The human gut is home to a complex community of bacteria that play a vital role in maintaining health.
Among these bacteria are members of the Enterobacteriaceae family, including Klebsiella pneumoniae, Shigella, and E. coli. At low levels, they coexist peacefully as part of a balanced gut microbiome.
However, when their numbers increase—due to inflammation, illness, or contaminated food—they can cause serious diseases, and in extreme cases, life-threatening conditions.
A recent study, published in Nature Microbiology and led by researchers at the University of Cambridge, reveals how diet, particularly fiber intake, can influence the balance of gut bacteria and reduce the risk of infections caused by harmful Enterobacteriaceae.
Using artificial intelligence and computational tools, the research team analyzed the gut microbiomes of over 12,000 individuals from 45 countries, using stool samples to study bacterial populations.
They found that the composition of a person’s gut microbiome could predict whether Enterobacteriaceae would thrive in their gut.
The researchers identified 135 bacterial species commonly found in healthy guts that seem to protect against harmful Enterobacteriaceae. Among the most notable are bacteria from the Faecalibacterium group, which produce beneficial short-chain fatty acids (SCFAs).
These compounds are created when Faecalibacterium break down dietary fiber and help create an environment in the gut that is hostile to harmful bacteria.
The findings suggest that increasing dietary fiber by eating vegetables, beans, whole grains, and other fiber-rich foods can support the growth of protective bacteria like Faecalibacterium. This, in turn, helps crowd out harmful bacteria and reduces the risk of infections caused by pathogens such as Klebsiella pneumoniae.
In contrast, the study found that taking probiotics, which do not significantly alter the gut environment, is less likely to prevent infections from Enterobacteriaceae.
The implications are especially significant as antibiotic resistance continues to rise globally. Bacteria like Klebsiella pneumoniae, which can cause pneumonia, meningitis, and other infections, are becoming increasingly resistant to antibiotics.
As Dr. Alexandre Almeida, senior author of the study, explained, “With fewer treatment options due to rising antibiotic resistance, the best strategy now is to prevent infections by reducing the conditions that allow harmful bacteria to thrive in the gut.”
Interestingly, the study also challenged some earlier beliefs about gut bacteria interactions. Previous research, often conducted on mice, suggested that bacteria competing for the same nutrients would prevent harmful species from establishing themselves in the gut.
However, this study identified 172 gut microbe species that can coexist with Enterobacteriaceae. Many of these species share similar nutrient needs with the harmful bacteria, but their presence does not necessarily prevent infections.
This finding suggests that changing the overall environment of the gut—rather than simply introducing competing bacteria through probiotics—is a more effective way to control harmful bacterial growth.
Dr. Qi Yin, the study’s lead author, emphasized the importance of studying pathogens within the context of the entire gut microbiome. Understanding how harmful and beneficial bacteria interact can guide better strategies for preventing and treating infections.
This research offers new insights into the role of diet in shaping the gut microbiome and preventing infections. By focusing on creating a healthy gut environment through fiber-rich diets, individuals can support beneficial bacteria that protect against harmful pathogens.
These findings highlight the potential of dietary changes as a simple and effective tool for improving gut health and reducing the risk of diseases caused by antibiotic-resistant bacteria.
If you care about gut health, please read studies about how junk food harms your gut health, and how probiotics can protect gut health.
For more information about health, please see recent studies about how fiber affects weight loss and your overall health, and results showing why a glass of red wine is good for your gut.
The research findings can be found in Nature Microbiology.
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