Probiotics and Other Sources of Microorganisms


Lactobacillus acidophilus from a commercially-sold nutritional supplement tablet.

An avalanche of studies linking alterations in the human microbiome to all sorts of diseases suggest that it’s hard to overstate the importance of the microbes that live in and on our bodies. Coming in contact with new species of beneficial bacteria seems to be especially important in regards to maintaining a healthy microbiome. Probiotics are microorganisms that have claimed health benefits when consumed, and there are several possible sources of these beneficial germs.

A recent review looking into the role of probiotics in health and disease found the following:
“The mechanism of action of probiotics is related to their ability to compete with pathogenic microorganisms for adhesion sites, to antagonize these pathogens or to modulate the host’s immune response. The potential application of probiotics includes prevention and treatment of various health conditions and diseases such as gastrointestinal infections, inflammatory bowel disease, lactose intolerance, allergies, urogenital infections, cystic fibrosis, various cancers, reduction of antibiotic side effects, in oral health such as prevention of dental caries, periodontal diseases and oral malodour and many other effects which are under investigation. The results of many of these clinical investigations suggests that probiotics may be useful in preventing and treating various health conditions and diseases. However, many of these clinical studies require validation so as to apply these results to clinical realm. (1)”

While probiotics often are associated with supplements, several other sources of bacteria could also be considered as probiotics since they provide microorganisms that have claimed health benefits when consumed. It also seems that our immune system expects a certain exposure to both “good” and “bad” microbes, and that although isolated probiotic bacteria provide some benefits, exposure to more complex communities of microbes (e.g., soil, dirt) seems to be especially important.

Probiotics and other sources of microorganisms

Probiotic supplements

pills-containersSome species of microorganisms are beneficial to human health, and well-studied strains are often isolated and used in probiotic supplements. Most probiotic supplements contain lactic acid bacteria and bifidobacteria, and these germs are able to compete with pathogenic microorganisms for adhesion sites and modulate the host’s immune response (1,2).
Probiotic supplements with soil based organism’s are also getting more popular, and although few studies have investigated the benefits of these products, there’s definitely an evolutionary precedent for the ingestion of soil microbes. It seems that soil-based organisms improve immune function, and one of the most well-researched soil bacteria, bacillus subtilis, has been shown to improve symptoms of IBS, suppress the growth of harmful pathogens, and enhance the growth of Lactobacillus (3).
I’m not a big fan of most probiotic supplements since they only contain a couple of strains of bacteria that seem to have minor impact on the gut bacterial community. Probiotics containing soil based organisms are more promising, and advanced probiotics containing entire ecosystems of bacteria could be available sometime soon.

Fermented food

sauerkrautTraditionally prepared fermented foods such as sauerkraut, kefir and kimchi are rich-bacterial resources that contain several strains of probiotic organisms. All fermented foods have an unique bacterial profile, but lactobacillus acidophilus and other species of bacteria with well-known probiotic properties are usually involved in the fermentation process. While our paleolithic ancestors probably ate overripe fruits, rotting vegetation, and other foods subject to natural fermentation, humans soon learned to control the fermentation process and we now know that pretty much all foods can be fermented.
Since most fermented foods at the typical grocery store or supermarket are of poor quality, it’s best to make these probiotic superfoods at home or look for high-quality products online or at the health food store, farmer’s market or some other trusted vendor.

Food and water

dirty_carrotsMicroorganisms are on the surface of spices, herbs, vegetables, and fruits, and it seems that these germs should be considered a part of the food. Plants contain complex polysaccharides that are digested by gut bacteria in the colon, and several species of bacteria are involved in the breakdown of different fermentable substrates. When we cook or clean plants before we eat them, we also remove microbes that could have a positive impact on our digestion and health. Even though there are some risks associated with eating uncleaned plants, adding some microbes into the diet from high-quality untreated drinking water and/or from plants found at the farmers market or backyard garden could be a way to mimic our ancestors, “priming” the immune system, and getting some prebiotics and probiotics into the colon.

Other humans, animals, and the rest of the environment

dog_kissingMicroorganisms are transferred to our hands, body and clothes from other people and pets, and we’re also exposed to germs from the rest of the environment. It’s unclear to which extent these microbes actually inhabit the body, but it seems that health is contagious in a sense that the microbiome is affected by other people you’re in close contact with. Even though the incidence of infectious and contagious disease has declined partly because of the use of hand sanitizers, soaps, and cleaning detergents, modern hygiene also has some hidden costs. Humans have co-evolved with certain types of microorganisms, and removing these microbes from our environment has been linked to a dramatic increase in autoimmune disease, allergies, and inflammatory conditions.


bacteriaFecal microbiota transplantation involves transferring an entire ecosystem of microbes from one person to another, and studies show that these transplants are especially effective in the treatment of c.difficile infection (4). DNA sequencing of the microorganisms that live in and on our bodies has made it clear that each person has an unique composition of bacteria. The risks associated with transferring this unique microbiome from one person to another is not fully established, and there are some legitimate concerns regarding fecal transplants. A lot of patients stay away from fecal bacteriotherapy because of the obvious “ick” factor of the procedure, but hopefully advanced probiotics could be available for these patients sometime in the future.


  1. The second genome: Bacteria we receive from our family shape our health - Organic Fitness says:

    […] birth, breast milk quickly becomes the major source of beneficial bacteria and prebiotic fibers. Since breast milk contains over 700 species of bacteria, it’s no […]

  2. […] care of your microbiome by eating prebiotics and probiotics. Avoid antibiotics and don’t be too […]

  3. […] both the quantity of some beneficial microorganisms and the production of short-chain fatty acids. Probiotics also increase the quantity of beneficial critters in the body, but they are usually more important […]


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