mkdoherty
commented
8 years ago Data sets from shotgun sequencing projects have been deposited in the DNA Data Bank of Japan–European Molecular Biology Laboratory–GenBank under the accession numbers 39857 (C. innocuum strain SB23) and 39859 (humanized mouse gut microbiome). 454 and Illumina sequencing reads have been deposited in the National Center for Biotechnology Information Short Read Archive. Nearly full-length 16S rRNA gene sequences are deposited in GenBank under the accession numbers GQ491120 to GQ493997. The annotated SB23 genome is available for further analysis in RAST (http://rast.nmpdr.org/). Additional Supplementary data can be found at http://gordonlab.wustl.edu/TurnbaughSE_10_09/STM_2009.html.
Turnbaugh, P. J. Ridaura, V. K. Faith, J. J. Rey, F. E. Knight, R. Gordon, J. I. 2009. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice
http://dx.doi.org/10.1126/scitranslmed.3000322
Diet and nutritional status are among the most important modifiable determinants of human health. The nutritional value of food is influenced in part by a person's gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelations among diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology, and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent metagenomic analysis of the temporal, spatial, and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized and reproduced much of the bacterial diversity of the donor's microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a high-fat, high-sugar "Western" diet shifted the structure of the microbiota within a single day, changed the representation of metabolic pathways in the microbiome, and altered microbiome gene expression. Reciprocal transplants involving various combinations of donor and recipient diets revealed that colonization history influences the initial structure of the microbial community but that these effects can be rapidly altered by diet. Humanized mice fed the Western diet have increased adiposity; this trait is transmissible via microbiota transplantation. Humanized gnotobiotic mice will be useful for conducting proof-of-principle "clinical trials" that test the effects of environmental and genetic factors on the gut microbiota and host physiology. Nearly full-length 16S rRNA gene sequences are deposited in GenBank under the accession numbers GQ491120 to GQ493997.