Eating more fiber-rich foods can strengthen beneficial gut bacteria that protect against harmful Enterobacteriaceae, reducing infection risk more effectively than probiotics.
The Enterobacteriaceae family of bacteria—which includes Klebsiella pneumoniae, Shigella, Escherichia coli (E. coli), and others—naturally exists in small amounts within a healthy human gut microbiome. However, when these bacteria grow excessively, often due to factors like increased inflammation or consumption of contaminated food, they can lead to illness and disease. In severe cases, an overgrowth of Enterobacteriaceae in the gut can become life-threatening.
To better understand this risk, researchers analyzed the gut microbiome composition of over 12,000 individuals from 45 countries using computational methods, including artificial intelligence (AI), based on stool samples. Their findings revealed that a person’s unique microbiome profile can predict the likelihood of Enterobacteriaceae colonization. This pattern was consistent across various health conditions and geographic regions.
Protective Gut Bacteria and the Role of Fiber
The researchers identified 135 gut microbe species that are commonly found in the absence of Enterobacteriaceae, likely protecting against infection.
Notable among the protective gut species is a group of bacteria called Faecalibacterium, which produces beneficial compounds called short-chain fatty acids by breaking down fiber in the foods we eat. This seems to protect against infection by a range of disease-causing Enterobacteriaceae bugs.
The researchers suggest that eating more fiber in our diet will support the growth of good bacteria and crowd out the bad ones to significantly reduce the risk of illness.
Probiotics Offer Limited Protection
In contrast, taking probiotics, which don’t directly change the environment in the gut, is less likely to affect the likelihood of Enterobacteriaceae infection.
The results are published in the journal Nature Microbiology.
“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,” said Dr. Alexandre Almeida, a researcher at the University of Cambridge’s Department of Veterinary Medicine and senior author of the paper.
He added: “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.”
Klebsiella pneumonia can cause pneumonia, meningitis, and other infections. The alarming global rise in antibiotic resistance to this bacterial pathogen has led scientists to look for new ways of keeping it, and other similar infectious bacteria, under control.
“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,” said Almeida.
A new understanding of gut microbe interactions
Earlier research to understand interactions between the different bacteria in our gut has used mouse models. But some of these new results are at odds with previous findings.
The new study revealed that 172 species of gut microbe can coexist with disease-causing Enterobacteriaceae bugs. Many of these species are functionally similar to the bugs: they need the same nutrients to survive. Previously it was thought that competition for resources would stop the disease-causing bacteria from getting established in the gut.
This has important implications for treatment: taking probiotics that compete for the same nutrients with the bad bacteria to try and starve them out isn’t going to work. The researchers say that it will be more beneficial to change the environment in the gut, for instance through diet, to reduce the risk of infection with Enterobacteriaceae.
“This study highlights the importance of studying pathogens not as isolated entities, but in the context of their surrounding gut microbiome,” said Dr. Qi Yin, a visiting researcher at the University of Cambridge’s Department of Veterinary Medicine and first author of the report.
Reference: “Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations” by Qi Yin, Ana C. da Silva, Francisco Zorrilla, Ana S. Almeida, Kiran R. Patil and Alexandre Almeida, 10 January 2025, Nature Microbiology.
DOI: 10.1038/s41564-024-01912-6
The study was funded by the Medical Research Council.
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2 Comments
It barely mentioned what we should eat: beans, grains and something else.
Bottom Line – Eat a plant based diet that provides the fiber we humans need in our gut. Beans, grains, nuts, seeds, fruits and vegetables. That doe not mean that you cannot eat a little meat and eggs. If you can afford eggs.