Background: Roux-en-Y gastric bypass (RYGB) is an effective means to achieve sustained weight loss for morbidly
obese individuals. Besides rapid weight reduction, patients achieve major improvements of insulin sensitivity and
glucose homeostasis. Dysbiosis of gut microbiota has been associated with obesity and some of its co-morbidities,
like type 2 diabetes, and major changes of gut microbial communities have been hypothesized to mediate part of
the beneficial metabolic effects observed after RYGB. Here we describe changes in gut microbial taxonomic
composition and functional potential following RYGB.
Methods: We recruited 13 morbidly obese patients who underwent RYGB, carefully phenotyped them, and had
their gut microbiomes quantified before (n = 13) and 3 months (n = 12) and 12 months (n = 8) after RYGB.
Following shotgun metagenomic sequencing of the fecal microbial DNA purified from stools, we characterized the
gut microbial composition at species and gene levels followed by functional annotation.
Results: In parallel with the weight loss and metabolic improvements, gut microbial diversity increased within
the first 3 months after RYGB and remained high 1 year later. RYGB led to altered relative abundances of 31
species (P < 0.05, q < 0.15) within the first 3 months, including those of Escherichia coli, Klebsiella pneumoniae,
Veillonella spp., Streptococcus spp., Alistipes spp., and Akkermansia muciniphila. Sixteen of these species maintained
their altered relative abundances during the following 9 months. Interestingly, Faecalibacterium prausnitzii was
the only species that decreased in relative abundance. Fifty-three microbial functional modules increased their
relative abundance between baseline and 3 months (P < 0.05, q < 0.17). These functional changes included
increased potential (i) to assimilate multiple energy sources using transporters and phosphotransferase systems,
(ii) to use aerobic respiration, (iii) to shift from protein degradation to putrefaction, and (iv) to use amino acids
and fatty acids as energy sources.
Conclusions: Within 3 months after morbidly obese individuals had undergone RYGB, their gut microbiota
featured an increased diversity, an altered composition, an increased potential for oxygen tolerance, and an
increased potential for microbial utilization of macro- and micro-nutrients. These changes were maintained for
the first year post-RYGB.