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In newly published research, CU �ֲ���ý scientist Matthew Olm and colleagues map the gut microbiome’s hidden global diversity

When Matthew Olm’s daughter was born, he did something most parents never consider. He gave her a type of experimental probiotic designed to nudge her infant gut microbiome in a healthy direction.��

Then again, most new parents don’t have a PhD in microbiology or run their own research lab studying microbes from around the world.��

“It was fascinating in terms of how well it worked to colonize my daughter’s gut, and it really validated a lot of the science that I’d read about,” he says.��

Matthew Olm, a CU �ֲ���ý assistant professor of integrative physiology, recently collaborated on a study examining the gut microbiomes of eight tribal communities across India.��

At the time, Olm was a postdoc in , curious to know more about what happens to the human gut microbiome as one’s lifestyle industrializes.��

“There’s a lot of reason to suspect that the way industrialization changes the microbiome opens you up to immune disease. Many studies also show that the infant microbiome is especially important in this regard,” he says.��

Olm, now running his own lab and serving as an assistant professor of integrative physiology at the �ֲ���ý, recently collaborated on a study examining the gut microbiomes of eight tribal communities across India.��

While trying to understand what these communities’ relative isolation from industrialization may have preserved, the data revealed an unexpected story.��

A better global picture

Now a paper , the project first found Olm while he was at Stanford.��

“A graduate�� student, , came up to my (principal investigator) Justin at a conference and asked if we wanted to help out with the analysis. He had done this sampling campaign across all of these different tribes in India and had a lot of microbiome samples,” Olm recalls.��

It was a unique proposition.��

Some come from the United States, Europe or Canada. Almost half of all samples come from the United States despite the country accounting for just 4.3% of the global population. Samples from more populous areas like Africa and Southeast Asia, particularly communities outside urban hubs, are studied far less often.��

One challenge of acquiring samples from less developed areas, Olm says, is that the sample material must be frozen immediately lest the microbes inside keep growing and distort the snapshot.��

Rather than freezing in the field, the team preserved each sample on-site with a chemical stabilization buffer that halts microbial growth until the samples could be frozen back at the lab. Olm then catalogued the samples and ran the initial analysis, doing much of the work with , a genome analysis tool he had written during his PhD work at UC Berkeley.��

He points out that a single microbe most people have heard of, like the E. coli found naturally in your gut, isn’t really one thing at all.��

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Geographic and dietary diversity of the eight sampled tribal populations in India. A, Photographs of traditional dwellings, residents, and unique foods in participating villages. B, Geographical locations of the eight sampled populations. Map is from Survey of India. Green shading indicates tribal populations as a percentage of state population in the 2011 Census of India. C, Food items consumed daily by at least one population.��

“That’s millions, billions, trillions of cells, and each individual cell is slightly different from the others,” Olm says.

inStrain allows researchers to see the hidden variations so they can trace the lineage of bacterial strains within communities, regions and even family trees.��

Where do our microbes come from?

The study’s most striking finding centers on Bifidobacterium, a genus prized for its health benefits. Analysis showed it in much greater abundance among dairy-consuming Trans-Himalayan communities than anywhere else in the study. The microbes were also genetically distinct from Bifidobacterium strains found in industrialized populations.

Olm says this result speaks to a long-running debate over where we get our gut microbes from. Does everyone share the same global pool of microbes, altered by our diet and lifestyle, or does physical exposure determine our gut’s unique makeup?��

“Actually, the physical source matters a lot. Even if you eat a lot of potatoes, if you don’t interact with a microbe that specializes in digesting potatoes, you’re never going to pick that strain up,” Olm explains.��

The findings from these communities suggest their unique gut microbiome strains co-evolved alongside the populations themselves, passed down from generation to generation, rather than being acquired because of a shared diet. An American who started eating more dairy today, Olm says, would likely never achieve a similar microbiome through diet alone.��

The cost of a cleaner world

Science has proven the benefits of a diverse microbiome. Yet, industrialized societies are notorious for a lack of gut diversity, even among individuals who do everything “right” when it comes to diet and lifestyle factors.��

Olm says this traces back to a handful of compounding factors.��

“We have a lot more antibiotic exposure, birth by C-section and these other medical things. Diet plays a role too,” he says.��

But the biggest factor is one most people aren’t as comfortable discussing: modern sanitation.��

Olm explains that acquiring new microbes from other people typically requires a level of everyday exposure that handwashing and modern plumbing have all but eliminated in industrialized societies.��

“A hundred years ago, the number one causes of death were all infectious disease, because we didn't have this hygiene,” Olm says. “Hygiene is definitely a good thing, but the downside is you're also not exposed to the way you'd naturally pick up healthy microbes from other people and other people’s poop.”

In other words, our cleaner world is also one with less microbial diversity.��

“The more you sanitize the environment, maybe the less diverse microbiome you have, but also the less infectious disease you have,” Olm says.

He’s careful to reiterate that this isn’t an argument against modern medicine. It’s simply a reminder that everything has a trade-off.��

“If you’re prescribed antibiotics for an ear infection, it’s important to take it. You should be washing your hands regularly and practicing good hygiene. Yes, it will have some harm on your microbiome, but in the cost-benefit analysis, modern medicine and sanitation still win,” he says.��

Racing to preserve a moving target

As the world moves further along the path of industrialization, we risk losing much of the gut diversity our ancestors had. Once that diversity is gone, Olm says, it’s very difficult to bring it back—let alone study it.��

This is why some researchers have begun freezing and banking fecal samples from non-industrialized populations, similar to preserving seed banks for crop diversity. Others have taken to studying ancient fossilized fecal matter to recover snapshots of gut microbiomes lost millennia ago.��

While projects like the one Olm collaborated on can reveal some hidden secrets of humanity’s gut health, he is careful not to frame traditional communities as something to be preserved for the benefit of research.��

Pointing to the Hadza hunter-gatherers of Tanzania, he says it’s tempting to romanticize the lifestyle as something worth protecting, but adds, “If you talk to some of these communities, they want education, they want modern medicine.”��

Industrialization, he says, is “part of the human condition.”��

“I don’t think it’s right to discourage these non-industrialized populations from becoming industrialized with the rest of the world just so it benefits our microbiomes,” Olm adds.

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“Most of the microbes in our gut, they eat fiber, and it's the primary food source for our microbiome," says CU �ֲ���ý scientist Matthew Olm. "The more fiber you eat, the more substrate there is to sustain a healthy microbiome." (Photo: iStock)

Instead of discouraging it, his lab publishes its sequencing data publicly, serving as what he calls a computational resource for future researchers to study before these unique microbiomes change further.��

What about your gut?��

As for the rest of us, Olm’s advice on a healthy microbiome is refreshingly unglamorous in a world where we are constantly bombarded by ads and influencers pushing one supplement or the next.��

“Eat more fiber. That’s definitely the number one recommendation,” he says.��

Recommended daily fiber intake in the U.S. is about 25 to 28 grams per day for women and between 28 and 34 grams per day for men, .��

Olm says most Americans get just 10 grams of fiber from their diet each day. Traditional hunter-gatherer communities may eat up to 200 grams a day during certain bountiful seasons.��

“Most of the microbes in our gut, they eat fiber, and it's the primary food source for our microbiome. The more fiber you eat, the more substrate there is to sustain a healthy microbiome,” Olm adds.��

It’s not a flashy recommendation, but that’s the point. In a field full of trendy probiotics that are more marketing than science, the answer may be as simple as supporting the system our bodies have relied on for thousands of years.��

For Olm and his lab moving forward, the real promise of gut microbiome research lies in building a fuller picture of what a healthy gut can look like and how we can support it with science-backed interventions.��

As more of the world's underrepresented microbiomes get studied, that picture, and our knowledge of our own health, can only be clearer.

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