There are several exciting projects/studies that have started which may result in a clear understanding of gut bacteria and the human over the next decades. A quick review of these and results to date is warranted. Our lack of knowledge about gut bacteria is shocking, and may explain why many autoimmune diseases are not understood.
Washington University in St. Louis: Project: Human Gut Microbiome
“The total number of genes in the various species represented in our internal microbial communities (microbiome) likely exceeds the number of our human genes by at least two orders of magnitude… Our microbiome is largely unexplored… The HGMI seeks to deliver a more comprehensive view of our biology by providing deep draft whole genome sequences for 100 species representing the bacterial divisions known to reside in the distal gut. Fifteen of these genomes will be selected for finishing…” White Paper
National Institute of Health: Human Microbiome Project
“Within the body of a healthy adult, microbial cells are estimated to outnumber human cells ten to one. This community, however, remains largely unstudied, leaving their influence upon human development, physiology, immunity, and nutrition almost entirely unknown… the vast majority of microbial species have never been successfully isolated as viable specimens for analysis, presumably because their growth is dependent upon a specific microenvironment that has not been, or cannot be, reproduced experimentally.”
US Department of Energy Join Genome Institute
“They found that the gut microbial communities are species-specific, and have tracked with their hosts over evolutionary timescales. This evolutionary signal appears to be discernable even when gut communities are disturbed by such factors as disease…Host phylogeny is the overriding factor determining the microbial composition of the great ape gut microbiota,” Ochman and his colleagues concluded in their study, adding that the finding “contrasts with previous notions that diet is the most important factor governing the gut microbiotae within primates.” “