scholarly journals A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid

2018 ◽  
Vol 84 (19) ◽  
Author(s):  
María Esteban-Torres ◽  
Laura Santamaría ◽  
Raúl Cabrera-Rubio ◽  
Laura Plaza-Vinuesa ◽  
Fiona Crispie ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gallic Acid ◽  
High Throughput Sequencing ◽  
Human Gut ◽  
Diverse Range ◽  
Fecal Samples ◽  
Content Type ◽  
Human Gut Microbiota ◽  
Human Microbiota ◽  
Phenolic Components

ABSTRACTThe human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota wereFirmicutes(74.6%),Proteobacteria(17.6%), andActinobacteria(7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera,AnaerostipesandKlebsiellaaccounted for the majority of reads (40%). The usefulness of the HTS-lpdCmethod was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCEDespite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives ofBacteroidetes. The presence of functional gallate decarboxylases was demonstrated in representativeProteobacteriaandFirmicutesstrains from the human microbiota, an observation that could be of considerable relevance to thein vivoproduction of pyrogallol, a physiologically important bioactive compound.

scholarly journals From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Eugen Bauer ◽  
Ines Thiele
Keyword(s):  
Systems Biology ◽  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Computational Systems Biology ◽  
Human Gut ◽  
Novel Treatments ◽  
Human Gut Microbiota ◽  
Microbe Interactions ◽  
Constraint Based Modeling ◽  
Computational Systems

ABSTRACTAn important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities. Common approaches to investigate the human microbiota include high-throughput sequencing with subsequent correlative analyses. However, to understand the ecology of the human gut microbiota and consequently design novel treatments for diseases, it is important to represent the different interactions between microbes with their associated metabolites. Computational systems biology approaches can give further mechanistic insights by constructing data- or knowledge-driven networks that represent microbe interactions. In this minireview, we will discuss current approaches in systems biology to analyze the human gut microbiota, with a particular focus on constraint-based modeling. We will discuss various community modeling techniques with their advantages and differences, as well as their application to predict the metabolic mechanisms of intestinal microbial communities. Finally, we will discuss future perspectives and current challenges of simulating realistic and comprehensive models of the human gut microbiota.

scholarly journals Revealing microbial species diversity using sequence capture by hybridization

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Sophie Marre ◽  
Cyrielle Gasc ◽  
Camille Forest ◽  
Yacine Lebbaoui ◽  
Pascale Mosoni ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rdna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Human Gut ◽  
Content Type ◽  
Innovative Strategy ◽  
Human Gut Microbiota ◽  
Rare Biosphere

Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales , 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.

scholarly journals Substrate Use Prioritization by a Coculture of Five Species of Gut Bacteria Fed Mixtures of Arabinoxylan, Xyloglucan, β-Glucan, and Pectin

2019 ◽  
Vol 86 (2) ◽  
Author(s):  
Yafei Liu ◽  
Anne-Louise Heath ◽  
Barbara Galland ◽  
Nancy Rehrer ◽  
Lynley Drummond ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Fiber ◽  
Bacterial Species ◽  
Short Chain ◽  
Emergent Properties ◽  
Human Gut ◽  
Fermentation Products ◽  
Plant Polysaccharides ◽  
Content Type ◽  
Human Gut Microbiota

ABSTRACT Dietary fiber provides growth substrates for bacterial species that belong to the colonic microbiota of humans. The microbiota degrades and ferments substrates, producing characteristic short-chain fatty acid profiles. Dietary fiber contains plant cell wall-associated polysaccharides (hemicelluloses and pectins) that are chemically diverse in composition and structure. Thus, depending on plant sources, dietary fiber daily presents the microbiota with mixtures of plant polysaccharides of various types and complexity. We studied the extent and preferential order in which mixtures of plant polysaccharides (arabinoxylan, xyloglucan, β-glucan, and pectin) were utilized by a coculture of five bacterial species (Bacteroides ovatus, Bifidobacterium longum subspecies longum, Megasphaera elsdenii, Ruminococcus gnavus, and Veillonella parvula). These species are members of the human gut microbiota and have the biochemical capacity, collectively, to degrade and ferment the polysaccharides and produce short-chain fatty acids (SCFAs). B. ovatus utilized glycans in the order β-glucan, pectin, xyloglucan, and arabinoxylan, whereas B. longum subsp. longum utilization was in the order arabinoxylan, arabinan, pectin, and β-glucan. Propionate, as a proportion of total SCFAs, was augmented when polysaccharide mixtures contained galactan, resulting in greater succinate production by B. ovatus and conversion of succinate to propionate by V. parvula. Overall, we derived a synthetic ecological community that carries out SCFA production by the common pathways used by bacterial species for this purpose. Systems like this might be used to predict changes to the emergent properties of the gut ecosystem when diet is altered, with the aim of beneficially affecting human physiology. IMPORTANCE This study addresses the question as to how bacterial species, characteristic of the human gut microbiota, collectively utilize mixtures of plant polysaccharides such as are found in dietary fiber. Five bacterial species with the capacity to degrade polymers and/or produce acidic fermentation products detectable in human feces were used in the experiments. The bacteria showed preferential use of certain polysaccharides over others for growth, and this influenced their fermentation output qualitatively. These kinds of studies are essential in developing concepts of how the gut microbial community shares habitat resources, directly and indirectly, when presented with mixtures of polysaccharides that are found in human diets. The concepts are required in planning dietary interventions that might correct imbalances in the functioning of the human microbiota so as to support measures to reduce metabolic conditions such as obesity.

scholarly journals Wood-Derived Dietary Fibers Promote Beneficial Human Gut Microbiota

mSphere ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Sabina Leanti La Rosa ◽  
Vasiliki Kachrimanidou ◽  
Fanny Buffetto ◽  
Phillip B. Pope ◽  
Nicholas A. Pudlo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Well Being ◽  
Gut Health ◽  
Human Gut ◽  
Content Type ◽  
Human Gut Microbiota ◽  
Lignocellulosic Feedstocks ◽  
Host Health ◽  
Clostridial Cluster ◽  
Gut Microbiota Composition

The architecture of the gut bacterial ecosystem has a profound effect on the physiology and well-being of the host. Modulation of the gut microbiota and the intestinal microenvironment via administration of prebiotics represents a valuable strategy to promote host health. This work provides insights into the ability of two novel wood-derived preparations, AcGGM and AcAGX, to influence human gut microbiota composition and activity. These compounds were selectively fermented by commensal bacteria such as Bifidobacterium, Bacteroides-Prevotella, F. prausnitzii, and clostridial cluster IX spp. This promoted the microbial synthesis of acetate, propionate, and butyrate, which are beneficial to the microbial ecosystem and host colonic epithelial cells. Thus, our results demonstrate potential prebiotic properties for both AcGGM and AcAGX from lignocellulosic feedstocks. These findings represent pivotal requirements for rationally designing intervention strategies based on the dietary supplementation of AcGGM and AcAGX to improve or restore gut health.

scholarly journals Evaluation of an Oral Subchronic Exposure of Deoxynivalenol on the Composition of Human Gut Microbiota in a Model of Human Microbiota-Associated Rats

PLoS ONE ◽  
2013 ◽  
Vol 8 (11) ◽  
pp. e80578 ◽  
Author(s):  
Manuel J. Saint-Cyr ◽  
Agnès Perrin-Guyomard ◽  
Paméla Houée ◽  
Jean-Guy Rolland ◽  
Michel Laurentie
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Subchronic Exposure ◽  
Human Gut Microbiota ◽  
Human Microbiota

scholarly journals Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population

2021 ◽  
Author(s):  
Hao Chung The ◽  
Chau Nguyen Ngoc Minh ◽  
Chau Tran Thi Hong ◽  
To Nguyen Thi Nguyen ◽  
Lindsay J. Pike ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Antimicrobial Susceptibility ◽  
Genomic Diversity ◽  
Human Gut ◽  
Content Type ◽  
Human Gut Microbiota ◽  
Probiotic Potential ◽  
Vietnamese Population ◽  
Strain Dependent ◽  
Biochemical Features

Bifidobacterium pseudocatenulatum is a beneficial member of the human gut microbiota. The organism can modulate inflammation and has probiotic potential, but its characteristics are largely strain dependent and associated with distinct genomic and biochemical features.

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.

scholarly journals Sharing a β-Glucan Meal: Transcriptomic Eavesdropping on a Bacteroides ovatus-Subdoligranulum variabile-Hungatella hathewayi Consortium

2020 ◽  
Vol 86 (20) ◽  
Author(s):  
Manuela Centanni ◽  
Ian M. Sims ◽  
Tracey J. Bell ◽  
Ambarish Biswas ◽  
Gerald W. Tannock
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Dietary Fiber ◽  
Bacterial Species ◽  
Human Gut ◽  
Additional Energy ◽  
Content Type ◽  
Human Gut Microbiota ◽  
Bacteroides Ovatus

ABSTRACT Whole-transcriptome analysis was used to investigate the molecular interplay between three bacterial species that are members of the human gut microbiota. Bacteroides ovatus, Subdoligranulum variabile, and Hungatella hathewayi formed associations in cocultures fed barley β-glucan, a constituent of dietary fiber. B. ovatus depolymerized β-glucan and released, but did not utilize, 3-O-β-cellobiosyl-d-glucose (DP3) and 3-O-β-cellotriosyl-d-glucose (DP4). These oligosaccharides provided growth substrates for S. variabile and H. hathewayi with a preference for DP4 in the case of the latter species. There was increased transcription of a B. ovatus mixed-linkage-β-glucan utilization locus, as well as carbohydrate transporters in S. variabile and H. hathewayi when in batch coculture. Increased transcription of the β-glucan utilization locus did not occur in continuous culture. Evidence for interactions relating to provision of cobalamin, alterations to signaling, and modulation of the “stringent response” (an adaptation to nutrient deprivation) were detected. Overall, we established a bacterial consortium based on barley β-glucan in vitro, which can be used to investigate aspects of the functional blueprint of the human gut microbiota. IMPORTANCE The microbial community, mostly composed of bacterial species, residing in the human gut degrades and ferments polysaccharides derived from plants (dietary fiber) that would not otherwise be digested. In this way, the collective metabolic actions of community members extract additional energy from the human diet. While the variety of bacteria present in the microbial community is well known, the formation of bacterial consortia, and the consequent interactions that result in the digestion of dietary polysaccharides, has not been studied extensively. The importance of our work was the establishment, under laboratory conditions, of a consortium of gut bacteria that formed around a dietary constituent commonly present in cereals. This enabled the metabolic interplay between the bacterial species to be studied. This kind of knowledge is required to construct an interactive, metabolic blueprint of the microbial community that inhabits the human gut.

scholarly journals A Putative Type V Pilus Contributes toBacteroides thetaiotaomicronBiofilm Formation Capacity

2019 ◽  
Vol 201 (18) ◽  
Author(s):  
Jovana Mihajlovic ◽  
Nathalie Bechon ◽  
Christa Ivanova ◽  
Florian Chain ◽  
Alexandre Almeida ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Selection Procedure ◽  
Bacteroides Thetaiotaomicron ◽  
Human Gut ◽  
Healthy Human ◽  
Content Type ◽  
Human Gut Microbiota ◽  
Type V

ABSTRACTBacteroides thetaiotaomicronis a prominent anaerobic member of the healthy human gut microbiota. While the majority of functional studies onB. thetaiotaomicronaddressed its impact on the immune system and the utilization of diet polysaccharides,B. thetaiotaomicronbiofilm capacity and its contribution to intestinal colonization are still poorly characterized. We tested the natural adhesion of 34B. thetaiotaomicronisolates and showed that although biofilm capacity is widespread amongB. thetaiotaomicronstrains, this phenotype is masked or repressed in the widely used reference strain VPI 5482. Using transposon mutagenesis followed by a biofilm positive-selection procedure, we identified VPI 5482 mutants with increased biofilm capacity corresponding to an alteration in the C-terminal region of BT3147, encoded by theBT3148-BT3147locus, which displays homology with Mfa-like type V pili found in manyBacteroidetes. We show that BT3147 is exposed on theB. thetaiotaomicronsurface and that BT3147-dependent adhesion also requires BT3148, suggesting that BT3148 and BT3147 correspond to the anchor and stalk subunits of a new type V pilus involved inB. thetaiotaomicronadhesion. This study therefore introducesB. thetaiotaomicronas a model to study proteinaceous adhesins and biofilm-related phenotypes in this important intestinal symbiont.IMPORTANCEAlthough the gut anaerobeBacteroides thetaiotaomicronis a prominent member of the healthy human gut microbiota, little is known about its capacity to adhere to surfaces and form biofilms. Here, we identify that alteration of a surface-exposed protein corresponding to a type of pili found in manyBacteroidetesincreasesB. thetaiotaomicronbiofilm formation. This study lays the ground for establishing this bacterium as a model organism forin vitroandin vivostudies of biofilm-related phenotypes in gut anaerobes.

scholarly journals Complete Genome Sequence of Alistipes indistinctus Strain 2BBH45, Isolated from the Feces of a Healthy Japanese Male

2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Yusuke Ogata ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
Masahira Hattori ◽  
Wataru Suda
Keyword(s):  
Gut Microbiota ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Human Gut ◽  
Content Type ◽  
Human Gut Microbiota ◽  
Japanese Male

ABSTRACT The genus Alistipes is one of the members of the human gut microbiota. Here, we report the complete genome sequence of Alistipes indistinctus strain 2BBH45, harboring plasmid p2BBH45.

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