Gut health is now sold in probiotic pills and at-home microbiome tests. According to a group of leading scientists who study gut microbes, both have grown faster than the evidence behind them.

The habits they do support are much simpler. Eat many kinds of plants, choose fiber and fermented foods, and skip antibiotics that aren’t medically needed.

The microbiome is the community of microbes living in the human body.

These scientists see it as one of the most practical tools for fighting chronic disease, but one big question is still open.

Studies keep linking gut microbes to illness. Proving that the microbes actually help cause illness in people, the scientists wrote, is still the main job ahead.

Scientists propose microbiome plan

Thirteen researchers wrote the new commentary in Nature Medicine after a public roundtable held by the U.S. Department of Health and Human Services in September.

It reviews existing research and doesn’t report a new experiment.

The lead author is Martin Blaser of Rutgers University, who directs its Center for Advanced Biotechnology and Medicine.

Suchitra Hourigan, a microbiome researcher at the National Institutes of Health, chaired the group, whose members work in fields ranging from immunology and cancer biology to brain science.

A link is not proof

Twenty years ago, microbiome research was mostly about listing which microbes lived where on the body.

Better DNA sequencing and computing have since tied those microbes to immunity, metabolism, the brain and how people respond to drugs.

Studies have linked the microbiome to metabolic disease, cancer, allergies and diseases that destroy brain cells. But most studies in people only compare groups, without changing anything about how they live or eat.

A comparison like that can show a pattern. It can’t prove that the microbes helped cause the disease.

Major research gaps remain

The clearest proof of cause still comes from animal experiments and a small number of treatments, mostly for gut infections.

Most studies also identify microbes by reading their DNA. That shows which microbes are present, but not what they’re doing.

Microbiome research has also mostly been done in wealthy Western countries, so much of the world’s microbial variety is still unmapped.

Even the body’s viruses, including those that infect bacteria, remain largely unstudied. The group backed the Human Virome Program to study this virome.

Simple habits have support

Not everything is uncertain, though. The panel listed several habits that current evidence supports.

The first is variety. Eating a wide variety of plant foods, with some research pointing to 30 or more types a week, is associated with greater gut microbial diversity.

Diets built mostly on fiber-rich plants also favor helpful microbes. Fermented foods add live organisms to the diet, and eating them has been linked to lower markers of inflammation.

Antibiotics matter too. Taking them when they aren’t needed disrupts the microbiome, especially in young children, so the authors want them avoided whenever that’s medically possible.

When medically possible, vaginal birth and breastfeeding also help build a healthier microbiome. Staying active and managing sleep and stress help too.

Do gut tests and probiotics help?

Home microbiome tests have spread quickly. But the panel found too little evidence that their results lead to meaningful improvements in health.

Part of the problem is that there are no proven medical standards for reading the results yet.

Without them, the authors wrote, these tests risk misleading people instead of informing them.

Probiotics and other supplements got a similar warning. Their market has grown far ahead of the evidence, and marketing claims often promise more than the science can back up.

The authors also warned that broad use of these products may cause harm.

Early life was singled out

Of all ten priorities, the authors singled out the first 1,000 days of life, from pregnancy to a child’s second birthday.

They called it the most important period for the developing microbiome, and the one most open to change.

Antibiotics before age two and cesarean birth both change a baby’s microbiome. Both have also been linked to a higher risk of metabolic and allergy-related conditions later in life.

“The microbiome develops during this period, creating an opportunity to investigate whether protecting the initial development can improve health years later,” said Maria Gloria Dominguez-Bello, one of the authors.

Dominguez-Bello is a professor of microbiome and health in Rutgers’ School of Environmental and Biological Sciences.

She and her co-authors wrote that stepping in early offers the best long-term return on public health spending.

Treatments show what’s possible

In cancer, microbiome research has moved fast.

Evidence increasingly suggests that the gut microbiome influences how patients respond to immunotherapy, a treatment that helps the immune system attack tumors.

Dietary fiber, antibiotic use and the mix of gut microbes have all been linked to how well patients respond to treatment.

The clearest success is against Clostridioides difficile, a gut infection that can keep coming back.

Moving a donor’s stool microbes into a patient can be highly effective at preventing recurrent infections, and the Food and Drug Administration has approved treatments based on this.

Brain diseases are another target. Gut microbes have been linked to Parkinson’s disease, Alzheimer’s disease, ALS and autism.

By 2060, nearly 14 million Americans will have Alzheimer’s, the authors wrote. Yet fewer than 15% of research money for diseases that destroy brain cells goes to prevention.

Unlike genes, the microbiome can be changed. That makes it a promising target for prevention, in the group’s view.

What comes next

Large microbiome studies in the United States are clearly underfunded, according to the panel. Other countries currently lead the biggest efforts.

“We hope to move quickly, with detailed proposals for particular studies and programs in this next fiscal year,” said Blaser.

Some steps could come sooner. The authors want microbiome and nutrition science taught in medical schools, nutrition lessons in schools, and harmful ultra-processed foods removed from federally funded school meals.

“Altogether, I see this agenda as short-term as well as medium and long-term,” said Dominguez-Bello.

Four of the 13 authors reported ties to companies or foundations. Tim Spector co-founded the gut health science company ZOE and holds equity in it, and Nicola Segata consults for ZOE and sits on its board.

The biggest open question is whether a disrupted microbiome early in life actually causes disease years later.

The study is published in the journal Nature Medicine.

—–

Like what you read? Subscribe to our newsletter for engaging articles, exclusive content, and the latest updates.

Check us out on EarthSnap, a free app brought to you by Eric Ralls and Earth.com.

—–