Health focus shifts to gut microbiome and nurturing ‘good’ bacteria

A diverse diet, including fermented foods such as yogurt and sauerkraut, may help promote a healthy gut.
(Bryan Chan / Los Angeles Times)

Our guts are at the height of their glory. Most health-conscious humans accept, somewhat blindly, that our gut bacteria — or the gut microbiome — are key to our overall health and ability to fight disease. That’s what fuels the $1.3 billion North American probiotics industry and spurs about 150 companies to search for the next fermented concoction promising to nurture those “good” bacteria.

And it’s a tall order: Microbiomes comprise the 50 billion bacteria that live on our skin and in our mouths, noses, vaginas and intestines, outnumbering our human cells by 10 to 1, according to the National Institutes of Health Human Microbiome Project. Our gut microbiome rightly gets the most attention: There is evidence linking it to diseases such as colitis and inflammatory bowel disease, but also to obesity, autoimmune diseases like diabetes and rheumatoid arthritis, and chronic inflammatory-related conditions.

Still, most of us don’t understand how it rules our immune system.

Enter Stanford microbiologist and infectious disease physician David Relman. “Think of [the gut microbiome] as a community that for millions of years has taken advantage of the environment we’ve created for them in our bodies,” Relman said, “and that in turn is helping us humans take advantage of our time on Earth. It’s all about [the microbiota] adapting to untoward challenges and learning how to protect us, and us them.”


For example, he said, “when humans are exposed to arsenic, our microbes use their genes and proteins to convert it to something less toxic — or more toxic, it can go either way — and we don’t know exactly why. But we do know that there must be some advantage to the microbiota, or they wouldn’t do it.”

And the bacteria in our gut have specific jobs, said Dr. Alejandro Junger, author of “Clean Gut: The Breakthrough Plan for Eliminating the Root Cause of Disease and Revolutionizing Your Health.” “The gut flora train and interact with the neurons in the immune system and give them signals to be alert, strong and protective.”

Healthy bacteria aid in detoxification, Junger said. There also is evidence that bacteria play an important role in the integrity of the intestinal wall, which, if it becomes hyperpermeable, leads to leaky gut syndrome, in turn linked to chronic inflammation — because our bodies attack these foreigners that get into our bloodstream — and disease.

So, our quest for a healthy gut environment appears to be well-founded. New York Dr. Raphael Kellman talks about how food fits into that in his book “The Microbiome Diet.”

“Anything that changes the microbiome — for instance, our Western diet of unhealthful, highly processed food, full of chemicals and hormones — can stress the immune system and in turn affect the microbiota,” he said. “This is an ancient system that has evolved to be incredibility elastic and is the key to our survival. But there is so much we really don’t know.”

Some scientists feel that a return to a clean, old and “healthy” microbiome is the secret to modern-day health, going so far as injecting the feces of Hadza villagers in Africa into their own bowels to try to replicate the richly diverse and buggy bacteria — the Hadza eat the stomachs of their prey — that live there.


“For one specific, dire disease — an infection of Clostridium difficile that causes severe diarrhea and inflammation of the colon — fecal transplant is shockingly successful,” Relman said. “These are people who are close to death, and current therapies can do nothing. But for other, less-extreme conditions, it doesn’t seem to work as well. I think the answer is you have to start with a microbial system that’s unstable and in great turmoil, so that it is receptive to the transplant. Otherwise the existing bacteria will fight [the bacteria] that’s introduced, and they will win.”

Indeed, Relman isn’t so sure our quest to return to the gut microbiome of our hunter-gatherer ancestors is a good idea. “There would be a huge trade-off, because if we could put those ancient microbiota in our gut, we’d be in a real jam — we would no longer have all the newly acquired functions life on modern Earth requires us to have.”

The experts agree on a few things. “I would be happy if people would stop using antibacterial soap,” said Marlene Zuk, a professor of evolutionary biology at the University of Minnesota. “It’s very clear that trying to clean everything constantly is not only purposeless, it might be downright bad for us.”

Antibiotic overuse also has the sweeping effect of wiping out the “good” bacteria with the bad. Experts suggest limiting antibiotic use and taking a probiotic along with the antibiotic.

A diverse diet also seems to be key, including probiotics and fermented foods like yogurt and sauerkraut.

In short, think more dirt and more diversity.

Peg Moline is author of “The Doctor’s Book of Natural Health Remedies.”