by Wei Li
figures by MacKenzie Mauger

Microbial communities, known as microbiomes, are everywhere—on our bodies, in our food, and in the environment—and they are as important as they are prevalent. The gut microbiome interacts with our body and influences our health, the bacteria composition in cheese and other fermented products shapes their taste, and the bacteria in the soil helps plants grow faster. 

These microbial communities are often diverse, with a multitude of bacteria interacting and communicating with one another. This diversity can determine the impact of the bacteria on their habitat. For example, taking antibiotics or changing diets can eliminate or perturb our gut microbiome, potentially causing unexpected side effects. Moreover, there has been increased interest in recent decades in the various therapeutic strategies that target our gut microbiome to improve our health, such as probiotics or fecal transplants. Therefore, studying the complexities of these bacterial communities can help us better understand their impact on the environment they are in, as well as teach us how to develop and maintain a beneficial microbiome for therapeutic purposes. 

Given the large diversity within most microbial communities, you might think that the relative abundances of bacterial species within a microbiome would go through a slew of changes over time. However, these microbial communities can be very stable and resilient, often returning to their original composition after a minor perturbation. In other words, despite having potentially thousands of species coexisting with one another, some bacterial populations rarely change unless seriously perturbed by an outside force. So, how do bacterial communities regulate their populations and maintain this high level of diversity? Why do they even exist in a community, instead of having one species take over and dominate? 

In order to answer these questions, we must first take a look at what allows a community to thrive while having a stable, diverse population.

Stable diversity: a trade-off between competition and cooperation

When a group of bacteria co-exists, there are two driving forces that keep the community in balance: (1) resource competition and (2) microbial cooperation. On one hand, resources can be scarce, and thus bacteria have to fight and compete for the resources around them. On the other hand, bacteria are microorganisms that may not have all the functions they need to survive on their own. Therefore, they rely on other bacterial species for their genes and metabolites that are necessary for their growth but that they do not have or cannot make themselves. This push and pull of competition and cooperation are important during the development of a stable microbiome.

A recent study shows that different microbial communities strike different balances between competition and cooperation. A microbiome with bacteria that have smaller genomes, containing fewer genes and proteins inside their cells than other bacteria, requires a lot more intraspecies cooperation to thrive. Each bacterial species in a community is responsible for having at least one set of genes that makes metabolites crucial for the entire community. On the other hand, bacteria with larger genomes are more likely to be self-sufficient and have overlapping genes with other bacteria in the community. Therefore, they tend to be in more competitive microbial communities, as they do not need to rely on one another. 

Kefir: an example of a cooperative microbial community

Kefir is a fermented milk drink that has a thick, yogurt-like consistency. It is made by fermenting kefir grains in milk overnight. Kefir grains are small clusters of bacteria and yeast that contain a microbial community of about 30 to 50 species that are very easy to cultivate and maintain. The community is also very resilient, able to be preserved for years and to survive under a lot of environmental changes—this is why kefir milk can be easily made at home!

Within the microbial community of the kefir grain, Lactobacillus kefiranofaciens is a dominant bacteria. It is also a bacteria that has no other known habitat beyond the kefir grain and kefir milk. However, L. kefiranofaciens is unable to survive on its own in milk, suggesting that its ability to thrive in kefir milk is endowed by the rest of the microbial community.

In a recent study analyzing the metabolites produced in kefir milk, scientists uncovered how each species in the kefir grain contributes to milk fermentation. L. kefiranofaciens makes the “shell” of the kefir grain—a matrix of polysaccharides and proteins—giving the rest of the microbial community a “house” to live in. Although the grain is cultured in milk, L. kefiranofaciens is unable to digest the nutrients within milk and thus is unable to grow. However, other bacteria like Lactobacillus mesenteroides (a bacteria in the same family as L. kefiranofaciens) can break down the lactose in milk into lactate, a nutrient that L. kefiranofaciens can use and proliferate with. 

The kefir microbial community is thus shaped by this unique cooperation: one group of bacteria builds the grain that houses and preserves the community for a long time, while the other breaks down the nutrients in milk to help everyone thrive and grow.

Soil: an example of a competitive microbial community

On the opposite end of the spectrum from kefir, the microbial community in soil is highly competitive. The nutrients in soil are limited, and foreign microbes or organisms can invade the habitat at any time. Therefore, the bacteria in soil have evolved to focus on traits that enable them to outcompete their neighbors—in other words, “take down” their rivals in the community. For example, bacteria in soil can develop the ability to secrete enzymes that help harvest nutrients that they need, to stab neighboring bacteria, or, most notably, to make antibiotics that kill other bacterial species.

One such soil bacteria is called Streptomyces. These bacteria produce antibiotics to ward off competitors, as well as to protect the plants they live near against pathogens. In turn, the plants provide a nutritious environment for the bacteria to grow in. In fact, most of the antibiotics that we use today, such as streptomycin, tetracycline, vancomycin, and erythromycin, are isolated from Streptomyces. These antibiotics are the bacteria’s arsenal against their neighbors in a competitive microbial community, and we have adapted these into our arsenal against deadly infections. Our ability to treat infectious diseases has greatly improved since the discoveries of these antibiotics.

Every microbial community is different

There are pros and cons for both ends of the cooperation versus competition spectrum. Competitive communities can better resist the invasion of foreign species than cooperative communities, but they’re not as good at adapting to nutrient changes in the environment, and vice versa. Generally, microbial communities lie in between these two extremes, and the degree of cooperation and competition will depend on the size of the community. A small, niche community like the kefir grain will be more cooperative, while a large, free-for-all community like that found in soil will be more competitive.

But why is it necessary to understand the diversity and interactions in a microbial community? If we want to be able to perturb any microbiome in a beneficial manner, it is essential to understand how cooperative or competitive the community is. For example, probiotics are live microorganisms that are consumed with the intent to regulate the microbiome in the gut. They are a rising trend among people with gastrointestinal issues potentially caused by the gut bacteria community. However, if we want a probiotic species to be accepted into a community, we need to first ensure that it is a species that is cooperative towards the community. Therefore, learning how they would interact in a microbiome is key.

Microbial communities are all around us and impact us in various ways. As we continue to study the bacteria in our bodies, environment, and food, it is imperative to understand these communities and what makes them work. 

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Wei Li is a fifth-year Ph.D. student in the Chemistry and Chemical Biology program at Harvard University, where she is studying the gut microbiome and their chemical transformations. You can find her on Twitter as @miniboe.

MacKenzie Mauger is a fourth-year Ph.D. student in the Biological and Biomedical Sciences program at Harvard Medical School, where she is studying cell type-specific gene repression. You can find her on Twitter as @MacKenzieMauger

Cover image by allyartist on pixabay

For More Information: 

• Read more about the cooperation in the kefir microbial community here.
• For more information about microbes making antibiotics, read here.
• Read more about the stability of microbial communities here, here, and here.
• Find out about the stability of the human gut microbiome here.

This article is part of our special edition on diversity. To read more, check out our special edition homepage!