The hidden guardians in your gut: How beneficial bacteria shield your health

Could eating more fiber be the answer to fighting infection?

CAMBRIDGE, England — Inside your intestines lives a bustling community of trillions of microorganisms that play a vital role in your health. While most of these tiny tenants are beneficial, some have the potential to cause serious infections if they grow out of control. A new large-scale study has revealed fascinating insights into how “good” gut bacteria help keep potentially harmful ones in check.

The research focused on a family of bacteria called Enterobacteriaceae that includes well-known troublemakers like E. coli and Klebsiella pneumoniae, the bacteria behind pneumonia.

Researchers from the University of Cambridge analyzed gut bacteria data from over 12,000 people across 45 countries to better understand what prevents these opportunistic pathogens from multiplying to dangerous levels. Published in Nature Microbiology, this global investigation identified specific bacterial species that appear to naturally suppress Enterobacteriaceae growth, as well as others that tend to coincide with their presence.

When Enterobacteriaceae overgrow in the gut, they can cause severe infections and have been linked to inflammatory conditions like Crohn’s disease. What’s especially concerning is that many are becoming resistant to multiple antibiotics. In fact, some particularly problematic strains have been classified as “priority 1 pathogens” by the World Health Organization due to their growing resistance to treatment.

“With higher rates of antibiotic resistance, there are fewer treatment options available to us. The best approach now is to prevent infections occurring in the first place, and we can do this by reducing the opportunities for these disease-causing bacteria to thrive in our gut,” says Dr. Alexandre Almeida from the University of Cambridge’s Department of Veterinary Medicine, in a statement.

The research team discovered that about 66% of people naturally harbor some level of Enterobacteriaceae in their gut microbiome. While this may sound alarming, these bacteria typically don’t cause problems when kept in balance by other microbes, much like how a garden stays healthy when no single plant species overgrows. The study identified 172 “co-colonizer” bacterial species that frequently appear alongside Enterobacteriaceae, as well as 135 “co-excluder” species that seem to naturally suppress them.

Among the most effective co-excluders were bacteria from the Faecalibacterium genus. These beneficial microbes produce compounds called short-chain fatty acids which are essentially bacterial byproducts that help maintain gut health. These acids create an inhospitable environment for Enterobacteriaceae growth.

“Our results suggest that what we eat is potentially very important in controlling the likelihood of infection with a range of bacteria, including E.coli and Klebsiella pneumoniae, because this changes our gut environment to make it more hostile to invaders,” says Dr. Almeida.

Of particular concern is Klebsiella pneumoniae, which can cause pneumonia, meningitis, and other severe infections. The global rise in antibiotic resistance to this pathogen has pushed scientists to search for alternative control methods, making the study’s findings especially timely.

The bacteria that commonly coexist with Enterobacteriaceae showed greater diversity in how they process nutrients and energy, or what scientists call metabolic capabilities. Imagine different businesses in a shopping center — while some compete directly, others might complement each other by offering different services. These co-colonizing relationships varied by geographic region, possibly reflecting differences in diet, lifestyle, and healthcare practices.

Rather than engaging in all-out warfare, the bacterial communities organize themselves more like neighborhoods where similar residents tend to cluster together. This is a phenomenon scientists call habitat filtering. Just as you might find artists congregating in certain city districts, bacteria with similar resource needs and processing capabilities tend to group together naturally.

These findings challenge some previous assumptions about gut bacteria interactions. While earlier research using mouse models suggested that competition for resources would prevent harmful bacteria from establishing themselves, this study revealed that many species can actually coexist with Enterobacteriaceae despite needing similar nutrients. This has important implications for treatment approaches: taking probiotics that merely compete for nutrients with harmful bacteria may be less effective than changing the gut environment through diet.

“By eating fiber in foods like vegetables, beans, and whole grains, we can provide the raw material for our gut bacteria to produce short-chain fatty acids — compounds that can protect us from these pathogenic bugs,” explains Dr. Almeida. The research suggests that dietary interventions targeting the gut environment may prove more effective than traditional probiotics in preventing Enterobacteriaceae infections.