Data from: Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

There is growing interest in understanding how diet affects the intestinal
microbiota, including its possible associations with systemic diseases
such as metabolic syndrome. Here we report a comprehensive and deep
microbiota analysis of fourteen obese males consuming fully controlled
diets supplemented with resistant starch (RS) or non-starch
polysaccharides (NSP), and a weight-loss diet (WL). We analyzed the
composition, diversity and dynamics of the faecal microbiota on each
dietary regime by phylogenetic microarray and quantitative PCR analysis.
Additionally, we analyzed faecal short chain fatty acids (SCFA) as a proxy
of colonic fermentation, and indices of insulin sensitivity from blood
samples. The diet explained around 10% of the total variance in microbiota
composition, which was substantially less than the inter-individual
variance. Yet, each of the study diets induced clear and distinct changes
in the microbiota. Multiple Ruminococcaceae phylotypes increased on the RS
diet, whereas mostly Lachnospiraceae phylotypes increased on the NSP diet.
Bifidobacteria decreased significantly on the WL diet. The RS diet
decreased significantly diversity of the microbiota. The total 16S rRNA
gene signal estimated by qPCR correlated positively with the three major
SCFAs, while the amount of propionate specifically correlated with the
Bacteroidetes. The dietary responsiveness of the individual’s microbiota
varied substantially and associated inversely with its diversity,
suggesting that individuals can be stratified into responders and
non-responders based on the features of their intestinal microbiota.