Microbial Archives

Yogurt, rice, and orange peels—a classic combination, right?

No? Well, it is for me. The deepest recesses of my memories recall the taste of my grandma’s yogurt rice: the very specific tang of her yogurt, the exact mushiness of her Jasmine, not Basmati, rice. And, the magical ingredient, a dollop of orange peel oorugai, a Tamil savory pickle condiment that, to this day, I’ve only seen in my grandma’s kitchen (though a cursory Google search shows it’s not a totally obscure item).

My visits to my grandparents’ home revolved around food. As soon as I’d walk in the door, I’d grab my stainless steel plate from the same cabinet as always and plop down at the kitchen table. A variety of cooking vessels covered by an assortment of mismatched plates-as-lids sat waiting for me. I’d lift a plate to take a peek at what sat beneath, aromas wafting into the air. I’d start by laying down a hefty helping of rice, then place vegetable dishes around the rim of my plate. Finally, I crown the rice with two ladles of rasam. I’d scarf down one plate, then another, and then the grand finale: theyir chadam (yogurt rice) with orange peel oorugai.

My grandma passed away last year. I won’t have another helping of her theyir chadam and orange peel oorugai again. I have her recipes. I can get close, but it’s not quite the same. I wonder if, floating in the air and crawling on the surfaces around us, the invisible world of microbes might provide us the information we need to recreate the smells and tastes of our past.

Fermentation is as close to alchemy as we’ll get. Throw some milk in a pot, heat it up, let it cool a bit, add a spoon of yogurt, and overnight, you’ll have a new batch of yogurt. Magic.

The true magicians in this trick are lactobacillus – a kind of bacteria that eats the sugar in milk and excretes lactic acid. They like warmth – ~110 degrees is perfect – and multiply in droves when they’re both well fed and comfortable. As they multiply, more and more of them excrete lactic acid, we not only start to taste the tartness of the acid, but the proteins in milk also start to denature and reform into a matrix that takes on the texture that we associate with yogurt.

The lactobacillus that turns milk into yogurt remains active in yogurt, so we’re able to use yogurt as a starter culture when making new batches. And lactobacillus can be found in many other places: on our skin, in our bodies, on the surface of many fruits and vegetables, to name a few. We can make yogurt by replacing our yogurt starter with, say, a piece of ginger with the skin unwashed and unpeeled. It might be less reliable than a yogurt starter, but if there’s enough lactobacillus crawling around, it should work.

But – it’ll taste a bit different. In fact, your homemade yogurt and mine will probably taste different from each other. Yes, some of that variance has to do with the milks we used and the exact temperatures at which we took our milk to and incubated the yogurt. But some of that variance will likely also be due to the exact combination of microorganisms present in our yogurts. Our yogurts, and all other fermented foods, have some microbial terroir.

Taste and smell are often linked with memories: one whiff of a glass of Frank Cornelissen Nerello Mascalese wine can take you directly to the summertime slopes of Mount Etna. A glass of wine encodes information about climate, time, geography and soil health in what the wine world calls “terroir.” Chocolate and mezcal, among many other fermented foods, also have a notion of “terroir” among well-adjusted palettes. How and why humans have been able to taste that encoded information has been a bit of a mystery. To some, it’s voodoo, yet trained palettes have been able to ID wines blind, all the way down to the producer, time of year, and plot of land. How?

Emerging genomics research¹ shows a couple of promising signals: 1) that microbial activity could be a strong factor in the production of tastes and smells that create what we perceive as flavor; and 2) that specific microbiomes may function as the unique identifiers for particular terroirs. Put simply, the microorganisms that ferment our wines (and cheeses, chocolates, mezcals, and yogurts) may be the link to understanding “terroir.”

This research points towards a future where we can demonstrably identify terroirs of wines and other food products transformed by microbes. However, there are miles to go in research to understand the interactions between different microorganisms and their metabolic inputs and outputs – the precursors to what we might eventually taste and associate as the terroir of a food or drink.

How might this emerging research about microbial terroir help me rediscover my grandma’s special touch in her yogurt and oorugai? And how might we contribute to pushing this research forward without PhDs and wet labs?

Imagine if it were simple to take a swab of my grandma’s kitchen and get back a reading of the microorganisms present in that sample. That may have given me some more insight into the particular strains of lactobacillus that could have made their way into my grandma’s yogurt. The makeup of her kitchen’s microenvironment could have changed fairly often; after cleaning, after visitors after, at different times of day. So, we’d want to build up a collection of samples over time and understand how the microbiome of her kitchen evolved over time, and how that might have impacted (or not impacted!) her yogurt’s terroir.

Imagine if it were simple to take a swab of my grandma’s kitchen and get back a reading of the microorganisms present in that sample. That may have given me some more insight into the particular strains of lactobacillus that could have made their way into my grandma’s yogurt.

As more and more of these microbial archives of different kitchens, and different environments more broadly, are recorded we might be able to start understanding more of the links between the microbial world and our human-scale world.

Data-collection focused on understanding microbiomes does happen today – it just predominantly happens in university and commercial laboratories. However, both the cost of sequencing microbial genomes and the accessibility of DIY hardware and services have improved greatly over the last decade. Not so long ago, it cost billions of dollars to do genome sequencing; now it costs hundreds. Handheld sequencing devices like the MinIon are within-reach for at-home tinkerers and would-be microbial archivists. Community labs like Genspace NYC make these tools and knowledge even more accessible.

Other artists, researchers, tinkerers, and businesses have brought parts of this vision together already. Here are some examples:

• Dogfish Head, a Delaware-based brewery, recovered molecular material from King Midas’ tomb and made a beer that aimed to give us a sense of what that beer might have tasted like then. It wasn’t recreated from microbial material – but illustrates an analogous idea. They’ve turned this approach of bringing beers from the past back to life into their Ancient Ales series.

• Sissel Tolaas is an artist focused on exploring smell and scent. She’s archived over 7000 smells from around the world and draws upon them to create art experiences that ask us to engage with the unseen world and memory in novel ways. She also teamed up with artist Alexandra Daisy Ginsberg and the biodesign company Gingko Bioworks to recreate the smell of extinct flowers from small amounts of DNA recovered from museum archives.

• Elizabeth Henaff, professor at NYU’s Integrated Design and Media (IDM) Program (who I was fortunate enough to study with) collaborated with Cornell’s Christopher Mason on a project that showed how microbial samples from NYC’s subway system could tell us about New York City itself. Subway stops near pizza shops, for example, left trails of yeast from cheese and dough.

Affordable tools for doing DIY microbial sampling and sequencing may lead to non-commercial, non-medical, surprising research. With inspiration from researchers and artists also exploring the unseen world around them and the unseeable memories from our pasts, we can expect a diversity of explorations unlike the medical and commercial ones we’ve predominantly seen today.

With greater archiving of the microbial world around us, we may deepen our understanding of the ways other lifeforms, especially the invisible microbial ones in and around us, are so intertwined with humanity… for purposes more important and substantial than trying to replicate my grandma’s yogurt. With deeper empathy for lifeforms of all kinds, perhaps we will choose to design human constructs with more than just human life in mind.

¹ In “Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate (2014),” Nicholas Bokulich and his collaborators suggest that there are significant correlations between each of temperature, geolocation and temporality with corresponding unique microbial communities. As a result, the same grapes grown by one winemaker down the coast from another demonstrate significantly different microbiomes.