8 things you need to know about your gut microbiome

1. It's hard to define what a 'healthy' gut microbiome is

Within healthy people, the specific makeup of the gut microbiome can vary significantly based on geography, lifestyle, diet, genetics, and other factors.

While the field has made major strides, there's "no clinical or scientific consensus around what constitutes a healthy microbiome," said Hannah Holscher, a professor of nutrition at the University of Illinois in Urbana-Champaign.

However, experts do have clues about what typically are desirable characteristics for the microbiome.

Research has found that a higher diversity of microorganisms can be an indicator of a healthy gut. You can also see how well the microbiome resists change in the face of disruptions like illness or antibiotics, and its ability to bounce back after that. Experts have also identified certain bacteria groups that are correlated with health.

None of these are universal markers, but taken together, they can be markers of how well the microbiome is doing.

2. It's not just which bacteria are present — it's what they're doing

Certain groups of bacteria are associated with better health, and research has revealed some of the important jobs they're doing. But experts caution against simple ideas that you can separate the bacteria in the gut into "good" and "bad" microbes.

"There's a new understanding that we're not necessarily talking about just one microbe at a time causing problems," said Alexander Khoruts, a professor at the University of Minnesota who directs the UMN Microbiota Therapeutics Program.

"It could be an entire microbial community as a unit that may be dysfunctional," he added.

In a study published last year, researchers surveyed more than 40,000 human gut microbiomes from dozens of countries and ranked various groups of bacteria that seem to be "keystones" of health and resilience, like Roseburia, Eubacterium, Faecalibacterium, Allistipes, and Bacteroides.

While the study was unable to prove causation, Holscher noted there are some common themes among the top-ranking microbes. This helps explain why bacteria are beneficial, including their ability to ferment fiber, produce healthful metabolites, and make short-chain fatty acids.

However, two healthy people can have microbiomes that look and behave very differently, meaning it's possible they could respond to the same diets and interventions in different ways.

3. While the modern microbiome has problems, it's not broken

While social media might convince you that the modern person's microbiome is irreversibly destroyed, Fergus Shanahan, a researcher in the field and an emeritus professor of medicine at the National University of Ireland in Cork, said the truth is more nuanced.

"There are many features of our industrialized microbiome that are suboptimal, but it may be the best we have because our microbiome has changed and adapted to our environment," he said.

Studies have found that living in industrialized societies has taken its toll on our gut health, as has the wide use of antibiotics, diets heavy in refined food and low in fiber, sedentary lifestyles, and other environmental factors.

However, the fact that our microbiome looks different from our ancestors doesn't mean we'd be better off if we had their microbiomes. When people who live in a pre-industrialized setting move to one that's more industrialized, Shanahan said it seems their microbiome might actually become a liability, potentially increasing their risk of obesity and other chronic diseases.

It's also worth noting that what may have been normal at one point in history might not necessarily have been "healthy." For example, it's well-established that the bacteria species Helicobacter pylori is a risk factor for peptic ulcers and stomach cancer. Not long ago, most people had this bacterium in their stomach, and scientists speculated it might've had a protective effect against certain autoimmune and allergic diseases.

"So there's a yin-yang with everything," Shanahan said. "What's good at a certain time in human evolution isn't necessarily good at a later time."

4. Over-the-counter microbiome tests might provide questionable results

As technology has advanced, the development of products to determine your gut health have advanced alongside it. Typically, these tests rely on stool samples, cost a few hundred dollars, and provide hundreds of measurements related to microbes and metabolites, sometimes even giving you a gut health score.

Khoruts said that in his practice, it's not unusual for patients to present him with results from these tests.

"I think the message the patient gets is 'gee, my doctor never did this kind of testing — it must mean something,'" he said. "The reality is, unfortunately, it's not very informative at all."

5. Be careful with probiotics

There are many probiotic options out there aimed at supporting various organ systems and aspects of your well-being, and experts have outlined the three core requirements of a probiotic: the microbes must be alive, present in sufficient quantities, and have a proven health benefit.

Shanahan said the last criteria is typically the one that commercial products gloss over by claiming they've been "clinically tested" but omitting the fact that the actual findings were underwhelming.

"I'm afraid the consumer has to be really careful about that," Shanahan said.

Researchers agree that probiotics have potential, and some strains are backed by high-quality data that shows they can be effective in some circumstances. For example, some strains of probiotics can lower the risk of diarrhea from antibiotics and severe complications for preterm infants.

A common misconception is that probiotics are supposed to head straight to the gut, take root, and fight against unwelcome microbes, but in reality, they temporarily trigger "our immune system, our intestinal lining and our gut brain-axis" to make compounds that are beneficial while we're taking them, according to Maria Marco, a professor of food technology at the University of California, Davis.

"Through my own work, I have seen that they have made a difference in people's lives," she said. "The challenge probiotics face is the same issue with gut microbiome — that it depends on which microbe, for which person, at which time."

Research has found you can change the composition of the microbiome fairly quickly by significantly upping your fiber intake. However, Holscher recommends you take it slowly.

Her lab has found that even small additions to the diet, like a handful of nuts or an avocado, can enrich certain beneficial bacteria over the course of a few weeks. There's also evidence that adding fermented food to your diet, like kimchi, kefir, and sauerkraut can be especially effective.

One study from Stanford University found that adults who added extra fermented foods over the course of two-and-a-half months had increased microbial diversity and a decrease in markers of inflammation.

Yogurt is another easy way to add probiotics to your diet, though it's best to look for products with live cultures in them and avoid those with a lot of sugar.

7. Avoid highly processed snacks

While there are plenty of foods demonized online, gut health experts emphasize that the sum of what you eat matters more than any single food. As long as you have a diverse diet, Holscher said there's room to indulge in the occasional sugary treat.

However, she and other experts advise that most of what you should eat consist of whole foods, whether from plants or animals, and to minimize foods high in refined sugars and saturated fats.

There's also an increasing amount of evidence linking ultra-processed foods to gut diseases and changes within the microbiome. Studies, mostly done in animals, have found that artificial sweeteners, food additives, and emulsifiers can be harmful, though what's responsible for the link is still unsettled.

Holscher also recommended limiting alcohol if you're concerned about your gut microbiome, as research suggests heavy drinking can disrupt the microbiome, damage the gut lining, and contribute to other problems.

8. Lifestyle is important

Our gut microbiome is entwined with our physiology, so when we're thriving, it's likely the microbes inside of us are as well. Research has found that sleep, exercise, and psychological well-being are all lifestyle factors that can meaningfully alter your gut microbiome for better or worse.

Khoruts says that people with gut problems like bloating, cramps, and constipation can expect significant improvement from making fairly simple lifestyle changes, assuming they don't have some diagnosed condition.

"Microbiome science has not found us some magic little trick that you can take and you're going to be perfect," Shanahan said. "So there isn't any need for some health guru to come along and say, 'Oh, I've got some potion that is going to improve your microbiome.'"