Decided to write a microbe post every Monday [that I get around to it.] since I liked doing so last week. For reference I don’t have an advanced degree in microbiology or anything, I just have a BSc. and a special interest in bacteria. I did ace all my microbio and biochem courses and did undergraduate bacterial ecology research but please take what I say with a grain of salt. I still work in biology, but am currently in medical research unconnected to microbio (although I'd argue nothing on earth is seperable from microbiology. That may just be the ASD though). I do keep up with the research thanks to our mutual friend Alexandra Elbakyan.

For this one, we’re going to be looking at a broader concept than a single microbe. You may have heard the term SCOBY (or “the Mother”) in reference to home fermenting things like kombucha or sourdough. SCOBY stands for Symbiotic Culture of Bacteria and Yeast.

The SCOBY is an absolutely incredible work of biological engineering. They are functionally, ecologically, and morphologically diverse so I am going to focus on the SCOBY present in kombucha (fermented tea). Symbiotic bacteria-yeast cultures are also present in certain types of vinegar production (think of apple cider vinegar including “the mother”), sour beers, kefir, and honestly most fermented products.

The SCOBY itself is a biofilm (according to IUPAC at least but that is a whole can of worms — It isn't a biofilm if you consider biofilm as needing a solid substrate). Biofilms are microbial communities, some of which can be seen with the naked eye. Dental plaque, pond scum, assorted bits of “gunk”, the pretty colors near hot springs, and the like. Microbes, especially bacteria, are discussed as “single-celled organisms” but in nature most are found in biofilm communities. Many bacteria even have unique functionality at scale when you get into stuff like quorum sensing.

Kombucha SCOBY is composed of several main types of organism: Acetic Acid Bacteria (AAB), Lactic Acid Bacteria (LAB), and yeasts. They grow in the fairly sweet medium and fill the environment with a diverse array of acids: acetic, glutonic, malic, tartaric, and a bit of citric. The ecological composition varies between the pellicle (think the actual physical SCOBY, a sort of cellulose disc) and the tea media itself.

Yeasts can convert sugar to ethanol. This is how most alcohol is made, though in the modern day we use a monoculture of Saccharomyces cerevisiae for most beer since it is efficient and predictable. Lambic and other sour beers (i.e. the best beers) are made with more complex communities which in turn produces more complex flavors. More biochemistry is happening, basically, so you get a different and unique medley of stuff. This is the case for kombucha, which harbors many different yeasts. Most of the ethanol is used for other metabolic processes, especially in bacteria. which is why it doesn’t usually get too alcoholic.

Bacteria are split mostly into AAB and LAB as mentioned. AAB make up the majority, and are aerobic (i.e. need oxygen) alcohol-metabolizers. They make kombucha’s distinctive acetic acid out of yeastmade alcohol. They’re precious, needy little dears and need way more oxygen than yeast which can just sort of vibe and ferment without worrying about it much. The various acids produced by bacteria in kombucha help contribute to its antimicrobial nature, essentially helping prevent further colonization by toxic bacteria, mold, etc. Only acidophilic/acidotolerant (and at first, osmotolerant) organisms can survive the kombucha environment.

The pellicle is cool. Basically, a diverse array of unrelated microbes come together to build this structure. There’s not a fully coherent “why,” but it may have something to do with oxygen access or protection. The thing is, it’s genuinely not that important to actual fermentation. People just like it because of our macroscopic biases. It is easy to see, and certainly is convenient in that it is among the bits most prone to mold growth so it helps as a diagnostic tool. Fermentation doesn’t need it though; it is just a byproduct.

The pellicle made largely of bacterial cellulose. This is chemically identical to plant cellulose but differs in physical structure — It’s more porous and crystalline than plant stuff. This is because bacteria are cooler than plants.

While several bacteria produce it, Komagataeibacter xylinus, an acetobacteria, is of particular interest in this case. It can use a lot of different carbon sources including ethanol, glucose, sucrose, and glycerol. Depending on what it uses it starts at a different phase of the reaction but ultimately transforms it into UDPGlc, then cellulose. Cellulose is actually produced outside the cell on these little fibers. Every cell has 50-80 or thereabouts and extrudes the cellulose in long chains.

There are two main types — Cellulose I and Cellulose II. I is a sort of bundle of microfibrils forming a whip or ribbonlike structure whereas II is an amorphous polymer with more thermodynamic stability.

These cellulose makers explode in population at the beginning of fermentation, devouring dissolved oxygen ferociously, the little scamps. They grow the pellicle in progressive layers, each superimposed over the last, but eventually becomes dormant as it entraps most of the cellulose makers who eventually run out of enough oxygen to produce a relevant amount of cellulose.

The pellicle is, again, insane. Like most bacterial cellulose, it’s very crystalline in nature, highly polymerized, has much thinner layers than plant cellulose, can take in much more water, and has just absurd tensile strength and insolubility. This thing would survive exposure to the mythical alkahest. The chemical properties of bacterial cellulose are so cool that they’re an active topic of study for medical applications. Though it may not matter much to the actual fermentation process, the weird cellulose pellicle has really unique chemical properties that just make it a cool bit of materials science!

I was a bit pressed for time this morning so this one wasn’t as thorough as I would like. There is so much more to talk about in terms of kombucha biochemistry pathways and the interlinkage between that and its ecological communities but I tried to cover some interesting bacteria and mechanisms involved.

Have a happy microbe monday! Remember the world is less sterile and more beautiful than you realize.