We ferment foods for a variety of health reasons. We ferment foods like sauerkraut, kimchi, and kefir because the process of room temperature fermentation causes bacterial species such as Leuconostoc mesenteroides, Pediococcus pentosaceus, and Weisella species to proliferate and, upon ingestion, pass through the gastrointestinal (GI) tract and into the toilet, (usually) not taking up residence in any part of the GI tract. But in their passage through the 30-some feet of GI tract, these fermenting species somehow provoke the proliferation of bacterial species that do take up residence and provide numerous health benefits, many mediated via production of the fatty acid, butyric acid. We also ferment microbes that proliferate at human body temperature and play other significant roles in health. These are species such as Lactobacillus reuteri, Lactobacillus gasseri, and Bifidobacterium infantis. So our fermentation efforts fall into two broad categories: microbes that ferment at room temperature and microbes that ferment at human (mammalian) body temperature. Recognizing this distinction will help you better navigate the world of food fermentation and health. There are exceptions such as Lactobacillus plantarum that is so adaptable that it will ferment at either temperature range. But, in general, bearing the above distinction in mind can be very helpful.

But some people still encounter difficulties or uncertainties when they ferment foods at either end of the temperature spectrum. So here are some Frequent-Asked Questions (FAQs) that you may find helpful to help you succeed in navigating this hugely important aspect of health.

Q: If I ferment veggies like cucumbers or radishes, do I need a starter culture?
A: No, as you can rely on the microbes normally resident on the surface of vegetables and fruit, though present at low counts. The vegetables and fruit will need to be organic and not covered by waxes or other coatings. Because of the low microbial counts, relying on such resident microbes means that fermentation will generally require weeks to ferment. By adding a starter culture, you can abbreviate the process to a few days (though it varies depending on the mix of veggies and fruits and their sugar and fiber content). You can purchase a commercial starter culture or you can just use, for instance, the brine from a commercially-fermented food like sauerkraut or pickles. So you do not need a starer culture, but it can significantly accelerate the process of fermentation for you.

Q: Do vegetables or fruit need to be sliced to ferment?
A: No, but you will experience greater release of nutrients and higher bacterial counts if, for instance, you slice or chop cucumbers or onions, exposing greater surface area for fermentation.

Q: Can fermented foods alone serve as a source of probiotics?
A: Probably not. As explained in the opening comments, consuming fermented foods results in significant changes in the overall composition of the GI microbiome. But fermented foods alone likely do not fully restore all microbes lost due to factors such as exposure to antibiotics. We therefore purposefully and specifically restore important species such as L. reuteri and L. gasseri in our yogurt projects.

Q: My first attempt at making L. reuteri yogurt yielded a lot of separation into curds (solids) and whey (liquid). What did I do wrong?
A: Nothing. We call this “the first batch effect,” i.e., the tendency to separate when “yogurt” is first made from a probiotic capsule or starter culture. Making subsequent batches from a prior batch tends to yield a more uniform, thicker end-result? We don’t know why this happens, but one way to manage this effect is to make a smaller first batch in case you do not want to consume it, then use a bit of this first batch to make a larger second batch.

Q: I’ve been having good results with my yogurts. But one batch turned out awful: it smelled rotten and was inedible. What happened?
A: The most common cause is contamination with another organism. In this case, discard and start from scratch, i.e., start with a known probiotic or starter culture. Also, be sure that the heating device you are using is delivering your desired temperature, as these devices can occasionally fail. If neither of these solve the problem, consider a new source of prebiotic fiber because the fiber may contain a contaminant.

Q: Why do you say this isn’t “yogurt”?
Many years ago, the FDA issued regulations that defined what can be called “yogurt.” Among the requirements: Anything called yogurt must be fermented with Lactobacillus bulgaricus and Streptococcus thermophilus, two microbes used in traditional fermentation of yogurt. Other microbes can be added but the two traditional species must be included. In this age of growing appreciate of fermenting microbes, this regulations is clearly outdated and arbitrary—but it still stands. So we cannot call our yogurts “yogurt” in the strict regulatory sense. Provided we are not selling it, of course, we can call it anything we like, but it remains that, in the conventional use of the word, it is not yogurt.

Q: Can I ferment more than one species of bacteria together?
A: Yes, absolutely. But there are some issues you should know about. If you are trying to achieve the highest number of microbes of a specific species, then a single species is the way to go. If you co-ferment more than one species, you will experience a reduced number of each microbe. If, for instance, you want the maximum rise in oxytocin possible in order to generate love and empathy or sleep augmenting effects and you obtain this by fermenting L. reuteri alone but fail to experience it when fermenting with three other species, you know that you’ve reduced the number of L. reuteri too far. I liken our yogurts to a backyard garden in springtime: If you plant only tomatoes, you will have lots of tomatoes at the end of the season. But what if you plant eggplant, zucchini, squash and tomatoes—how many tomatoes will you have at the end of the season? Far fewer, of course. Another issue to be aware of when fermenting more than one species is that some species can, over time and several batches, come to dominate, changing the relative proportions of each species. If the final composition of the end product matters to you, then consider starting from scratch every several batches.

Q: How necessary is the addition of a prebiotic fiber like inulin?
A: It is helpful but not essential. When we’ve made L. reuteri yogurt, for instance, without prebiotic fiber, the end result is not as thick and microbial counts are lower. If you do choose to include prebiotic fiber and you add too much, don’t worry: It just means that any residual prebiotic fiber will remain available to you when you consume the yogurt.

Q: How do we know the final result is really L. reuteri (or whatever other species you are fermenting)?
A: Think of it this way: If you plant tomato seeds in your garden, should you expect cucumbers? No, of course not. Species cannot just morph into other species. Such fermentation efforts have been conducted millions of times in laboratories and in fermenting facilities. Unless you obtain the occasional contamination (e.g., poorly-cleaned utensils previously used to make a spore-forming species like Bacillus subtilis, or you introduced another microbe from a contaminated batch of inulin), if you start with L. reuteri, you end up with L. reuteri. In general, bacteria that ferment as yogurt are not airborne and do not contaminate. Fungi and mold can, however, but that will be obvious as pink, red, green, or black discoloration that can be scraped off and discarded and the yogurt will be perfectly fine.

Q: Can we expect similar results when consuming store-bought yogurts?
A: No, not even close. Commercially produced yogurts employ microbes with minimal benefits (L. bulgaricus, S. thermophilus), low counts of microbes because of the short fermentation time, contain thickening agents like gellan gum and xanthan gum since fermentation is incomplete, often use low- or non-fat dairy, and have added sugars, high-fructose corn syrup and other undesirable additives. You cannot expect effects such as small intestinal colonization, bacteriocin production, oxytocin provocation, or reduction in endotoxemia. The differences between the yogurts we make with specific choice of bacterial species, prolonged fermentation, and addition of prebiotic fiber yield something that is completely different from what you find in the supermarket refrigerator.