How modern life depletes our gut microbes – ‘The concern is that we’re losing keystone species’

Desdemona Despair

By Michaeleen Doucleff
21 April 2015

(NPR) – Looks like many of us don’t have the right stomach for a paleodiet. Literally.

Two studies give us a glimpse into our ancestors’ microbiome — you know, those trillions of bacteria that live in the human gut.

And the take-home message of the studies is clear: Western diets and modern-day hygiene have wiped a few dozen species right out of our digestive tracts. One missing microbe helps metabolize carbohydrates. Other bygone bacteria act as prebiotics. And another communicates with our immune system.

In other words, Americans’ digestive tracts look like barren deserts compared with the lush, tropical rain forest found inside indigenous people.

“The concern is that we’re losing keystone species,” says microbiologist M. Gloria Dominguez-Bello, at the New York University School of Medicine. “That’s a hypothesis, but we haven’t proved it.”

Dominguez-Bello and her colleagues are the first to characterize the gut bacteria of people completely isolated from modern medicine, food and culture.

In 2009, her colleagues and a medical team with the Venezuelan government took a helicopter to a remote Yanomami tribe at the border of Venezuela and Brazil. Members of the tribe have lived as hunter-gatherers for more than 11,000 years in a mountainous area of the Amazon rain forest.

The visit was the first time that particular tribe had direct contact with modern society. “They knew about us, but we didn’t know about them,” Dominguez-Bello says. “They had names [in their language] for our helicopters and planes.”

Dominguez-Bello’s colleagues took samples from 12 of the villagers’ fecal matter. Back in New York City, the team used DNA analysis to figure out which species thrived in the hunter-gatherers’ guts.

The biggest surprise was how many different species were present in the Yanomami’s microbiome. The tribe had about 50 percent more ecological diversity than the average American has, Dominguez-Bello and her colleagues reported Friday in the journal Science Advances.

As cultures around the world become more “Western,” they lose bacteria species in their guts, Dominguez-Bello says. At the same time, they start having higher incidences of chronic illnesses connected to the immune system, such as allergies, Crohn’s disease, autoimmune disorders and multiple sclerosis.

“So the big question is: Are these two facts related?” Dominguez-Bello asks. “It’s not clear if more diversity in the microbiome is healthier. But maybe we have lost species with important functions.” [more]

How Modern Life Depletes Our Gut Microbes

ABSTRACT: Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.

The microbiome of uncontacted Amerindians