Spooky by name, friendly by nature: microbes that keep us healthy

The invisible world within us

Microbes often have a bad reputation. When you hear the words bacteria, virus, or fungus, your first thought might be “infection” or “disease.” After all, in popular culture, microbes have long been cast as invisible agents that make us sick. But today’s science tells a different story.

Our gut is home to a complex community of bacteria, fungi, viruses, and archaea collectively known as the gut microbiota. Far from being a threat, these microorganisms living in the gut are our allies, as many carry out functions that play a crucial role in the body¹. They help us digest fiber, produce essential nutrients (e.g., short-chain fatty acids, vitamin K, as well as most B vitamins), train our immune system, and protect us from harmful pathogens. Scientists are now uncovering that what matters most is not whether a microbe sounds “good” or “bad,” but whether it’s in the right place and at the right balance. Indeed, an unbalanced microbial community can allow certain members to become harmful. However, when present in a healthy and well-balanced gut microbiota, its members provide protective or health-promoting effectsWith that in mind, this Halloween we’re shining a light on some gut residents whose names might sound spooky — but whose functions are anything but frightening.

Meet some of these not-so-scary microbes

Akkermansia muciniphila

Discovered relatively recently in 2004, Akkermansia muciniphila has quickly become one of the most studied members of the gut microbiota. This bacterium is far from threatening. It lives close to the intestinal lining, where it feeds on the mucus layer, not to harm it, but to keep it healthy, stimulating the renewal of the gut wall and strengthening the intestinal barrier.

What makes Akkermansia truly fascinating is its potential as a “next-generation probiotic.”². This type of new probiotics is under research and development with a more precise focus on addressing specific diseases, compared to traditional probiotics such as Lactobacillus and Bifidobacterium that focus mainly on gut health. Scientists are now exploring its ability to influence both gut and metabolic health — helping regulate glucose levels, body weight, and immune responses.

Research has linked higher levels of Akkermansia with a lower risk of obesity and type 2 diabetes, positioning it as a promising candidate to reshape the future of probiotic therapies, aimed at improving mucosal health and overall metabolic balance. In the context of inflammatory bowel diseases or a disrupted gut microbiota after antibiotic treatment, some evidence in mice caution against the use of A. muciniphila as a potential probiotic.

Clostridium butyricum

Clostridium butyricum is a human commensal bacterium that naturally inhabits the gut and provides multiple benefits. It grows by fermenting dietary fiber and other materials that are not degraded by the host and, in so doing, it produces butyrate, a short-chain fatty acid essential for nourishing intestinal cells, strengthening the gut barrier, and reducing inflammation.

Beyond its role in producing butyrate, C. butyricum also forms spores, which allow it to survive the acidic environment of the stomach and reach the intestines alive, even when taken orally. Once there, it supports gut balance by increasing the levels of bacteria that protect against disease, while inhibiting those that may cause disease. This potential probiotic is being studied for diseases associated with epithelial gut damage for preserving gut health, maintaining the integrity of the gut barrier, inhibiting pathogenic bacteria, and reducing the risk of translocation, i.e. the shift of microorganisms from the gut to the blood^3-5.

Escherichia coli

E. coli is one of the most familiar names in microbiology — and often misunderstood. While certain strains can cause infections, most Escherichia coli living in the human gut are harmless and even beneficial. These commensal strains contribute to essential functions like vitamin K production, metabolism of nutrients, and maintaining microbial balance by preventing harmful bacteria from taking over.

One particular strain, E. coli Nissle 1917, has been studied for more than a century and is now recognized as one of the best-known probiotic bacteria for gut health. It has been used in various clinical contexts to support intestinal balance and help prevent gastrointestinal disturbances. Despite its success, and similar to other probiotics, there is a small risk of infection for individuals with a weakened immune system. This potential ‘Jekyll and Hyde’ aspect of probiotics should — referring to their double-edged nature — encourage patients and consumers to discuss their use with a healthcare provider, especially if they are immune compromised due to conditions like cancer, HIV, or organ transplants.⁶

Saccharomyces boulardii

First discovered in 1923 by French scientist Henri Boulard from tropical fruits such as lychee and mangosteen, Saccharomyces boulardii is a yeast that has earned its reputation as a well-established probiotic. Yes, you read that right! We also host fungi as part of our intestinal ecosystem, collectively known as the gut mycobiome.

Although there are far fewer fungi in the gut microbiota compared to other microbes, they are much bigger than bacteria and viruses. Unlike bacteria, S. boulardii doesn’t permanently colonize the gut; instead, it acts as a temporary ally that helps limit alteration and restore balance during times of disruption, especially after antibiotic treatment.

Clinical studies have shown that S. boulardii helps restore microbial balance, supports the intestinal barrier, and can help prevent and treat certain infections, such as traveler’s diarrhea and those caused by Helicobacter pylori⁷.

Streptococcus thermophilus

Streptococcus thermophilus is best known as one of the starter cultures used in yogurt and cheese fermentation. But beyond its culinary fame, this bacterium plays a valuable role in human health. By fermenting lactose into lactic acid, it helps people with mild lactose intolerance digest dairy products more easily (without symptoms) while contributing to overall gut balance⁸.

Emerging studies⁸ suggest that S. thermophilus may also influence gut microbial composition and support immune regulation by interacting with bile salt metabolism and digestive enzymes. Its dual role — in both food and gut health — makes it a true example of how consuming live microbes everyday via fermented foods can benefit the host in multiple ways.

Candida albicans

Candida albicans is a yeast that naturally lives in the gut of around 50–60% of adults⁹. Under balanced conditions, it coexists peacefully with the rest of the microbiota and even offers benefits — such as helping protect against bacterial pathogens like Clostridioides difficile, a highly contagious bacterium that causes diarrhea and colitis when the normal gut microbiota is disrupted, and supporting immune regulation.

When this balance is disturbed — for instance, by antibiotic use or stress — C. albicans can shift from a harmless guest to a troublemaker. Its overgrowth has been linked to gut inflammation, and in people with weakened immune systems, it can sometimes lead to serious infections. Many women would be familiar with C. albicans infections (thrush) that flourish after they use antibiotics¹⁰. It’s a good reminder that keeping this “opportunist” in check is part of maintaining overall microbial harmony¹¹.

It’s all about balance

Other microbes like Helicobacter pylori, Fusobacterium nucleatum, or Clostridioides difficile also sound threatening. They can cause disease under certain conditions (e.g., a bloom of C. difficile after antibiotics) or if they are outside their natural habitat (e.g., when F. nucleatum is found in the intestine rather than in the mouth). But researchers are discovering that context matters: some of these species play regulatory or protective roles when they coexist in harmony with others.

The microbial world isn’t divided into villains and heroes. It’s made of dynamic ecosystems and our health depends on maintaining their balance. Diet, stress, sleep, antibiotics and even other medications, though not antibiotic, can all shift that balance. Eating fiber-rich foods, fermented products, and maintaining a healthy lifestyle are key ways to support the trillions of microbes that keep our gut — and the rest of us — in good shape.

This Halloween, instead of fearing the invisible, let’s celebrate it.

References:

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