gut microbiome pyrosequences from 15 subjects in choline study
The human gut microbiome predicts susceptibility to choline deficiency induced fatty liver
Healthy female subjects (n=15), a subset of those enrolled in an NIH-funded study (DK55965) investigating the effects of genetic polymorphisms, menopausal status and estrogen therapy on choline deficiency, were brought into the hospital and fed a proscribed, standard experimental diet ofver a two-month time period.  Time series stool samples were collected at specific points in the study that corresponded to dietary manipulations.  By sampling under these rigorously controlled conditions as choline levels were altered, we observed the effects of dietary challenge on microbial community stability, identifying changes in specific bacterial taxa that were coincident with controlled dietary manipulations and disease states in human beings.
Identifying how factors, such as diet and nutrition, affect the human gut microbiome is key to understanding the role of symbiont microbes in human health and disease.  To investigate the gut microbial response to dietary change, we used 454 pyrosequencing to characterize the impact of diet standardization, choline deficiency and recovery from choline deprivation in human subjects (n=15).  Despite exposure to a common diet, the subjects in our study maintained distinct microbial communities, even though those communities changed within each subject as diets changed.  Our findings identify specific bacterial biomarkers for the development of choline deficiency induced fatty liver, adding to the accumulating evidence of the influence of gut microbes in the variety of related metabolic disorders that are epidemic in Western society.