gained in this study shed light on the potential therapeutic use of SCFAs for conferring colonization resistance against invading pathogens in a dysbiotic gut.IMPORTANCERising antimicrobial resistance has made treatment of bacterial infections increasingly difficult. According to the World Health Organization, it has become a burgeoning threat to hospital and public health systems worldwide. This threat is largely attributed to the global rise of carbapenem-resistant Enterobacteriaceae in recent years, with common hospital-acquired pathogens growing increasingly resistant to last-line antibiotics. Antibiotics disrupt the homeostatic balance of the gut microbiota, resulting in the loss of colonization resistance against enteric pathogens. This work describes the ability of short-chain fatty acids (SCFAs) produced by gut microbiota to be effective against a wide panel of enteric pathogens without major impact on common gut commensal species. We also demonstrate a previously undescribed link between alkyl chain length and antibacterial effects of SCFAs. SCFAs, thus, hold promise as an alternative therapeutic option leveraging on the antimicrobial activity of these endogenously produced gut metabolites without disrupting gut microbiota homeostasis.
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Affiliation(s)
- Kai Chirng Chang
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Niranjan Nagarajan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yunn-Hwen Gan
- Department of Biochemistry, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Tarracchini C, Milani C, Lugli GA, Mancabelli L, Turroni F, van Sinderen D, Ventura M. The infant gut microbiota as the cornerstone for future gastrointestinal health. ADVANCES IN APPLIED MICROBIOLOGY 2024; 126:93-119. [PMID: 38637108 DOI: 10.1016/bs.aambs.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
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5
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Argentini C, Lugli GA, Tarracchini C, Fontana F, Mancabelli L, Viappiani A, Anzalone R, Angelini L, Alessandri G, Longhi G, Bianchi MG, Taurino G, Bussolati O, Milani C, van Sinderen D, Turroni F, Ventura M. Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota. Front Microbiol 2024; 15:1349391. [PMID: 38426063 PMCID: PMC10902438 DOI: 10.3389/fmicb.2024.1349391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.
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Affiliation(s)
- Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano G. Bianchi
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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6
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Kuntz S, Kunz C, Borsch C, Hill D, Morrin S, Buck R, Rudloff S. Influence of microbially fermented 2´-fucosyllactose on neuronal-like cell activity in an in vitro co-culture system. Front Nutr 2024; 11:1351433. [PMID: 38389793 PMCID: PMC10881714 DOI: 10.3389/fnut.2024.1351433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Scope 2´-Fucosyllactose (2´-FL), the most abundant oligosaccharide in human milk, plays an important role in numerous biological functions, including improved learning. It is not clear, however, whether 2´-FL or a cleavage product could influence neuronal cell activity. Thus, we investigated the effects of 2´-FL, its monosaccharide fucose (Fuc), and microbial fermented 2´-FL and Fuc on the parameters of neuronal cell activity in an intestinal-neuronal transwell co-culture system in vitro. Methods Native 13C-labeled 2´-FL and 13C-Fuc or their metabolites, fermented with Bifidobacterium (B.) longum ssp. infantis and B. breve, which were taken from the lag-, log- and stationary (stat-) growth phases of batch cultures, were applied to the apical compartment of the co-culture system with Caco-2 cells representing the intestinal layer and all-trans-retinoic acid-differentiated SH-SY5Y (SH-SY5YATRA) cells mimicking neuronal-like cells. After 3 h of incubation, the culture medium in the basal compartment was monitored for 13C enrichment by using elemental analysis isotope-ratio mass spectrometry (EA-IRMS) and effects on cell viability, plasma, and mitochondrial membrane potential. The neurotransmitter activation (BDNF, GABA, choline, and glutamate) of SH-SY5YATRA cells was also determined. Furthermore, these effects were also measured by the direct application of 13C-2´-FL and 13C-Fuc to SH-SY5YATRA cells. Results While no effects on neuronal-like cell activities were observed after intact 2´-FL or Fuc was incubated with SH-SY5YATRA cells, supernatants from the stat-growth phase of 2´-FL, fermented by B. longum ssp. infantis alone and together with B. breve, significantly induced BDNF release from SH-SY5YATRA cells. No such effects were found for 2´-FL, Fuc, or their fermentation products from B. breve. The BDNF release occurred from an enhanced vesicular release, which was confirmed by the use of the Ca2+-channel blocker verapamil. Concomitant with this event, 13C enrichment was also observed in the basal compartment when supernatants from the stat-growth phase of fermentation by B. longum ssp. infantis alone or together with B. breve were used. Conclusion The results obtained in this study suggest that microbial products of 2´-FL rather than the oligosaccharide itself may influence neuronal cell activities.
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Affiliation(s)
- Sabine Kuntz
- Department of Nutritional Science, Justus Liebig University Giessen, Giessen, Germany
| | - Clemens Kunz
- Department of Nutritional Science, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Borsch
- Department of Nutritional Science, Justus Liebig University Giessen, Giessen, Germany
| | - David Hill
- Abbott, Nutrition Division, Columbus, OH, United States
| | - Sinéad Morrin
- Abbott, Nutrition Division, Columbus, OH, United States
| | - Rachael Buck
- Abbott, Nutrition Division, Columbus, OH, United States
| | - Silvia Rudloff
- Department of Nutritional Science, Justus Liebig University Giessen, Giessen, Germany
- Department of Pediatrics, Justus Liebig University Giessen, Giessen, Germany
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7
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Rizzo SM, Vergna LM, Alessandri G, Lee C, Fontana F, Lugli GA, Carnevali L, Bianchi MG, Barbetti M, Taurino G, Sgoifo A, Bussolati O, Turroni F, van Sinderen D, Ventura M. GH136-encoding gene (perB) is involved in gut colonization and persistence by Bifidobacterium bifidum PRL2010. Microb Biotechnol 2024; 17:e14406. [PMID: 38271233 PMCID: PMC10884991 DOI: 10.1111/1751-7915.14406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Bifidobacteria are commensal microorganisms that typically inhabit the mammalian gut, including that of humans. As they may be vertically transmitted, they commonly colonize the human intestine from the very first day following birth and may persist until adulthood and old age, although generally at a reduced relative abundance and prevalence compared to infancy. The ability of bifidobacteria to persist in the human intestinal environment has been attributed to genes involved in adhesion to epithelial cells and the encoding of complex carbohydrate-degrading enzymes. Recently, a putative mucin-degrading glycosyl hydrolase belonging to the GH136 family and encoded by the perB gene has been implicated in gut persistence of certain bifidobacterial strains. In the current study, to better characterize the function of this gene, a comparative genomic analysis was performed, revealing the presence of perB homologues in just eight bifidobacterial species known to colonize the human gut, including Bifidobacterium bifidum and Bifidobacterium longum subsp. longum strains, or in non-human primates. Mucin-mediated growth and adhesion to human intestinal cells, in addition to a rodent model colonization assay, were performed using B. bifidum PRL2010 as a perB prototype and its isogenic perB-insertion mutant. These results demonstrate that perB inactivation reduces the ability of B. bifidum PRL2010 to grow on and adhere to mucin, as well as to persist in the rodent gut niche. These results corroborate the notion that the perB gene is one of the genetic determinants involved in the persistence of B. bifidum PRL2010 in the human gut.
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Affiliation(s)
- Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Laura Maria Vergna
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Ciaran Lee
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of IrelandCorkIreland
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- GenProbio srlParmaItaly
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
| | - Luca Carnevali
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Massimiliano G. Bianchi
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Margherita Barbetti
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Giuseppe Taurino
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Andrea Sgoifo
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Ovidio Bussolati
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of IrelandCorkIreland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
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8
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Bakshani CR, Crouch LI. Human milk oligosaccharides and Bifidobacterium species. Trends Microbiol 2024; 32:118-119. [PMID: 38087708 DOI: 10.1016/j.tim.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 02/09/2024]
Abstract
Several bacterial species initially colonise the infant gut, but are outcompeted. Human milk oligosaccharides (HMOs) in breast milk create an environment for Bifidobacterium to flourish. Laursen and Roager recently showed a clear link between breast milk and the dominance of Bifidobacterium longum subsp. infantis in the infant gut.
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Affiliation(s)
- Cassie R Bakshani
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lucy I Crouch
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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9
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Walsh C, Owens RA, Bottacini F, Lane JA, van Sinderen D, Hickey RM. HMO-primed bifidobacteria exhibit enhanced ability to adhere to intestinal epithelial cells. Front Microbiol 2023; 14:1232173. [PMID: 38163079 PMCID: PMC10757668 DOI: 10.3389/fmicb.2023.1232173] [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: 05/31/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024] Open
Abstract
The ability of gut commensals to adhere to the intestinal epithelium can play a key role in influencing the composition of the gut microbiota. Bifidobacteria are associated with a multitude of health benefits and are one of the most widely used probiotics for humans. Enhanced bifidobacterial adhesion may increase host-microbe, microbe-nutrient, and/or microbe-microbe interactions, thereby enabling consolidated health benefits to the host. The objective of this study was to determine the ability of human milk oligosaccharides (HMOs) to enhance bifidobacterial intestinal adhesion in vitro. This study assessed the colonisation-promoting effects of HMOs on four commercial infant-associated Bifidobacterium strains (two B. longum subsp. infantis strains, B. breve and B. bifidum). HT29-MTX cells were used as an in vitro intestinal model for bacterial adhesion. Short-term exposure of four commercial infant-associated Bifidobacterium strains to HMOs derived from breastmilk substantially increased the adherence (up to 47%) of these probiotic strains. Interestingly, when strains were incubated with HMOs as a four-strain combination, the number of viable bacteria adhering to intestinal cells increased by >90%. Proteomic analysis of this multi-strain bifidobacterial mixture revealed that the increased adherence resulting from exposure to HMOs was associated with notable increases in the abundance of sortase-dependent pili and glycosyl hydrolases matched to Bifidobacterium bifidum. This study suggests that HMOs may prime infant gut-associated Bifidobacterium for colonisation to intestinal epithelial cells by influencing the expression of various colonization factors.
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Affiliation(s)
- Clodagh Walsh
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- Health and Happiness Group, H&H Research, Cork, Ireland
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | | | - Francesca Bottacini
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
- Biological Sciences and ADAPT Research Centre, Munster Technological University, Cork, Ireland
| | | | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Rita M. Hickey
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
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10
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Gavzy SJ, Kensiski A, Lee ZL, Mongodin EF, Ma B, Bromberg JS. Bifidobacterium mechanisms of immune modulation and tolerance. Gut Microbes 2023; 15:2291164. [PMID: 38055306 PMCID: PMC10730214 DOI: 10.1080/19490976.2023.2291164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
Bifidobacterium is a widely distributed commensal bacterial genus that displays beneficial pro-homeostatic and anti-inflammatory immunomodulatory properties. Depletion or absence of Bifidobacterium in humans and model organisms is associated with autoimmune responses and impaired immune homeostasis. At the cellular level, Bifidobacterium upregulates suppressive regulatory T cells, maintains intestinal barrier function, modulates dendritic cell and macrophage activity, and dampens intestinal Th2 and Th17 programs. While there has been a large volume of literature characterizing the probiotic properties of various Bifidobacterial species, the likely multifactorial mechanisms underlying these effects remain elusive, in particular, its immune tolerogenic effect. However, recent work has shed light on Bifidobacterium surface structural polysaccharide and protein elements, as well as its metabolic products, as commensal mediators of immune homeostasis. This review aims to discuss several mechanisms Bifidobacterium utilizes for immune modulation as well as their indirect impact on the regulation of gut microbiome structure and function, from structural molecules to produced metabolites. These mechanisms are pertinent to an increasingly networked understanding of immune tolerance and homeostasis in health and disease.
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Affiliation(s)
- Samuel J Gavzy
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Allison Kensiski
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zachariah L Lee
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jonathan S Bromberg
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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11
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Laursen MF, Roager HM. Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy. THE ISME JOURNAL 2023; 17:2452-2457. [PMID: 37816852 PMCID: PMC10689826 DOI: 10.1038/s41396-023-01525-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023]
Abstract
Despite the significant role of the gut microbiota in infant health and development, little is known about the ecological processes determining gut microbial community assembly. According to ecology theory, the timing and order of arrival of microbial species into an ecosystem affect microbial community assembly, a phenomenon termed priority effects. Bifidobacterium species are recognized as highly abundant early colonizers of the infant's gut, partly due to their ability to selectively utilize human milk oligosaccharides (HMOs) from breast milk. However, the role of priority effects in Bifidobacterium community assembly remains unclear. Here, we investigated the Bifidobacterium community assembly in the gut of 25 breastfed Danish infants longitudinally sampled throughout the first 6 months of life. Our results showed that the breastfed infants were often initially, but temporarily, dominated by suboptimal HMO-utilizing Bifidobacterium taxa, such as B. longum subsp. longum, before more efficient HMO-utilizers such as B. longum subsp. infantis, replaced the first colonizer as the dominant Bifidobacterium taxon. Subsequently, we validated this observation using gnotobiotic mice sequentially colonized with B. longum subsp. longum and B. longum subsp. infantis or vice versa, with or without supplementation of HMOs in the drinking water. The results showed that in the absence of HMOs, order of arrival determined dominance. Yet, when mice were supplemented with HMOs the strength of priority effects diminished, and B. longum subsp. infantis dominated regardless of colonization order. Our data demonstrate that the arrival order of Bifidobacterium taxa and the deterministic force of breast milk-derived HMOs, dictate Bifidobacterium community assembly in the infant's gut.
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Affiliation(s)
- Martin F Laursen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark.
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12
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Kiely LJ, Busca K, Lane JA, van Sinderen D, Hickey RM. Molecular strategies for the utilisation of human milk oligosaccharides by infant gut-associated bacteria. FEMS Microbiol Rev 2023; 47:fuad056. [PMID: 37793834 PMCID: PMC10629584 DOI: 10.1093/femsre/fuad056] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
A number of bacterial species are found in high abundance in the faeces of healthy breast-fed infants, an occurrence that is understood to be, at least in part, due to the ability of these bacteria to metabolize human milk oligosaccharides (HMOs). HMOs are the third most abundant component of human milk after lactose and lipids, and represent complex sugars which possess unique structural diversity and are resistant to infant gastrointestinal digestion. Thus, these sugars reach the infant distal intestine intact, thereby serving as a fermentable substrate for specific intestinal microbes, including Firmicutes, Proteobacteria, and especially infant-associated Bifidobacterium spp. which help to shape the infant gut microbiome. Bacteria utilising HMOs are equipped with genes associated with their degradation and a number of carbohydrate-active enzymes known as glycoside hydrolase enzymes have been identified in the infant gut, which supports this hypothesis. The resulting degraded HMOs can also be used as growth substrates for other infant gut bacteria present in a microbe-microbe interaction known as 'cross-feeding'. This review describes the current knowledge on HMO metabolism by particular infant gut-associated bacteria, many of which are currently used as commercial probiotics, including the distinct strategies employed by individual species for HMO utilisation.
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Affiliation(s)
- Leonie Jane Kiely
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61C996, Ireland
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - Kizkitza Busca
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
| | - Jonathan A Lane
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - Rita M Hickey
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61C996, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
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13
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Nogacka AM, Cuesta I, Gueimonde M, de los Reyes-Gavilán CG. 2-Fucosyllactose Metabolism by Bifidobacteria Promotes Lactobacilli Growth in Co-Culture. Microorganisms 2023; 11:2659. [PMID: 38004671 PMCID: PMC10673426 DOI: 10.3390/microorganisms11112659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Breastfeeding is recognized as the gold standard in infant nutrition, not only because of breastmilk's intrinsic nutritional benefits but also due to the high content of different bioactive components such as 2-fucosyllactose (2'FL) in the mother's milk. It promotes the growth of its two major consumers, Bifidobacterium longum ssp. infantis and Bifidobacterium bifidum, but the effect on other intestinal microorganisms of infant microbiota remains incompletely understood. pH-uncontrolled fecal cultures from infants donors identified as "fast 2'FL -degrader" microbiota phenotype were used for the isolation of 2'FL-associated microorganisms. The use of specific selective agents allowed the successful isolation of B. bifidum IPLA20048 and of Lactobacillus gasseri IPLA20136. The characterization of 2'FL consumption and its moieties has revealed more pronounced growth, pH drop, and lactic acid production after 2'FL consumption when both microorganisms were grown together. The results point to an association between B. bifidum IPLA20048 and L. gasseri IPLA20136 in which L. gasseri is able to use the galactose from the lactose moiety after the hydrolysis of 2'FL by B. bifidum. The additional screening of two groups of bifidobacteria (n = 38), fast and slow degraders of 2'FL, in co-culture with lactobacilli confirmed a potential cross-feeding mechanism based on degradation products released from bifidobacterial 2'FL break-down. Our work suggests that this phenomenon may be widespread among lactobacilli and bifidobacteria in the infant gut. More investigation is needed to decipher how the ability to degrade 2'FL and other human milk oligosaccharides could influence the microbiota establishment in neonates and the evolution of the microbiota in adult life.
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Affiliation(s)
- Alicja M. Nogacka
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (I.C.); (M.G.); (C.G.d.l.R.-G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain
| | - Isabel Cuesta
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (I.C.); (M.G.); (C.G.d.l.R.-G.)
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (I.C.); (M.G.); (C.G.d.l.R.-G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain
| | - Clara G. de los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (I.C.); (M.G.); (C.G.d.l.R.-G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain
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14
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Gutierrez A, Pucket B, Engevik MA. Bifidobacterium and the intestinal mucus layer. MICROBIOME RESEARCH REPORTS 2023; 2:36. [PMID: 38045921 PMCID: PMC10688832 DOI: 10.20517/mrr.2023.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 12/05/2023]
Abstract
Bifidobacterium species are integral members of the human gut microbiota and these microbes have significant interactions with the intestinal mucus layer. This review delves into Bifidobacterium-mucus dynamics, shedding light on the multifaceted nature of this relationship. We cover conserved features of Bifidobacterium-mucus interactions, such as mucus adhesion and positive regulation of goblet cell and mucus production, as well as species and strain-specific attributes of mucus degradation. For each interface, we explore the molecular mechanisms underlying these interactions and their potential implications for human health. Notably, we emphasize the ability of Bifidobacterium species to positively influence the mucus layer, shedding light on its potential as a mucin-builder and a therapeutic agent for diseases associated with disrupted mucus barriers. By elucidating the complex interplay between Bifidobacterium and intestinal mucus, we aim to contribute to a deeper understanding of the gut microbiota-host interface and pave the way for novel therapeutic strategies.
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Affiliation(s)
- Alyssa Gutierrez
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Brenton Pucket
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Melinda A. Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
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15
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Shiver AL, Sun J, Culver R, Violette A, Wynter C, Nieckarz M, Mattiello SP, Sekhon PK, Friess L, Carlson HK, Wong D, Higginbottom S, Weglarz M, Wang W, Knapp BD, Guiberson E, Sanchez J, Huang PH, Garcia PA, Buie CR, Good B, DeFelice B, Cava F, Scaria J, Sonnenburg J, Sinderen DV, Deutschbauer AM, Huang KC. A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555234. [PMID: 37693407 PMCID: PMC10491234 DOI: 10.1101/2023.08.29.555234] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Bifidobacteria commonly represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest as a probiotic therapy, predicting the nutritional requirements and health-promoting effects of Bifidobacteria is challenging due to major knowledge gaps. To overcome these deficiencies, we used large-scale genetics to create a compendium of mutant fitness in Bifidobacterium breve (Bb). We generated a high density, randomly barcoded transposon insertion pool in Bb, and used this pool to determine Bb fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. To enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1462 genes. We leveraged these tools to improve models of metabolic pathways, reveal unexpected host- and diet-specific requirements for colonization, and connect the production of immunomodulatory molecules to growth benefits. These resources will greatly reduce the barrier to future investigations of this important beneficial microbe.
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Affiliation(s)
- Anthony L. Shiver
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Rebecca Culver
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Arvie Violette
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Charles Wynter
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Marta Nieckarz
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Samara Paula Mattiello
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- College of Mathematics and Science, The University of Tennessee Southern, Pulaski TN 38478, USA
| | - Prabhjot Kaur Sekhon
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Lisa Friess
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Hans K. Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel Wong
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
| | - Steven Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, California, USA
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, Stanford CA 94305, USA
| | | | - Emma Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Po-Hsun Huang
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Paulo A. Garcia
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Cullen R. Buie
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Benjamin Good
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
| | | | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Douwe Van Sinderen
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
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16
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Kartjito MS, Yosia M, Wasito E, Soloan G, Agussalim AF, Basrowi RW. Defining the Relationship of Gut Microbiota, Immunity, and Cognition in Early Life-A Narrative Review. Nutrients 2023; 15:2642. [PMID: 37375546 DOI: 10.3390/nu15122642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Recently, the immune system has been identified as one of the possible main bridges which connect the gut-brain axis. This review aims to examine available evidence on the microbiota-immunity-cognitive relationship and its possible effects on human health early in life. This review was assembled by compiling and analyzing various literature and publications that document the gut microbiota-immune system-cognition interaction and its implications in the pediatric population. This review shows that the gut microbiota is a pivotal component of gut physiology, with its development being influenced by a variety of factors and, in return, supports the development of overall health. Findings from current research focus on the complex relationship between the central nervous system, gut (along with gut microbiota), and immune cells, highlighting the importance of maintaining a balanced interaction among these systems for preserving homeostasis, and demonstrating the influence of gut microbes on neurogenesis, myelin formation, the potential for dysbiosis, and alterations in immune and cognitive functions. While limited, evidence shows how gut microbiota affects innate and adaptive immunity as well as cognition (through HPA axis, metabolites, vagal nerve, neurotransmitter, and myelination).
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Affiliation(s)
| | - Mikhael Yosia
- Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Erika Wasito
- Medical and Science Affairs Division, Danone Specialized Nutrition Indonesia, Jakarta 12950, Indonesia
| | - Garry Soloan
- Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | | | - Ray Wagiu Basrowi
- Medical and Science Affairs Division, Danone Specialized Nutrition Indonesia, Jakarta 12950, Indonesia
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17
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Fernandez-Julia P, Black GW, Cheung W, Van Sinderen D, Munoz-Munoz J. Fungal β-glucan-facilitated cross-feeding activities between Bacteroides and Bifidobacterium species. Commun Biol 2023; 6:576. [PMID: 37253778 DOI: 10.1038/s42003-023-04970-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/23/2023] [Indexed: 06/01/2023] Open
Abstract
The human gut microbiota (HGM) is comprised of a very complex network of microorganisms, which interact with the host thereby impacting on host health and well-being. β-glucan has been established as a dietary polysaccharide supporting growth of particular gut-associated bacteria, including members of the genera Bacteroides and Bifidobacterium, the latter considered to represent beneficial or probiotic bacteria. However, the exact mechanism underpinning β-glucan metabolism by gut commensals is not fully understood. We show that mycoprotein represents an excellent source for β-glucan, which is consumed by certain Bacteroides species as primary degraders, such as Bacteroides cellulosilyticus WH2. The latter bacterium employs two extracellular, endo-acting enzymes, belonging to glycoside hydrolase families 30 and 157, to degrade mycoprotein-derived β-glucan, thereby releasing oligosaccharides into the growth medium. These released oligosaccharides can in turn be utilized by other gut microbes, such as Bifidobacterium and Lactiplantibacillus, which thus act as secondary degraders. We used a cross-feeding approach to track how both species are able to grow in co-culture.
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Affiliation(s)
- Pedro Fernandez-Julia
- Microbial Enzymology Lab, Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, NE1 8ST, Tyne & Wear, England, UK
| | - Gary W Black
- Microbial Enzymology Lab, Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, NE1 8ST, Tyne & Wear, England, UK
| | - William Cheung
- Microbial Enzymology Lab, Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, NE1 8ST, Tyne & Wear, England, UK
| | - Douwe Van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jose Munoz-Munoz
- Microbial Enzymology Lab, Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, NE1 8ST, Tyne & Wear, England, UK.
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18
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Martin AJ, Serebrinsky-Duek K, Riquelme E, Saa PA, Garrido D. Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium. MICROBIOME RESEARCH REPORTS 2023; 2:17. [PMID: 38046822 PMCID: PMC10688804 DOI: 10.20517/mrr.2023.10] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 12/05/2023]
Abstract
The human gut is home to trillions of microorganisms that influence several aspects of our health. This dense microbial community targets almost all dietary polysaccharides and releases multiple metabolites, some of which have physiological effects on the host. A healthy equilibrium between members of the gut microbiota, its microbial diversity, and their metabolites is required for intestinal health, promoting regulatory or anti-inflammatory immune responses. In contrast, the loss of this equilibrium due to antibiotics, low fiber intake, or other conditions results in alterations in gut microbiota composition, a term known as gut dysbiosis. This dysbiosis can be characterized by a reduction in health-associated microorganisms, such as butyrate-producing bacteria, enrichment of a small number of opportunistic pathogens, or a reduction in microbial diversity. Bifidobacterium species are key species in the gut microbiome, serving as primary degraders and contributing to a balanced gut environment in various ways. Colonization resistance is a fundamental property of gut microbiota for the prevention and control of infections. This community competes strongly with foreign microorganisms, such as gastrointestinal pathogens, antibiotic-resistant bacteria, or even probiotics. Resistance to colonization is based on microbial interactions such as metabolic cross-feeding, competition for nutrients, or antimicrobial-based inhibition. These interactions are mediated by metabolites and metabolic pathways, representing the inner workings of the gut microbiota, and play a protective role through colonization resistance. This review presents a rationale for how microbial interactions provide resistance to colonization and gut dysbiosis, highlighting the protective role of Bifidobacterium species.
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Affiliation(s)
- Alberto J.M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago 8580702, Chile
| | - Kineret Serebrinsky-Duek
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago 833115, Chile
| | - Erick Riquelme
- Department of Respiratory Diseases, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Pedro A. Saa
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago 833115, Chile
- Institute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago 833115, Chile
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19
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Crouch LI. N-glycan breakdown by bacterial CAZymes. Essays Biochem 2023; 67:373-385. [PMID: 37067180 PMCID: PMC10154615 DOI: 10.1042/ebc20220256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 04/18/2023]
Abstract
The modification of proteins by N-glycans is ubiquitous to most organisms and they have multiple biological functions, including protecting the adjoining protein from degradation and facilitating communication or adhesion between cells, for example. Microbes have evolved CAZymes to deconstruct different types of N-glycans and some of these have been characterised from microbes originating from different niches, both commensals and pathogens. The specificity of these CAZymes provides clues as to how different microbes breakdown these substrates and possibly cross-feed them. Discovery of CAZymes highly specific for N-glycans also provides new tools and options for modifying glycoproteins.
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Affiliation(s)
- Lucy I Crouch
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, U.K
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20
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Zheng J, Zhu T. Polymorphism of fucosyltransferase 3 gene is associated with inflammatory bowel disease: a systematic review. ASIAN BIOMED 2023; 17:45-54. [PMID: 37719320 PMCID: PMC10505062 DOI: 10.2478/abm-2023-0044] [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] [Indexed: 09/19/2023]
Abstract
Background Inflammatory bowel disease (IBD) is a condition with an unclear genetic basis. Fucosyltransferase 3 (FUT3) could potentially be linked to IBD susceptibility. Objective To investigate the association between FUT3 gene polymorphisms and IBD. Methods Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 checklist and Population, Intervention, Comparison, Outcomes, and Study (PICOS) guidelines, case-control studies published until April 30, 2020 was searched. Two independent reviewers conducted screening, data extraction, and quality assessment using the Newcastle-Ottawa Scale. Meta-analysis, sensitivity analysis, and Egger tests were performed using RevMan and Stata12.0. Results The review included 5 articles and 12 case-control studies involving 1712 IBD patients and 1903 controls. The meta-analysis revealed the following combined odds ratios [95% confidence intervals]: rs3745635 genotype (GA+AA vs GG) 0.84 (0.72-0.97), (GG+GA vs AA) 1.93 (1.23-3.05), (GG vs AA) 2.38 (1.52-3.74), (A vs G) 0.84 (0.73-0.96); rs3894326 genotype (TA+AA vs TT) 1.03 (0.87-1.23), (TT+TA vs AA) 1.19 (0.56-2.51), (TT vs AA) 1.19 (0.56-2.51), (A vs T) 1.02 (0.86-1.20); rs28362459 genotype (TG+GG vs TT) 0.98 (0.85-1.12), (TT+TG vs GG) 1.20 (0.90-1.61), (TT vs GG) 1.21 (0.90-1.62), (G vs T) 0.96 (0.86-1.07). Sensitivity analysis indicated the stability of the results, and Egger analysis showed no significant publication bias. Conclusions The rs3745635 gene polymorphism may be associated with IBD susceptibility, whereas the rs3894326 and rs28362459 gene polymorphisms may not be associated with IBD.
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Affiliation(s)
- Jiansheng Zheng
- Department of Public Health, School of Basic Medical Science, Putian University, Putian, Fujian351100, China
| | - Tang Zhu
- Key Laboratory of Translational Tumor Medicine in Fujian Province, School of Basic Medical Science, Putian University, Putian, Fujian351100, China
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Morozumi M, Wada Y, Tsuda M, Tabata F, Ehara T, Nakamura H, Miyaji K. Cross-feeding among bifidobacteria on glycomacropeptide. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
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22
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Lee KW, Shin JS, Lee CM, Han HY, O Y, Kim HW, Cho TJ. Gut-on-a-Chip for the Analysis of Bacteria-Bacteria Interactions in Gut Microbial Community: What Would Be Needed for Bacterial Co-Culture Study to Explore the Diet-Microbiota Relationship? Nutrients 2023; 15:nu15051131. [PMID: 36904133 PMCID: PMC10005057 DOI: 10.3390/nu15051131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Bacterial co-culture studies using synthetic gut microbiomes have reported novel research designs to understand the underlying role of bacterial interaction in the metabolism of dietary resources and community assembly of complex microflora. Since lab-on-a-chip mimicking the gut (hereafter "gut-on-a-chip") is one of the most advanced platforms for the simulative research regarding the correlation between host health and microbiota, the co-culture of the synthetic bacterial community in gut-on-a-chip is expected to reveal the diet-microbiota relationship. This critical review analyzed recent research on bacterial co-culture with perspectives on the ecological niche of commensals, probiotics, and pathogens to categorize the experimental approaches for diet-mediated management of gut health as the compositional and/or metabolic modulation of the microbiota and the control of pathogens. Meanwhile, the aim of previous research on bacterial culture in gut-on-a-chip has been mainly limited to the maintenance of the viability of host cells. Thus, the integration of study designs established for the co-culture of synthetic gut consortia with various nutritional resources into gut-on-a-chip is expected to reveal bacterial interspecies interactions related to specific dietary patterns. This critical review suggests novel research topics for co-culturing bacterial communities in gut-on-a-chip to realize an ideal experimental platform mimicking a complex intestinal environment.
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Affiliation(s)
- Ki Won Lee
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Jin Song Shin
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Chan Min Lee
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Hea Yeon Han
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Yun O
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Hye Won Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tae Jin Cho
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Correspondence: ; Tel.: +82-44-860-1433
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23
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Dahal S, Hurst GB, Chourey K, Engle NL, Burdick LH, Morrell-Falvey JL, Tschaplinski TJ, Doktycz MJ, Pelletier DA. Mechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas- Rahnella Co-Culture. Metabolites 2023; 13:metabo13020140. [PMID: 36837758 PMCID: PMC9959693 DOI: 10.3390/metabo13020140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Pseudomonas fluorescens GM16 associates with Populus, a model plant in biofuel production. Populus releases abundant phenolic glycosides such as salicin, but P. fluorescens GM16 cannot utilize salicin, whereas Pseudomonas strains are known to utilize compounds similar to the aglycone moiety of salicin-salicyl alcohol. We propose that the association of Pseudomonas to Populus is mediated by another organism (such as Rahnella aquatilis OV744) that degrades the glucosyl group of salicin. In this study, we demonstrate that in the Rahnella-Pseudomonas salicin co-culture model, Rahnella grows by degrading salicin to glucose 6-phosphate and salicyl alcohol which is secreted out and is subsequently utilized by P. fluorescens GM16 for its growth. Using various quantitative approaches, we elucidate the individual pathways for salicin and salicyl alcohol metabolism present in Rahnella and Pseudomonas, respectively. Furthermore, we were able to establish that the salicyl alcohol cross-feeding interaction between the two strains on salicin medium is carried out through the combination of their respective individual pathways. The research presents one of the potential advantages of salicyl alcohol release by strains such as Rahnella, and how phenolic glycosides could be involved in attracting multiple types of bacteria into the Populus microbiome.
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Affiliation(s)
- Sanjeev Dahal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN 37996, USA
- Department of Chemical Engineering, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Gregory B. Hurst
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Leah H. Burdick
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Correspondence:
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24
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Chen C, Li T, Chen G, Chen D, Peng Y, Hu B, Sun Y, Zeng X. Prebiotic effect of sialylated immunoglobulin G on gut microbiota of patients with inflammatory bowel disease by in vitro fermentation. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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25
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Human Milk Microbiome and Microbiome-Related Products: Potential Modulators of Infant Growth. Nutrients 2022; 14:nu14235148. [PMID: 36501178 PMCID: PMC9737635 DOI: 10.3390/nu14235148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Infant growth trajectory may influence later-life obesity. Human milk provides a wide range of nutritional and bioactive components that are vital for infant growth. Compared to formula-fed infants, breastfed infants are less likely to develop later-onset obesity, highlighting the potential role of bioactive components present in human milk. Components of particular interest are the human milk microbiota, human milk oligosaccharides (HMOs), short-chain fatty acids (SCFAs), and antimicrobial proteins, each of which influence the infant gut microbiome, which in turn has been associated with infant body composition. SCFAs and antimicrobial proteins from human milk may also systemically influence infant metabolism. Although inconsistent, multiple studies have reported associations between HMOs and infant growth, while studies on other bioactive components in relation to infant growth are sparse. Moreover, these microbiome-related components may interact with each other within the mammary gland. Here, we review the evidence around the impact of human milk microbes, HMOs, SCFAs, and antimicrobial proteins on infant growth. Breastfeeding is a unique window of opportunity to promote optimal infant growth, with aberrant growth trajectories potentially creating short- and long-term public health burdens. Therefore, it is important to understand how bioactive components of human milk influence infant growth.
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26
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Using difference-in-difference to understand the downside to antibiotic use during infancy. Pediatr Res 2022; 92:1500-1501. [PMID: 36008596 DOI: 10.1038/s41390-022-02280-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/21/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022]
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27
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Arzamasov AA, Osterman AL. Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics. Crit Rev Biochem Mol Biol 2022; 57:562-584. [PMID: 36866565 PMCID: PMC10192226 DOI: 10.1080/10409238.2023.2182272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/11/2023] [Accepted: 02/15/2023] [Indexed: 03/04/2023]
Abstract
Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain Bifidobacterium species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides (HMOs) and N-linked glycans. Therefore, these carbohydrates serve as promising prebiotic dietary supplements to stimulate the growth of bifidobacteria in the guts of children suffering from impaired gut microbiota development. However, the rational formulation of milk glycan-based prebiotics requires a detailed understanding of how bifidobacteria metabolize these carbohydrates. Accumulating biochemical and genomic data suggest that HMO and N-glycan assimilation abilities vary remarkably within the Bifidobacterium genus, both at the species and strain levels. This review focuses on the delineation and genome-based comparative analysis of differences in respective biochemical pathways, transport systems, and associated transcriptional regulatory networks, providing a foundation for genomics-based projection of milk glycan utilization capabilities across a rapidly growing number of sequenced bifidobacterial genomes and metagenomic datasets. This analysis also highlights remaining knowledge gaps and suggests directions for future studies to optimize the formulation of milk-glycan-based prebiotics that target bifidobacteria.
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Affiliation(s)
- Aleksandr A Arzamasov
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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28
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Ojima MN, Jiang L, Arzamasov AA, Yoshida K, Odamaki T, Xiao J, Nakajima A, Kitaoka M, Hirose J, Urashima T, Katoh T, Gotoh A, van Sinderen D, Rodionov DA, Osterman AL, Sakanaka M, Katayama T. Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides. THE ISME JOURNAL 2022; 16:2265-2279. [PMID: 35768643 PMCID: PMC9381805 DOI: 10.1038/s41396-022-01270-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022]
Abstract
Bifidobacteria are among the first colonizers of the infant gut, and human milk oligosaccharides (HMOs) in breastmilk are instrumental for the formation of a bifidobacteria-rich microbiota. However, little is known about the assembly of bifidobacterial communities. Here, by applying assembly theory to a community of four representative infant-gut associated Bifidobacterium species that employ varied strategies for HMO consumption, we show that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis, two avid HMO consumers, dominate through inhibitory priority effects. On the other hand, Bifidobacterium breve, a species with limited HMO-utilization ability, can benefit from facilitative priority effects and dominates by utilizing fucose, an HMO degradant not utilized by the other bifidobacterial species. Analysis of publicly available breastfed infant faecal metagenome data showed that the observed trends for B. breve were consistent with our in vitro data, suggesting that priority effects may have contributed to its dominance. Our study highlights the importance and history dependency of initial community assembly and its implications for the maturation trajectory of the infant gut microbiota.
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Affiliation(s)
- Miriam N Ojima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Keisuke Yoshida
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Toshitaka Odamaki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Jinzhong Xiao
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Aruto Nakajima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Junko Hirose
- School of Human Cultures, The University of Shiga Prefecture, Hikone, Shiga, Japan
- Department of Food and Nutrition, Kyoto Women's University, Kyoto, Japan
| | - Tadasu Urashima
- Department of Food and Life Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Toshihiko Katoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Aina Gotoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, Food Science Building, University College Cork, Cork, Ireland
| | - Dmitry A Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
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29
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Yokoi T, Nishiyama K, Kushida Y, Uribayashi K, Kunihara T, Fujimoto R, Yamamoto Y, Ito M, Miki T, Haneda T, Mukai T, Okada N. O-acetylesterase activity of Bifidobacterium bifidum sialidase facilities the liberation of sialic acid and encourages the proliferation of sialic acid scavenging Bifidobacterium breve. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:637-645. [PMID: 35581157 DOI: 10.1111/1758-2229.13083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Bifidobacterium bifidum possesses two extracellular sialidases (SiaBb1 and SiaBb2) that release free sialic acid from mucin sialoglycans, which can be utilized via cross-feeding by Bifidobacterium breve that, otherwise, is prevented from utilizing this nutrient source. Modification of sialic acids with O-acetyl esters is known to protect mucin glycans from degradation by bacterial sialidases. Compared to SiaBb2, SiaBb1 has an additional O-acetylesterase (Est) domain. We aimed to elucidate the role of the SiaBb1 Est domain from B. bifidum in sialic acid cross-feeding within Bifidobacterium. Pre-treatment of mucin secreted from bovine submaxillary glands (BSM) using His6 -tagged-Est and -SiaBb2 released a higher amount of sialic acid compared to the pre-treatment by His6 -SiaBb2. Growth of B. breve increased with an increase in nanE expression when supplemented with both His6 -Est- and His6 -SiaBb2-treated BSM. These results indicate that the esterase activity of the SiaBb1 Est domain enhances the efficiency of SiaBb2 to cleave sialic acid from mucin. This free sialic acid can be utilized by coexisting sialic acid scavenging B. breve via cross-feeding. Here, we provide the molecular mechanism underlying the unique sialoglycan degradation property of B. bifidum which is mediated by the complementary activities of SiaBb1 and SiaBb2 in the context of sialic acid cross-feeding.
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Affiliation(s)
- Tatsunari Yokoi
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Keita Nishiyama
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuka Kushida
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Kazuya Uribayashi
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Takahiro Kunihara
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Rika Fujimoto
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuji Yamamoto
- Laboratory of Biomolecular Science, School of Veterinary Medicine and Animal Sciences, Kitasato University, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Masahiro Ito
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Tsuyoshi Miki
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Takeshi Haneda
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Takao Mukai
- Laboratory of Biomolecular Science, School of Veterinary Medicine and Animal Sciences, Kitasato University, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Nobuhiko Okada
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
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Exploring the Ecological Effects of Naturally Antibiotic-Insensitive Bifidobacteria in the Recovery of the Resilience of the Gut Microbiota during and after Antibiotic Treatment. Appl Environ Microbiol 2022; 88:e0052222. [PMID: 35652662 DOI: 10.1128/aem.00522-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Amoxicillin-clavulanic acid (AMC) is the most widely used antibiotic, being frequently prescribed to infants. Particular members of the genus Bifidobacterium are among the first microbial colonizers of the infant gut, and it has been demonstrated that they exhibit various activities beneficial for their human host, including promotion/maintenance of the human gut microbiota homeostasis. It has been shown that natural resistance of bifidobacteria to AMC is limited to a small number of strains. In the current study, we investigated the mitigation effects of AMC-resistant bifidobacteria in diversity preservation of the gut microbiota during AMC treatment. To this end, an in vitro coculture experiment based on infant fecal samples and an in vivo study employing a rodent model were performed. The results confirmed the ability of AMC-resistant bifidobacterial strains to bolster gut microbiota resilience, while specific covariance analysis revealed strain-specific and variable impacts on the microbiota composition by individual bifidobacterial taxa. IMPORTANCE The first microbial colonizers of the infant gut are members of the genus Bifidobacterium, which exhibit different activities beneficial to their host. Amoxicillin-clavulanic acid (AMC) is the most frequently prescribed antibiotic during infancy, and few strains of bifidobacteria are known to show a natural resistance to this antibiotic. In the present work, we evaluated the possible positive effects of AMC-resistant bifidobacterial strains in maintaining gut microbiota diversity during AMC exposure, performing an in vitro and in vivo experiment based on an infant gut model and a rodent model, respectively. Our results suggested the ability of AMC-resistant bifidobacterial strains to support gut microbiota restoration.
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Wang J, Chen MS, Wang RS, Hu JQ, Liu S, Wang YYF, Xing XL, Zhang BW, Liu JM, Wang S. Current Advances in Structure-Function Relationships and Dose-Dependent Effects of Human Milk Oligosaccharides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6328-6353. [PMID: 35593935 DOI: 10.1021/acs.jafc.2c01365] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
HMOs (human milk oligosaccharides) are the third most important nutrient in breast milk. As complex glycans, HMOs play an important role in regulating neonatal intestinal immunity, resisting viral and bacterial infections, displaying anti-inflammatory characteristics, and promoting brain development. Although there have been some previous reports of HMOs, a detailed literature review summarizing the structure-activity relationships and dose-dependent effects of HMOs is lacking. Hence, after introducing the structures and synthetic pathways of HMOs, this review summarizes and categorizes identified structure-function relationships of HMOs. Differential mechanisms of different structural HMOs utilization by microorganisms are summarized. This review also emphasizes the recent advances in the interactions between different health benefits and the variance of dosage effect based on in vitro cell tests, animal experiments, and human intervention studies. The potential relationships between the chemical structure, the dosage selection, and the physiological properties of HMOs as functional foods are vital for further understanding of HMOs and their future applications.
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Affiliation(s)
- Jin Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Meng-Shan Chen
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Rui-Shan Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Jia-Qiang Hu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Shuang Liu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Yuan-Yi-Fei Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Xiao-Long Xing
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Bo-Wei Zhang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Jing-Min Liu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, No. 94 Weijin Road, Tianjin 300071, China
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Samara J, Moossavi S, Alshaikh B, Ortega VA, Pettersen VK, Ferdous T, Hoops SL, Soraisham A, Vayalumkal J, Dersch-Mills D, Gerber JS, Mukhopadhyay S, Puopolo K, Tompkins TA, Knights D, Walter J, Amin H, Arrieta MC. Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants. Cell Host Microbe 2022; 30:696-711.e5. [PMID: 35550672 DOI: 10.1016/j.chom.2022.04.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 11/19/2022]
Abstract
Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium-driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants.
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Affiliation(s)
- Jumana Samara
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Health Sciences Centre, Winnipeg, MB, Canada
| | - Shirin Moossavi
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Microbiome and Microbial Ecology Interest Group (MMEIG), Universal Scientific Education and Research Network (USERN), Calgary, Canada
| | - Belal Alshaikh
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Van A Ortega
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Veronika Kuchařová Pettersen
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tahsin Ferdous
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Suzie L Hoops
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Amuchou Soraisham
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Joseph Vayalumkal
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Deonne Dersch-Mills
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Jeffrey S Gerber
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sagori Mukhopadhyay
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karen Puopolo
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Dan Knights
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jens Walter
- School of Microbiology, Department of Medicine, and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Harish Amin
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada.
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Fernandez-Julia P, Commane DM, van Sinderen D, Munoz-Munoz J. Cross-feeding interactions between human gut commensals belonging to the Bacteroides and Bifidobacterium genera when grown on dietary glycans. MICROBIOME RESEARCH REPORTS 2022; 1:12. [PMID: 38045648 PMCID: PMC10688802 DOI: 10.20517/mrr.2021.05] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/20/2022] [Accepted: 02/25/2022] [Indexed: 12/05/2023]
Abstract
Elements of the human gut microbiota metabolise many host- and diet-derived, non-digestible carbohydrates (NDCs). Intestinal fermentation of NDCs salvages energy and resources for the host and generates beneficial metabolites, such as short chain fatty acids, which contribute to host health. The development of functional NDCs that support the growth and/or metabolic activity of specific beneficial gut bacteria, is desirable, but dependent on an in-depth understanding of the pathways of carbohydrate fermentation. The purpose of this review is to provide an appraisal of what is known about the roles of, and interactions between, Bacteroides and Bifidobacterium as key members involved in NDC utilisation. Bacteroides is considered an important primary degrader of complex NDCs, thereby generating oligosaccharides, which in turn can be fermented by secondary degraders. In this review, we will therefore focus on Bacteroides as an NDC-degrading specialist and Bifidobacterium as an important and purported probiotic representative of secondary degraders. We will describe cross-feeding interactions between members of these two genera. We note that there are limited studies exploring the interactions between Bacteroides and Bifidobacterium, specifically concerning β-glucan and arabinoxylan metabolism. This review therefore summarises the roles of these organisms in the breakdown of dietary fibre and the molecular mechanisms and interactions involved. Finally, it also highlights the need for further research into the phenomenon of cross-feeding between these organisms for an improved understanding of these cross-feeding mechanisms to guide the rational development of prebiotics to support host health or to prevent or combat disease associated with microbial dysbiosis.
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Affiliation(s)
- Pedro Fernandez-Julia
- Microbial Enzymology Group, Department of Applied Sciences, Ellison Building A, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Daniel M. Commane
- Microbial Enzymology Group, Department of Applied Sciences, Ellison Building A, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Jose Munoz-Munoz
- Microbial Enzymology Group, Department of Applied Sciences, Ellison Building A, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
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Human milk oligosaccharide-sharing by a consortium of infant derived Bifidobacterium species. Sci Rep 2022; 12:4143. [PMID: 35264656 PMCID: PMC8907170 DOI: 10.1038/s41598-022-07904-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/24/2022] [Indexed: 11/08/2022] Open
Abstract
Bifidobacteria are associated with a host of health benefits and are typically dominant in the gut microbiota of healthy, breast-fed infants. A key adaptation, facilitating the establishment of these species, is their ability to consume particular sugars, known as human milk oligosaccharides (HMO), which are abundantly found in breastmilk. In the current study, we aimed to characterise the co-operative metabolism of four commercial infant-derived bifidobacteria (Bifidobacterium bifidum R0071, Bifidobacterium breve M-16V, Bifidobacterium infantis R0033, and Bifidobacterium infantis M-63) when grown on HMO. Three different HMO substrates (2'-fucosyllactose alone and oligosaccharides isolated from human milk representing non-secretor and secretor status) were employed. The four-strain combination resulted in increased bifidobacterial numbers (> 21%) in comparison to single strain cultivation. The relative abundance of B. breve increased by > 30% during co-cultivation with the other strains despite demonstrating limited ability to assimilate HMO in mono-culture. HPLC analysis revealed strain-level variations in HMO consumption. Metabolomics confirmed the production of formate, acetate, 1,2-propanediol, and lactate with an overall increase in such metabolites during co-cultivation. These results support the concept of positive co-operation between multiple bifidobacterial strains during HMO utilisation which may result in higher cell numbers and a potentially healthier balance of metabolites.
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Wei B, Xia W, Wang L, Jin X, Yang W, Rao D, Chen S, Wu J. Diverse prebiotic effects of isomaltodextrins with different glycosidic linkages and molecular weights on human gut bacteria in vitro. Carbohydr Polym 2022; 279:118986. [PMID: 34980347 DOI: 10.1016/j.carbpol.2021.118986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022]
Abstract
Isomaltodextrin (IMD) is a novel dietary fiber enzymatically produced by reconstructing the molecular chain structure of starch using glycosyltransferases. In this study, the specific prebiotic effects of α-1,6 linear and α-1,2 or α-1,3 branched IMDs with different molecular weights (Mw) on human intestinal bacteria were investigated by pure culture of single strains and mixed fermentation of human fecal microflora in vitro. The results showed that α-1,6 linear IMDs markedly promoted beneficial Bifidobacterium and Lactobacillus in both pure culture and mixed fermentation. α-1,3 branching exhibited similar selectivity with α-1,6 linkage but yielded more butyrate in pure cultures. In contrast, IMDs containing α-1,2 branches were utilized efficiently only during mixed fermentation, which was speculated to result from metabolic cross-feeding. Regarding Mw, IMDs with lower Mw showed better prebiotic effects in pure cultures but no differences in mixed culture. These findings provide a theoretical basis for their application as functional foods.
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Affiliation(s)
- Beibei Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Wei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xuewei Jin
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Weikang Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Deming Rao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
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36
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Efficient isolation of membrane-associated exopolysaccharides of four commercial bifidobacterial strains. Carbohydr Polym 2022; 278:118913. [PMID: 34973732 DOI: 10.1016/j.carbpol.2021.118913] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/27/2021] [Accepted: 11/14/2021] [Indexed: 11/23/2022]
Abstract
Bifidobacteria confer many health effects, such as fiber digestion, pathogen inhibition and immune system maturation, especially in the newborn infant. The bifidobacterial exopolysaccharides (EPS) are often associated with important health effects, but their thorough investigation is hampered by lack of knowledge of the EPS localization, which is important for efficient EPS isolation. Here we present a straightforward isolation procedure to obtain EPS of four commercial bifidobacterial strains (B. adolescentis, B. bifidum, B. breve, and B. infantis), that are localized at the cell membrane (evidenced using cryo-EM). This procedure can be applied to other bifidobacterial strains, to facilitate the easy isolation and purification for biological experiments and future application in nutraceuticals. In addition, we demonstrate structural differences in the EPS of the four bifidobacterial strains, in terms of monosaccharide composition and size, highlighting the potential of the isolated EPS for determining specific structure-activity effects of bifidobacteria.
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37
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Why Are Bifidobacteria Important for Infants? Microorganisms 2022; 10:microorganisms10020278. [PMID: 35208736 PMCID: PMC8880231 DOI: 10.3390/microorganisms10020278] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
The presence of Bifidobacterium species in the maternal vaginal and fecal microbiota is arguably an evolutionary trait that allows these organisms to be primary colonizers of the newborn intestinal tract. Their ability to utilize human milk oligosaccharides fosters their establishment as core health-promoting organisms throughout life. A reduction in their abundance in infants has been shown to increase the prevalence of obesity, diabetes, metabolic disorder, and all-cause mortality later in life. Probiotic strains have been developed as supplements for premature babies and to counter some of these ailments as well as to confer a range of health benefits. The ability to modulate the immune response and produce short-chain fatty acids, particularly acetate and butyrate, that strengthen the gut barrier and regulate the gut microbiome, makes Bifidobacterium a core component of a healthy infant through adulthood.
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Zhang B, Li LQ, Liu F, Wu JY. Human milk oligosaccharides and infant gut microbiota: Molecular structures, utilization strategies and immune function. Carbohydr Polym 2022; 276:118738. [PMID: 34823774 DOI: 10.1016/j.carbpol.2021.118738] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
Abstract
Human milk oligosaccharides (HMOs) are a unique class of non-digestible carbohydrates present in the mother milk, which play a key role in the development of infant gut microbiota, epithelial barrier and immune function. The deficiency of HMOs in the bovine milk-based infant formula has been widely recognized as a major culprit for the much higher incidence of immune disorders of formula-fed infants. This report was to give an up-to-date review on the structure characteristics of HMOs and the possible mechanisms, and strategies for their cellular uptake, and metabolism by the gut bacteria and the associated effects on the infant gut microbiome, and immune function. Most previous studies have been carried out in animals or in vitro model systems on the utilization strategies for HMOs in infant bacteria and their roles in infant microbiome, and gut immune function. A few HMO molecules have been synthesized artificially and applied in infant formulas.
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Affiliation(s)
- Bin Zhang
- SCUT-Zhuhai Institute of Modern Industrial Innovation, School of Food Science and Engineering, Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health, South China University of Technology, Guangzhou 510640, China; Research Institute for Future Food, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Long-Qing Li
- Research Institute for Future Food, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Feitong Liu
- H&H Group Global Research and Technology Center, Guangzhou 510700, China.
| | - Jian-Yong Wu
- Research Institute for Future Food, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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39
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Saa P, Urrutia A, Silva-Andrade C, Martín AJ, Garrido D. Modeling approaches for probing cross-feeding interactions in the human gut microbiome. Comput Struct Biotechnol J 2021; 20:79-89. [PMID: 34976313 PMCID: PMC8685919 DOI: 10.1016/j.csbj.2021.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 12/16/2022] Open
Abstract
Microbial communities perform emergent activities that are essentially different from those carried by their individual members. The gut microbiome and its metabolites have a significant impact on the host, contributing to homeostasis or disease. Food molecules shape this community, being fermented through cross-feeding interactions of metabolites such as lactate, acetate, and amino acids, or products derived from macromolecule degradation. Mathematical and experimental approaches have been applied to understand and predict the interactions between microorganisms in complex communities such as the gut microbiota. Rational and mechanistic understanding of microbial interactions is essential to exploit their metabolic activities and identify keystone taxa and metabolites. The latter could be used in turn to modulate or replicate the metabolic behavior of the community in different contexts. This review aims to highlight recent experimental and modeling approaches for studying cross-feeding interactions within the gut microbiome. We focus on short-chain fatty acid production and fiber fermentation, which are fundamental processes in human health and disease. Special attention is paid to modeling approaches, particularly kinetic and genome-scale stoichiometric models of metabolism, to integrate experimental data under different diet and health conditions. Finally, we discuss limitations and challenges for the broad application of these modeling approaches and their experimental verification for improving our understanding of the mechanisms of microbial interactions.
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Affiliation(s)
- Pedro Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860 Santiago, Chile
| | - Arles Urrutia
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia Silva-Andrade
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Alberto J. Martín
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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40
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Turroni F, van Sinderen D, Ventura M. Bifidobacteria: insights into the biology of a key microbial group of early life gut microbiota. MICROBIOME RESEARCH REPORTS 2021; 1:2. [PMID: 38045555 PMCID: PMC10688781 DOI: 10.20517/mrr.2021.02] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/15/2021] [Indexed: 12/05/2023]
Abstract
The establishment and development of the human gut microbiota constitutes a dynamic and non-random process, which involves positive and negative interactions between key microbial taxa and their host. Remarkably, these early life microbiota-host communications include key events with long-term health consequences. Bifidobacteria arguably represent the most emblematic microbial taxon of the infant gut microbiota. In this context, the interactions among bifidobacteria, their human host, and other members of the human gut microbiota are far from completely understood, despite the crucial role they play in the development and maintenance of human physiology and immune system. Here, we highlight the ecological as well as genetic and functional features of bifidobacteria residing in the human gut using genomic and ecology-based information.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43126, Italy
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork Co. Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43126, Italy
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
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41
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Ishikawa E, Yamada T, Yamaji K, Serata M, Fujii D, Umesaki Y, Tsuji H, Nomoto K, Ito M, Okada N, Nagaoka M, Gomi A. Critical roles of a housekeeping sortase of probiotic Bifidobacterium bifidum in bacterium-host cell crosstalk. iScience 2021; 24:103363. [PMID: 34825137 PMCID: PMC8603203 DOI: 10.1016/j.isci.2021.103363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/09/2021] [Accepted: 10/25/2021] [Indexed: 10/30/2022] Open
Abstract
Bifidobacterium bifidum YIT 10347 (BF-1) is adhesive in vitro. Here we studied the molecular aspects of the BF-1 adhesion process. We identified and characterized non-adhesive mutants and found that a class E housekeeping sortase was critical for the adhesion to mucin. These mutants were significantly less adhesive to GCIY cells than was the wild type (WT), which protected GCIY cells against acid treatment more than did a non-adhesive mutant. The non-adhesive mutants aberrantly accumulated precursors of putative sortase-dependent proteins (SDPs). Recombinant SDPs bound to mucin. Disruption of the housekeeping sortase influenced expression of SDPs and pilus components. Mutants defective in a pilin or in an SDP showed the same adhesion properties as WT. Therefore, multiple SDPs and pili seem to work cooperatively to achieve adhesion, and the housekeeping sortase is responsible for cell wall anchoring of its substrates to ensure their proper biological function.
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Affiliation(s)
- Eiji Ishikawa
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Tetsuya Yamada
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Kazuaki Yamaji
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Masaki Serata
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Daichi Fujii
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Yoshinori Umesaki
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Hirokazu Tsuji
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Koji Nomoto
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan.,Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masahiro Ito
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Nobuhiko Okada
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Masato Nagaoka
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Atsushi Gomi
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
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42
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Nishiyama K, Yokoi T, Sugiyama M, Osawa R, Mukai T, Okada N. Roles of the Cell Surface Architecture of Bacteroides and Bifidobacterium in the Gut Colonization. Front Microbiol 2021; 12:754819. [PMID: 34721360 PMCID: PMC8551831 DOI: 10.3389/fmicb.2021.754819] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
There are numerous bacteria reside within the mammalian gastrointestinal tract. Among the intestinal bacteria, Akkermansia, Bacteroides, Bifidobacterium, and Ruminococcus closely interact with the intestinal mucus layer and are, therefore, known as mucosal bacteria. Mucosal bacteria use host or dietary glycans for colonization via adhesion, allowing access to the carbon source that the host’s nutrients provide. Cell wall or membrane proteins, polysaccharides, and extracellular vesicles facilitate these mucosal bacteria-host interactions. Recent studies revealed that the physiological properties of Bacteroides and Bifidobacterium significantly change in the presence of co-existing symbiotic bacteria or markedly differ with the spatial distribution in the mucosal niche. These recently discovered strategic colonization processes are important for understanding the survival of bacteria in the gut. In this review, first, we introduce the experimental models used to study host-bacteria interactions, and then, we highlight the latest discoveries on the colonization properties of mucosal bacteria, focusing on the roles of the cell surface architecture regarding Bacteroides and Bifidobacterium.
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Affiliation(s)
- Keita Nishiyama
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Tatsunari Yokoi
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Makoto Sugiyama
- Laboratory of Veterinary Anatomy, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Ro Osawa
- Research Center for Food Safety and Security, Kobe University, Kobe, Japan
| | - Takao Mukai
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Nobuhiko Okada
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
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Abstract
The neonatal body provides a range of potential habitats, such as the gut, for microbes. These sites eventually harbor microbial communities (microbiotas). A "complete" (adult) gut microbiota is not acquired by the neonate immediately after birth. Rather, the exclusive, milk-based nutrition of the infant encourages the assemblage of a gut microbiota of low diversity, usually dominated by bifidobacterial species. The maternal fecal microbiota is an important source of bacterial species that colonize the gut of infants, at least in the short-term. However, development of the microbiota is influenced by the use of human milk (breast feeding), infant formula, preterm delivery of infants, caesarean delivery, antibiotic administration, family details and other environmental factors. Following the introduction of weaning (complementary) foods, the gut microbiota develops in complexity due to the availability of a diversity of plant glycans in fruits and vegetables. These glycans provide growth substrates for the bacterial families (such as members of the Ruminococcaceae and Lachnospiraceae) that, in due course, will dominate the gut microbiota of the adult. Although current data are often fragmentary and observational, it can be concluded that the nutrition that a child receives in early life is likely to impinge not only on the development of the microbiota at that time but also on the subsequent lifelong, functional relationships between the microbiota and the human host. The purpose of this review, therefore, is to discuss the importance of promoting the assemblage of functionally robust gut microbiotas at appropriate times in early life.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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44
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Berkhout MD, Plugge CM, Belzer C. How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding. Glycobiology 2021; 32:182-200. [PMID: 34939101 PMCID: PMC8966484 DOI: 10.1093/glycob/cwab105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 11/12/2022] Open
Abstract
The intestinal epithelium is protected from direct contact with gut microbes by a mucus layer. This mucus layer consists of secreted mucin glycoproteins. The outer mucus layer in the large intestine forms a niche that attracts specific gut microbiota members of which several gut commensals can degrade mucin. Mucin glycan degradation is a complex process that requires a broad range of glycan degrading enzymes, as mucin glycans are intricate and diverse molecules. Consequently, it is hypothesised that microbial mucin breakdown requires concerted action of various enzymes in a network of multiple resident microbes at the gut mucosa. This review investigates the evolutionary relationships of microbial CAZymes that are potentially involved in mucin glycan degradation and focuses on the role that microbial enzymes play in the degradation of gut mucin glycans in microbial cross-feeding and syntrophic interactions.
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Affiliation(s)
- Maryse D Berkhout
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
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45
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Evolution of milk oligosaccharides: Origin and selectivity of the ratio of milk oligosaccharides to lactose among mammals. Biochim Biophys Acta Gen Subj 2021; 1866:130012. [PMID: 34536507 DOI: 10.1016/j.bbagen.2021.130012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The carbohydrate fraction of mammalian milk is constituted of lactose and oligosaccharides, most of which contain a lactose unit at their reducing ends. Although lactose is the predominant saccharide in the milk of most eutherians, oligosaccharides significantly predominate over lactose in the milk of monotremes and marsupials. SCOPE OF REVIEW This review describes the most likely process by which lactose and milk oligosaccharides were acquired during the evolution of mammals and the mechanisms by which these saccharides are digested and absorbed by the suckling neonates. MAJOR CONCLUSIONS During the evolution of mammals, c-type lysozyme evolved to α-lactalbumin. This permitted the biosynthesis of lactose by modulating the substrate specificity of β4galactosyltransferase 1, thus enabling the concomitant biosynthesis of milk oligosaccharides through the activities of several glycosyltransferases using lactose as an acceptor. In most eutherian mammals the digestion of lactose to glucose and galactose is achieved through the action of intestinal lactase (β-galactosidase), which is located within the small intestinal brush border. This enzyme, however, is absent in neonatal monotremes and macropod marsupials. It has therefore been proposed that in these species the absorption of milk oligosaccharides is achieved by pinocytosis or endocytosis, after which digestion occurs through the actions of several lysosomal acid glycosidases. This process would enable the milk oligosaccharides of monotremes and marsupials to be utilized as a significant energy source for the suckling neonates. GENERAL SIGNIFICANCE The evolution and significance of milk oligosaccharides is discussed in relation to the evolution of mammals.
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Sauvaitre T, Etienne-Mesmin L, Sivignon A, Mosoni P, Courtin CM, Van de Wiele T, Blanquet-Diot S. Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections. FEMS Microbiol Rev 2021; 45:5918835. [PMID: 33026073 DOI: 10.1093/femsre/fuaa052] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively referred as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonise the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely, the gut microbiota, under health and disease situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.
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Affiliation(s)
- Thomas Sauvaitre
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France.,Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
| | - Adeline Sivignon
- Université Clermont Auvergne, UMR 1071 Inserm, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Pascale Mosoni
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
| | - Christophe M Courtin
- KU Leuven, Faculty of Bioscience Engineering, Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium
| | - Tom Van de Wiele
- Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
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Turroni F, Milani C, Ventura M, van Sinderen D. The human gut microbiota during the initial stages of life: insights from bifidobacteria. Curr Opin Biotechnol 2021; 73:81-87. [PMID: 34333445 DOI: 10.1016/j.copbio.2021.07.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 12/18/2022]
Abstract
Current scientific literature has identified the infant gut microbiota as a multifaceted organ influencing a range of aspects of host-health and development. Many scientific studies have focused on characterizing the main microbial taxa that constitute the resident bacterial population of the infant gut. This has generated a wealth of information on the bacterial composition of the infant gut microbiota, and on the functional role/s exerted by their key microbial members. In this context, one of the most prevalent, abundant and investigated microbial taxon in the human infant gut is the genus Bifidobacterium, due to the purported beneficial activities is bestows upon its host. This review discusses the most recent findings regarding the infant gut microbiota with a particular focus on the molecular mechanisms by which bifidobacteria impact on host health and well-being.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy; Microbiome Research Hub, University of Parma, Parma, Italy.
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy; Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy; Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
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Olvera-Rosales LB, Cruz-Guerrero AE, Ramírez-Moreno E, Quintero-Lira A, Contreras-López E, Jaimez-Ordaz J, Castañeda-Ovando A, Añorve-Morga J, Calderón-Ramos ZG, Arias-Rico J, González-Olivares LG. Impact of the Gut Microbiota Balance on the Health-Disease Relationship: The Importance of Consuming Probiotics and Prebiotics. Foods 2021; 10:1261. [PMID: 34199351 PMCID: PMC8230287 DOI: 10.3390/foods10061261] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 02/07/2023] Open
Abstract
Gut microbiota is a group of microorganisms that are deposited throughout the entire gastrointestinal tract. Currently, thanks to genomic tools, studies of gut microbiota have pointed towards the understanding of the metabolism of important bacteria that are not cultivable and their relationship with human homeostasis. Alterations in the composition of gut microbiota could explain, at least in part, some epidemics, such as diabetes and obesity. Likewise, dysbiosis has been associated with gastrointestinal disorders, neurodegenerative diseases, and even cancer. That is why several studies have recently been focused on the direct relationship that these types of conditions have with the specific composition of gut microbiota, as in the case of the microbiota-intestine-brain axis. In the same way, the control of microbiota is related to the diet. Therefore, this review highlights the importance of gut microbiota, from its composition to its relationship with the human health-disease condition, as well as emphasizes the effect of probiotic and prebiotic consumption on the balance of its composition.
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Affiliation(s)
- Laura-Berenice Olvera-Rosales
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Alma-Elizabeth Cruz-Guerrero
- Departamento de Biotecnología, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de Mexico 09340, Mexico
| | - Esther Ramírez-Moreno
- Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda, La Concepción S/N, Carretera Pachuca Actopan, San Agustín Tlaxiaca 42060, Hidalgo, Mexico; (E.R.-M.); (Z.-G.C.-R.)
| | - Aurora Quintero-Lira
- Área Académica de Ingeniería Agroindustrial e Ingeniería en alimentos, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Av. Universidad km. 1, Ex-Hacienda de Aquetzalpa, Tulancingo 43600, Hidalgo, Mexico;
| | - Elizabeth Contreras-López
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Judith Jaimez-Ordaz
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Araceli Castañeda-Ovando
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Javier Añorve-Morga
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Zuli-Guadalupe Calderón-Ramos
- Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda, La Concepción S/N, Carretera Pachuca Actopan, San Agustín Tlaxiaca 42060, Hidalgo, Mexico; (E.R.-M.); (Z.-G.C.-R.)
| | - José Arias-Rico
- Área Académica de Enfermería, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda, La Concepción S/N, Carretera Pachuca Actopan, San Agustín Tlaxiaca 42060, Hidalgo, Mexico;
| | - Luis-Guillermo González-Olivares
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
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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: 3.3] [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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50
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Gene-Phenotype Associations Involving Human-Residential Bifidobacteria (HRB) Reveal Significant Species- and Strain-Specificity in Carbohydrate Catabolism. Microorganisms 2021; 9:microorganisms9050883. [PMID: 33919102 PMCID: PMC8143103 DOI: 10.3390/microorganisms9050883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 12/17/2022] Open
Abstract
Bifidobacteria are among the first colonizers of the human gastrointestinal tract. Different bacterial species use different mechanisms for utilization of various carbon sources in order to establish themselves in the complex microbial ecosystem of the gut. However, these mechanisms still need to be explored. Here, a large gene–phenotype correlation analysis was carried out to explore the metabolic and genetic diversity of bifidobacterial carbohydrate utilization abilities. In this study, we used 21 different carbohydrates to determine the growth phenotypes, the distribution of glycoside hydrolases (GHs), and gene clusters related to the utilization of multiple carbon sources in six human-residential Bifidobacterium species. Five carbohydrates significantly stimulated growth of almost all strains, while the remaining sugars exhibited species- and strain-specificity. Correspondingly, different Bifidobacterium species also had specific GHs involved in fermentation of plant or host glycans. Moreover, we analyzed several carbohydrate utilization gene clusters, such as 2-fucosyllactose (2′FL), sialic acid (SA), and fructooligosaccharide (FOS). In summary, by using 217 bifidobacterial strains and a wide range of growth substrates, our research revealed inter- and intra-species differences in bifidobacterial in terms of carbohydrate utilization. The findings of this study are useful for the process of developing prebiotics for optimum growth of probiotics, especially Bifidobacterium species.
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