About the Microbiome
What is this ‘human microbiota’, anyway? How is it different from the 'human microbiome'?
The microbiota consists of all the microscopic things living in a particular place, so the ‘human microbiota’ is all the microbes found in and on people. As with a lot of biology, the phrase isn’t absolutely precise. For example, living cells of soil-dwelling microbes will surely be found on and in people who have a lot of contact with the soil, even if those microbes are ‘transplants’ that can’t actually grow and divide in the body sites where they’re found – so are they part of the human microbiota or not? Fortunately, phrases like ‘human microbiota’ (and ‘skin microbiota’, ‘gut microbiota’, etc.) are generally useful, despite such ambiguity around the edges.
The term ‘microbiome’ has recently been used in two different ways. One definition is the same as ‘microbiota’, explained above. The other usage of ‘microbiome’ (the recent Human Microbiome Project used this definition) means not the living organisms, but rather all the genetic information of all the microbes that live in a particular place. Since a ‘genome’ refers to all the genetic information of an organism, and ‘metagenome’ means all the genomes of the different types of organisms in an ecological community, this second meaning of ‘microbiome’ could be expressed as ‘microbial metagenome’. (See Elio Schaecter's poll on his Small Things Considered blog on the definition of ‘microbiome’.)
Why should we pay attention to the human microbiota? Since it evolved with us to keep us healthy, won’t it just keep doing so?
It is true that humans and our microbiota have coevolved to have mostly mutualistic interactions, a process that happened without us needing to pay any attention to it at all. However, most humans today live in conditions that simply didn’t exist over most of our evolutionary history, and those differences have the potential to change our microbial interactions.
A child growing up in an American city today, for example, is probably exposed to far fewer microbes from soil and animals, but far more microbes from unrelated humans, compared to her farming grandparents, or to her nomadic, hunter-gatherer ancestors. She may encounter a different mixture of human-derived microbes than they did, with a higher proportion of respiratory and skin microbes but a lower proportion of gut microbes, due to the combined effects of crowded spaces and flush toilets.
Her diet includes more processed and refined foods, with higher sugar and salt content, than that of her forebearers. On the other hand, it may also include a more diverse array of fresh fruits and vegetables throughout the year. She quite likely consumes more meat and more animal fat, but less plant fiber than her ancestors; almost certainly she is less physically active.
She may have been born via cesarean section, fed mainly with infant formula, and exposed, perhaps repeatedly, to potent antibiotics. And while those practices certainly don't guarantee an unhealthy outcome (and sometimes, in fact, they are life-saving), they are also situations that are completely new in our evolutionary history...for us and our microbiota.
We know enough to realize that all these elements of a modern lifestyle have the potential to change our microbiota, and to change our interactions with our microbiota. However, we often don't know enough to predict what the consequences of those changes may be. The correlations that have been found thus far, between various aspects of the microbiota and particular diseases, suggest that at least some of the evolutionarily-recent changes to the human microbiota have important health effects. However, the microbiota can vary a lot between apparently healthy people, so it’s quite possible that some recent changes to the microbiota won't affect our health at all. It would be good to be able to tell the difference.
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