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A cuddly-looking ball of a crocheted microbe with big eyes.

Could most of the microorganisms found our digestive systems be as friendly as this guy? Photo and microbe by Stacey Trock of

What’s living in your gut? Are the microorganisms in there good for you? And how does your diet influence them? These are interesting questions for fans of living, fermented foods, and science is just beginning to answer them as it investigates the microbiome. The fact that we’re asking them at all is pretty cool.

The diversity of bacteria that live on the body is staggering. The Human Microbiome Project claims there are about 10,000 spices altogether, found everywhere from our mouths to our bellybuttons and that they outnumber human cells ten to one. In our digestive systems, it’s possible that we have “enterotypes” in the same way we have blood types. And it’s possible that different people have different populations depending on their diet, or where they grew up. Right now, anybody can find out what they’ve got inside by joining the American Gut campaign, which is wrapping up in a few days.

Why care? Maintaining and even cultivating our digestive diversity could be healthy, and learning how our microbiome works and reacts could open a whole new area of disease treatments, something that’s covered in depth in this excellent article in the New Yorker. As that article makes clear, we’re still really early in understanding the ins and outs of our bodies’ relationships to the many microorganisms they host.

One thing is becoming more clear, though: We need healthy microbiomes, which means we should carefully consider the use of antibiotics. It’s starting to look like taking them is akin to swallowing a grenade that can blow up a lot of beneficial bystanders at the same time that it hits the bad guys. If many of the microbes we harbor contribute to our health, then wiping them out by mistake with drugs could allow other harmful microbes to take root, produce autoimmune disorders, or trigger other problems. It’s possible that digestive bacteria protect against celiac disease, for example. They could help determine body weight. And, in some studies, fecal transplants have cured the diarrhea caused by Clostridium difficile infections, showing that changing the population in the gut can bring about health results.

I’m looking forward to the news that comes in the next few years, but I’m especially curious to learn how our diets, especially oes that include fermented foods and lots of live microorganisms, influence the microbiome and our health. Is there a change in our guts if we load up on kraut and yogurt every day? And do those little beasts stick around inside us and do good things? I can’t wait to find out.

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A partial image of a New York Times graphic showing some microbes mapped by the Human Microbiome Project

Find out even more about the human microbiome and the relation between microbes and health in a second, more detailed article the New York Times published last week. Here’s a snippet.

In a study published last week in the journal PLoS One, Dr. Kjersti Aagaard-Tillery, an obstetrician at Baylor College of Medicine, and her colleagues described the vaginal microbiome in pregnant women. Before she started the study, Dr. Aagaard-Tillery expected this microbiome to be no different from that of women who weren’t pregnant.

“In fact, what we found is the exact opposite,” she said.

Early in the first trimester of pregnancy, she found, the diversity of vaginal bacteria changes significantly. Abundant species become rare, and vice versa.

One of the dominant species in the vagina of a pregnant woman, it turns out, is Lactobacillus johnsonii. It is usually found in the gut, where it produces enzymes that digest milk. It’s an odd species to find proliferating in the vagina, to say the least. Dr. Aagaard-Tillery speculates that changing conditions in the vagina encourage the bacteria to grow. During delivery, a baby will be coated by Lactobacillus johnsonii and ingest some of it. Dr. Aagaard-Tillery suggests that this inoculation prepares the infant to digest breast milk.

The baby’s microbiome continues to grow during breast-feeding. In a study of 16 lactating women published last year, Katherine M. Hunt of the University of Idaho and her colleagues reported that the women’s milk had up to 600 species of bacteria, as well as sugars called oligosaccharides that babies cannot digest. The sugars serve to nourish certain beneficial gut bacteria in the infants, the scientists said. The more the good bacteria thrive, the harder it is for harmful species to gain a foothold.

Plus: viruses and fungi may be in on the action; strongly worded quotes suggesting that antibiotics could disrupt healthy bacteria in unhealthy ways; and fecal transplants seem to be gaining approval and could be coming to you in pill form someday. Oh and there’s a sweet graphic.

Researchers suspect that, by harming healthy microflora in children, antibiotics can lead to asthma and allergies later in life. Microbes could also influence the weight of the mammals that host them—scientists have made thin mice obese by giving them the gut bacteria of other obese mice. So where do these obesity-causing bacteria come from? Probably a variety of places. Even the food you eat can change your microflora. According to the Economist, a study found that a sugary, fat-laden diet could change a child’s gut bacteria profile, leading to an increased risk of asthma, allergies and other inflammatory diseases. Food for thought.


An adult body carries four to five pounds of bacteria, and many of them are good bacteria that keep you healthy. Now scientists are trying to get a snapshot of what that healthy human microbiomes look like. If they succeed, we could get a deeper insight into how to live disease-free. The New York Times has an article on what they’re finding and how they’re doing it:

Researchers have taken a detailed look at … the 100 trillion good bacteria that live in or on the human body.

No one really knew much about them. They are essential for human life, needed to digest food, to synthesize certain vitamins, to form a barricade against disease-causing bacteria. But what do they look like in healthy people, and how much do they vary from person to person?

In a new five-year federal endeavor, the Human Microbiome Project, which has been compared to the Human Genome Project, 200 scientists at 80 institutions sequenced the genetic material of bacteria taken from nearly 250 healthy people.

They discovered more strains than they had ever imagined — as many as a thousand bacterial strains on each person. And each person’s collection of microbes, the microbiome, was different from the next person’s.

It sounds like this will be even more complicated than sequencing the human genome, but it will be a great baseline from which we can start to understand how all these microbes we carry around keep us alive.

I particularly like this bit:

Humans, said Dr. David Relman, a Stanford microbiologist, are like coral, “an assemblage of life-forms living together.”

Dr. Barnett Kramer, director of the division of cancer prevention at the National Cancer Institute, who was not involved with the research project, had another image. Humans, he said, in some sense are made mostly of microbes. From the standpoint of our microbiome, he added, “we may just serve as packaging.”

People are like planets, brought to life by all the critters living on them.

Here are two articles in Nature, one about the study and one about the diversity of the human microbiome.


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