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More than food in your stomach

By David Steinkraus

Starting from clues first noticed about 20 years ago, medical science has concluded that a stomach infection with a bacterium called Helicobacter pylori causes inflammation and is a major cause of peptic ulcers. It turns out that this may be far from the only resident of human stomachs.

Although the stomach is an inhospitable place to live, full of hydrochloric acid and digestive enzymes, research published last week in the Proceedings of the National Academy of Sciences suggests that stomachs host many different kinds of bacteria whose benefit or detriment is unknown. Researchers got stomach samples from 23 patients at a Veterans Affairs hospital in New York City, isolated the DNA they wanted, multiplied it by inserting it into common bacteria, and then determined the sequence of amino acids in those strands of DNA.

We talked to Elisabeth Bik, 39, a research associate in the Department of Microbiology and Immunology at the Stanford University School of Medicine and the lead author on the paper. She spoke by phone from her lab in the VA hospital in Palo Alto, Calif.

Just give me a summary of what you found.

"We have looked at which bacteria are present in the stomach and we have found DNA of 128 different, let's say, species." (Scientifically speaking these are not properly defined species because the classification is based only on DNA, but for common use it's close enough.) "We have found a lot of species that are present in the mouth of people, and that's not surprising because every time you swallow a lot of bacteria will leave your mouth and kind of flow down into your stomach."

"About 10 percent of the species that we found were ... never seen before by other people; their DNA sequences are new. And one of the species that we found (Deinococcus) was related to a bacterium that is found in extreme environments."

"Previously people thought that in the stomach, which is a very acid environment Š that no bacteria could exist. Š And now we have found that many other bacteria are probably present there as well."

Are these bacteria living in or just under the mucous coating on the wall? They're not free-living in the acid are they? "No, they're kind of attached we think. Well, first of all, we have found the DNA. We have not proved they're alive. Š But we know that Helicobacter at least is living there."

"We haven't actually looked with a microscope, so I cannot really say whether they're in the mucous or whether they're really attached to the cell wall, but they're kind of between that space.

And not all 128 species were found in all samples; bacterial populations varied widely from person to person.

One of your cautions was that you had to be careful interpreting this because these were people undergoing medical procedures so their conditions were almost by definition not normal.

"Yes, they had some gastric complaints or some reason to go to the doctor and have this endoscopy procedure Š and we were very happy these people were willing to donate one sample extra for research, but it's definitely not a set of healthy people."

I want to get back to Deinococcus. This is the same kind of organism that grows in the hot springs in Yellowstone? "That's probably the Thermus (a related bacterium.) Š This (Deinococcus) definitely is a bacterium that is able to grow in a lot of inhospitable environments. So you could kind of say the stomach is part of that. The conditions are kind of harder for bacteria to grow in, very acid, a lot of enzymes capable of digesting food."

"We only found it in one patient Š So it's not something very common, we think. But it is definitely the first time it has been observed in or associated with the human body."

What's the ultimate goal of the project? Is it to find disease-causing organisms or kind of get an idea of what's going on? "Well I guess both, but in order to understand whether certain bacteria play a role in disease or health, you have to know what is present in healthy people. And of course you can say that our study is not really looking at a healthy part of the population, but at least we have an idea of which bacteria are there."

"So this is not a knowledge we have, and knowing that we can move on to see if we can maybe find healthy people or people with a defined disease and compare those two."

What's your next step in the process? "We're probably, to be honest, not going to do much more on the stomach project. Š The technique that we've used to do this, that's our specialty. And other people can now pick that up and maybe investigate more, using microscopy Š are we able to grow some of these bacteria to prove there they're really alive? That might be research that might be interesting to do, but I don't have personally the expertise to do that."

"But one of the things that we're looking at, for example, is how babies are colonized. Š From day one, when a baby is born, when it's born it's sterile - so you look at the poop samples, there's nothing in there. Then (we'll be) following those babies and seeing how their GI tract is being colonized."

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