Evolutie^? & my microbes made me do it ;)

[Cees Binkhorst]

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http://judson.blogs.nytimes.com/2009/07/21/microbes-r-us/
July 21, 2009, 9:30 pm
Microbes ‘R’ Us by Olivia Judson

There are 150 species right at your fingertips.

This week, the 40th anniversary of the first moon landing, there’s much
talk of exploring other worlds. Which is exciting and grand; such is the
stuff that dreams are made on. Yet we don’t need to go abroad to find
amazing new life forms. We just need to look at the palms of our hands,
the tips of our fingers, the contents of our guts.

The typical human is home to a vast array of microbes. If you were to
count them, you’d find that microbial cells outnumber your own by a factor
of 10. On a cell-by-cell basis, then, you are only 10 percent human. For
the rest, you are microbial. (Why don’t you see this when you look in the
mirror? Because most of the microbes are bacteria, and bacterial cells are
generally much smaller than animal cells. They may make up 90 percent of
the cells, but they’re not 90 percent of your bulk.)

This much has been known for a long time. Yet it’s only now, with the
revolution in biotechnology, that we’re able to do detailed studies of
which microbes are there, which genes they have, and what they’re doing.
We’re just at the start, and there are far more questions than answers.
But already, the results are astonishing, and the implications profound.

Even on your skin, the diversity of bacteria is prodigious. If you were to
have your hands sampled, you’d probably find that each fingertip has a
distinct set of residents; your palms probably also differ markedly from
each other, each home to more than 150 species, but with fewer than 20
percent of the species the same. And if you’re a woman, odds are you’ll
have more species than the man next to you. Why should this be? So far, no
one knows.

But it’s the bacteria in the digestive tract, especially the gut, that
intrigue me most. Many of these appear to be true symbionts: they have
evolved to live in guts and (as far as we know) are not found elsewhere.
In providing their habitat — a constant temperature, some protection from
hostile lifeforms and regular influxes of food — we are as essential to
them as they are to us.

And they definitely are essential to us. Gut bacteria play crucial roles
in digesting food and modulating the immune system. They make small
molecules that we need in order for our enzymes to work properly. They
interact with us, altering which of our genes get turned on and off in
cells in the intestinal walls. Some evidence suggests that they are
essential for the building of a normal heart. Finally, it seems likely
that gut bacteria will turn out to affect appetite, as well as other
aspects of our behavior, though no one has shown this yet. (Imagine the
plea: I’m sorry, sir, my microbes made me do it.)

Together, your gut microbes provide you with a pool of genes far larger
than that found in the human genome. Indeed, the gut “microbiome,” as it
is known, is thought to contain at least 100 times more genes than the
human genome. Moreover, whereas humans are extremely similar to one
another at the level of the genome, the microbiome appears to differ
markedly from one person to the next.

What determines these differences? Good question. Diet has some effect: a
diet rich in sugars and fats reduces the diversity of gut bacteria, and
shifts the balance towards those that are more efficient at extracting
energy. Start eating more plants and you can shift the balance back, and
increase the diversity of your gut microbes. Your own genetic background
may play a role as well, though we are far from understanding how, or how
much. It probably also matters which other microbes are present: as in any
ecosystem, relationships among different inhabitants are likely to be
complex.

(At this point, I’d like to introduce a caveat. We know that the diversity
of microbial species differs between your gut and mine, and that the less
related we are, the more that will be true. Family members tend to have
more similar gut microbes than nonrelatives, and preliminary evidence
suggests that geography matters, too. So the gut microbes of people in
China are different from those of people in the United States — though
whether this is due to diet, human genes or geography is entirely unknown.
But despite this variation at the species level, we don’t yet know how
much variation there is at the genetic level. It may be that different
sets of gut microbes provide broadly equivalent sets of genes.)

Naturally, a huge effort is now under way to see whether differences in
gut bacteria are responsible for differences in health. But what interests
me most about all this is that it suggests another mode of human
evolution. Bacteria evolve quickly: they can go through many thousands of
generations for every human one.

This has two potential consequences. First, during your lifetime, your
bacteria can change their genes even though you cannot change yours. (You
do have some flexibility: your immune system has a built-in capacity to
change.) It may be that gut bacteria evolve in response to short-term
changes in the environment, especially exposure to food-borne diseases.
They may thus act as an evolving supplement to the immune system.

The second potential consequence is further reaching. Because bacteria can
evolve so fast, it may be that some of what we think of as human evolution
— like the ability to digest new diets that accompanied the invention of
agriculture — is actually bacterial evolution. We know that hostile
bacteria — those that cause diseases in ourselves and our domestic plants
and animals — have undergone dramatic genetic changes in the last 10,000
years. Perhaps our friendly bacteria have, too.

Notes:

For human cells being outnumbered by microbial cells by a factor of 10,
see Savage, D. C. 1977. “Microbial ecology of the gastrointestinal tract.”
Annual Review of Microbiology 31: 107-133. For new techniques in analyzing
microbes that we cannot grow in the laboratory see, for example, Marcy, Y.
et al. 2007. “Dissecting biological ‘dark matter’ with single-cell genetic
analysis of rare and uncultivated TM7 microbes from the human mouth.”
Proceedings of the National Academy of Sciences USA 104: 11889-11894.

For bacteria living on hands, see Fierer, N. et al. 2008. “The influence
of sex, handedness, and washing on the diversity of hand surface
bacteria.” Proceedings of the National Academy of Sciences USA 105:
17994-17999. For gut microbes not being found elsewhere, see Ley, R. E. et
al. 2008. “Worlds within worlds: evolution of the vertebrate gut
microbiota.” Nature Reviews Microbiology 6: 776-788.

For a summary of the essential roles that gut microbes play, see
Turnbaugh, P. J. et al. 2007. “The human microbiome project.” Nature 449:
804-810. For estimates of the number of genes contained in the microbiome,
see Gill, S. R. et al. 2006. “Metagenomic analysis of the human distal gut
microbiome.” Science 312: 1355-1359.

For diet affecting human microbial diversity, see Ley, R. E. et al. 2006.
“Human gut microbes associated with obesity.” Nature 444: 1022-1023. For
“obese” microbes harvesting more energy, see Turnbaugh, P. J. et al. 2006.
“An obesity-associated gut microbiome with increased capacity for energy
harvest.” Nature 444: 1027-1031. For initial evidence that the genetic
background of the host affects which microbes are present, see Rawls, J.
F. et al. 2006. “Reciprocal gut microbiota transplants from zebrafish and
mice to germ-free recipients reveal host habitat selection.” Cell 127:
423-433.

For differences in gut microbes between people in China and the United
States, see Li, M. et al. 2008. “Symbiotic gut microbes modulate human
metabolic phenotypes.” Proceedings of the National Academy of Sciences USA
105: 2117-2123. For evidence that different sets of gut microbes can
provide broadly equivalent sets of genes, see Turnbaugh, P. J. et al.
2009. “A core gut microbiome in obese and lean twins.” Nature 457:
480-484.

For recent and dramatic genetic changes to our hostile bacteria, see Mira,
A., Rushker, R. and Rodriguez-Valera F. 2006. “The Neolithic revolution of
bacterial genomes.” Trends in Microbiology 14: 200-206.

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