Studying the Human Microbiome

Scientists have known since Pasteur times that our bodies and environment are awash in other species, microbial bystanders that seem to grow everywhere. But the techniques for uncovering which organisms are where and what they are doing was revolutionized in the first decade of the 2000s by those new-fangled gene sequencers that were so usefully applied to human genes.

Traditional methods: culturing

The old technique, in use since Pasteur's days, was essentially a version of farming. Take a sample of what you want to grow, plant it in a "soil" made of a food source known to be good for that microbe, and wait to see what grows (or doesn’t). That’s still a common way to study microbes, and that couple-of-day incubation period is one reason you don’t get your lab tests back for a few days.

This method of growing the microbes in culture has the advantage of being cheap and easy. It requires little specialized equipment: in fact you regularly perform a variant of this experiment a few times a week with your refrigerator leftovers.

But culturing also has several serious limitations. It only works if the microbes are still alive, which usually means they must be in their original environment; many microbes don’t culture well or at all outside their native habitat. Anaerobes, for example, are organisms that can’t survive in the presence of oxygen, not a problem deep inside the airless gut, but it won’t work in a normal lab. While you can take some precautions to preserve the original environment as much as possible – you can set the organisms in a specially-sealed oxygen-free container –the cost and expense rises quickly.

Even if, somehow, you were able to overcome all the other challenges, many (perhaps most) microbes don’t grow well unless they are in close proximity to other specific species.

Methanobrevibacter smithii, for example, which plays a critical role in the efficient digestion of complex sugars, removes hydrogen from its environment, providing a habitat for organisms that don’t like hydrogen, like Firmicutes and Bacterodetes. Plus, it converts all that excess hydrogen to methane, which in turn is needed by yet other organisms. Culturing any of those microbes on their own would be difficult, if not impossible.


Fortunately, thanks to new machines originally developed for mass DNA sequencing, it’s now possible to search for new life forms without growing them in a culture, and this has made possible a major shift in how to think about life.

Gene sequencing


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