The case of the missing bacteria in Bay Area poop

Our gut is experiencing its own extinction event.

New Stanford research has discovered that the gut of the average Bay Area resident has only half as many species of bacteria as hunter-gatherers in remote northern Tanzania, a decline attributed to the industrialized world’s changing diets and lifestyles.

And while it’s not yet proven what role these missing bacteria play, scientists know that our body’s complex inner ecosystem of bacteria, known as the microbiome, helps digest food, synthesize vitamins, and fend off infections.

“It’s very clear that industrialization has impacted our gut microbiome in a profound way,” said microbiologist Justin Sonnenburg, co-author of findings reported this month in the journal Cell. “We have lost species that were part of human biology for most, or all, of our evolutionary history.”

How are we different? The poop of a dozen Bay Area volunteers was home to an average of only 277 bacterial species, compared to 730 species in the nomadic Hazda people of the central Rift Valley of Tanzania, among the last remaining hunter-gatherer populations in Africa, according to a detailed genomic analysis by the Stanford team.

We also have fewer bacterial species than rural people who live in the Himalayas. The study tallied between 317 and 436 species in residents of Nepal, depending on their lifestyle.

We acquire bacteria through water, food and soil.

What’s killing our bacteria? Scientists don’t yet know. “There are a range of lifestyle changes that occur with industrialization,” such as eating low-fiber foods, Sonnenburg said. “It’s really hard to disentangle which ones are having the biggest impact.”

To be sure, Western-style dietary changes and modern medicines have solved some of humanity’s biggest problems, said Sonnenburg, assistant professor in the Department of Microbiology and Immunology at the Stanford University School of Medicine.

Processed food is cheap and abundant, feeding more hungry mouths. Antibiotics have conquered many deadly infectious diseases.

“But, at the same time, they’ve been enacted with complete ignorance of the importance of the gut microbiome,” he said. “And now we’re realizing that there’s been collateral damage.”

The Stanford team also sequenced the genomes of more than 90,000 different specimens. The sequences could help reveal the function of each species of microbe — and suggest, perhaps, why some have perished.

While some species are gone forever, they could be reintroduced, said Sonnenburg. Other species are hanging on, and populations could be boosted.

We’re not likely to adopt a diet similar to the Hadza, who forage for tubers, berries and the seeds of baobob trees, eating between 100 and 150 grams of dietary fiber per day, compared to an average of 15 grams per day for the average American.

But an earlier study found that fermented foods like yogurt, kimchi, sauerkraut and kombucha, which teem with live microorganisms, also may help maintain gut health, Sonnenburg said.

“We should avoid highly processed and very starchy foods, like white rice and potatoes,” he said, “and eat more legumes, whole grains, vegetables, fruits and nuts.”

Although previous research has found that human gut microbiomes vary across regions and lifestyles, the new study paints a more dramatic picture.

It is the first major study to sequence the genomes of bacteria in non-industrialized populations – and found more pronounced losses in industrialized nations than previously thought — although we do not know if the loss hurts or helps us.

What’s missing? Among others, a corkscrew-shaped bacterium called Treponema succinifaciens. Abundant in the Tanzanians, only some of the Nepali contained this microbe, suggesting that the bacterium is dying out as societies become more industrialized.

We also have fewer members of the bacterial Prevotella species, which loves fiber. Previous research has found that ethnic immigrants from Laos, Vietnam and Thailand begin losing Prevotella and other native microbes almost immediately after arriving in the U.S. and then acquire microbes that are more common in European-American people.

While we’ve lost hundreds of species, we’ve also gained others.

Akkermansia muciniphila, a mucus-loving bacterium that colonizes the intestines in the absence of high levels of dietary fiber, is flourishing.