Nothing is easier to get hold of than samples of human feces and nothing is harder to obtain that samples from undisturbed portions of the gut of people, both along the tract and across its various layers. It is widely recognized that fecal samples represent the end of a highly complex process of feces formation (turdopoiesis). They do not reflect the major aspects of composition and transactions of the intestinal microbiome in its many compartments. What to do?
Samples obtained from intestinal surgery don't count because patients have been "prepped" by being given antibiotics designed to rid the intestine of its microbes. This leaves only a few possibilities:
- Sampling the intestines of people undergoing emergency surgery or hurried post-mortems
- Sampling from ileostomies or colostomies
- Working with lab animals
In the future, small submarines may be engineered to travel to various parts of the intestines, sample the local microbiota, and rapidly deliver the samples to the hands of the investigator. In the meanwhile, take the data on the location of human intestinal microbiome with a grain of salt.