A groundbreaking study has revealed that the composition of your gut microbiome plays a significant role in predicting the likelihood of succumbing to potentially life-threatening infections caused by bacteria such as Klebsiella pneumoniae and E. coli. The findings suggest that altering your diet could change the microbiome environment, potentially reducing the risk of infection.
The gut microbiome includes bacteria like Enterobacteriaceae, which consists of species such as Klebsiella pneumoniae, Shigella, and E. coli. While these bacteria are present at low levels in a healthy gut, an overgrowth of these microbes is often triggered by inflammation or contaminated food. In extreme cases, it can lead to illness or be life-threatening.
Researchers at the University of Cambridge and international collaborators studied over 12,000 people from 45 countries, using AI-driven computational approaches to analyze the gut microbiome composition in stool samples. Their analysis revealed that a person’s unique microbiome ‘signature’ could predict whether their gut was more likely to be colonized by harmful Enterobacteriaceae bacteria. These patterns were surprisingly consistent across different health statuses and geographies.
Another surprise was the 135 gut microbes commonly associated with the Enterobacteriaceae absence, possibly conferring a protective effect against infection. A particularly notable group of protective bacteria is Faecalibacterium, which produces short-chain fatty acids by breaking down fiber in food. These fatty acids have a vital function in protecting against disease-causing Enterobacteriaceae.
The researchers suggest that increasing fiber intake—through vegetables, beans, and whole grains—can promote the growth of beneficial bacteria like Faecalibacterium. This helps crowd out harmful microbes and creates a gut environment less hospitable to pathogens. This diet change may significantly limit the risk of infections from dangerous bacteria like Klebsiella pneumoniae and E. coli.
The study found that the probiotics, which do not alter the gut environment directly, are unlikely to influence the susceptibility to Enterobacteriaceae infection.
“Our results suggest that what we eat is crucial in controlling the likelihood of infection with bacteria such as E. coli and Klebsiella pneumonia,” said Dr. Alexandre Almeida, senior author of the study and researcher at the University of Cambridge’s Department of Veterinary Medicine. “By eating fiber-rich foods, we provide the raw material for our gut bacteria to produce protective short-chain fatty acids, helping defend against harmful bugs.”
Klebsiella pneumoniae is a dangerous pathogen responsible for conditions such as pneumonia, meningitis, and bloodstream infections. The rise in antibiotic resistance for this and many other bacteria means that infections can no longer be treated as before, and global health is experiencing a growing health crisis. With this in mind, scientists have focused on preventing the multiplication of these detrimental bacteria in the gut.
“With the increasing rates of antibiotic resistance, fewer treatment options are available,” said Almeida. “The best approach now is prevention—reducing the chances for these disease-causing bacteria to thrive in the first place.”
The study also shows how different gut microbes interact with harmful Enterobacteriaceae species. Previous studies explain how competition between good and bad bacteria for nutrients would not allow disease-causing bacteria to thrive in the gut. However, the new research suggests that 172 gut microbes can coexist with Enterobacteriaceae based on their similar nutritional needs. This finding challenges earlier assumptions and has important implications for treatment strategies.
Rather than focusing on probiotics that compete for the same nutrients, the researchers emphasize that changing the gut’s environment—primarily through diet—could be a more effective way to prevent infection by harmful bacteria.
“This study highlights the importance of studying pathogens in the context of their surrounding gut microbiome, rather than in isolation,” said Dr. Qi Yin, first author of the study and visiting researcher at the University of Cambridge.
The study offers insights into the role of the gut microbiome in bacterial infections. It highlights the power of dietary interventions to shape the gut environment and reduce the risk of disease.
Journal Reference:
- Yin, Q. et al: ‘Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.’ Jan 2025, Nature Microbiology. DOI: 10.1038/s41564-024-01912-6
