Fiber-rich foods boost good bacteria and reduce infection risks, study shows

Eating a high-fiber diet can help protect against infections as it encourages the growth of beneficial gut bacteria to outnumber harmful pathogens like E. coli and Klebsiella, recent research suggests.

The University of Cambridge, UK, study in the journal Nature Microbiology has also found that knowing a person’s microbiome “signature” can allow scientists to predict whether someone’s gut is at risk of Enterobacteriaceae colonization. This group of bacteria can cause illness and disease, explain the researchers.

 The scientists identified 135 gut microbe species that are likely to protect against infection and are more commonly found without Enterobacteriaceae.

Using stool samples, they analyzed the gut microbiome composition of 12,238 people across 45 countries. They employed computational approaches, including AI for analysis.

The researchers suggest that eating more fiber will support the growth of good bacteria and crowd out the bad ones, eventually significantly reducing the risk of illness.

Pathogenic imbalance 

The scientists explain that Enterobacteriaceae species are naturally present in the gut but at low levels in healthy microbiomes. 

Dr. Almeida sees huge potential for using the gut microbiome to improve medical diagnostics and treatment (Image credit: University of Cambridge).However, the number of bacteria in this species can rise due to inflammation in the body and eating contaminated food, which can cause illness and disease. The paper warns that in extreme cases, too many Enterobacteriaceae can be life-threatening.

An example is Klebsiella pneumonia, which can cause pneumonia, meningitis and other infections.

“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 lead author Dr. Alexandre Almeida, a researcher at the University of Cambridge’s Department of Veterinary Medicine.

“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 protect us from these pathogenic bugs.”

Supporting protective bacteria 

Among the protective bacteria in the gut, researchers spotlight Faecalibacterium due to its ability to produce beneficial compounds called short-chain fatty acids. The bacteria do this by breaking down the fiber in foods, which scientists believe helps protect against infection and disease-causing Enterobacteriaceae.

The breakdown of food is why scientists suggest eating more fiber, which may reduce the risk of illness as it would support the growth of good bacteria.

However, they believe consuming probiotics does not directly change the gut environment, making them less likely to help against Enterobacteriaceae infection.

Probiotics does not directly change the gut environment, making them less likely to help against Enterobacteriaceae infection.Altering gut environment 

The new study suggests that changing the gut environment — through diet changes, for instance — would be more effective in reducing the risk of Enterobacteriaceae infection compared to consuming probiotics.

Explaining the significance of their study, the authors highlight previous research that concluded taking probiotics competing for the same nutrients as bad bacteria would starve them out. However, based on the new findings, this will not work.

“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,” adds Almeida.

The authors add that earlier understandings of bacteria in the gut were based on mouse models, however, the findings differ from those of the new study. It reveals that 172 species of gut microbes can coexist with the disease-causing Enterobacteriaceae.

“This study highlights the importance of studying pathogens not as isolated entities but in the context of their surrounding gut microbiome,” adds first author Dr. Qi Yin, a visiting researcher at the University of Cambridge’s Department of Veterinary Medicine.

Nutrition Insight recently spoke to researchers in the US using supercomputers to map the unique microorganisms in each person’s digestive system. The team says they can create personalized diets to improve and optimize overall health, underlining that almost 90% of all diseases are rooted in the gut health of the microbiome.

In other research, chicory root fiber intake was found to promote a “significant reduction” in body weight, body mass index, fat mass, waist circumference and, to a certain extent, body fat percentage.

Innova Market Insights data indicates an 18% year-over-year growth in sports nutrition launches with fiber claims between September 2022 and October 2024. Europe was on the frontlines of these launches. Nearly two-thirds of launches were sports bars, and key fibers used were oligofructose, inulin and chicory root fiber.