From almost the moment they were discovered, bacteria have had a rotten reputation. “Germs,” people called them. “Bugs.” People scrubbed them away, developed drugs to kill them, cursed them for causing sickness and death. It turns out, however, that the 100 trillion microbes living in and on people — that’s ten single-cell organisms for every one human cell — are a fundamental component of human physiology. In a very real sense, the human microbiome is as much a functioning organ as are the intestines into which so many of them are packed. But their influence goes way beyond the digestive tract, into such sites as the skin, eyes, urogenital tract, nose, and lungs.
Researchers studying this cloud of microbes have called them the “second genome.” A person’s microbiome starts to grow at birth — in fact, it may gain a toehold even before a person is born — and ultimately develops into a collection of on-board ecological systems somewhat akin to coral, with distinct colonies living in symbiosis. Even though bacteria are one-tenth to one-hundredth the size of a human cell, every person carries around up to five pounds of them. In other words, the microbes a person hosts weigh more than the three-pound brain does.
Until the advent of the Human Microbiome Project, which launched in 2007, very little was known about these stowaways. There was evolving understanding that many of them are essential to human life, that they help to synthesize certain nutrients, form a defense network against harmful microbes, and play an important role in digesting food. But they were tough to study. Many simply couldn’t be grown outside the body, and even those that could be cultured in the lab failed to behave the way researchers thought they might in vivo, or inside the body.
Gene sequencing technology developed during the race to map the human genome, however, has created a new field of research called metagenomics that lets researchers study microbial communities without having to culture them in the lab. New discoveries are being published regularly, including the following:
There are more than 10,000 microbial species within the human ecosystem — several times more than previously thought — and every human is host to a unique collection of more than 1,000 species.
Every human hosts one of only three distinct ecosystems of gut microbes, which in the future may allow microbiome “typing” similar to what has been done since the identification of blood types.
While the human genome includes roughly 22,000 genes that code for proteins, the microbiome has more than 8 million unique protein-coding genes, which means there are 360 times more active bacterial genes than human genes in the body.
The microbiome provides crucial components for digesting and absorbing nutrients, but different species play the same role in different people.
Even healthy adults play host to pathogenic microbes known to cause illness, but these pathogens simply coexist harmlessly in the microbiome.
Researchers in 2014 published an expanded catalog of nearly 9.8 million genes from the human gut microbiome that is three times larger than any previous list of genes.