scholarly journals Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Ana Martínez-del Campo ◽  
Smaranda Bodea ◽  
Hilary A. Hamer ◽  
Jonathan A. Marks ◽  
Henry J. Haiser ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gene Cluster ◽  
Gut Bacteria ◽  
Functional Gene ◽  
Metagenomic Data ◽  
Human Gut ◽  
Bacterial Gene ◽  
Human Gut Microbiota ◽  
Choline Metabolism

ABSTRACTElucidation of the molecular mechanisms underlying the human gut microbiota's effects on health and disease has been complicated by difficulties in linking metabolic functions associated with the gut community as a whole to individual microorganisms and activities. Anaerobic microbial choline metabolism, a disease-associated metabolic pathway, exemplifies this challenge, as the specific human gut microorganisms responsible for this transformation have not yet been clearly identified. In this study, we established the link between a bacterial gene cluster, the choline utilization (cut) cluster, and anaerobic choline metabolism in human gut isolates by combining transcriptional, biochemical, bioinformatic, and cultivation-based approaches. Quantitative reverse transcription-PCR analysis andin vitrobiochemical characterization of twocutgene products linked the entire cluster to growth on choline and supported a model for this pathway. Analyses of sequenced bacterial genomes revealed that thecutcluster is present in many human gut bacteria, is predictive of choline utilization in sequenced isolates, and is widely but discontinuously distributed across multiple bacterial phyla. Given that bacterial phylogeny is a poor marker for choline utilization, we were prompted to develop a degenerate PCR-based method for detecting the key functional gene choline TMA-lyase (cutC) in genomic and metagenomic DNA. Using this tool, we found that new choline-metabolizing gut isolates universally possessedcutC. We also demonstrated that this gene is widespread in stool metagenomic data sets. Overall, this work represents a crucial step toward understanding anaerobic choline metabolism in the human gut microbiota and underscores the importance of examining this microbial community from a function-oriented perspective.IMPORTANCEAnaerobic choline utilization is a bacterial metabolic activity that occurs in the human gut and is linked to multiple diseases. While bacterial genes responsible for choline fermentation (thecutgene cluster) have been recently identified, there has been no characterization of these genes in human gut isolates and microbial communities. In this work, we use multiple approaches to demonstrate that the pathway encoded by thecutgenes is present and functional in a diverse range of human gut bacteria and is also widespread in stool metagenomes. We also developed a PCR-based strategy to detect a key functional gene (cutC) involved in this pathway and applied it to characterize newly isolated choline-utilizing strains. Both our analyses of thecutgene cluster and this molecular tool will aid efforts to further understand the role of choline metabolism in the human gut microbiota and its link to disease.

scholarly journals A benzoxazole derivative as an inhibitor of anaerobic choline metabolism by human gut microbiota

2020 ◽  
Vol 11 (12) ◽  
pp. 1402-1412
Author(s):  
Moustafa T. Gabr ◽  
David Machalz ◽  
Szymon Pach ◽  
Gerhard Wolber
Keyword(s):  
Gut Microbiota ◽  
Metabolic Pathways ◽  
Therapeutic Targets ◽  
Gut Bacteria ◽  
Human Diseases ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Choline Metabolism

Metabolic pathways mediated by human gut bacteria have emerged as potential therapeutic targets because of their association with the pathophysiology of various human diseases.

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

PROTEOMICS ◽  
2015 ◽  
Vol 15 (20) ◽  
pp. 3474-3485 ◽  
Author(s):  
Alessandro Tanca ◽  
Antonio Palomba ◽  
Salvatore Pisanu ◽  
Maria Filippa Addis ◽  
Sergio Uzzau
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
The Impact

scholarly journals Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

Science ◽  
2015 ◽  
Vol 350 (6256) ◽  
pp. aac5992 ◽  
Author(s):  
Meng Wu ◽  
Nathan P. McNulty ◽  
Dmitry A. Rodionov ◽  
Matvei S. Khoroshkin ◽  
Nicholas W. Griffin ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Genetic Determinants ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Gene Level ◽  
Transposon Mutants ◽  
Gnotobiotic Mice ◽  
Stability And Resilience

Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in different ordered sequences. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability, and resilience and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness.

scholarly journals Bacterial Atlas of Mouse Gut Microbiota

2021 ◽  
Author(s):  
Mengqi Chu ◽  
Xiaobo Zhang
Keyword(s):  
Complex System ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Large Scale ◽  
Gut Bacteria ◽  
Human Gut ◽  
The Core ◽  
Human Gut Microbiota ◽  
Human Immunity ◽  
Mouse Gut Microbiota

Abstract Background: Mouse model is one of of the most widely used animal models for exploring the roles of human gut microbiota, a complex system involving in human immunity and metabolism. However, the structure of mouse gut bacterial community has not been explored at a large scale. To address this concern, the diversity and composition of the gut bacteria of 600 mice was characterized in this study. Results: The results showed that the bacteria belonging to 8 genera were found in the gut microbiota of all mouse individuals, indicating that the 8 bacteria were the core bacteria of mouse gut microbiota. The dominant genera of the mouse gut bacteria contained 15 bacterial genera. It was found that the bacteria in the gut microbiota were mainly involved in host’s metabolisms via the collaborations between the gut bacteria. The further analysis demonstrated that the composition of mouse gut microbiota was similar to that of human gut microbiota. Conclusion: Our study presented a bacterial atlas of mouse gut microbiota, providing a solid basis for investing the bacterial communities of mouse gut microbiota.

scholarly journals Glycan complexity dictates microbial resource allocation in the large intestine

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Artur Rogowski ◽  
Jonathon A. Briggs ◽  
Jennifer C. Mortimer ◽  
Theodora Tryfona ◽  
Nicolas Terrapon ◽  
...  
Keyword(s):  
Resource Allocation ◽  
Gut Microbiota ◽  
Large Intestine ◽  
Side Chains ◽  
Dietary Carbohydrates ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Bacteroides Ovatus ◽  
Complex Carbohydrates

Abstract The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan. Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains. Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.

scholarly journals Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown

2019 ◽  
Author(s):  
Lucy I. Crouch ◽  
Marcelo V. Liberato ◽  
Paulina A. Urbanowicz ◽  
Arnaud Baslé ◽  
Christopher A. Lamb ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Current Model ◽  
Initial Step ◽  
Gut Bacteria ◽  
Glycoside Hydrolases ◽  
Gut Health ◽  
New Paradigm ◽  
Human Gut ◽  
Peptide Backbone ◽  
Human Gut Microbiota

AbstractThe human gut microbiota (HGM) are closely associated with health, development and disease. The thick intestinal mucus layer, especially in the colon, is the key barrier between the contents of the lumen and the epithelial cells, providing protection against infiltration by the microbiota as well potential pathogens. The upper layer of the colonic mucus is a niche for a subset of the microbiota which utilise the mucin glycoproteins as a nutrient source and mucin grazing by the microbiota appears to play a key role in maintaining barrier function as well as community stability. Despite the importance of mucin breakdown for gut health, the mechanisms by which gut bacteria access this complex glycoprotein are not well understood. The current model for mucin degradation involves exclusively exo-acting glycosidases that sequentially trim monosaccharides from the termini of the glycan chains to eventually allow access to the mucin peptide backbone by proteases. However, this model is in direct contrast to the Sus paradigm of glycan breakdown used by the Bacteroidetes which involves extracellular cleavage of glycans by surface located endo-acting enzymes prior to import of the oligosaccharide products. Here we describe the discovery and characterisation of endo-acting family 16 glycoside hydrolases (GH16s) from prominent mucin degrading gut bacteria that specifically target the oligosaccharide side chains of intestinal mucins from both animals and humans. These endo-acting O-glycanases display β1,4-glactosidase activity and in several cases are surface located indicating they are involved in the initial step in mucin breakdown. The data suggest a new paradigm for mucin breakdown by the microbiota and the endo-mucinases provide a potential tool to explore changes that occur in mucin structure in intestinal disorders such as inflammatory bowel disease and colon cancer.

scholarly journals Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Guillaume Déjean ◽  
Kazune Tamura ◽  
Adriana Cabrera ◽  
Namrata Jain ◽  
Nicholas A. Pudlo ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Cell Surface ◽  
Gut Microbiota ◽  
Dietary Fiber ◽  
Binding Proteins ◽  
Functional Characterization ◽  
Human Gut ◽  
Content Type ◽  
Human Gut Microbiota

ABSTRACT The human gut microbiota (HGM) has far-reaching impacts on human health and nutrition, which are fueled primarily by the metabolism of otherwise indigestible complex carbohydrates commonly known as dietary fiber. However, the molecular basis of the ability of individual taxa of the HGM to address specific dietary glycan structures remains largely unclear. In particular, the utilization of β(1,3)-glucans, which are widespread in the human diet as yeast, seaweed, and plant cell walls, had not previously been resolved. Through a systems-based approach, here we show that the symbiont Bacteroides uniformis deploys a single, exemplar polysaccharide utilization locus (PUL) to access yeast β(1,3)-glucan, brown seaweed β(1,3)-glucan (laminarin), and cereal mixed-linkage β(1,3)/β(1,4)-glucan. Combined biochemical, enzymatic, and structural analysis of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) illuminates a concerted molecular system by which B. uniformis recognizes and saccharifies these distinct β-glucans. Strikingly, the functional characterization of homologous β(1,3)-glucan utilization loci (1,3GUL) in other Bacteroides further demonstrated that the ability of individual taxa to utilize β(1,3)-glucan variants and/or β(1,3)/β(1,4)-glucans arises combinatorially from the individual specificities of SGBPs and GHs at the cell surface, which feed corresponding signals to periplasmic hybrid two-component sensors (HTCSs) via TonB-dependent transporters (TBDTs). These data reveal the importance of cooperativity in the adaptive evolution of GH and SGBP cohorts to address individual polysaccharide structures. We anticipate that this fine-grained knowledge of PUL function will inform metabolic network analysis and proactive manipulation of the HGM. Indeed, a survey of 2,441 public human metagenomes revealed the international, yet individual-specific, distribution of each 1,3GUL. IMPORTANCE Bacteroidetes are a dominant phylum of the human gut microbiota (HGM) that target otherwise indigestible dietary fiber with an arsenal of polysaccharide utilization loci (PULs), each of which is dedicated to the utilization of a specific complex carbohydrate. Here, we provide novel insight into this paradigm through functional characterization of homologous PULs from three autochthonous Bacteroides species, which target the family of dietary β(1,3)-glucans. Through detailed biochemical and protein structural analysis, we observed an unexpected diversity in the substrate specificity of PUL glycosidases and glycan-binding proteins with regard to β(1,3)-glucan linkage and branching patterns. In combination, these individual enzyme and protein specificities support taxon-specific growth on individual β(1,3)-glucans. This detailed metabolic insight, together with a comprehensive survey of individual 1,3GULs across human populations, further expands the fundamental roadmap of the HGM, with potential application to the future development of microbial intervention therapies.

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