Keystone species: Meet the good bacteria shaping your health

You may have heard about the good bacteria in your gut that promote health. But are you aware that there are a few keystone species doing most of the work?

In biology, a keystone species is one that plays a key role in defining an ecosystem. Their presence plays a disproportionately large role in regulating the entire system. Therefore, their loss can cause that ecosystem to change dramatically, or even collapse.

For example, a healthy ecosystem has a balance between predators, prey, and vegetation that stabilize it. Predators keep the prey in check so they don’t wipe out the vegetation. Both fertilize the soil to help the vegetation grow.

But if you remove all the predators, the prey wipe out the vegetation. This decreases the abundance of their food and can actually lead to population decline of the prey. Don’t worry, something will eventually take everyone’s place.

It’s not a terribly difficult concept to grasp. Humans are, after all, a keystone species. If we ceased to exist, the World would be a radically different place. Buildings would become overgrown and collapse, roads would crumble, and other forms of life would fill the gap.

In much the same way, your gut microbiome contains keystone species. When these good bacteria populate your gut, they make the gastrointestinal ecosystem healthier.

They tamp down inflammation, help break down our food, prevent leaky gut, crowd out the bad guys, and make metabolites that attract the good guys. These metabolites even have a direct effect on other systems, and our overall health.

Clearly, you want these keystone microbes in your gut. The best part is, you don’t need a ton of them to reap their benefits.

But what are they and what do they do? Furthermore, what are the consequences of their loss?.

How the gut and keystone species shape one another

While keystone members of our microbiome shape our gut health, the reverse is true as well. Certain environmental factors within a healthy gut draw these keystone members in.

Consequently, it’s important that these functions be intact to attract keystone species to the gut. On the other hand, when the keystone members interact with these environmental factors, this supports the entire ecosystem. Let me explain.

Historically speaking, humans have eaten a higher carbohydrate diet. We know this from the types of bacteria found in preserved dental plaque and stool samples.

Of course, it’s important to point out that we’re not talking about Corn Flakes. These carbohydrates are highly complex, many of which we cannot break down. This is known as dietary fiber.

Dietary fiber makes its way into our colon without being absorbed, where our good bacteria metabolize it. Keystone members create short chain fatty acids(SCFAs), some of which attract other bacteria via cross-feeding.

But one SCFA in particular, butyrate, it the preferred energy source for the cells in the colon. This is likely due to the long term exposure of our species to these fiber-derived metabolites and the microbes that make them.

In addition to fueling these colonocytes, butyrate lowers inflammation, alters gene expression, and seals the gut up tightly to prevent “leakage”. As you can probably guess, some of our keystone members make butyrate.

But that’s not all. Some microbes create metabolites from the amino acid tryptophan, which also strongly regulate gut health. Additionally, some microbes alter the bile acids we use to help break down fat.

Finally, some snack on the mucus layer that helps keep them away. This normally happens when fiber is not available. It’s not a bad thing. In fact, it’s probably an essential part of keeping the gut healthy.

Meet the keystone cops in your gut

We certainly aren’t aware of every keystone species living in our gut. But we’ve identified several which are essential to help create gut stability and a healthy microbiome. They include:

Faecalbacterium prausnitzii-Breaks down fiber and converts acetate in to butyrate. Inhibits inflammation, and plays a role in preventing intestinal permeability. Lack of this microbe is associated with Crohn’s disease and ulcerative colitis.

Akkermansia muciniphila-Ferments our mucus layer. You’d think this is a bad thing, but it actually helps maintain a thicker mucus layer. Low A. muciniphila is associated with obesity and metabolic disease.

Bacteroides thetaiotamicron-Resilient, and can switch from breaking down fiber to breaking down mucus depending on conditions in the gut. Works with both the above to maintain a healthy mucus layer.

Bifidobacterium longum & pseudolongum-Create a healthy intestinal environment, attract good bacteria via crossfeeding, and deconjugate bile acids. Both break down human milk oligosaccharides while P. pseudolongum also breaks down starch.

Christensenella minuta-Promotes diversity and deconjugates bile acids. High levels are protective against metabolic disease, obesity, and Crohn’s disease.

Ruminococcus bromii-Ferments resistant starch, increasing butyrate and liberating energy for other species. Forms spores making it highly resilient.

Common features of these good bacteria

It’s clear that these keystone species have a diverse range of abilities. But it’s important to point out that, in general, their commonalities are what make them keystone species that promote a healthy gut and attract good bacteria.

First and foremost, they digest things other microbes can’t. This creates metabolites that other good bacteria can now access via cross-feeding.

Second, they regulate the gut environment in a way that makes it conducive to the growth of other beneficial bacteria. For example, promoting a healthy mucus layer prevents inflammation and intestinal permeability. It also provides sustenance for microbes that consume the mucus layer.

Finally, they interact with the many cell types in our gut to help repair damaged tissue, promote immune tolerance to the good guys, turn the immune system on the bad guys, and provide enough energy so the gut can do it’s job.

But, it’s important to point out that they can only do so much. The perception most people have of gut health is that they can fix it, and many other problems, by simply taking a probiotic or prebiotic supplement.

You can absolutely do enough damage to your gut to make it inhospitable to these keystone species and other beneficial bacteria. Even if you take them in probiotic form or feed them with prebiotics.

Drinking alcohol to excess, eating too much, over-relying on processed foods, and neglecting fibrous whole foods will all prevent the establishment of a healthy gut environment. This is effectively what the modern diet is for most people.

Attracting the good bacteria to your gut

One of the benefits of identifying keystone species is that the research generally begins to focus on them. As such, there are human studies to help us determine how to attract them to our gut.

For example, we recently covered a paper that shows raisins increase the abundance F. prausnitzii in humans. You can check that out here to learn how much and for how long.

Fructoligosaccharides(FOS), FODMAPs, and the diabetes drug Metformin all increase the abundance of A. muciniphila. FOS occur naturally in foods such as onions, garlic, asparagus, and bananas.

Yeast mannan increases the abundance of B. thetaiotamicron. Interestingly, this improved skin dryness in an 8 week study of female volunteers.

In general Bifidobacteria subsist on fiber, so consuming more fiber should promote their abundance. Additionally, since they also subsist on human milk oligosaccharides, goat’s milk may attract them to the gut. Goats’ milk contains 5 OS similar to human milk OS.

Christensenella are associated with being lean, and getting there may promotes their abundance. Weight loss of 10% via a very low calorie diet was shown to increase Christensenella in obese postmenopausal women.

Finally, increasing resistant starch in the diet increases the abundance of R. bromii. In particular, resistant starch 3 found in cooked and cooled potatoes seems to be preferentially fermented by R. bromii.


Building a microbiome enriched in good bacteria helps promote healthy gut function, and protects against gastrointestinal and metabolic disease. However, it’s important to provide a tidy gut environment to attract the right microbes.

Keystone species are members of the gut microbiome that help shape the entire ecosystem. Having these residents helps establish a healthy gut, and helps break down foods that other beneficial bacteria can’t.

As a result, these keystone species release metabolites that feed other beneficial microbes. Therefore, it’s important to make sure they are prevalent and that you feed them.

To do this, focus mostly on whole, unprocessed foods as the cornerstone of your diet. And remember, maintain a healthy lifestyle and work to maintain a healthy weight. Then, focus on the individual factors mentioned in this blog to increase their abundance.

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