Microflora and Fermented Foods


The impact of the microflora that all humans are host to on health has become a hot topic. Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment including toxin exposure, host genetics, and early microbial exposure have all been implicated.

Specific types of bacteria in the intestine have been linked to obesity1, circulatory disease2, inflammatory bowel disease3, and autism4. While progress is being made, our understanding of a truly healthy microbial balance in the human gut is still in its infancy. Nonetheless, research on the health benefits of probiotic supplementation and probiotic in foods has started to shed light on ways that we might be able to influence our gut microbes in a positive way. If you’re interested, you can view some of this research here, here, and here.

However, in this article I’d like to focus on something more basic, more immediate, and potentially, more beneficial in many respects. That is getting back to our roots; getting back in touch with the way that our ancestors not only preserved food but also inoculated their intestines with some probably pretty beneficial bugs. With the advent of pasteurization, refrigeration, alimentary (alongside cultural) homogenization, many of the healthful traditions in food preparation and preservation have become lost in the flurry of lives too busy to find time for the very stuff of life: our food. Let me share a passage with you from the book “Wild Fermentation” written by my favourite fermentation enthusiast, Sandor Ellix Katz:

“Microbial cultures are essential to life’s processes, such as digestion and immunity. We humans are in a symbiotic relationship with these single-cell life-forms. Microflora, as they are often called, digest food into nutrients our bodies can absorb, protect us from potentially dangerous organisms, and teach our immune system how to function.”

And try as we may to eradicate microscopic bacteria, they are everywhere. Instead of waging war on these little critters, it’s time to enter the enlightened post-pasteurean era wherein we learn to culture and nurture the bugs that will help us to both maintain health and ward off potentially threatening microorganisms, not to mention bring a diverse array of exciting new flavours to our palates, instead of indiscriminately eradicating all things microscopic. Indeed, it could be argued that learning to work with microbes instead of embarking on an all out blitzkrieg is essential to the future wellbeing of human beings.


Incidence of autism, IBD, obesity and its cousin type 2 diabetes, and many other chronic health conditions are increasing at alarming rates; rates that cannot be explained by changes in genetic make-up or better diagnostic criteria. We know that factors such as poor diet, antibiotic use, and widespread use of pesticides like roundup (glyphosate)5 can cause undesirable shifts in the human microbiome. Though the etiologies of increased incidence of chronic disease are undoubtedly multifaceted, it seems quite plausible that one of the driving forces of the alarming acceleration of disease could very well be a shifting human microbiome. So let’s take a moment in our busy lives to slow down, to nurture some anaerobic lactobacilli in our kitchens using some simple tools, a bit of patience, and an inspired aspiration for a healthier microbiome and some tantalizing new flavours.



1. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI: An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444:1027-1031.

2. Holmes E, Loo RL, Stamler J, Bictash M, Yap IK, Chan Q, Ebbels T, De Iorio M, Brown IJ, Veselkov KA, Daviglus ML, Kesteloot H, Ueshima H, Zhao L, Nicholson JK, Elliott P: Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 2008, 453:396-400.

3. Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y: Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 2007, 6:546-551.

4. Finegold SM: Therapy and epidemiology of autism – clostridial spores as key elements. Med Hypotheses 2008, 70:508-511.

5.Samsel M, Seneff S Glyphosate’s Suppression of Cytochrome P450 Enzymes and Amino Acid Biosynthesis by the Gut Microbiome: Pathways to Modern Diseases. Entropy 2014. 15(4), 1416-1463