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 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet. We analyzed the composition, diversity and dynamics of the fecal microbiota on each dietary regime by phylogenetic microarray and quantitative PCR (qPCR) analysis. In addition, we analyzed fecal short chain fatty acids (SCFAs) 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 the diversity of the microbiota significantly. The total 16S ribosomal RNA 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.

Describes the implementation of a system that is able to organize vast document collections according to textual similarities. It is based on the self-organizing map (SOM) algorithm. As the feature vectors for the documents statistical representations of their vocabularies are used. The main goal in our work has been to scale up the SOM algorithm to be able to deal with large amounts of high-dimensional data. In a practical experiment we mapped 6840568 patent abstracts onto a 1002240-node SOM. As the feature vectors we used 500-dimensional vectors of stochastic figures obtained as random projections of weighted word histograms.

Persistence of fecal transplants: Fecal microbiota transplantation is a successful way of treating the distressing symptoms of irritable bowel disease or Clostridium difficile infection. The procedure is done by administering a concentrate of colonic bacteria from a healthy donor. Li et al. used metagenomic data to look at single-nucleotide variants after transplants in humans. Donor and recipient strains coexisted for at least 3 months. Some donor strains replaced related strains of the same species, but totally novel species from a donor were unlikely to thrive in a recipient. Rational design of personalized fecal transplant “cocktails” will therefore rely on resolution beyond the species level. Science , this issue p. 586