Human gut microbiota in obesity and after gastric bypass

Husen Zhang, John K DiBaise, Andrea Zuccolo, Dave Kudrna, Michele Braidotti, Yeisoo Yu, Prathap Parameswaran, Michael D Crowell, Rod Wing, Bruce E Rittmann, Rosa Krajmalnik-Brown, Husen Zhang, John K DiBaise, Andrea Zuccolo, Dave Kudrna, Michele Braidotti, Yeisoo Yu, Prathap Parameswaran, Michael D Crowell, Rod Wing, Bruce E Rittmann, Rosa Krajmalnik-Brown

Abstract

Recent evidence suggests that the microbial community in the human intestine may play an important role in the pathogenesis of obesity. We examined 184,094 sequences of microbial 16S rRNA genes from PCR amplicons by using the 454 pyrosequencing technology to compare the microbial community structures of 9 individuals, 3 in each of the categories of normal weight, morbidly obese, and post-gastric-bypass surgery. Phylogenetic analysis demonstrated that although the Bacteria in the human intestinal community were highly diverse, they fell mainly into 6 bacterial divisions that had distinct differences in the 3 study groups. Specifically, Firmicutes were dominant in normal-weight and obese individuals but significantly decreased in post-gastric-bypass individuals, who had a proportional increase of Gammaproteobacteria. Numbers of the H(2)-producing Prevotellaceae were highly enriched in the obese individuals. Unlike the highly diverse Bacteria, the Archaea comprised mainly members of the order Methanobacteriales, which are H(2)-oxidizing methanogens. Using real-time PCR, we detected significantly higher numbers of H(2)-utilizing methanogenic Archaea in obese individuals than in normal-weight or post-gastric-bypass individuals. The coexistence of H(2)-producing bacteria with relatively high numbers of H(2)-utilizing methanogenic Archaea in the gastrointestinal tract of obese individuals leads to the hypothesis that interspecies H(2) transfer between bacterial and archaeal species is an important mechanism for increasing energy uptake by the human large intestine in obese persons. The large bacterial population shift seen in the post-gastric-bypass individuals may reflect the double impact of the gut alteration caused by the surgical procedure and the consequent changes in food ingestion and digestion.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Taxonomic breakdown of human intestinal bacterial V6 tags obtained by pyrosequencing in the normal-weight (nw1, nw2, and nw3), obese (ob1, ob2, and ob3), and post-gastric bypass (gb1, gb2, and gb3) subjects.
Fig. 2.
Fig. 2.
Bacterial families enriched in the ob and gb groups. (A) Significant (P < 0.05) difference between the nw and ob groups. (B) Significant difference between the ob and gb groups. (C) Significant difference between the gb and nw groups. Error bars represent the standard error of the mean (n = 3). The P values are based on the 2-sample t-test assuming equal variances.
Fig. 3.
Fig. 3.
Correlation of Sanger sequence- and pyrosequencing tag- predicted taxonomic assignments. The number of sequences within a taxon by full-length sequences is plotted against the number of tags from the same taxon using pyrosequencing.
Fig. 4.
Fig. 4.
The numbers of Bacteria, Archaea, and Methanobacteriales quantified by real-time QPCR. Error bars represent the standard error of the mean (n = 3).
Fig. 5.
Fig. 5.
Clustering of human intestinal microbial communities in the 3 test groups (nw, ob, and gb), based on the unweighted UniFrac analysis of the phylogenetic tree shown in Fig. S1. The branch length represents the distance between environments in UniFrac units, as indicated by the scale bar. Jackknife counts are based on 100 replicates, and only values > 50 are shown.

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