‘Good’ Gut Bacteria Linked to Lower Infection Risk

What constitutes a healthy gut microbiome can look different for each individual. But new research suggests that having high levels of one certain gut bacteria could keep you protected from pathogens that might otherwise cause infection.

The gut microbiome is a complex ecosystem containing trillions of bacteria, viruses, and other microbial organisms that help break down food and support healthy gut and immune function. These bacteria in the gut often have complex relationships with one another, and scientists are working to figure out how each of these species influences our health.

To that end, a new study published on Jan. 10 in Nature Microbiology found that people with high levels of the “good” bacteria Faecalibacterium in their gut also had lower levels of Enterobacteriaceae, which can lead to illness at high concentrations.

Bacteria that fall under the Enterobacteriaceae umbrella include E. coli and Klebsiella pneumoniae, which have the “potential to cause severe, life-threatening infections.”

The study’s findings indicate that the gut microbiome can be used to provide clues as to “whether a person is more or less likely to be colonized by potentially harmful bacteria,” senior study author Alexandre Almeida, PhD, a researcher at the University of Cambridge, told Health.

And because the Faecalibacteria feed on fiber—found in fruits, vegetables, and whole grains—increasing your fiber intake might be one way to protect against gut infections. However, more research needs to be done.

“Our results suggest this protective effect may be modulated by changing our gut environment through diet,” Almeida said.

For this study, Almeida and his colleagues analyzed gut microbiome data collected from stool samples belonging to over 12,200 participants across 65 other studies in 45 countries. None of the participants had active infections or had been using antibiotics when the samples were collected.

The researchers then used a computer program to determine the amount of different types of gut bacteria in the samples. They looked for any overlapping or co-occurrences of different bacteria—this allowed them to see if people with high levels of certain microbes had lower levels of others.

Across all the studies and samples, the researchers found that when higher levels of various species of Faecalibacterium were present in a person’s sample, gram-negative Enterobacteriaceae bacteria—such as E. coli, Shigella, and Klebsiella pneumoniae—were less common.

These gram-negative bacteria can cause infections in immunocompromised individuals and are linked to inflammatory bowel disease and other gastrointestinal conditions.

Though the study included samples from people around the world, Almeida noted that the majority of these samples were taken from people living in North America and Europe. More research needs to be done to determine if the same trends hold true in other diverse populations.

With the study establishing a link between higher concentrations of Faecalibacteria and lower levels of Enterobacteriaceae, the next question for researchers to tackle is whether there’s anything people can do to support the growth of this good bacteria.

The role that Faecalibacteria play in the gut microbiome offers a possible solution—these bacteria feed on dietary fiber in the colon and, in the process, produce short-chain fatty acids (SCFAs).

These SCFAs “have been shown to have various beneficial effects, such as reducing levels of inflammation and protecting the gut epithelial barrier,” said Almeida. They can also regulate the growth of E. coli and Klebsiella in the gut.

So in theory, eating more fiber could help support Faecalibacteria as they produce SCFAs, keeping these harmful gut pathogens at bay.

However, experts agreed that more research is needed before we can definitively say that fiber consumption reduces the risk of gut infections.

“This work was an observational study performed on the gut microbiome of people at one point in time, so we need to be mindful that most of our results are based on associations,” Almeida said. “Future work is needed to experimentally test whether certain things like fiber and other nutrients directly prevent the incidence of infections in a longer timespan.”

Daniel Freedberg, MD, gastroenterologist and assistant professor of medicine and epidemiology at the Columbia University Irving Medical Center, also cautioned that the study doesn’t show that eating more fiber reduces infection risk.

“People who drive red sports cars may be more likely to smoke, but driving a red sports car does not cause smoking,” he told Health. “Similarly, people who have more good bacteria may have other habits that make it less likely that they have bad bacteria.”

Fiber may not even play a significant role in the relationship between these bacteria. Another potential explanation is that healthy gut microbiomes simply maintain colonization resistance against harmful pathogens, said Tom Schmidt, PhD, professor of ecology and evolutionary biology at the University of Michigan.

That means that “all the resources are being consumed by the resident microbes in a healthy gut ecosystem, so they are not available to support invasion and growth of pathogen[s],” Schmidt told Health. “But when the ecosystem is perturbed—for instance by antibiotics, malnutrition, or a dysfunctional immune system—that disruption in the ecosystem creates opportunities for pathogenic microbes to invade and flourish.”

Your gut microbiome is powered by what you eat, but you can’t necessarily feed the “good” bacteria while depriving the rest.

“There is not a universal difference between them,” said Almeida. “Some bacteria may be good in some situations but then could be harmful in others.”

In fact, some of these “bad” bacteria—including E. coli—are present in almost every person’s gut and can be beneficial in certain contexts.

The gut microbiome is a complex ecosystem with bacteria, viruses, fungi, and other microorganisms fulfilling specific niches. Like a rainforest, tundra, or jungle, if the balance of species is disrupted, it affects the health of the ecosystem.

So, rather than trying to build your diet around promoting one specific type of bacteria, it’s best to stick with a diet high in fruits, vegetables, whole grains, poultry, and fish, which have been linked to gut microbiome diversity.

Fiber also plays a key role. Though “we currently do not know what is the ideal amount of [fiber] needed to elicit the potential benefits from our gut microbiome,” Almeida said, evidence suggests that getting enough fiber helps regulate gut health overall.

Adults should consume about 22 to 36 grams of fiber per day, depending on age, sex, and pregnancy status. To do that, Freedberg recommended choosing fruits and vegetables over simple carbohydrates, which are often found in less-nutritious foods.

These dietary swaps are likely a better way to improve your gut microbiome, rather than relying on probiotics or other trendy gut health products. There’s “no strong evidence suggesting that they are really helpful,” said Almeida. “In fact, studies have shown that probiotics do not usually colonize the intestinal tract of people who take them, so it raises some questions on what are they actually doing.”