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New research has revealed that consuming fiber-rich foods could play a significant role in preventing the growth of harmful gut bacteria, particularly a group known as Enterobacteriaceae. This group includes bacteria such as Klebsiella pneumoniae, Shigella, and E. coli—pathogens that can cause severe illnesses ranging from pneumonia and meningitis to gastrointestinal infections. While these bacteria are typically present in small, manageable amounts as part of a healthy gut microbiome, their overgrowth, often triggered by factors like inflammation or contaminated food, can lead to serious health complications.
The study, published in Nature Microbiology, is the result of a comprehensive analysis of over 12,000 stool samples from individuals across 45 countries. Using advanced computational methods, including artificial intelligence, the researchers were able to identify patterns in the gut microbiomes of participants. Their findings suggest that the composition of a person’s microbiome—its “signature”—can predict whether or not the gut is likely to become colonized by Enterobacteriaceae.
The researchers also identified 135 species of gut microbes that tend to be present in the absence of harmful Enterobacteriaceae. These microbes may act as a defense mechanism, protecting the gut from infection. Among the most notable protective species is a group of bacteria called Faecalibacterium, which break down fiber from food to produce short-chain fatty acids (SCFAs). These compounds are believed to help safeguard against the overgrowth of disease-causing bacteria.
Dr. Alexandre Almeida, a researcher at the University of Cambridge and senior author of the study, emphasized the importance of diet in modulating the gut microbiome. “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,” Almeida said. He advocates for fiber-rich foods like vegetables, beans, and whole grains to help nurture beneficial gut bacteria and promote the production of SCFAs.
The research also suggests that probiotics, which have become popular as a means of boosting gut health, are less effective in preventing Enterobacteriaceae infections. Unlike fiber, which can alter the gut’s environment and provide the raw materials for beneficial bacterial growth, probiotics do not significantly change the gut’s overall ecosystem.
The study is particularly timely given the rising global concerns over antibiotic resistance. Klebsiella pneumoniae and other pathogens in the Enterobacteriaceae family have become increasingly resistant to antibiotics, leading scientists to explore alternative prevention methods. Dr. Almeida stresses that reducing the growth of these bacteria in the gut, rather than relying solely on antibiotics, is crucial in controlling infections. “With higher rates of antibiotic resistance, there are fewer treatment options available to us. The best approach now is to prevent infections from occurring in the first place,” he noted.
The study also challenges previous research on gut bacteria interactions. Earlier studies suggested that competition for nutrients between good and bad bacteria would prevent harmful bacteria from thriving. However, this new research shows that 172 species of gut microbes can coexist with disease-causing Enterobacteriaceae, many of which require similar nutrients. This insight has significant implications for treatment strategies, suggesting that simply competing for resources through probiotics may not be effective. Instead, the focus should be on altering the gut environment, primarily through dietary changes, to make it less conducive to pathogenic growth.
Dr. Qi Yin, a visiting researcher at the University of Cambridge and first author of the paper, highlighted the importance of understanding pathogens within the broader context of the gut microbiome. “This study highlights the importance of studying pathogens not as isolated entities, but in the context of their surrounding gut microbiome,” Yin said.
The findings of this groundbreaking research offer new insights into the complex interactions between diet, gut microbiomes, and disease prevention. By promoting the growth of beneficial bacteria through fiber consumption, individuals may be able to reduce the risk of infections caused by harmful gut bacteria, including those with antibiotic resistance.
For more details, the study is available in Nature Microbiology, with the full citation: Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations, DOI: 10.1038/s41564-024-01912-6.
