scholarly journals Gut microbiome of capybara, the Amazon master of the grasses, harbors unprecedented enzymatic strategies for plant glycans breakdown

2021 ◽  
Author(s):  
Lucelia Cabral ◽  
Gabriela F. Persinoti ◽  
Douglas A. A. Paixao ◽  
Marcele P. Martins ◽  
Mariana Chinaglia ◽  
...  
Keyword(s):  
Amazon Basin ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Short Chain Fatty Acids ◽  
Ecological Niches ◽  
Metabolic Reconstruction ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Fermentation Products ◽  
Plant Polysaccharides

Abstract Background: Plant biomass is a promising feedstock to replace fossil-based products including fuels, chemicals and materials. However, the high resistance of plant biomass to either physicochemical or biological deconstruction has been hampering its broad industrial utilization and, consequently, the transition to a sustainable bioeconomy. The gut system from herbivores are formidable bioreactors in nature for lignocellulose breakdown and the diverse ecological niches where herbivores are found have led to the rise of a myriad of molecular strategies to cope with the sheer complexity of plant polysaccharides. This study illuminates how the underexplored microbiota of the largest living rodent, capybara, found in Pantanal wetlands and the Amazon basin, can efficiently depolymerize and utilize lignocellulosic biomass.Results: Here, we have elucidated the gut microbial structure and composition of the semiaquatic herbivorous capybara through multi-omics approaches. Metabolic reconstruction of this microbiota showed that cellulose degradation is likely performed by Fibrobacter bacteria, whereas hemicelluloses and pectins are processed by a broad arsenal of Carbohydrate-Active enZymes (CAZymes) organized in polysaccharide utilization loci (PULs) identified in the multiple metagenome-assembled genomes from the phylum Bacteroidetes. Furthermore, metabolomics analysis showed short chain fatty acids as major fermentation products, which are key markers of digestion performance of plant polysaccharides. Exploring the genomic dark matter of this gut microbial community, two novel CAZymes families were unveiled including a glycoside hydrolase family of β-galactosidases (GHXXX) and a carbohydrate-binding module family (CBMXX) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to CAZymes. Conclusions: Our results reveal how the capybara gut microbiota orchestrates the depolymerization and utilization of dietary plant polysaccharides, representing an untapped reservoir of new and intricate enzymatic strategies to overcome the recalcitrance of plant polysaccharides, a central challenge toward a circular and sustainable economy.

Gut Microbiome of the Amazon Master of the Grasses Harbors Unprecedented Enzymatic Strategies for Plant Glycans Breakdown

2020 ◽  
Author(s):  
Lucelia Cabral ◽  
Gabriela F Persinoti ◽  
Douglas A Paixao ◽  
Marcele P Martins ◽  
Mariana Chinaglia ◽  
...  
Keyword(s):  
Amazon Basin ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Short Chain Fatty Acids ◽  
Ecological Niches ◽  
Metabolic Reconstruction ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Fermentation Products ◽  
Plant Polysaccharides

Abstract BackgroundPlant biomass is a promising feedstock to replace fossil-based products including fuels, chemicals and materials. However, the high resistance of plant biomass to either physicochemical or biological deconstruction has been hampering its broad industrial utilization and, consequently, the transition to a sustainable bioeconomy. The gut system from herbivores are formidable bioreactors in nature for lignocellulose breakdown and the diverse ecological niches where herbivores are found have led to the rise of a myriad of molecular strategies to cope with the sheer complexity of plant polysaccharides. This study illuminates how the unexplored microbiota of the largest living rodent, capybara, found in Pantanal wetlands and the Amazon basin, can efficiently depolymerize and utilize lignocellulosic biomass. ResultsHere, we have elucidated the gut microbial structure and composition of the semiaquatic herbivorous capybara through multi-omics approaches. Metabolic reconstruction of this microbiota showed that cellulose degradation is chiefly performed by Fibrobacter bacteria, whereas hemicelluloses and pectins are processed by a broad arsenal of Carbohydrate-Active enZymes (CAZymes) organized in polysaccharide utilization loci (PULs) identified in multiple metagenome-assembled genomes from the phylum Bacteroidetes. Furthermore, metabolomics analysis showed short chain fatty acids as major fermentation products, which are key markers of digestion performance of plant polysaccharides. Exploring the genomic dark matter of this gut microbial community, two novel CAZymes families were unveiled including a glycoside hydrolase family of β-galactosidases and a carbohydrate-binding module family involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to CAZymes. ConclusionsOur results unveil how the capybara gut microbiota orchestrates the depolymerization and utilization of dietary plant polysaccharides, representing an untapped reservoir of new and intricate enzymatic strategies to overcome the recalcitrance of plant polysaccharides, a central challenge toward a circular and sustainable economy.

scholarly journals S-Layer Homology Domain Proteins Csac_0678 and Csac_2722 Are Implicated in Plant Polysaccharide Deconstruction by the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus

2011 ◽  
Vol 78 (3) ◽  
pp. 768-777 ◽  
Author(s):  
Inci Ozdemir ◽  
Sara E. Blumer-Schuette ◽  
Robert M. Kelly
Keyword(s):  
Cellular Localization ◽  
Catalytic Domain ◽  
Plant Biomass ◽  
Thermophilic Bacteria ◽  
Biochemical Properties ◽  
Crystalline Cellulose ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Caldicellulosiruptor Saccharolyticus ◽  
Content Type

ABSTRACTThe genusCaldicellulosiruptorcontains extremely thermophilic bacteria that grow on plant polysaccharides. The genomes ofCaldicellulosiruptorspecies reveal certain surface layer homology (SLH) domain proteins that have distinguishing features, pointing to a role in lignocellulose deconstruction. Two of these proteins inCaldicellulosiruptor saccharolyticus(Csac_0678 and Csac_2722) were examined from this perspective. In addition to three contiguous SLH domains, the Csac_0678 gene encodes a glycoside hydrolase family 5 (GH5) catalytic domain and a family 28 carbohydrate-binding module (CBM); orthologs to Csac_0678 could be identified in all genome-sequencedCaldicellulosiruptorspecies. Recombinant Csac_0678 was optimally active at 75°C and pH 5.0, exhibiting both endoglucanase and xylanase activities. SLH domain removal did not impact Csac_0678 GH activity, but deletion of the CBM28 domain eliminated binding to crystalline cellulose and rendered the enzyme inactive on this substrate. Csac_2722 is the largest open reading frame (ORF) in theC. saccharolyticusgenome (predicted molecular mass of 286,516 kDa) and contains two putative sugar-binding domains, two Big4 domains (bacterial domains with an immunoglobulin [Ig]-like fold), and a cadherin-like (Cd) domain. Recombinant Csac_2722, lacking the SLH and Cd domains, bound to cellulose and had detectable carboxymethylcellulose (CMC) hydrolytic activity. Antibodies directed against Csac_0678 and Csac_2722 confirmed that these proteins bound to theC. saccharolyticusS-layer. Their cellular localization and functional biochemical properties indicate roles for Csac_0678 and Csac_2722 in recruitment and hydrolysis of complex polysaccharides and the deconstruction of lignocellulosic biomass. Furthermore, these results suggest that related SLH domain proteins in otherCaldicellulosiruptorgenomes may also be important contributors to plant biomass utilization.

scholarly journals Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

2021 ◽  
Author(s):  
Xuefeng Peng ◽  
St. Elmo Wilken ◽  
Thomas S. Lankiewicz ◽  
Sean P. Gilmore ◽  
Jennifer L. Brown ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Cellulose Degradation ◽  
Anaerobic Bacteria ◽  
Short Chain Fatty Acids ◽  
Division Of Labour ◽  
Microbial Consortia ◽  
Bacterial Consortia ◽  
Green Biotechnology ◽  
Enrichment Experiments ◽  
Bacteria And Fungi

AbstractThe herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.

scholarly journals Characterization of a galactosyl-binding protein module from a Cellvibrio japonicus endo-xyloglucanase defines a new family of Carbohydrate Binding Modules

2020 ◽  
pp. AEM.02634-20
Author(s):  
Mohamed A. Attia ◽  
Harry Brumer
Keyword(s):  
Binding Protein ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Substrate Affinity ◽  
Carbohydrate Binding ◽  
Carbohydrate Active Enzymes ◽  
Plant Polysaccharides ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
Cellvibrio Japonicus

Carbohydrate-binding modules (CBMs) are usually appended to carbohydrate-active enzymes (CAZymes) and serve to potentiate catalytic activity, e.g. by increasing substrate affinity. The Gram-negative soil saprophyte Cellvibrio japonicus is valuable source for CAZyme and CBM discovery and characterization, due to its innate ability to degrade a wide array of plant polysaccharides. Bioinformatic analysis of the CJA_2959 gene product from C. japonicus revealed a modular architecture consisting of a fibronectin type III (Fn3) module, a cryptic module of unknown function (“X181”), and a Glycoside Hydrolase Family 5 subfamily 4 (GH5_4) catalytic module. We previously demonstrated that the last of these, CjGH5F, is an efficient and specific endo-xyloglucanase [Attia et al. 2018. Biotechnol. Biofuels, 11: 45]. In the present study, C-terminal fusion of superfolder green fluorescent protein in tandem with the Fn3-X181 modules enabled recombinant production and purification from Escherichia coli. Native affinity gel electrophoresis revealed binding specificity for the terminal galactose-containing plant polysaccharides galactoxyloglucan and galactomannan. Isothermal titration calorimetry further evidenced a preference for galactoxyloglucan polysaccharide over short oligosaccharides comprising the limit-digest product of CjGH5F. Thus, our results identify the X181 module as the defining member of a new CBM family, CBM88. In addition to directly revealing the function of this CBM in the context of xyloglucan metabolism by C. japonicus, this study will guide future bioinformatic and functional analyses across microbial (meta)genomes.Importance This study reveals Carbohydrate Binding Module Family 88 (CBM88) as a new family of galactose-binding protein modules, which are found in series with diverse microbial glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases. The definition of CBM88 in the Carbohydrate-Active Enzymes classification (http://www.cazy.org/CBM88.html) will significantly enable future microbial (meta)genome analysis and functional studies.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a trimodular endo-β-1,4-glucanase (Cel5B) fromBacillus halodurans

2014 ◽  
Vol 70 (12) ◽  
pp. 1628-1630 ◽  
Author(s):  
Immacolata Venditto ◽  
Helena Santos ◽  
James Sandy ◽  
Juan Sanchez-Weatherby ◽  
Luis M. A. Ferreira ◽  
...  
Keyword(s):  
Diffraction Analysis ◽  
Plant Biomass ◽  
Organic Polymer ◽  
Major Constituent ◽  
Bacillus Halodurans ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
X Ray Diffraction ◽  
X Ray ◽  
Carbohydrate Binding Modules

Cellulases catalyze the hydrolysis of cellulose, the major constituent of plant biomass and the most abundant organic polymer on earth. Cellulases are modular enzymes containing catalytic domains connected,vialinker sequences, to noncatalytic carbohydrate-binding modules (CBMs). A putative modular endo-β-1,4-glucanase (BhCel5B) is encoded at locus BH0603 in the genome ofBacillus halodurans. It is composed of an N-terminal glycoside hydrolase family 5 catalytic module (GH5) followed by an immunoglobulin-like module and a C-terminal family 46 CBM (BhCBM46). Here, the crystallization and preliminary X-ray diffraction analysis of the trimodularBhCel5B are reported. The crystals ofBhCel5B belonged to the orthorhombic space groupP21212 and data were processed to a resolution of 1.64 Å. A molecular-replacement solution has been found.

scholarly journals CalkGH9T: A Glycoside Hydrolase Family 9 Enzyme from Clostridium alkalicellulosi

Catalysts ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1011
Author(s):  
Paripok Phitsuwan ◽  
Sengthong Lee ◽  
Techly San ◽  
Khanok Ratanakhanokchai
Keyword(s):  
Glycoside Hydrolase ◽  
Cellulose Degradation ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Type I ◽  
Amorphous Cellulose ◽  
Carbohydrate Binding Modules ◽  
Glycoside Hydrolase Family 9 ◽  
Hydrolysis Of ◽  
Hydrolase Family

Glycoside hydrolase family 9 (GH9) endoglucanases are important enzymes for cellulose degradation. However, their activity on cellulose is diverse. Here, we cloned and expressed one GH9 enzyme (CalkGH9T) from Clostridium alkalicellulosi in Escherichia coli. CalkGH9T has a modular structure, containing one GH9 catalytic module, two family 3 carbohydrate binding modules, and one type I dockerin domain. CalkGH9T exhibited maximal activity at pH 7.0–8.0 and 55 °C and was resistant to urea and NaCl. It efficiently hydrolyzed carboxymethyl cellulose (CMC) but poorly degraded regenerated amorphous cellulose (RAC). Despite strongly binding to Avicel, CalkGH9T lacked the ability to hydrolyze this substrate. The hydrolysis of CMC by CalkGH9T produced a series of cello-oligomers, with cellotetraose being preferentially released. Similar proportions of soluble and insoluble reducing ends generated by hydrolysis of RAC indicated non-processive activity. Our study extends our knowledge of the molecular mechanism of cellulose hydrolysis by GH9 family endoglucanases with industrial relevance.

scholarly journals Genome-centric metagenomics revealed the spatial distribution and the diverse metabolic functions of lignocellulose degrading uncultured bacteria

2018 ◽  
Author(s):  
Panagiotis G. Kougias ◽  
Stefano Campanaro ◽  
Laura Treu ◽  
Panagiotis Tsapekos ◽  
Andrea Armani ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Lignocellulose Degradation ◽  
Pig Manure ◽  
Carbohydrate Binding ◽  
Lignocellulosic Substrate ◽  
Polysaccharide Degradation ◽  
Carbohydrate Binding Modules ◽  
Metabolic Strategies

AbstractThe mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material allowing them to efficiently decompose the organic matter are far to be elucidated. To circumvent this issue, the microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads followed by binning process recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution into the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes can vary depending on the number and functional roles of carbohydrate-binding modules. On contrary, members of Bacteroidetes are able to adhere and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics allowing a functional and taxonomical exploration of the biogas microbiome.ImportanceThis work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales. Even though structural elements of cellulosome were restricted to Clostridiales, our study identified in Bacteroidetes a putative mechanism for biomass decomposition based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose and transport to cytoplasm.

scholarly journals Expression, crystal structure and cellulase activity of the thermostable cellobiohydrolase Cel7A from the fungusHumicola griseavar.thermoidea

2014 ◽  
Vol 70 (9) ◽  
pp. 2356-2366 ◽  
Author(s):  
Majid Haddad Momeni ◽  
Frits Goedegebuur ◽  
Henrik Hansson ◽  
Saeid Karkehabadi ◽  
Glareh Askarieh ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Plant Biomass ◽  
Cellulase Activity ◽  
Hydrolysis Rate ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Fungal Host ◽  
Industrial Processing ◽  
Industrial Utilization ◽  
Catalytic Module

Glycoside hydrolase family 7 (GH7) cellobiohydrolases (CBHs) play a key role in biomass recycling in nature. They are typically the most abundant enzymes expressed by potent cellulolytic fungi, and are also responsible for the majority of hydrolytic potential in enzyme cocktails for industrial processing of plant biomass. The thermostability of the enzyme is an important parameter for industrial utilization. In this study, Cel7 enzymes from different fungi were expressed in a fungal host and assayed for thermostability, includingHypocrea jecorinaCel7A as a reference. The most stable of the homologues,Humicola griseavar.thermoideaCel7A, exhibits a 10°C higher melting temperature (Tmof 72.5°C) and showed a 4–5 times higher initial hydrolysis rate thanH. jecorinaCel7A on phosphoric acid-swollen cellulose and showed the best performance of the tested enzymes on pretreated corn stover at elevated temperature (65°C, 24 h). The enzyme shares 57% sequence identity withH. jecorinaCel7A and consists of a GH7 catalytic module connected by a linker to a C-terminal CBM1 carbohydrate-binding module. The crystal structure of theH. griseavar.thermoideaCel7A catalytic module (1.8 Å resolution;RworkandRfreeof 0.16 and 0.21, respectively) is similar to those of other GH7 CBHs. The deviations of several loops along the cellulose-binding path between the two molecules in the asymmetric unit indicate higher flexibility than in the less thermostableH. jecorinaCel7A.

scholarly journals Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics

2018 ◽  
Vol 84 (18) ◽  
Author(s):  
Panagiotis G. Kougias ◽  
Stefano Campanaro ◽  
Laura Treu ◽  
Panagiotis Tsapekos ◽  
Andrea Armani ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Lignocellulose Degradation ◽  
Pig Manure ◽  
Carbohydrate Binding ◽  
Content Type ◽  
Polysaccharide Degradation ◽  
Carbohydrate Binding Modules ◽  
Metabolic Strategies

ABSTRACTThe mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material, allowing them to efficiently decompose organic matter, have yet to be elucidated. To circumvent this issue, microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads, followed by a binning process, recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution in the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of theBacteroidetesandFirmicutesfollow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome inFirmicutesspecies can differ depending on the number and functional roles of carbohydrate-binding modules. In contrast, members of theBacteroidetesare able to adhere to and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics, allowing a functional and taxonomical exploration of the biogas microbiome.IMPORTANCEThis work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species ofBacteroidetesandClostridiales. Even though structural elements of cellulosome were restricted toClostridialesspecies, our study identified a putative mechanism inBacteroidetesspecies for biomass decomposition, which is based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose, and transport to cytoplasm.

scholarly journals Muribaculaceae genomes assembled from metagenomes suggest genetic drivers of differential response to acarbose treatment in mice

2020 ◽  
Author(s):  
Byron J. Smith ◽  
Richard A. Miller ◽  
Thomas M. Schmidt
Keyword(s):  
Small Intestine ◽  
Short Chain Fatty Acids ◽  
Ecological Niches ◽  
Gut Health ◽  
Fermentation Products ◽  
Starch Fermentation ◽  
The Family ◽  
Acarbose Treatment ◽  
Genes Encoding ◽  
Study Sites

AbstractThe drug acarbose (ACA) is used to treat diabetes, and, by inhibiting α-amylase in the small intestine, increases the amount of starch entering the lower digestive tract. This results in changes to the composition of the microbiota and their fermentation products. Acarbose also increases longevity in mice, an effect that has been correlated with increased production of the short-chain fatty acids propionate and butyrate. In experiments replicated across three study sites, two distantly related species in the bacterial family Muribaculaceae were dramatically more abundant in ACA-treated mice, distinguishing these responders from other members of the family. Bacteria in the family Muribaculaceae are predicted to produce propionate as a fermentation end product and are abundant and diverse in the guts of mice, although few isolates are available. We reconstructed genomes from metagenomes (MAGs) for nine populations of Muribaculaceae to examine factors that distinguish species that respond positively to acarbose. We found two closely related MAGs (B1A and B1B) from one responsive species that both contain a polysaccharide utilization locus with a predicted extracellular α-amylase. These genomes also shared a periplasmic neopullulanase with another, distantly related MAG (B2) representative of the only other responsive species. This gene differentiated these three MAGs from MAGs representative of non-responding species. Differential gene content in B1A and B1B may be associated with the inconsistent response of this species to acarbose across study sites. This work demonstrates the utility of culture-free genomics for inferring the ecological roles of gut bacteria including their response to pharmaceutical perturbations.ImportanceThe drug acarbose is used to treat diabetes by preventing the breakdown of starch in the small intestine, resulting in dramatic changes in the abundance of some members of the gut microbiome and its fermentation products. In mice, several of the bacteria that respond most positively are classified in the family Muribaculaceae, members of which produce propionate as a primary fermentation product. Propionate has been associated with gut health and increased longevity in mice. We found that genomes of the most responsive Muribaculaceae showed signs of specialization for starch fermentation, presumably providing them a competitive advantage in the large intestine of animals consuming acarbose. Comparisons among genomes enhance existing models for the ecological niches occupied by members of this family. In addition, genes encoding one type of enzyme known to participate in starch breakdown were found in all three genomes from responding species, but none of the other genomes.

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