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Common Bacteria and Yeast in Everyday Foods

An overview of some of the microbes that we encounter every day


At ZBiotics, we are obsessed with the gut microbiome. Crucial to our overall health, the microbiome is teeming with a complex balance of microflora that are the foundation of many of our bodies’ key processes. Those microorganisms didn’t appear out of nowhere; they are abundant in our environment. In fact, we reencounter them every day in some of our favorite foods and drinks. In this post, we’ll explore some of the most common bacteria and yeast in day-to-day life. And we’ll dive into how they function in creating the foods we love and how they interact with the human microbiome.

Here are some of the microbes and yeast you could encounter in everyday life:

  • Lactobacillales (lactic acid bacteria)
  • Acetic acid bacteria
  • Bifidobacteria
  • Saccharomyces cerevisiae and the Candida genus
  • Bacillus subtilis


Fans of kimchi, cheese, yogurt, sauerkraut, pickles, sourdough bread, and many other fermented foods have the Lactobacillales order of bacteria (lactic acid-producing bacteria; not to be confused with “Lactobacillus”, which is just one of many genera within the Lactobacillales order) to thank. This enormous order of bacteria – comprising dozens of genera and thousands of species  metabolizes carbohydrates into lactic acid. This acid, which gives fermented foods their signature tart flavor, prevents the growth of harmful bacteria that would otherwise cause food to spoil (citation).

The human body is host to a wide variety of Lactobacillales bacteria with differing functions, including but not limited to protecting the lining of the gut from damage, digesting carbohydrates, and preventing infection. They aren’t confined to the gut either. Lactobacillales bacteria comprise the vast majority of the vaginal microbiome, acidifying the vaginal canal and protecting it from unwanted colonization by pathogens (citation).

Acetic acid bacteria (a group within the Acetobacteraceae family)

Used in chocolate and coffee production, the true star product of acetic acid bacteria is vinegar. Composed of 10 specific genera within a larger bacterial family, the acetic acid bacteria convert sugar and/or alcohol into acetic acid. This is the ingredient that gives vinegars as well as kombuchas, water kefirs, and lambic beers their sour flavor (citation). While they do not populate the human gut, their acetic acid byproduct is excellent at preventing the growth of harmful bacteria, making them incredibly useful for food preservation in the form of pickling. They are present, however, in the guts of an animal typically close to fermenting foods: the fruit fly (citation).


Bifidobacteria are lactic acid producing bacteria (though not part of the Lactobacillales order) and are often added to dairy products like kefir and yogurt (citation). It also can be a valuable member of the human microbiome, due in part to its ability to ferment prebiotic fiber into short-chain fatty acids, which are beneficial for gut health and nutrient absorption (citation).

Bifidobacteria prevent overgrowth of harmful bacteria, help to modulate immune responses in the gut, and assist in the production of vitamins and nutrients from otherwise non-bioactive substances (see previous citation).

Saccharomyces cerevisiae and the Candida genus

Bacteria are not the only microorganisms we interact with regularly. Saccharomyces cerevisiae and the Candida genus are two groups of yeasts that are crucial to the food system.

The millions of people who took up baking during the pandemic will be familiar with Saccharomyces cerevisiae. Familiarly known as baker’s yeast or brewer’s yeast, Saccharomyces cerevisiae has two main functions in food production: leavening bread and fermenting beer and wine. It converts sugar to alcohol and carbon dioxide, creating the bubbles that cause bread to rise. This also transforms grains and fruits into beer, cider, and wine (citation). Saccharomyces cerevisiae has also recently grown in popularity in the form of nutritional yeast, a protein- and vitamin B12-rich supplement created by washing, pasteurizing, and drying yeast that has been left to ferment cane and beet molasses. This product, however, does not contain any living microbes.

Several species within the Candida genus are used to ferment foods, most notably cheese. Various strains of Candida yeasts are used in the making of cotija, Fontina, pecorino, Camembert, brie, Taleggio and many other artisanal cheeses (citation).

While these yeasts are generally benign and normal constituents of our microbiomes, as with many of the microbes in our bodies, they can become opportunistic pathogens when out of balance with the rest of the microbiome. Candida overgrowth in particular can be harmful, especially as a vaginal infection; 75% of women of childbearing age are affected at some point by vulvovaginal candidiasis (VVC) (citation). Interestingly though, there is some data to suggest that Saccharomyces cerevisiae could possibly be helpful in resolving VVC (citation).

Bacillus subtilis

A species from a genus used in foods like natto, chocolate, and kombucha, Bacillus subtilis is found abundantly in healthy soil (citation). Bacillus subtilis co-evolved alongside the human digestive tract and can help in the body’s defense against parasites and other infections (e.g. citation).

B. subtilis is also the bacteria we use in our products at ZBiotics. There are many aspects of B. subtilis that make it an ideal bacteria for us to work with: it’s one of the safest and most common microbes we encounter in our daily lives; it is easy to grow and work with; it’s great at producing enzymes and performing useful biological functions that can have a positive impact on our health; and it’s a spore-former. This last part in particular is especially valuable. B. subtilis can go into a dormant, shell-like spore that allows it to tolerate harsh conditions like extreme heat, pH and other things that would be lethal to many cells. This enables it to pass safely through our stomach acid unharmed and make it into our intestines ready for action. But it is also naturally evolved to pass through our intestines without taking up residence. This makes it perfect for the creation of our genetically engineered probiotic drink, able to perform specific beneficial functions without disrupting the rest of your gut microbiome.

In Conclusion

There is an intricate relationship between the microbial world and our everyday lives. Whether they’re giving yogurt its tang, helping our favorite bread to rise, or making sure our immune system functions properly, these common microbes are integral to sustaining both our food system and also our general wellbeing. While focusing on maintaining a healthy gut microbiome is a more recent lens for wellness for many people, luckily, most of the core tenets of good living still apply. Getting lots of good rest, staying active, and eating a wide variety of fresh, diverse, and minimally processed foods helps to ensure that these everyday microbes can do their job effectively.