Richard Peet, J.D., Ph.D.

DOES A DIVERSE ARRAY OF BACTERIA IN THE GUT MICROBIOTA CONTRIBUTE TO PROTECTION AGAINST PATHOGEN INFECTION?

If so, how do we nourish and maintain a diverse group of bacteria in the gut microbiota?

The presence of a diverse array of bacteria in the gut microbiome contributes to protection against pathogen infection.  Among the mechanisms of protection, the presence of gut bacteria with diverse metabolic requirements makes it difficult for pathogens to find sufficient food thereby reducing the incidence of disease.  Protection from infection is a team sport.  

What more do we know about pathogen protection by diverse gut bacteria?  Many scientific studies have revealed a correlation between diversity in the gut microbiota and good health outcomes. More and more scientific studies are investigating the biological mechanisms that are at play. In a recent scientific publication, researchers at University of Oxford and University of Strasbourg explored the mechanisms underlying why a diverse array of bacteria in the gut microbiome protect against infection by Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium. Each of K. pneumoniae and S. enterica serovar Typhimurium infect humans but do so in very different ways.  The researchers investigated which non-pathogenic bacteria in the human gut microbiota are best able to protect against infection by K. pneumoniae and S. enterica serovar Typhimurium and whether the non-pathogenic bacteria are more effective in protecting against infection alone or in groups. In short, the researchers found the non-pathogenic bacteria were most effective in protecting against infection when in groups. The researchers determined one mechanism of protection involved the non-pathogenic bacteria outcompeting pathogens for the same food sources in the gut.

Let’s dig a little deeper into what the research scientists found, and how they found it. The gut microbiota is comprised of bacteria, fungi, viruses, archaea, and protists.  The collective DNA sequences of these microorganisms is referred to as the microbiome. A lot of the current scientific studies on the gut microbiota are focused on the bacteria living there.  DNA sequencing is relatively cheap, rapid, and reliable, and can be used to identify the bacteria in the gut microbiota. This is done by isolating DNA from feces, sequencing the DNA present in stool samples, and constructing the DNA sequence of each species of bacteria found in the samples using sophisticated computer software. Each DNA sequence is compared to the DNA sequence of known bacteria.

Typically, there are between 500 and 1,000  different bacterial species in the gut microbiota. We can think of different species of bacteria as different models of cars. Each species of bacteria has unique characteristics that are determined by its DNA sequence. Each DNA sequence, sometimes called a genome, is similar to a cookbook. This cookbook contains recipes, which are instructions for everything the bacterium can do. Just like a recipe can tell you if a dish is sweet or spicy, the DNA sequence can tell us what kind of chemicals the bacterium can make, what kinds of chemicals the bacterium can use as food, or how the bacterium reacts to different environments. The non-pathogenic bacteria most effective in protecting against infection by K. pneumoniae and S. enterica serovar Typhimurium used the same chemicals as food as the pathogens and therefore inhibited, or outcompeted, the growth of the pathogens.

How do we nourish and maintain a diverse gut microbiota?  Dr Megan Rossi, a Research Fellow at King’s College in London, is a leading advocate for the importance of dietary diversity, particularly in the consumption of diverse fruits, vegetables, whole grains, legumes, nuts, seeds, and fermented foods, all of which contribute to a diverse and health-promoting diet.  Dr. Rossi’s research has shown that each type of plant food contains different types of prebiotics, fibers, vitamins, minerals, and other bioactive compounds, which various microbes in our gut can utilize.  By eating a wide range of these foods, we provide a feast for a diverse array of gut bacteria, promoting a more balanced and resilient gut microbiota. In her book entitled How to Eat More Plants, Dr. Rossi recommends eating 30 different plant-based foods per week to nourish and sustain the diverse gut microbiota needed for health and wellness.  Unfortunately, in the U.S. and other countries, it is hard for many people to achieve this goal because they lack access to fresh fruits and vegetables and/or cannot afford them. We will explore this important issue in future blog posts. 

1. Spragge et al., Microbiome diversity protects against pathogens by nutrient blocking, Science 382 (2023)
2. So et al., Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. The American Journal of Clinical Nutrition, 107(6), 965-983 (2018) and Barranco et al., Dietary fibre in gastrointestinal health and disease. Nature Reviews Gastroenterology & Hepatology, 18, 101-116 (2020).
3. Rossi, Megan, How to Eat More Plants, The Experiment LLC (2022) ISBN-10 1615198784