Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

Abstract

Summary The intestinal microbiota impacts many facets of human health and is associated with human diseases. Diet impacts microbiota composition, yet mechanisms that link dietary changes to microbiota alterations remain ill-defined. Here we elucidate the basis of Bacteroides proliferation in response to fructans, a class of fructose-based dietary polysaccharides. Structural and genetic analysis disclosed a fructose-binding, hybrid-two-component signaling sensor that controls the fructan utilization locus in Bacteroides thetaiotaomicron. Gene content of this locus differs among Bacteroides species and dictates the specificity and breadth of utilizable fructans. BT1760, an extracellular β2-6 endo-fructanase, distinguishes B. thetaiotaomicron genetically and functionally, and enables the use of the β2-6-linked fructan levan. The genetic and functional differences between Bacteroides species are predictive of in vivo competitiveness in the presence of dietary fructans. Genes that differentiate function serve as potential biomarkers in microbiomic datasets to enable rational manipulation of the microbiota via diet.

The effect of microbial colonization on the host proteome varies by gastrointestinal location

“…BT was chosen based on its status as a common and abundant member of the human microbiota that has been extensively characterised (Hooper et al, 2000;Martens et al, 2008;Mahowald et al, 2009;Sonnenburg et al, 2010). We analyzed the luminal contents of five GI regions dissected from each experimental animal: (1) stomach, (2) jejunum, (3) ileum, (4) cecum and (5) proximal colon.…”

A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice

“…Mice GF Swiss-Webster (SW) and C57BL/6J and conventional (RF, Taconic Inc., Cambridge city, IN, USA) SW mice were maintained as previously described (Sonnenburg et al, 2010). Humanization was performed using human fecal samples obtained from healthy anonymous donors.…”

“…Frozen feces were thawed by dilution in an equal volume of prereduced phosphate-buffered saline in anerobic conditions and 0.2 ml non-settling material was gavaged into GF-recipient mice. Mice were fed standard diet (Purina LabDiet 5K67) or polysaccharide-deficient diet (Bio-Serv, Frenchtown, NJ, USA; Sonnenburg et al, 2010). GF mice were mono-or bi-associated using oral gavage with 10 8 colony-forming units of Bacteroides thetaiotaomicron (Bt) VPI-5482 and/or Bifidobacterium longum (Bl) NCC2705.…”

“…GF mice were mono-or bi-associated using oral gavage with 10 8 colony-forming units of Bacteroides thetaiotaomicron (Bt) VPI-5482 and/or Bifidobacterium longum (Bl) NCC2705. Bacteria were cultured under anerobic conditions at 37 1C in tryptone-yeast extract-glucose medium (Sonnenburg et al, 2010) or Reinforced Clostridial Medium (Becton Dickinson and Company, Sparks, MD, USA). All experiments were done according to the A-PLAC, the Stanford IACUC.…”

Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes

“…Metagenomic studies and experiments with isolated strains revealed that members of the genus Bacteroides are broadly adapted to the degradation of host glycans and terrestrial plant material (2). This adaptation is exemplified by the enzyme systems devoted to starch, pectin, hemicelluloses, and other plant carbohydrates as well as host glycans (2,3); the wide variety of genes encoding enzymes for the degradation of these carbohydrates dominate carbohydrate active enzyme, or CAZyme, arsenals in human gut metagenome datasets. Hence, the evolution of this carbohydrate catabolizing machinery is key for host and microbiome mutualism.…”