Fermented Foods & the Gut

Ask someone why fermented foods are good for them and they’ll probably shrug and mumble something about “healthy bacteria?”.

And while they’re not necessarily wrong, some of the putative benefits of fermented foods may be available notwithstanding any potential probiotic effect. In order to get those benefits though, it’s best to be consistent and eat a variety of fermented food every day or so.

Some (Microscopic) Navel-Gazing

Let’s take a brief pause to survey our own internal landscape. The human gastrointestinal or “GI” tract is a series of hollow organs extending in a long twisted tube from the mouth to the anus. In a very real sense, while deeply embedded within us, the lumen of the GI tract is outside of our bodies and an open ecosystem - meaning that the stable population of resident gut microbes (given the tongue-confounding moniker of “autochthonous” microbes) is regularly challenged by the ingestion of exogenous microbes from sources such as the diet and living environment (Derrien et al., 2015).

The ability of the resident gut microbes to prevent these external or '“allochthonous” microbes, especially pathogens, taking up residence is known as “colonization resistance” or “the barrier effect” (Lawley & Walker, 2013).

This inhospitality notwithstanding, some allochthonous microbes may temporarily integrate into the gut microbiota population and, while transient, emerging evidence suggests they may play a significant role in gut microbiota structure and function. The composition at any one point in time of this transient microbiota is highly dynamic and individual and is the result of recent exposure, the gut ecosystem conditions, diet, and the fitness of the ingested organisms (Derrien et al., 2015).

But What Has the Microbiota Ever Done For Us?

Since we are housing an outrageous number of these little beasts (approximately 100 trillion), what’s the quid pro quo of this arrangement?

Well, their extensive metabolic repertoire complements the activity of our own digestive enzymes secreted by our liver and gut mucosa (the gut wall) contributing enzymes otherwise absent in humans that breakdown polysaccharides, polyphenols and synthesize vitamins, notably vitamin K and B group vitamins (Rowland et al., 2018).

This means that our microbiota play a key role in shaping the biochemical profile of our diet i.e. what we can absorb from our food. Add these and other metabolic functions to their impact on immune and neuro-behavioural traits and they can consequently influence our fitness, phenotype and health (Valdes et al., 2018).

That’s a pretty good deal for us hosts when the microbe population is well-balanced and happy.

The microbiota primarily rely on undigested carbohydrates (e.g. insoluble fiber, resistant starch: the “prebiotics”) for survival. Fermentation of these substrates by certain strains of bacteria produces short chain fatty acids (“SCFAs”) - butyrate, acetate, propanol - and gases.

SCFAs definitely need an article of their own but, for now, just know that they are vital for our well-being. Among other functions, SCFAs help to power the function of our gut cells, moderate the microbial population (by providing food substrate and an acidic-enough environment for those we want and a too-acidic environment for those we don’t) and support efficient regulation of blood sugar (Rowland et al., 2018).

Finally, lower bacterial diversity in humans has been reproducibly observed to be an indicator for disease - so the more diverse your microbiota (both resident and transient), the better (Valdes et al., 2018).

Are fermented foods Probiotics / Synbiotics?

Fermented foods are major sources of the environmental bacteria that enter the GI tract. After consumption, these ingested bacteria enter a hostile environment where subsequent passage through the stomach and small intestine exposes them to highly stressful physicochemical and biological conditions: the low pH of the stomach together with pepsin (the enzyme that breaks down protein) followed by exposure to bile, pancreatin and lipase in the duodenum (the first section of the small intestine)(Derrien et al., 2015).

The surrounding food matrix appears to play an important role in their survival or otherwise, but a number of studies have shown that microorganisms from fermented foods can reach the gastrointestinal tract. If they do make it this far, bacterial strains may recover and replicate to form part of the transient microbiome - but while strains may continue to be detected after a few days, they are rarely detected after a week (Dimidi et al., 2019).

Then there is the question of whether or not these bacteria fit the IASSP’s definition of “probiotic” or “synbiotic” - broadly whether the strains have been demonstrated to confer a health benefit and are present in sufficient numbers to have that effect (Hill et al. 2014, Swanson et al., 2020).

Most fermented foods will not be able to label themselves as a “fermented probiotic” or as containing “probiotic cultures” on this basis simply because the human studies aren’t there to support it. This is not to say that the effect definitely isn’t there though and you should look for fermented foods labelled as containing '“live and active cultures”.

There’s also the simple fact that live microbes take up (already limited) space: these microorganisms may still have the potential to exert a physiological benefit in the gut through competition with pathogenic bacteria. They tell bad bacteria “nah-uh, you can’t sit with us”. An example of our innate / barrier immunity at work.

So Why Else Should I be Eating Fermented Foods then?

There’s a clue in the IASSP’s (yes, them again) definition of a “fermented food”: foods or beverages produced through controlled microbial growth, and the conversion of food components through enzymatic action (Marco et al., 2021, emphasis added). Ahhh, now we’re getting somewhere.

The very process of being fermented may already confer some of the metabolic benefits we’ve been discussing. Microbial activity during food fermentation may have already generated SCFAs and other bioactive metabolites, reduced toxins and anti-nutrients (such as phytic acid in soybeans for example) and produced vitamins otherwise produced by the microbiota in the gut (natto, for example, is a good dietary source of vitamin K2 for this reason).

And as previously discussed, even if your fermented food of choice isn’t currently considered a probiotic, the diverse spectrum of bacterial strains may provide benefits through adding to microbiota diversity as part of the transient microbiome, supporting immune function through competition with pathogenic bacteria, (as well as viruses and fungi) and providing substrates to support the health and function of the resident microbiota. Woah! That’s pretty dang cool.

So Wait - Should I Eat them or Not?!

While the health benefits to humans from different types of fermented food have generally not been clinically demonstrated, given the promising animal and in vitro studies, it can surely only be a matter of time before this is corrected.

Fermented foods are to a large extent absent as a recommended category in dietary guidelines, but it nevertheless seems sensible to incorporate a wide variety of fermented foods into our daily diet. Remember, it doesn’t seem as though these bacteria hang about for a long time, so being consistent is the way to go.

So my advice is to go out there and have at it! The science will likely catch up eventually and fermented foods are tasty.

Summary of Fermented foods

Infographic from The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods (Marco et al., 2021)

ReferenceS

Derrien, M., & van Hylckama Vlieg, J. E. (2015). Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends in microbiology, 23(6), 354–366. https://doi.org/10.1016/j.tim.2015.03.002

Lawley, T. D., & Walker, A. W. (2013). Intestinal colonization resistance. Immunology, 138(1), 1–11. https://doi.org/10.1111/j.1365-2567.2012.03616.x

Dimidi, E., Cox, S. R., Rossi, M., & Whelan, K. (2019). Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease. Nutrients, 11(8), 1806. https://doi.org/10.3390/nu11081806

Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2018). Gut microbiota functions: metabolism of nutrients and other food components. European journal of nutrition, 57(1), 1–24. https://doi.org/10.1007/s00394-017-1445-8

Valdes A M, Walter J, Segal E, Spector T D. Role of the gut microbiota in nutrition and health BMJ 2018; 361 :k2179 doi:10.1136/bmj.k2179

Swanson, K.S., Gibson, G.R., Hutkins, R. et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics. Nature reviews. Gastroenterology & hepatology, 17(11), 687–701. https://doi.org/10.1038/s41575-020-0344-2

Hill, C., Guarner, F., Reid, G., Gibson, G. R., Merenstein, D. J., Pot, B., Morelli, L., Canani, R. B., Flint, H. J., Salminen, S., Calder, P. C., & Sanders, M. E. (2014). Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature reviews. Gastroenterology & hepatology, 11(8), 506–514. https://doi.org/10.1038/nrgastro.2014.66

Marco, M.L., Sanders, M.E., Gänzle, M. et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol 18, 196–208 (2021). https://doi.org/10.1038/s41575-020-00390-5