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SHARYL ATTKISSON: Not too long ago, people might have thought you were crazy if you said most stomach ulcers were caused by bacteria. But, thanks to the efforts of one persistent researcher, it's become a widely-accepted fact. And the role of germs in digestive diseases may not stop there. Now, a small group of doctors think bacteria may be to blame for a chronic intestinal disorder, called Crohn's Disease. Andrew Holtz reports on their controversial theory, and whether it may lead to the cure patients have been hoping for.

ANDREW HOLTZ: A normal family life is something Randy Bogani feared he might never have.

RANDY BOGANI: When we were married, I was sick, so I thought we were going to live a life of sickness.

ANDREW HOLTZ: For four years, Randy suffered from chronic diarrhea, fatigue, sleeplessness and other symptoms that he says were ten times as bad as the flu. His weight dropped almost 50 pounds.

RANDY BOGANI: What I felt I looked like is that I came out of a POW camp. I was really skinny, gaunt, it was not pleasant.

ANDREW HOLTZ: Repeated exams of his digestive tract eventually pointed to Crohn's disease, a chronic inflammation of the intestinal wall. Randy was put on medications, including the steroid Prednisone.

RANDY BOGANI: At one point, I was up to 30 pills a day. This went on for years. The treatment wasn't helping at all, it was just giving me more symptoms.

ANDREW HOLTZ: Unfortunately, many Crohn's patients, like Randy, aren't helped by standard treatments. There is no cure, and the cause of the condition is unknown. But now one doctor is promoting a radical, and surprisingly simple, explanation: bacteria. Gastroenterologist Ira Shafran is a one of a handful of doctors who believe many cases of Crohn's are caused by mycobacterium avium paratuberculosis... MAP for short.

It causes a Crohn's-like disease in cattle, which has led some to conclude the bacteria may be transmitted through milk, though most experts say pasteurization kills MAP.

It's also present in soil and water, but only some who come into contact with it seem to get sick. Until recently, it was very hard to detect MAP in people. Now a few labs across the country have the technology to do so.

For Crohn's patients who test positive, Dr. Shafran prescribes a combination of antibiotics intended to target MAP.

IRA SHAFRAN, MD, GASTROENTEROLOGIST: And in that process, 80 percent of patients get well in a period of six months.

ANDREW HOLTZ: Randy was one of those patients. He was given antibiotics as part of a study conducted by Dr. Shafran. Within weeks, he began to feel much better.

RANDY BOGANI: It was great, because then I realized what it felt like to feel good. After four years, when you feel bad all the time, you just think, you know, you forget what it is to feel well.

ANDREW HOLTZ: But stories like Randy's aren't enough to convince most Crohn's experts.

GARY GRAY, MD, STANFORD UNIVERSITY MEDICAL CENTER: I wouldn't be willing to take the same antibiotics and say, "here, try this, because it may have worked in a few patients."

ANDREW HOLTZ: Dr. Gary Gray says the fact that Crohn's symptoms can come and go on their own makes it hard to tell whether antibiotics really have any effect.

GARY GRAY, MD: It's very important that multi-centered controlled trials, probably with hundreds and hundreds of people, at least, be established before we could put any real credence into antibiotics actually helping the patients.

ANDREW HOLTZ: Indeed, not every patient is helped. Tony Glaser, who has Crohn's, went to Dr. Shafran, tested positive for MAP, and was put on antibiotics. The treatment was no fun.

TONY GLASER: The side-effects of the antibiotics are pretty brutal, you know, you get severe flu symptoms, headaches, joint pains, the whole nine yards.

ANDREW HOLTZ: Patients have to take the drugs, twice a day for a year... or longer. Tony stuck it out, and eventually began to feel better. But then after a full year on the antibiotics, his Crohn's symptoms came back.

TONY GLASER: All of a sudden, I started to get sick again. And then you say, "ok, fine, what've I got to do to be done with this?"

ANDREW HOLTZ: Still, Tony's sticking with the antibiotics.

TONY GLASER: I'm still not back to where I'd ideally like to be, you know, healthy, but it's better than it was.

ANDREW HOLTZ: Dr. Shafran says he doesn't expect to cure every case of Crohn's, but thinks ultimately, his theory will be proven true.

IRA SHAFRAN, MD: It's very easy to throw treatment at a disease, but to find the root cause, to identify that cause, and then to be to able to eradicate it and make a patient well, that's all I need.

SHARYL ATTKISSON: A large clinical trial is getting underway at 12 VA hospitals across the country. Half of the 200 patients are getting antibiotics; the others, placebo pills.

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