Scientists map bacteria living inside us

A consortium of scientists has nearly completed cataloguing the 10,000 microbial species living on and in the normal human body, potentially paving the way for research that could illuminate our understanding of how disease may be linked to changes in our bacterial make-up.

'We can actually add compounds or take food supplements or do other things…to either support the good bugs or minimize the impact of the aberrant bad bugs'  — Lila Proctor, co-ordinator for Humane Microbiome Project

Just as the Human Genome Project in 2001 mapped out every gene that makes us human, the Human Microbiome Project seeks to discover all the invisible, non-human bugs that inhabit just about every part of us — from the skin to the gut and up the nose.

The research, a co-ordinated effort from 200 scientists representing almost 80 U.S. universities and scientific institutions, will be published in Thursday's edition of Nature as well as several journals in the Public Library of Science.

Lila Proctor, program director at the U.S. National Institutes of Health and the co-ordinator for the project, said the work began five years ago, after a call from the research community to map "other" genomes — "a quick way of describing the microbes."

The NIH poured $154 million US into the project.

"We’ve known for a long time that we have many kinds of microbes that live in and on our bodies, but it was really daunting to even imagine trying to do this work 10 years ago when the genome was being done," she said.

'Gold standard' healthy subset studied

The idea was to study five major body sites — the oral cavity, the nostrils, the skin, the urogenital tract and the gut — from a "gold standard" group of "super healthy" individuals free of any infections, Proctor explained.

"It was meant to be a reference data set. The goal was, we could say these are the healthiest people we could find and these are the microbials we could find," she said.

"You need to get a sense for the boundary of conditions of what might be considered normal or healthy."

She noted that many illnesses, such as Crohn's disease and irritable bowel syndrome, appear to be microbiome-related, but the bacterial communities in our bodies also perform important and helpful functions, such as aiding with digestion.

Curtis Huttenhower, assistant professor of computational biology and bioinformatics at the Harvard School of Public Health, explained that a comprehensive census of bacterial communities within healthy bodies can show scientists what an abnormal presence of pathogens looks like.

"This research tells us the range of healthy variation in microbial function and in specific bugs. Knowing which sorts of microbes are normally found in healthy people can help us understand the roles they play during changes in disease," he said in a release.

The undertaking was no small feat, Proctor said. Her colleagues have compared the project to the discovery and exploration of a new continent, as trillions of micro-organisms are believed to populate each of our bodies.

For a bit of perspective, there are so many non-human microbial cells residing in our two-legged ecosystems that they outnumber our human cells 10 to one. If one were to mass together all the bacteria populating a 150-pound adult, it would weigh about 4.5 pounds.

81-99% of microbes mapped

Roughly 23,000 human genomes have been identified. By contrast, Proctor said there are eight million different kinds of unique microbial genes associated with the human body.

The project successfully identified between 81 and 99 per cent of the spectrum of microbes populating a group of 240 healthy subjects.

This was achieved through new advanced computational methods. About 350 of the most important organisms were first identified, then further analyzed with DNA sequencing.

"Just the data processing was a bear," Proctor said. "To manage the data, we were crashing computers left, right and centre."

Gaining a better grasp of the human microbiome could have benefits in terms of clinical use.

"You can change your microbiome to make it healthier," Proctor said. "We can actually add compounds or take food supplements or do other things once we understand better how the microbiome reacts, to either support the good bugs or minimize the impact of the aberrant bad bugs. So I think you're going to see the application of microbiome science as to how people manage their own health."