Gas Chamber: An Industrial Accident at a Poop Science Lab

The tale of my worst invention

I work at a microbiome startup, where we’re trying to cure depression with poop. Specifically, with individual strains of bacteria from poop. It’s really exciting, because it’s got a better shot of actually curing someone than SSRIs ever did, but it’s a dirty job—and sometimes things happen to you that should never, ever happen to anyone. This is a story of one of those things.

To set the stage: it’s a typical Tuesday afternoon in our BSL2 lab, and I’m growing some bacteria. This one’s a strain that produces GABA, the primary inhibitory neurotransmitter in your body. It’s a species of Bacteroides, which means it’s a strict anaerobe—exposure to any more than trace amounts of oxygen is lethal to it. (There’s practically zero oxygen inside your GI tract. Weird, isn’t it? Given that your body runs on the stuff.)

But this low oxygen tolerance is a big part of why, even though Bacteroides is much more important for gut health than any Lactobacillus or Bifidobacterium, you can’t buy it as a probiotic yet: it has to be grown in a zero-oxygen environment, and it’s expensive to build that kind of thing at an industrial scale. We have a lab-sized one at work, though; an anaerobic chamber. It’s a big plastic bubble full of nitrogen, with glove-ports so you can work inside it and an airlock that lets you move things in and out without introducing a bunch of room air.

This is what they generally look like. That’s the airlock on the right; the box with black doors is a temperature-controlled incubator.

So I’m growing a bunch of this bacterium, so that we can dose it into animals and see if it has an antidepressant effect. I make a few liters of nutrient broth, grab a vial of the bacterium from the freezer, and cycle them both into the chamber.

“Cycling it in” just means you open the outer door of the chamber’s little airlock, put your stuff inside it, close the door, and press a button. A loud vacuum pump starts buzzing for a few seconds, sucking all the air out of the airlock, then shuts off with a sound like someone letting out a huge breath.  That sound comes from the gas tank, which is letting pure nitrogen flow into the airlock, replacing the air that just got sucked out. The cycle repeats to get any oxygen it missed the first time, and then once more for good measure. After the third cycle, you hear a pleasant little beeeep.

I wriggle my hands into the glove-ports, open the inner door of the airlock, and bring the broth and bacteria into the chamber. I inoculate the broth, put it in the incubator since they like to be at 98.6℉, and leave it.

Harvest Day

A few days later, I put my hands back into the chamber’s glove ports, open the incubator, and pull the culture flasks out to examine them. It’s grown nice and thick—it looks like a few liters of hazy IPA, opaque and golden…even a little foam at the top from the gases produced in fermentation. It’s ready to be put in the centrifuge, and subjected to something like 20,000 times Earth’s gravity to concentrate all the bacteria into a sludgy mass that we can use in our experiments.

I carefully pour the hazy liquid into the special centrifuge bottles and move them to the airlock. I shut the inner airlock door. I open the outer airlock door and realize, shit, I forgot to weigh the bottles. You have to weigh the bottles. If the weight distribution in your centrifuge is lopsided, it can wreck the equipment in a truly spectacular and deadly way. So if one is heavier than the other, you pour a little off into the lighter one until they’re equal.

But you can’t pour liquid back and forth outside the anaerobic chamber without aerating it, and that’s bad for the bugs. Having realized my mistake, I quickly close the outer airlock door and hit the button to cycle them back in. As the first vacuum/flush cycle is buzzing away, I put my hands back in the glove ports and take the cover off the little weighing scale inside the chamber.

I notice a faint smell. I blink. Did I...fart?

I’m alone in the room, which—for reference—is about eight feet by ten feet. The first vacuum cycle ends and nitrogen whooshes into the airlock. I conclude at the back of my mind that I must have farted and not realized it, because the smell is definitely there, only now it’s slightly stronger.

The vacuum starts up again, and now something catches my eye: through the clear acrylic of the airlock door, I can see motion. The flasks are bubbling furiously, as if they’re boiling. I panic for a moment, wondering just how badly I’ve fucked things up. I realize I’ve never put a finished ferment through the airlock’s vacuum cycle before, since you don’t need to “cycle” things when you’re taking them out—only on the way in.

I’m suddenly transported back to undergrad. A physics class; some ruddy-faced TA in a ringer tee explaining partial pressures on an honest-to-god chalkboard.

You know how, when you crack a soda or a beer, it starts to fizz? When the bottle is sealed, the pressure is high enough that all the carbonation stays dissolved in the liquid—a 2-liter bottle of soda actually contains about six liters of dissolved CO2. Opening the bottle reduces the pressure, which lets the gas come out of solution, and it all starts to bubble to the surface.

The panic fades as I realize that the bacteria will probably be fine; the “boiling” I’m seeing must just be gas that they produced during the fermentation, pulled out of solution at hyper-speed by the vacuum. I marvel for a few seconds at the sheer volume being released.

The panic returns, as a few things occur to me in quick succession.

It occurs to me that the vacuum which pumps the air out of the airlock probably vents directly into the room.

It occurs to me that the smell I noticed earlier has continued to get stronger, and is rapidly approaching unbearable.

It occurs to me that, while the gas produced by human gut bacteria grown in a sulfur-rich medium is not technically a fart, this distinction is what most people would call “splitting hairs”.

The final realization, really a combination of the first three, is that I’ve just accidentally invented an industrial-scale Dutch oven. By the time this realization hits and I start the laborious process of extracting my hands from the glove ports, the third vacuum cycle is underway and I am gagging on the air.

Think of the last time you smelled a fart that could be neither ignored nor denied. The kind that, by its sheer foulness and intensity, demands an acknowledgement. The kind that makes you glare at the offending person, skipping over the customary, narrow-eyed “Did you…”, and go straight to “Awh, what did you eat?”

Think egg farts. Think meat farts. Imagine those smells, but magnified beyond anything achievable by the human body alone, subject as it is to the constraints of geometry. With this marvelous machine I’ve just inadvertently created, it’s suddenly as if four thousand people have squeezed into this 8’x10’ room with me, after a preparatory week of consuming nothing but hard-boiled eggs and beer, and have all simultaneously, on cue, ripped ass.

I retch. I begin to wonder if I can die from this. I start to hope so.

As I claw free from the chamber, there’s a weird moment where time seems to slow down. My body is scrambling towards the door, but my mind starts to wander, lost in a sulfurous haze.

I wonder about the person who this strain was isolated from, and experience a distinctly psychedelic feeling of connection to them. I’ll probably never meet you, I think, but across time and space, I’ve smelled your farts. The sense of profound awe is followed a wave of sadness, as I realize that the disgust I’m experiencing is disconnected from its natural equal-and-opposite, the gleeful schadenfreude typically afforded to the one who “dealt it”.

I hope that somehow, wherever they are, they feel the inexplicable urge to cackle.

My hand closes around the door handle and I burst into the hallway, gasping.  The world comes back into focus as I hear the end of the vacuum cycle signaled with a pleasant little beeeeep.

The entire series of events, from start to finish, has taken maybe twenty five seconds. I take a minute to come to grips with what’s just happened, catch my breath, and let the room air out a bit. A BSL2 facility during COVID has the saving grace of good air exchange, and within a few minutes I can reenter the room, weigh and balance the bottles, and load them into the floor centrifuge for a forty-five minute spin.

I drop my lab coat in the bin to be laundered, leave the lab, and walk to the hair salon next door. They have time for a walk-in.

“Can we do a shampoo?”

Epilogue

I was lucky enough to walk away from the event totally fine, if a little humiliated. My suffering wasn’t for nothing, either: the results of the animal experiments look promising.

And, on a personal note: the startup where this all went down, Holobiome, has been my scientific home for the past three years or so. It’s been a great ride, but as of this month I’m moving on to work at a company called Seed. (If you’ve ever googled anything to do with probiotics, they’ve likely shown up in your instagram feed.) This blog has taken a backseat as I’ve navigated that transition, but I’m back in action now, so you can look forward to more regular updates over the next few months.

—🖖🏼💩