Todd Atherly

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a ‘selfish’ model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet.

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.

Corrigendum: Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

This corrects the article DOI: 10.1038/nature13995

Dysbiosis Characterized by Reduced Abundance of Roseburia is Associated With Increased Severity of Colitis in IL-10−/− Mice

G A A b st ra ct s estimated by real-time PCR assay using oligonucleotide primers specific to immediate early gene. More than 10 copies/μg DNA of PCR amplicons were defined as positive. We compared the positive ratio of those colonoscopic findings of UC patients between positive and negative for CMV-DNA. Additionally, we examined the correlation between the number of CMVDNA amplicons [negative, low-copy group (10-100 copies/μg DNA), high-copy group (≧100 copies/μg DNA)], and colonoscopic features and their medications. Results: Positive ratio of ulcerative lesions was higher in CMV-DNA-positive group than in CMV-DNA-negative group [22/34 (64.7%) vs. 10/27 (37.0%), p<0.05]. Further analysis in limited to UC patients who had no ulcerative lesions revealed that the positive ratio of edema or redness in CMVDNA-positive groupwere significantly higher than in CMV-DNA-negative UC group [redness, 8/12 (66.7%) vs. 4/17 (23.5%); edema, 7/12 (58.3%) vs. 2/17 (11.8%)]. Moreover, the positive ratio of edema or redness is higher even in low-copy group of CMV-DNA-positive UC patients (Table). Ratio of UC patients treated with the combination of steroids and immunomodulators is significantly higher in the high-copy group than in other groups [negative, 3/27 (11.1%); low-copy group, 1/10 (10.0%); high-copy group, 11/24 (45.8%)]. Conclusions: In addition to ulcerative lesions, reddish and edematous colonic mucosa might be characteristic of early colonoscopic features in UC patients concomitant with CMV reactivation. CMV reactivation can be easily occurred in patients with UC refractory to the combined therapies of steroids and immunomodulators.