Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

McNulty, Nathan P.; Wu, Meng; Erickson, Alison R.; Pan, Chongle; Erickson, Brian K.; Martens, Eric C.; Pudlo, Nicholas A.; Muegge, Brian D.; Henrissat, Bernard; Hettich, Robert L.; Gordon, Jeffrey I.

doi:10.1371/journal.pbio.1001637

Cited by 253 publications

(256 citation statements)

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“…Narrowing measurements to the 18-species consortium MIBAC-1, which can be used as a proxy for native mouse gut ecosystems, revealed coverages of 55-75% (PFAM and sequence homologues) and 20% (close sequence matches). Minimal consortia of bacteria already exist in the literature, but strains were selected based on educated guesses or for specific purposes and either originated from the human intestinal tract or are not easily available 26,27,37 . In contrast, the minimal bacteriome presented here contains strains that originate from the mouse intestine, is publicly available, was selected on the basis of comprehensive sequence-based approaches, and was overall characterized by a higher coverage of mouse faecal metagenomes.…”

Section: Discussionmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

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Section: Discussionmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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“…We demonstrated the predictive capability of AGORA models using two models, Bacteroides caccae ATCC 34185 (a fiber-degrading symbiont common in microbiomes of Western individuals 29,30 ) and Lactobacillus rhamnosus GG (LGG), a common human probiotic strain 31 . No chemically defined medium has been reported for B. caccae.…”

Section: Validation Of Agora Model Predictionsmentioning

confidence: 99%

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

et al. 2016

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1 r e s o u r c eChanges in the composition of the human gut microbiota have been associated with the development of chronic diseases including type 2 diabetes, obesity, and colorectal cancer 1 . Gut bacterial functions, such as synthesis of amino acids and vitamins 2 , breakdown of indigestible plant polysaccharides 3 , and production of metabolites involved in energy metabolism 4 , have been linked to human health. The use of 'omics approaches to study human microbiome communities has led to the generation of enormous data sets whose interpretations require systems biology tools to shed light on the functional capacity of gut microbiomes and their interactions with the human host 5 .In order to infer the metabolic repertoire of a gut metagenome data set, researchers usually map sequenced genes or organisms onto metabolic networks derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 6 , and functional annotations from KEGG ontologies 7 . However, this approach cannot identify the contribution of each bacterial species to the metabolic repertoire of the whole gut microbiome, nor can it infer the effects of different gut microbial communities on host metabolism.A technique that can bridge this gap is constraint-based reconstruction and analysis (COBRA) 8 using genome-scale metabolic reconstructions (GENREs) of individual human gut microbes. GENREs are assembled using the genome sequence and experimental information 9 . These reconstructions form the basis for the development of condition-specific metabolic models whose functions are simulated and validated by comparison with experimental results. The models can be used to investigate genotype-phenotype relationships 10 , microbe-microbe interactions 11 , and host-microbe interactions 11 . Numerous tools can be used to automatically generate draft GENREs but such models contain errors 12 and are incomplete.Manual curation of draft reconstructions is time consuming because it involves an extensive literature review and experimental validation of metabolic functions 9 .To provide an extensive resource of GENREs for human gut microbes, we developed a comparative metabolic reconstruction method that enables any refinement to one metabolic reconstruction to be propagated to others. This accelerates reconstruction and improves model quality. We generated AGORA, which includes 773 gut microbes, comprising 205 genera and 605 species. All reconstructions were based on literature-derived experimental data and comparative genomics. The metabolic predictions of two AGORA reconstructions and their derived metabolic models were validated against experimental data. RESULTS Metabolic reconstruction pipelineWe devised a comparative metabolic reconstruction method (Fig. 1a,c), which is analogous to the comparative microbial genome annotation approach 13 that has enabled accelerated annotation by propagation of refinements to one genome to others. First, we downloaded draft GENREs using Model SEED 14 and KBase (US Department of Energy Systems Biology Knowledgebase, http:/...

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“…They are encoded together with mannoside-degrading enzymes by multigenic systems such as the polysaccharide utilization loci (PUL) characterized in Bacteroidetes and recently referenced in the PUL database , which is a highly useful resource to assess glycan catabolic functions in these organisms. Mannoside-specific PUL-like systems recently have been characterized, mainly in Bacteroides species but also in other bacteria (Martens, Chiang & Gordon, 2008;Sonnenburg et al, 2010;Martens et al, 2011;Senoura et al, 2011;Kawahara et al, 2012;McNulty et al, 2013;Abbott et al, 2015;Cuskin et al, 2015b). These genomic loci code for polysaccharide utilization systems which resemble the starch utilization system (Sus) found in Bacteroides thetaiotaomicron VPI-5482 (Reeves, Wang & Salyers, 1997;Shipman, Berleman & Salyers, 2000;Cho et al, 2001).…”

Section: Recognition Of Eukaryotic Mannosides By Bacteriamentioning

confidence: 99%

Mannoside recognition and degradation by bacteria

et al. 2016

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Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein-protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them. This review focuses on the various mannosides that can be found in nature and details their structure. It underlines their involvement in cellular interactions and finally describes the latest discoveries regarding the catalytic machinery and metabolic pathways that bacteria have developed to metabolize them.

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Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

Abstract: Artificial human gut microbial communities implanted into germ-free mice provide insights into how species-level responses to changes in diet give rise to community-level structural and functional reconfiguration and how types of bacteria prioritize use of available nutrients in vivo.

Cited by 253 publications

References 64 publications

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Mannoside recognition and degradation by bacteria

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