Bacteria, viruses and fungi (oh my!) on the human body

There has been lots of excitement this week as a horde of scientists released their first looks at the trillions of microbes that live in (or on) our bodies.

As well as the two main papers published in Nature, a slate of reports was published in other journals, containing all kinds of tidbits. One week earlier, another slate of “microbiome” papers was published in the journal Science.

We already covered the nuts and bolts of the Human Micriobiome Project report. Here’s more about the teeming zoo of life we carry around with us:

Ethnic differences: Researchers found a lot of variation in the microbe populations within their 242-person sample. But were there any patterns? The study didn’t find many, based on gender, body mass index, blood pressure and body temperature. But they did find different patterns of microorganisms and of genes contained in the microbe population based on race/ethnicity (the sample included people who were white, black and of Asian, Puerto Rican or Mexican roots. What’s behind the differences? Human genetic variation? Environmental exposures, such as where one was raised or what one was fed as a baby, etc.? They cannot yet tell. Nor do they know what the health consequences (if any) are for the differences they see.

The skin: This was another spot on the body where scientists found a lot of variation from one person to the next. Since it’s our interface with the outside world, “you might imagine it is the most easily perturbed by the environment as people walk around in their life day to day,” said Curtis Huttenhower of Harvard, one of the consortium scientists, in an interview. The skin is also a relative microbe desert compared with other parts of the body. There are fewer nutrients there. It’s dry. Unfriendly. Makes sense.

The scientists did find differences in the skin related with age (all the subjects were between18 and 40, so who knows what happens to skin of people from midlife to old age). Certain bacteria from a large group called the Firmicutes decreased with age in samples taken from behind the ear.   

The vagina: Not a great variety of microbes at this site -- it’s usually dominated by just one species of Lactobacillus. (It can be a different one from one woman to the next, however.) But there are differences one sees with pH. With higher pH (i.e. the less acidic), Lactobacillus amounts decrease and microbial diversity goes up.

When a woman is pregnant, the vaginal microbiome becomes even less diverse, scientists reported in a paper published in the journal PLOS ONE after comparing the vaginal flora of 24 healthy pregnant women to those of 60 women who weren’t pregnant. There are fewer bacteria there as well. The scientists speculate that the changes may have a role -- perhaps in protecting the baby who is soon to move through the vaginal canal from picking up infections.

Links to disease and disorders: You won’t find links to disease from the data from the five-year Human Microbiome Project, because all the subjects had to be in super-duper health. The volunteers couldn’t even have gum disease, which affects maybe 40% of Americans. There’s a reason why only healthy people were chosen. The scientists wanted to figure out a baseline healthy microbiome to compare against people with medical problems, and it’s expected that what they have found will inform a raft of future studies into disease and the microbes that we harbor. And yes, researchers are finding links to a lot of disorders: inflammatory bowel disease, asthma, psoriasis, obesity, rheumatoid arthritis and more. Such links have to be studied in depth before scientists can be sure that the microbes are actually contributing to the conditions.

If disorders are linked specifically to flora of the small intestine, the Human Microbiome Project might miss it, because only one gut sample was taken, from stool. Taking small intestine samples would have been trickier and pricier to do, explained consortium member Barbara Methe of the J. Craig Venter Institute. You’d have to use an endoscope. That adds to the cost and also makes it harder to get consent from volunteers because it is an invasive procedure and these people are not sick -- they’re just giving their microbes for the furtherance of science.

Fungus among us: Though bacteria are the dominant life forms in the microbiome, there are other microscopic critters inside us too -- such as fungi. In a paper published last week in Science and described in a post on The Times' Science Now blog, David Underhill of the Cedars Sinai Medical Center and colleagues described how some of them are linked to ulcerative colitis, an inflammatory bowel disease.

Viruses! They’re in our bodies too, though the microbiome project wasn’t optimized for picking them up, Methe said. In another PLOS ONE paper, researchers looked at a possible link between viruses and unexplained fever in children 3 and younger. Even though viruses are generally suspected to be the cause, they’re not usually tested for and there are plenty of antibiotics being asked for and prescribed. (Antibiotics do not eradicate viruses.) The researchers’ DNA analysis found that kids with fever contained 1.5 times more virus genetic material than healthy controls.  

Who lives where: Why is it that the microbial communities in one part of the body are different from ones in other parts? Researchers took a detailed look at all the genes our tiny tenants contained, and suggest that a key factor in setting up microbial communities is what kinds of carbohydrates are present at each body site. There is “an astounding diversity” of carbohydrates in nature -- sugars, starches, fibers, etc., with all kinds of different branching patterns and other chemicals stuck on them -- but they’re not all present at the same place. Whole communities of bacteria can grow up around the local carb offerings, the scientists say.

What the bugs do is handy for us: Our genome contains a positively paltry set of enzymes capable of digesting complex carbohydrates. Just 20!  And yet consider, the scientists say: “A single vegetable contains hundreds of different bonds that need to be cleaved” if a plant cell wall is to provide us with calories. Bacteria, working together as a community, can manage this digestion. We get some of the calories they don’t chomp.

Not that calories are necessarily something we lack. And on that note, as we mentioned there’s considerable interest these days in the relationship between gut flora and obesity. Some of that work is going on in L.A. in the lab of endocrinologist Ruchi Mathur of Cedars Sinai. She’s reported that women who are obese tend to have more methane on their breath, suggesting that their bodies contain more microbes called Archaea, which make methane. Methane increases the time it takes for food to move through our gastrointestinal tract … more time to absorb food, perhaps?

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