Microbes and Us - An Unknown Symbiosis

Microbiologists researching the human microbiome are fond of citing statistics and no wonder, for the numbers are jaw-dropping. The average person is home to about 100 trillion, 10¹⁴, microbes - mostly bacteria but also some viruses, fungi, protozoans and archaeans. You are in a minority in your own body: microbial cells outnumber your cells by 10 to 1. Your microbes contribute perhaps a couple of kilograms to your body weight and they are everywhere, colonising your gut, mouth, skin, mucous membranes and genitals. In fact, the only time anyone is free from microbes is in the womb. You are born 100 per cent human, but die 90 per cent microbial. Between these two events lies a vista of unexplored ecology that helps make us what we are.

Metagenomics, is exploring what these gut microbes are capable of. Unlike conventional genome studies, which focus on individual organisms, this entails collecting all the genes in an ecosystem to create a global "metagenome" - effectively a parts list for the biological functions of that ecosystem. The most detailed inventory to date was published in 2010 by Metagenomics of the Human Intestinal Tract (MetaHIT), a European Union-based consortium. The researchers studied faecal samples taken from 124 European adults and found a staggering 3.3 million different microbial genes, meaning that they outnumber our own human gene set about 150-fold (Nature, vol 464, p 59). Not everyone had every microbial gene, but by comparing the individuals in the study the team identified a set of genes we all share. Capable of more than 6000 biochemical functions, this "minimal metagenome" represents the core genes needed for the survival of the entire ecosystem.

It is not yet clear whether our gut microflora actually cause health problems or whether they simply change as a consequence. The system is so complex it will be hard to prove causation. With luck more detailed studies of the structure of the microbial communities in healthy and sick individuals will be a starting point for developing therapies. These might include drugs, probiotics, foods that alter the behaviour of our gut ecosystems, and even faecal transplants (New Scientist, 22 January, p 8). And this is just the beginning. The US Human Microbiome Project alone is being funded to the tune of $115 million. It aims to study the microbiomes of 300 individuals, in the gut as well as numerous other sites in the body, analysing some 12,000 samples and investigating diseases including Crohn's and necrotising enterocolitis.

Meanwhile, other researchers are wondering whether the link with gut microbes might help explain why obesity, diabetes, autoimmune diseases and certain cancers are on the rise in western cultures. Could our modern lifestyles be having detrimental effects on the ecology of our microbiome? "We're exposed to all kinds of weird and wonderful foods that we didn't have before, and our environment is much cleaner," says Nicholson. That's not all - our tendency to overuse antibiotics could be inflicting lasting damage on our microbiomes.

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