Ascertaining the biochemical function of an essential pectin methylesterase in the gut microbe Bacteroides thetaiotaomicron

Pectins are a major dietary nutrient source for the human gut microbiota. The prominent gut microbe Bacteroides thetaiotaomicron was recently shown to encode the founding member (BT1017) of a new family of pectin methylesterases essential for the metabolism of the complex pectin rhamnogalacturonan-II (RG-II). However, biochemical and structural knowledge of this family is lacking. Here, we showed that BT1017 is critical for the metabolism of an RG-II–derived oligosaccharide ΔBT1017oligoB generated by a BT1017 deletion mutant (ΔBT1017) during growth on carbohydrate extract from apple juice. Structural analyses of ΔBT1017oligoB using a combination of enzymatic, mass spectrometric, and NMR approaches revealed that it is a bimethylated nonaoligosaccharide (GlcA-β1,4-(2-O-Me-Xyl-α1,3)-Fuc-α1,4-(GalA-β1,3)-Rha-α1,3-Api-β1,2-(Araf-α1,3)-(GalA-α1,4)-GalA) containing components of the RG-II backbone and its side chains. We showed that the catalytic module of BT1017 adopts an α/β-hydrolase fold, consisting of a central twisted 10-stranded β-sheet sandwiched by several α-helices. This constitutes a new fold for pectin methylesterases, which are predominantly right-handed β-helical proteins. Bioinformatic analyses revealed that the family is dominated by sequences from prominent genera of the human gut microbiota, including Bacteroides and Prevotella. Our re-sults not only highlight the critical role played by this family of enzymes in pectin metabolism but also provide new insights into the molecular basis of the adaptation of B. thetaiotaomicron to the human gut.

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Clostridioides difficileuses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea

Science Translational Medicine ◽

10.1126/scitranslmed.aam7019 ◽

2018 ◽

Vol 10 (464) ◽

pp. eaam7019 ◽

Cited By ~ 43

Author(s):

Eric J. Battaglioli ◽

Vanessa L. Hale ◽

Jun Chen ◽

Patricio Jeraldo ◽

Coral Ruiz-Mojica ◽

...

Keyword(s):

Risk Factors ◽

Amino Acid ◽

Gut Microbiota ◽

Critical Role ◽

Human Gut ◽

Fecal Microbiota Transplant ◽

Germ Free ◽

Human Gut Microbiota ◽

Microbial Dysbiosis ◽

Amino Acid Availability

The gut microbiota plays a critical role in pathogen defense. Studies using antibiotic-treated mice reveal mechanisms that increase susceptibility toClostridioides difficileinfection (CDI), but risk factors associated with CDI in humans extend beyond antibiotic use. Here, we studied the dysbiotic gut microbiota of a subset of patients with diarrhea and modeled the gut microbiota of these patients by fecal transplantation into germ-free mice. When challenged withC. difficile, the germ-free mice transplanted with fecal samples from patients with dysbiotic microbial communities showed increased gut amino acid concentrations and greater susceptibility to CDI. AC. difficilemutant that was unable to use proline as an energy source was unable to robustly infect germ-free mice transplanted with a dysbiotic or healthy human gut microbiota. Prophylactic dietary intervention using a low-proline or low-protein diet in germ-free mice colonized by a dysbiotic human gut microbiota resulted in decreased expansion of wild-typeC. difficileafter challenge, suggesting that amino acid availability might be important for CDI. Furthermore, a prophylactic fecal microbiota transplant in mice with dysbiosis reduced proline availability and protected the mice from CDI. Last, we identified clinical risk factors that could potentially predict gut microbial dysbiosis and thus greater susceptibility to CDI in a retrospective cohort of patients with diarrhea. Identifying at-risk individuals and reducing their susceptibility to CDI through gut microbiota–targeted therapies could be a new approach to preventingC. difficileinfection in susceptible patients.

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Perturbation of the human gut microbiome by a non-antibiotic drug contributes to the resolution of autoimmune disease

10.1101/600155 ◽

2019 ◽

Cited By ~ 3

Author(s):

Renuka R. Nayak ◽

Margaret Alexander ◽

Kye Stapleton-Grey ◽

Carles Ubeda ◽

Jose U. Scher ◽

...

Keyword(s):

Gut Microbiota ◽

Drug Response ◽

Ex Vivo ◽

Critical Role ◽

Pharmaceutical Drugs ◽

Human Gut ◽

Human Gut Microbiota ◽

Antibiotic Drug ◽

Target Effects

AbstractThe trillions of microorganisms (microbiota) found within the human gut play a critical role in shaping the immune system, yet these complex microbial communities are also highly sensitive to numerous environmental factors. While much of the focus to date has been on dietary intake, emerging data has begun to suggest that the use of pharmaceutical drugs, even those that are not considered to be antibiotics, can alter the human gut microbiota with unknown consequences for treatment outcomes. Here, we use a combination ofin vitro, in vivo, andex vivomethods to demonstrate that the first-line therapy for rheumatoid arthritis (RA), methotrexate (MTX), has off-target effects on the human gut microbiota, resulting in a significant growth advantage for drug-resistant Firmicutes over the Bacteroidetes, which tend to be more sensitive. Longitudinal analyses of the gut microbiotas of RA patients revealed that MTX-induced shifts in bacterial relative abundance are associated with improved drug response and transplant experiments in gnotobiotic mice show that these shifts lead to reduced inflammation. Together, these results suggest that the mechanism-of-action of non-antibiotic drugs may be due in part to off-target effects on the gut microbiota, while providing a critical first step towards explaining long-standing differences in drug response between patients.

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A Putative Type V Pilus Contributes toBacteroides thetaiotaomicronBiofilm Formation Capacity

Journal of Bacteriology ◽

10.1128/jb.00650-18 ◽

2019 ◽

Vol 201 (18) ◽

Cited By ~ 3

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.

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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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