From Microbiology: The new germ theory in Nature news:

…collaborations are linking those exploring the human microbiota in the intestine, skin, mouth and other surfaces with microbial ecologists, such as Banfield, who have already made a career out of studying microbial universes in environments such as soil, ocean water and toxic waste sites.

The human microbiologists need the help. Although work by Relman and many others over the past five years has gone a long way to building up a genetic catalogue of human microbiota — what types of microbes live where — it has also revealed its staggering and previously unappreciated complexity. With hundreds of interacting, coevolving species living in and on every individual, and frustratingly little species overlap between each person’s microbial population, understanding the connection between microbes and health seems more daunting than ever. Researchers want to know what role the body’s microbial inhabitants have in immune function, nutrition, drug metabolism and conditions as diverse as obesity, cancer, autism and multiple sclerosis. But to do so, they have to sort through an avalanche of genetic sequence to find out what microbes are in the community, how they change over the course of a day, a lifetime or after a change in diet, and which functions are served by particular microbes, combinations of microbes or microbial metabolites (see ‘Exploring the superorganism’).

Microbial ecologists are supplying some of the expertise and bio-informatic tools to help make sense of the data mountain. They are also bringing to the human microbial field ecological principles such as colonization, succession, resilience to change, and competition and cooperation between community members. “It’s hard not to think about ecology when you enter the field,” says Jeff Gordon, a leader in gut microbiology at Washington University in St Louis, Missouri. In return, specialists in human microbiology are attracting funding and attention that ecologists have sometimes struggled to find. “The arbitrary and false barriers between environmental and medical microbiology are breaking down,” Gordon says.

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Other collaborations are also exploring how human microbial ecosystems adjust during illness, shifts in diet or after antibiotics. “They’re probably changing all the time in response to all sorts of perturbations,” says Claire Fraser-Liggett, a microbiologist at the University of Maryland School of Medicine in Baltimore, who, in collaboration with Janet Jansson, a soil microbiologist at the University of California, Berkeley, is studying microbiomes associated with the intestinal disorder Crohn’s disease in identical Swedish twins. “Are these communities resilient enough to rebound to where they were before a perturbation like antibiotics? What should we be measuring in order to answer that question? What’s going on in the recovery period? It leads to all these questions that ecologists have been dealing with for decades.”

Ecological concepts are also helping to account for the substantial differences that most studies have found between the microbiota of individuals — even, to a lesser extent, between identical twins. Ecology offered a likely explanation in the form of redundancy. The idea now is that every person’s microbes provide a core set of genes or biological functions, regardless of the specific species encoding them. “If you look at grasslands in different parts of the planet, there’s a common morphology and function,” says Gordon, drawing parallels. “But in different locales, the component species are quite distinct.” Gordon and other researchers hope that more extensive sequencing and analysis of many individuals’ microbiomes will reveal what those core functions are. Relman, meanwhile, has become interested in finding ‘keystone species’, rare species that nevertheless have a vital role in a community, and he is working with a colleague at Stanford, bioengineer Stephen Quake, to sequence the genomes of single microbial cells from the gut.