Microbiome Diversity May Be the Key to Preventing Illness


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It is well known that a diverse microbiome is a healthy microbiome. Increased microbial diversity in the gut is associated with benefits such as optimal immune function and the improved breakdown of nondigestible food components. A diverse microbial ecosystem can actually protect the host against disease-causing pathogens.

“…a diverse microbiome can out compete and inhibit the growth of foreign pathogens.”

A 2023 study by researchers at the University of Oxford and published in the journal Science found that a diverse microbiome can outcompete and inhibit the growth of foreign pathogens. One of the mechanisms through which this occurs is nutrient blocking, a process in which the gut microbial ecosystem restricts access to vital nutrients that pathogens require for their survival and proliferation.

In the study, researchers tested 100 gut bacteria strains either on their own or combined with other strains on their ability to inhibit two harmful bacterial pathogens: Klebsiella pneumoniae and Salmonella enterica. Testing was done both in vitro (e.g. in test tubes) and in vivo in mice.

Additionally, researchers found that single species of microbes did not show the same benefits, suggesting that community diversity greatly impacts the “colonization resistance.” Interestingly, however, some species that were not effective on their own were in fact essential for the success of the microbial community in protecting against pathogens.

“…specific strains may contribute more than others to protecting the host, rather than diversity alone…”

This suggests that specific strains may contribute more than others to protecting the host, rather than diversity alone, which is likely due to the similarities in nutrient requirements between the microbial community and pathogen. When specifically chosen communities were tested against an E.coli pathogen, those with the greatest nutrient requirement similarities were able to inhibit pathogen growth best.

These findings highlight the importance of building and maintaining a rich and diverse gut microbial ecosystem. One of the most helpful ways to increase microbial diversity is to consume a wide variety of plant based foods. Diet diversity is associated with microbial diversity as it allows for a plethora of different microbes to be fed and proliferate.

“…disruptions to the diversity and composition of the microbiome can weaken this protection.”

However, disruptions to the diversity and composition of the microbiome can weaken this protection. Antibiotic use, dietary changes (including but not limited to low percentage and variety of different fruits and vegetables), stress, and other factors can alter the health of the microbiome, reducing its richness (how many microbes are there) diversity (how many different microbes are there) and paving the way for opportunistic pathogens to thrive.

The findings from this study may shed light on possible methods of prevention and even treatment of diseases caused by pathogens. Perhaps future studies might investigate which specific microbial communities are optimal for pathogen-resistance. Until we have the results of such studies, the immediate consequence from the current results (together with overwhelming evidence from other studies emphasizing the importance of a varied largely plant based diet) consuming a Mediterranean-type diet is the simplest and most effective way of preventing pathogens from setting foot in our gut.

Fiona Riddle is a Certified Health Coach with a degree in Psychology from UCLA. She is passionate about a holistic approach to health when working with her private coaching clients. She is an avid cook, constantly creating and sharing new recipes on her Instagram (@feelgoodwithfi) to showcase simple clean home cooking.

This article was reviewed and approved by Emeran Mayer, MD