Different Bacteroides Species Colonise Human and Chicken Intestinal Tract

Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken-adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken-adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.

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A network-based data-mining approach to investigate indole-related microbiota-host co-metabolism

10.1101/602458 ◽

2019 ◽

Author(s):

Ana Luisa Neves ◽

Andrea Rodriguez-Martinez ◽

Rafael Ayala ◽

Joram M Posma ◽

MR Abellona U ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Species ◽

Human Gut ◽

New Members ◽

Human Gut Microbiota ◽

Genome Data ◽

Data Mining Approach ◽

Cardiometabolic Disorders ◽

Metabolic Reactions

AbstractMotivationIndoles have been shown to play a significant role in cardiometabolic disorders. While some individual bacterial species are known to produce indole-adducts, to our best knowledge no studies have made use of publicly available genome data to identify prokaryotes, specifically those associated with the human gut microbiota, contributing to the indole metabolic network.ResultsHere, we propose a computational strategy, comprising the integration of KEGG and BLAST, to identify prokaryote-specific metabolic reactions relevant for the production of indoles, as well as to predict new members of the human gut microbiota potentially involved in these reactions. By identifying relevant prokaryotic species for further validation studiesin vitro, this strategy represents a useful approach for those interrogating the metabolism of other gut-derived microbial metabolites relevant to human health.AvailabilityAll R scripts and files (gut microbial dataset, FASTA protein sequences, BLASTP output files) are available fromhttps://github.com/AndreaRMICL/Microbial_networks.ContactARM:[email protected]; LH:[email protected].

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

Applied and Environmental Microbiology ◽

10.1128/aem.01651-20 ◽

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.

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Dissecting Individual Interactions between Pathogenic and Commensal Bacteria within a Multispecies Gut Microbial Community

mSphere ◽

10.1128/msphere.00013-21 ◽

2021 ◽

Vol 6 (2) ◽

Author(s):

Jack Hassall ◽

Jeffrey K. J. Cheng ◽

Meera Unnikrishnan

Keyword(s):

Gut Microbiota ◽

Bacterial Species ◽

Single Species ◽

Commensal Bacteria ◽

Individual Species ◽

Human Gut ◽

Content Type ◽

Clostridioides Difficile ◽

Gut Pathogen

ABSTRACT Interactions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lack in vitro models to monitor community responses to pathogens at a single-species level. We have developed a multispecies community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a quantitative PCR (qPCR)-based approach. Introduction of the major nosocomial gut pathogen, Clostridioides difficile, to this community resulted in increased adhesion of commensals and inhibition of C. difficile multiplication. Interestingly, we observed an increase in individual Bacteroides species accompanying the inhibition of C. difficile. Furthermore, Bacteroides dorei reduced C. difficile growth within biofilms, suggesting a role for Bacteroides spp. in prevention of C. difficile colonization. We report here an in vitro tool with excellent applications for investigating bacterial interactions within a complex community. IMPORTANCE Studying interactions between bacterial species that reside in the human gut is crucial for gaining a better insight into how they provide protection from pathogen colonization. In vitro models of multispecies bacterial communities wherein behaviors of single species can be accurately tracked are key to such studies. Here, we have developed a synthetic, trackable, gut microbiota community which reduces growth of the human gut pathogen Clostridioides difficile. We report that Bacteroides spp. within this community respond by multiplying in the presence of this pathogen, resulting in reduction of C. difficile growth. Defined in vitro communities that can be tailored to include different species are well suited to functional genomic approaches and are valuable tools for understanding interbacterial interactions.

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In vitro study of the interaction between human gut microbiota and herbal extracts using willow bark extract as an example

Planta Medica ◽

10.1055/s-0036-1596386 ◽

2016 ◽

Vol 81 (S 01) ◽

pp. S1-S381

Author(s):

EM Pferschy-Wenzig ◽

K Koskinen ◽

C Moissl-Eichinger ◽

R Bauer

Keyword(s):

Gut Microbiota ◽

In Vitro Study ◽

Vitro Study ◽

Bark Extract ◽

Herbal Extracts ◽

Human Gut ◽

Human Gut Microbiota ◽

Willow Bark

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Metabolization of the herbal combination STW-5 by human gut microbiota in vitro

10.1055/s-0037-1608399 ◽

2017 ◽

Author(s):

EM Pferschy-Wenzig ◽

A Roßmann ◽

K Koskinen ◽

H Abdel-Aziz ◽

C Moissl-Eichinger ◽

...

Keyword(s):

Gut Microbiota ◽

Human Gut ◽

Human Gut Microbiota

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Substrate use prioritization by a coculture of five species of gut bacteria fed mixtures of arabinoxylan, xyloglucan, β-glucan, and pectin

10.26686/wgtn.12585620.v1 ◽

2020 ◽

Author(s):

Y Liu ◽

AL Heath ◽

B Galland ◽

N Rehrer ◽

L Drummond ◽

...

Keyword(s):

Gut Microbiota ◽

Dietary Fiber ◽

Plant Cell Wall ◽

Bacterial Species ◽

Short Chain ◽

Emergent Properties ◽

Human Gut ◽

Fermentation Products ◽

Plant Polysaccharides ◽

Human Gut Microbiota

© 2020 American Society for Microbiology. 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. 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.

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Preservation of Human Gut Microbiota Inoculums for In Vitro Fermentations Studies

Fermentation ◽

10.3390/fermentation7010014 ◽

2021 ◽

Vol 7 (1) ◽

pp. 14

Author(s):

Nelson Mota de Carvalho ◽

Diana Luazi Oliveira ◽

Mayra Anton Dib Saleh ◽

Manuela Pintado ◽

Ana Raquel Madureira

Keyword(s):

Gut Microbiota ◽

Metabolic Profile ◽

Bacterial Count ◽

Glycerol Solution ◽

Metabolic Profiles ◽

Human Gut ◽

Colonic Fermentation ◽

In Vitro Fermentation ◽

Fecal Samples

The use of fecal inoculums for in vitro fermentation models requires a viable gut microbiota, capable of fermenting the unabsorbed nutrients. Fresh samples from human donors are used; however, the availability of fresh fecal inoculum and its inherent variability is often a problem. This study aimed to optimize a method of preserving pooled human fecal samples for in vitro fermentation studies. Different conditions and times of storage at −20 °C were tested. In vitro fermentation experiments were carried out for both fresh and frozen inoculums, and the metabolic profile compared. In comparison with the fresh, the inoculum frozen in a PBS and 30% glycerol solution, had a significantly lower (p < 0.05) bacterial count (<1 log CFU/mL). However, no significant differences (p < 0.05) were found between the metabolic profiles after 48 h. Hence, a PBS and 30% glycerol solution can be used to maintain the gut microbiota viability during storage at −20 °C for at least 3 months, without interfering with the normal course of colonic fermentation.

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Wheat cell walls and constituent polysaccharides induce similar microbiota profiles upon in vitro fermentation despite different short chain fatty acid end-product levels.

Food & Function ◽

10.1039/d0fo02509g ◽

2021 ◽

Author(s):

Shiyi Lu ◽

Deirdre Mikkelsen ◽

Hong Yao ◽

Barbara Williams ◽

Bernadine Flanagan ◽

...

Keyword(s):

Fatty Acid ◽

Gut Microbiota ◽

Plant Cell ◽

Cell Walls ◽

Short Chain Fatty Acid ◽

Chain Fatty Acid ◽

Plant Cell Walls ◽

Human Gut ◽

In Vitro Fermentation

Plant cell walls as well as their component polysaccharides in foods can be utilized to alter and maintain a beneficial human gut microbiota, but it is not known whether the...

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