Michael Eisenstein in Nature:
What does a healthy forest look like? A seemingly thriving, verdant wilderness can conceal signs of pollution, disease or invasive species. Only an ecologist can spot problems that could jeopardize the long-term well-being of the entire ecosystem. Microbiome researchers grapple with the same problem. Disruptions to the community of microbes living in the human gut can contribute to the risk and severity of a host of medical conditions. Accordingly, many scientists have become accomplished bacterial naturalists, labouring to catalogue the startling diversity of these commensal communities. Some 500–1,000 bacterial species reside in each person’s intestinal tract, alongside an undetermined number of viruses, fungi and other microbes. Rapid advances in DNA sequencing technology have accelerated the identification of these bacteria, allowing researchers to create ‘field guides’ to the species in the human gut. “We’re starting to get a feeling of who the players are,” says Jeroen Raes, a bioinformatician at VIB, a life-sciences institute in Ghent, Belgium. “But there is still considerable ‘dark matter’.”
Currently, these field guides are of limited use in distinguishing a healthy microbiome from an unhealthy one. Part of the problem is the potentially vast differences between the microbiomes of apparently healthy people. These differences arise through a complex combination of environmental, genetic and lifestyle factors. This means that relatively subtle differences can have a disproportionate role in determining whether an individual is relatively healthy or at increased risk of developing disorders such as diabetes.