Microbes – in our guts, on our skin and elsewhere – outnumber our own cells by about 10 to 1 (Image: Henrik Sorensen/Getty)

People are more microbe than human, with microbes outnumbering our cells by 10 to 1. But strangely, scientists know more about the microbes that inhabit the soil and sea than those that call us home. Now, the genetic sequencing of 178 of these microbes will help close that gap.

Scientists have long known that our microbial inhabitants, collectively known as the microbiome, can contribute to disease. But culturing the cells outside of the human body can be difficult, complicating efforts to identify many of them, particularly rare species.

The Human Microbiome Project, funded by the US National Institutes of Health, has now used next-generation DNA sequencing technology to study these microbes straight from the source.


A sequel to the human genome project, the project is one of several around the world aiming to characterise the microbiome. It seeks to take a census of microbes from five key sites – the gut, skin, mouth, airways, and urogenital tract – to understand the way the microbes contribute to human health and disease.

So far, the project has sequenced the genomes of 178 microbes towards its ultimate goal of 900, identifying more than 500,000 new genes in the process.

Bacteria as balm

“By being able to characterise more of these species, I think we’re gaining more ground in terms of beneficial organisms on the human body and how we can use them to benefit our health,” says Karen Nelson, team leader at one of the project’s four main sequencing centres, the J. Craig Venter Institute in Rockville, Maryland.

The sequencing project could help pinpoint microbes that contribute to disease, which could lead to new treatment strategies. For example, previous research revealed that the bacterium Faecalibacterium prausnitzii helps counteract the misdirected immune response that ravages the gut in people with Crohn’s disease. Genetic sequencing may uncover other beneficial bacteria that could be used to treat – or prevent – disease, much as probiotic yogurt helps to regulate digestion.

So far, the project has focused on relatively simple microbes that do not have nuclei in their cells – bacteria and archaea. But project members are now turning their attention to larger organisms with nuclei, called eukaryotes, as well as viruses.

“To me, this is one of the most exciting projects I have worked on,” says team member Jane Peterson of the NIH National Human Genome Research Institute in Rockville. “It really is the unknown.”

Journal reference: Science (vol 328, p 994)