mkdoherty
commented
8 years ago COPRO-Seq and microbial RNA-Seq data are available in the Gene Expression Omnibus (accession number GSE26687). Processed data can be obtained at http://gordonlab.wustl.edu/modeling_microbiota/.
Faith, J. J. McNulty, N. P. Rey, F. E. Gordon, J. I. 2011 Predicting a human gut microbiota's response to diet in gnotobiotic mice http://dx.doi.org/10.1126/science.1206025
The interrelationships between our diets and the structure and operations of our gut microbial communities are poorly understood. A model community of 10 sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 60% of the variation in species abundance evoked by diet perturbations, and we were able to identify which factors in the diet best explained changes seen for each community member. The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods.