Food Fermentation: The Good, The Bad & The Infectious

Like wild & sour beers, fermented foods rely on a host of organisms to generate their flavourful and preservative properties. However, the diversity of organisms involved is much larger across the various fermented foods than you’ll find in any beer, wine, cider or mead. By one count, over 1500 species of microorganisms – both bacteria and fungi – are used in commercial production of fermented foods world-wide. Among hobbyists, that number is probably even larger. To make matters even more complex, the types of fermentation (and non-fermentative pathways) used to produce these foods is far larger than with beer and other alcoholic beverages.

Obviously I’m not going to be able to cover that diversity in a single blog post, but it is worth discussing briefly the general details surrounding these fermentations. To keep things manageable, I’m going to avoid talking about fermented milk products like yoghurt and cheese – these get quite complicated, and I’ll tackle them in future dedicated posts.


What is Fermentation?

Formally, fermentation is defined as energy-generating biochemical processes which do not utilise oxygen. When talking about fermented foods, we’re generally talking about fermentations where bacteria &/or fungi “eat” sugars from the foods to generate energy, and where flavourful/preservative chemicals are produces as a product of that fermentation. There are other fermentative pathways that allow some bacteria to ferment things like proteins and fats, but outside of milk fermentations, these pathways are not major players in the production of fermented foods.

When it comes to fermented foods, we’re generally talking about two types of fermentation – alcoholic and lactic. Alcoholic fermentation is what most people are familiar with – yeasts breakdown sugars, forming alcohol (ethanol) and carbon dioxide. This is what takes place in beer, wine, cider, mead and other alcoholic beverages. It also occurs in some fermented foods as well (e.g. kumbucha and vinegar). This contributes the flavour of alcohol to the food – semi-sweetness in lower amounts; solvent-like in higher, as well as a preservative effect. The CO2, if captures, results in carbonation.

Far more common in fermented foods is lactic acid fermentation. Like with alcohol fermentation, lactic acid fermentation begins with the breakdown of sugars by bacteria. But instead of producing alcohol and CO2, lactic acid fermentation produces lactic acid, and in some cases CO2 is also produced. Lactic acid has a characteristic flavour that many people enjoy (this is the predominant flavour in yoghurt, sour beers and some cheeses), and by dropping the pH of the food, also acts as a preservative.

Ethanol and lactic acid are not the only products of these fermentative organisms, with other flavour and aroma compounds often produced in smaller amounts alongside the alcohol/lactic acid. A shot and incomplete list would include butyric, propanoic and isovaleric acids, acetaldehyde, diacetyl, acetoin, acetone, and 2-butanone.

For some fermented foods, non-fermentative pathways are also used. Vinegar and kombuch are prime examples of this; both begin with yeast performing alcoholic fermentation, converting sugars into ethanol. And in both, acetobacter (or closely related bacteria) then use oxygen to consume that ethanol – forming acetic acid as a product. Cheeses too rely on oxidative metabolism for some of their character – the pungent taste (and blue veins) in blue cheese are a product of the oxidative growth of the fungi Penicillium roqueforti, as one example.


Synergy During Mixed Fermentation

Most fermented foods – especially those relying on the natural microbes present on the food being fermented – generally rely on multiple different species to complete fermentation. Sourdough bread fermentation is a prime example of this, where the sourness is produced by a range of lactic acid bacteria including Lactobacillus  and Weissella, while the leavening of the bread and some of the funky/earthy flavours are a product of the yeast Candida milleri. Any of these on their own fail to produce a proper sourdough bread, with the full flavour and texture requiring a mixture of organisms.

But while sourdough needs these organisms to achieve its full flavour and aroma profile, other fermentations don’t merely require a mixture of microbes – they require that those microbes assist each other in the fermentation. Kombucha is an example of this, where the yeast Zygosaccharomyces* ferments sugars into ethanol, while the acetic acid bacteria Acetobacter and Gluconacetobacter oxidize the alcohol to acetic acid. These bacteria, in turn, support the growth of the yeast by fixing nitrogen.

*Other yeasts are often found alongside Zygosaccharomyces in kombucha, including SaccharomycesSaccharomycodesSchizosaccharomycesBrettanomycesCandidaTorulosporaKoleckeraPichiaMycotorula, and Mycoderma.

There are exceptions to this “rule”. Sauerkraut is predominantly fermented by the lactic acid bacteria Leuconostoc mesenteroides, and sauerkraut can be prepared using pure cultures of this species. However, “wild” sauerkraut’s often contain other lactic acid bacteria alongside the Leuconostoc, including other members of the Leuconostoc genus, Lactobacillus paraplantarum, Lactobacillus coryniformis, and various Weissella species.


Major Organisms

As mentioned in the intro, there is no way I can introduce all of the organisms involved in the fermentation of foods. In fact, I’m not even going to try. Instead, I’d going to give you a brief introduction into the general classes of organisms involved. Future food-specific posts will then delve deeper into the microbiology specific to individual foods.

Lactic Acid Bacteria: These are the most common organisms found in fermented foods, and with only a few exceptions (e.g. kombucha), are ubiquitous in fermented foods. As their name suggests, their main contribution to these ferments is lactic acid, which acts both as a flavourant and as a preservative. The flavour of lactic acid is mellow in comparison to the more commonly encountered acetic acid (vinegar). The drop in pH which accompanies the production of lactic acid is what helps to preserve many foods.

The lactic acid bacteria (officially called the Lactobacillales) are a hugely diverse group of bacteria, with well over a hundred species spread across 13 genera falling into this group (Lactobacillus, Leuconostoc, Pediococcus, Lactococcus, Streptococcus, Aerococcus, Carnobacterium, Enterococcus, Oenococcus, Sporolactobacillus, Tetragenococcus, Vagococcus, and Weissella). The first 4 genera (Lactobacillus, Leuconostoc, Pediococcus, Lactococcus) are the ones responsible for most lactic acid fermentation in fermented foods, but some of the later appear in certain cases – Oenococcus in wine and cider fermentation, Weissella in sourdough breads. A few genera contain pathogens – Streptococcus and Enterococcus – although innocuous species are also found in these genera.

One aspect that separates those lactic acid bacteria that are found in fermented foods form those which are not is salt tolerance. Many of the Lactobacillus, Leuconostoc, Pediococcus and Lactococcus species are tolerant to high levels of salt – some can survive in brines containing more than 10% salt by weight. For many fermented foods, it is the combination of salt and lactic acid from these halo-tolerant (salt-loving) bacteria that ultimately preserve the food.

Acetobacter & related species: Technically, Acetobacter and related species of bacteria (Gluconacetobacter) do not ferment foods, but instead oxidize alcohols into acetic acids. However, they play a major role in some fermented foods – specifically vinegar and kombucha – where they produce the more intense and pungent acetic acid that gives these foods their particular characteristics. Like lactic acid, the acetic acid produced by these bacteria will acidify the food to provide a preservative effect. These bacteria are unable to produce vinegar on their own, and typically require a yeast to first convert sugars to ethanol, with the bacteria then converting the ethanol to acetic acid.

Yeasts: Yeast are a unique group of single-celled fungi. Yeast are not bacteria – in fact, they are evolutionary closer to humans than they are to bacteria. Regardless, yeast are found working alongside bacteria in many fermented foods. Again, there are hundreds of species spread across a number of genera potentially involved in fermented food production. These include species wihtin the genera Zygosaccharomyces, Saccharomyces, Saccharomycodes, Schizosaccharomyces, Brettanomyces, Candida, Torulospora, Koleckera, Pichia, Mycotorula and Mycoderma.

Depending on the species present, these yeasts perform different roles in fermented foods. Some are truly fermentative yeasts, and will convert sugars into ethanol (alcohol). Others, however, are oxidative yeasts – meaning they are not capable of extensive fermentation, and instead require oxygen for their growth. These yeasts can provide a leavening action to breads, and can contribute a broad range of flavours to the fermented foods. These oxidative yeasts are also sometimes unwanted guests…but more about that can be found below.

Moulds/Molds: In most fermented foods, moulds and other non-yeast fungi are unwatned guests. But there are a few exceptions. There are a number of moulds used in cheese making which provide the earthy and funky notes of many cheeses. Many rice wines, including saki and cheongju, rely on the mould Aspergillus oryzae to breakdown starches in rice into fermentable sugars. These sugars are then fermented by yeasts to form alcohol. But in most cases, moulds are unwated guests that can ruin a food fermentation.


Unwanted Guests

While there are a lot of players we do want in these ferments, there are also some organisms that occasionally make an unwanted appearance. With care these can be limited to those which are only inconvenient, but a failure to take proper preventative measures can rarely lead to vists by a few very hazardous – even lethal – organisms.

Kahm yeast growing on a pepper mash

Kahm: Kahm is a harmless, but unpleasant looking growth of yeast. This is not a single species of yeast, and instead kahm is formed by a number of oxidative yeasts including Pichia, Hansenula, Debaryomyce, Mycoderma and Candida. Kahm is often mistaken for mould, but once you know what to look for the two are easy to tell apart. Kahm appears as a waxy, often lumpy or broken film on the surface of a ferment. Importantly, kahm floats on top of the ferment and does not send any sort of filaments or streamers deeper into the food (see picture to the left).

Kahm is harmless, and indeed, many of these yeasts are part of some fermented foods. It is, however, unpleasant in appearance and can impart harsh flavours and aromas. Kahm usually occurs because air gets into the ferment, allowing these yeasts to grow. Ensuring you use a properly sealed lid with a quality airlock can prevent most cases of kahm yeast formation.

If you find kahm in your ferments you have a few options. First, carefully scrape as much of the yeast out as you can, and re-sanitise any fermentation weights you are using. Re-seal the jar, being careful to ensure a proper seal and ensure that your airlock is working properly. Increasing your salt content may help – I often sprinkle a little bit of salt across the kahm before re-sealing the jar. Any benefit of this is temporary. Many kahm yeasts are tolerant to over 10% salt, and thus will only be suppressed for the short period of time before the salt dissolves and distributes throughout the fermenting food. But this extra salt can limit the re-growth of kahm while you wait for the fermentation to re-establish an oxygen-free environment. Lastly, you can filter the brine portion of your ferment through cheesecloth to remove the kahm. The later option will not prevent regrowth of the kahm, but can be used to remove it prior to re-packaging into a storage/serving container, or before additional processing of the fermented food.

Mould/Mold: Moulds are a bigger issue, which I have written about previously. Many moulds are harmless, but others produce mycotoxins – compounds which have a range of toxic effects including being carcinogens. Unfortunately, there is no easy way to separate safe moulds from unsafe ones. if you have mould contamination your best bet is to throw away that ferment and to start over. Unfortunately, scraping the mould off does not work, as even a small mould island will send many near-invisible filaments deep into the ferment. And, of course, mycotoxins are free to spread throughout the ferment and cannot be removed.

The good news is that moulds are very easy to prevent. Moulds require oxygen, so as long as you ensure you have a well-sealed fermentation jar with a good airlock, you should be able to prevent these issues.

Enterobacteria: This is where things start to get scary. Enterobacteria refer to a range of species commonly found in our guts. These species go by well-known names – E. coliShigella, and Salmonella. Yes, these are the bacteria which commonly cause food poisoning. Contamination occurs through two main routes – the spraying of manure-based fertilisers onto plants too close to harvest, and they can often be found on your hands.

The solution here, luckily, is simple:

  1. Wash your damned hands before you prepare any fermented foods.
  2. Make sure that you are adding enough salt to form a proper brine.
  3. Make sure that you allow your food to complete fermentation before consuming it.

Generally speaking, these bacteria do poorly in salt concentrations above 2% (with the exception of E. coli), and the combination of salt and acidity found in many fermented foods is sufficient to kill them.

While a minor infection of these (which can still make you sick) may go unnoticed, there will be no doubt if you’ve had a serious infection – these bacteria create aromas of vomit, faeces and rot. If you ever smell these aromas coming from a ferment, dispose of it immediately and either toss the fermentation equipment or clean it judiciously before re-use.

Listeria: Listeria are a special case, as they are generally only an issue with fermented milk products or fermented meats. They are, however, a serious risk that you need to consider when preparing these kinds of foods. Listeria is especially scary as the salt and acidity which normally preserve foods are ineffective against it. To make matters worse, Listeria is perfectly happy to grow at refrigeration temperatures. Meaning that even a minute Listeria infection during preparation can result in a very dangerous food product a few weeks down the road. Listeriosis (food poisoning by Listeria) is very serious, and even with modern medical interventions can be fatal.

Preventing listeria is trivial. If preparing a fermented milk product, use pasteurized milk (or pasteurize it yourself). Unpasteurized products carry a high risk of listeria contamination, especially if consumed young. With cheese, the risk of listeria goes away after ~6 months of ageing, but younger cheeses are best prepared using pasteurised milk For fermented meats, these should be cooked to an appropriate internal temperature, and then inoculated with a clean and trusted lactobacillus culture.

Botulism: I’ve left the worst for last. Botulism is thankfully very rare. It is, however, a horrific disease when it occurs. Ironically, botulism itself cannot infect you (unless you are an infant) – the acidity and conditions in our stomach are too much for it to take. Unfortunately, botulism makes the most toxic compound known to human kind. A quantity the size of a pin head is more than enough to kill a busload of people.

The good news is that botulism will generally be killed off by the combination of acidity and salt found in the average food fermentation. But problems can arise if you can the food for long-term storage. Botulism spores can survive the fermentation and the heat of boiling, and can persist on surfaces for long periods of time. As such, unless there is enough salt in the brine and acidity, botulism can emerge post-canning. Many fermented foods use brines that are too weak to prevent botulism, so unless you are certain you have sufficient acidity, canning can be potentiality hazardous. If you are choosing the preserve your food by canning, can using a a pressure cooker as the higher canning heat will kill off any spores. Botulism is thankfully very rare – on average less than 20 cases/year in the USA. However, death is not uncommon and those who survive often experience long-term heath issues as a result.

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