The Time I Accidentally Destroyed My Armpit Microbiome

Sort of an origin story, come to think of it.

The year is 2017. It’s the middle of July, a characteristically sunny day in San Diego. I’m sitting in the jacuzzi of a community pool in one of the city’s outlying developments. I chat with my host—a scientist who lives in the neighborhood—who squats on the concrete nearby. Despite the hot tub, I am not relaxed. We’re here because I couldn’t come into his lab without raising a lot of eyebrows.

It’s uncomfortably warm to be in a jacuzzi, and I ask if it’s been long enough, if I can get out. He gives a kind of shrug which says: Your guess is as good as mine.

I get out, and take a thorough shower in the pool’s bathroom before going back over to meet him in the umbrella-shade of the table where our things are set. From his bag, he produces a box of waxing strips, which he hands to me, and a pair of gloves, which he puts on. He shows me how to apply the strips, and offers to do the first one.

Sure, I say. He yanks the strip away.

It stings, but less than I was expecting. That wasn’t bad at all, I think. I look down at my armpit. There’s still basically as much hair there as before.

Getting it all takes practically the whole box of strips—four or five tries on each side—and each subsequent yank is more painful than the last, eliciting stifled grunts of pain to accompany the distinct sound of adhesive paper being peeled from skin. The pool area is mercifully empty; the only other person there is an elderly woman swimming laps, who has apparently resolved to pretend that we’re not there. I can’t help wondering what she thinks is going on. Just one dude teaching another how to wax?¹

At last, the hairs are gone. I take a deep breath and inspect my armpits, noting with interest the thousand tiny droplets of red, welling up like gems where some of the hairs had been. I am bleeding from the pores.

My companion in this adventure reaches into his bag again, and produces a bottle of ethyl alcohol and some lime juice. My stomach lurches.

Hey, alright, shots! I quip. Where’s the salt?

In my heart, I know that I will not be so lucky.

*Record scratch*, I bet you’re wondering etc. etc.

The above is not, in fact, the story of how I destroyed my armpit microbiome; it was part of the quest to fix it. But we’ll get back to that. First, let’s rewind another three summers.

It’s 2014, and I’ve just graduated college. I’m living, for the summer, in the dorms of George Washington University in DC—courtesy of an internship with the Society of Physics Students.

It’s early in the day, but already clear that it’s going to be a stifling one. Outside the bars of my bathroom window, a busker with a saxophone is riffing on the Star Wars theme. I hop out of the shower, hurrying through my morning routine so I can catch the metro out to College Park, where the American Physical Society has its headquarters. I go to put on deodorant, only to wince as the plastic scrapes my pits; the stick I’m using has reached the end of its life.

I’d known this was coming—you never reach the end of your deodorant without being aware at least a few days in advance—and I curse myself a little for failing to get ahead of the problem. But then an idea strikes me. I remember reading somewhere that sweat itself isn’t actually responsible for the smell of body odor—rather, it’s bacteria living in the armpit, which eat the fatty acids in your sweat and excrete odorous byproducts.

Like any good intern fresh out of college, I had my priorities straight: no deodorant, but plenty of alcohol in the house. I even had some homebrew limoncello in the works, which at that point was just a bottle of vodka with a few lemons’ worth of zest steeping in it.

Hey, alcohol kills germs, I say to myself. If it’s the bacteria that smell, maybe this’ll do. I splash some of the lemon-scented vodka onto my hands and rub it into my armpits. I congratulate myself on my ingenuity and—lemony fresh—set out for work.

And it works! Despite the muggy summer heat, I go the whole day without catching an offensive whiff of myself, and don’t even think about the deodorant problem again until the next morning, when I’m faced with the same dilemma as the day before. I do the lemon vodka pat-down again, telling myself that I should probably go and get some actual deodorant sooner or later, but still pleased that I’ve found an interim solution that works so well.

After three or four days of this, I’m starting to seriously cut into the yield on this batch of limoncello. I skip the alcohol rinse and head for work, resolving that tonight is the night I’ll get my shit together and run to the store for some deodorant.

Halfway through the day, I realize: I have made a terrible mistake.

Body odor is one of those things that everyone seems to experience differently, but hopefully you understand what I mean when I say that most people’s sweat shares a characteristic undertone of funk. It’s a little spicy—somewhere near the smell of cumin, in olfactory space—but it’s not exactly unpleasant. On the right person and under the right circumstances, it can even be sexy. Being trapped on a train car with too much of it can start to get claustrophobic, but it’s fundamentally a sweaty human smell.

On this first day that I went without deodorant, I discovered that this smell—any semblance of a normal human body odor—was gone from my pits. In its place was what I can only describe as metal and onions with a side of mildew, although that doesn’t quite capture it. It was sharp, rank, and dank in all the wrong ways. What the Grinch would smell like, if you could smell him.

I was already aware of the concept of a microbiome by this point, thanks to an evolutionary biology class I had taken in my final year of undergrad. I knew that these ecosystems were often fragile, and could be tipped out of balance permanently by a single perturbation. I even had a strong hunch—bordering on a conviction—that such disturbances in the gut were behind a number of psychiatric diseases.

So it didn’t take long for me to realize what I had done: I had burned down the jungle. Whatever innocuous microbes had been living all my life in the verdant rainforests of my armpits, fermenting my sweat into those normal-funky-human byproducts—they were no more. Instead, all I had was whatever hardy bastards had survived the fire, or else grown back quickly enough to take over.

That night, after a train ride spent deliberately sitting as far from anyone else as possible, I bought a stick of deodorant—one of the crunchy, “natural”-branded ones, with some kind of vegetable wax as its main ingredient. I wanted something to keep the stink down, but was worried about doing even more damage to the ecosystem than I had already done. It did a fine job of keeping the problem in check. As long as I didn’t smell at all, I didn’t smell bad. I would check, periodically, to see if the situation had righted itself: Right out of the shower, when the previous day’s deodorant had been washed off, I would lift and sniff.

Bad. Bad, bad, bad, even fresh out of the shower.

A Visit with Dr. Armpit

Fast-forward to 2017, to the sunny poolside where we started this story. I’m in San Diego on a work trip, and—after years of experimenting with various remedies both natural and artificial—I’ve managed to find a researcher who studies the axillary² microbiome for a living, and happens to live in San Diego. He’s sympathetic to my situation, having found his way to the field through a story similar to my own: apparently, he had picked up a bad Corynebacterium from sharing a bed with a rather smelly girl. Still, he’s not keen to experiment on a random stranger from the internet. It takes pleading, cajoling, and—eventually—the promise of a few hundred dollars in cash to convince him to devise a protocol.

When we meet up, he does a quick sniff test and confirms that I’m likely dealing with the same type of organism: Corynebacteria are a part of most people’s axillary microbiome, but they’re usually a minor component, kept in check by native Staphylococci and other less malodorous microbes. It’s a hard problem to rectify, he explains, because these organisms dwell in some of the deepest layers of the skin—down near the base of the hair follicles in the tiny glands where sweat, oils, and a waxy secretion called sebum are produced.³

This is why the first step is a soak in the hot tub: to liquefy the waxy stuff at the base of my hair follicles and make it easier to clear them out. After the decidedly unpleasant waxing process, all that’s left is to take our best shot at sanitizing the turf, and then reinoculate with good bacteria.

Easier said than done. If the waxing had stung, the next part seared. As I swab the area with alcohol on a sterile gauze pad, I become exquisitely aware of just how sensitive a body part the armpit really is. My skin flushes hot, as alcohol mixes with the blood still seeping from thousands of freshly opened follicles—flowing into the tiny channels like liquid fire, then like ice as the fluid starts to evaporate and cool the skin. My nerve endings scream out to my brain in alarm and confusion. I swear through gritted teeth. I take a breather before doing the other side.

The lime juice is next. It seems like a cruel joke, and if I hadn’t initiated this whole thing I would wonder if I’m being pranked—but the man who devised this new and interesting form of torture explains to me that low pH plays a crucial role in biasing the environment against Corynebacterium and in favor of the “good guys”. By this point, either the nerves have given up on their distress signals, or the series of assaults has triggered such a rush of endorphins that I barely notice as the juice goes on.

The worst of it is over.

A little dazed but rapidly recovering, I watch with interest as my companion reaches into his bag and pulls out a stack of petri dishes wrapped in a waxy film.

Hesitantly, I ask: Are you sure we can’t just…I make a finger-twiddling gesture toward his armpits, then toward mine, accompanied by a little boodleoop noise. He gets a grave look on his face. Absolutely not.

In response to my disappointed expression, he elaborates. You’ve heard of MRSA?

I had. It nearly killed my mom, after a surgery a few years prior.

Better to be stinky than dead, right?

I had expected this. In our email exchange, he had explained to me that, with a complex community, there’s no telling what will take hold and what won’t. A transplant would run the risk of introducing an opportunistic pathogen like MRSA—while failing to transfer some other species that would prevent it from becoming problematic. Instead, the plan is to introduce one well-studied commensal called Staphylococcus epidermidis; a dominant species in the axillary microbiome of people who have an inoffensive body odor. There’s no way of knowing if it’ll work, but it’s a best guess—and if it goes wrong, we know which antibiotics can kill it.

I accept it, nodding as I lean back against the rubbery straps of the poolside chair. He carefully unwraps the plates, and through the clear plastic lid of the petri dish, I can see a beige substance stretching uniformly over the surface of the gelatinous material inside. He punches a sterile cotton swab out of its package, and runs it through the beige gunk with a rolling motion, picking up as much of the stuff as possible.

We inoculate my armpits.

The Way Back

The following week is a weird one. I work our booth at Comic Con, handing out physics-themed educational comics and little LED circuit kits to anybody who will take one. Under my shirt, the makeshift bandages chafe whenever I move my arms: we’ve rigged up an elaborate system of gauze pads and medical tape to keep as much of the inoculum on my skin as possible. I take them off to shower—no soap on the pits—and then put them back on with fresh tape.

By the time we’re packing up the booth to head home from San Diego, there’s a downright bizarre smell coming from the gauze. Almost cheeselike. The smell from my armpits themselves has maybe changed slightly—there’s definitely a note of the gauze smell in it now—but it’s by no means “normal”.

On the flight back east, I console myself with the knowledge that, on the ranked list of “craziest-smelling people at Comic Con”, I wasn’t even in the top quartile. At the end of the week, I trash the bandages, and the cheesy smell goes away overnight.

Slowly, my armpit hair starts to regrow (although I swear it’s less thick than it used to be, to this day) and I get on with my life, accepting that there are worse fates than a life of mandatory deodorant. Casual attempts to convince friends to let me steal their armpit bacteria go about as well as you’d expect. A few years later, recounting the story to an Uber driver earns me a laugh…and a worthwhile tip.

Where I come from, he says in a thick Ghanian accent, we just use limes.

I try it that night, and am surprised to discover how well it works: the smell disappears almost instantly. I recall “Dr. Armpit’s” comment about the pH preferences of different bacteria, but suspect this has more to do with chemistry than biology because of how quickly it happens—maybe changing the pH reduces the volatility of some of the smellier compounds. But over the next year or two, as I sub in lime juice for deodorant whenever life allows it, the smell seems to gradually improve even without the juice—and I wonder if I’m reshaping the ecosystem of my armpit microbiome.

But earlier this year, I came across a paper from 1953—one of the original treatises on bacteria and B.O.: Axillary odor; experimental study of the role of bacteria, apocrine sweat, and deodorants by Shelley, Hurley, and Nichols. It’s a scientific tour de force—the kind of exhaustive investigation that, these days, you rarely see outside a big-name journal like Nature or Science. They trained a team to perform blinded olfactory ratings, tested different deodorants, injected people with epinephrine to activate their apocrine glands, collected sterile sweat, inoculated that sweat with various bacteria to explore their impact on the odor profile, tested topical antimicrobials for their effects on B.O…they really left no stone unturned.

One key takeaway from their findings: there are some people with armpit bacteria that make them smell better than the rest of us.

Back then, it was okay to call them “Aerobacter”, rather than the more politically correct “Klebsiella” we would use in this enlightened era.

But the big finding—the one that made me smack my forehead? There’s a simple way to take the smell out of even the stinkiest sweat.

It’s aluminum. Normie deodorant.

It looks like this effect is also as much chemistry as it is biology, in that it’s an instantaneous change rather than one that reshapes the microbiome to produce less offensive odors to begin with. Still, it took me by surprise to realize I had succumbed to the naturalistic fallacy—assuming that “artificial” aluminum deodorants would necessarily make the problem worse.

I switched from my hippie deodorant to Degree, and—wouldn’t you know it—smelled more or less normal again within the hour. Sorry, Tom of Maine.

I still have hope that someday we’ll be able to figure out a natural solution: to find those happy few people blessed by nature with “pleasant” B.O., and convince them to share their gift with the world. It seems like the kind of product that would kill among a certain subset of the Silicon Valley crowd. It won’t necessarily be easy, though…the one genus reported by Shelley, et al—Klebsiella—is an opportunistic pathogen, frequently antibiotic-resistant and with a tendency to cause sepsis if it gets into your bloodstream. Getting clearance to sell it as a cosmetic seems like an uphill battle.

There are other layers of intrigue here, as well. Take the famous “sweaty t-shirt test”—an experiment which found that people can smell one another’s genes. The study involved giving a number of men new t-shirts, and having them get ‘em nice and gross by wearing them for a few days. Then, a panel of women were asked to huff the shirts and rate the smells on their attractiveness.

Sequencing the genomes of the participants revealed a consistent pattern in the results: a woman was more likely to rate a shirt’s odor as attractive when it came from a man whose genes were dissimilar from her own—specifically in a region of the genome called the major histocompatibility complex, or MHC. This is an immune locus, the bit of the genome which helps your body differentiate your own cells from those of other organisms. Curiously enough, it’s also where you find most of the risk genes for diseases like schizophrenia.

But we know for a fact: it’s not the sweat itself that smells. It’s the fermentation products of that sweat…so the results of the sweaty t-shirt test must be mediated by the armpit bacteria of the participants. This makes sense: if the MHC encodes the list of which cells get a pass from the immune system, it likely plays a role in determining which bacteria are allowed to stick around. One implication of this is that there may be no one-size-fits-all bacterial fix for B.O.; it’s possible that, if I tried inoculating my armpits with the Klebsiella described in that 1953 paper, my immune system would destroy it. Hell, maybe that Klebsiella only smelled pleasant to the researchers because they had MHCs very dissimilar from the people the bacteria came from.

As for what it means for schizophrenia…I have a theory. We’ll get to that next time.

-🖖🏼💩

1. I have since been informed that you are supposed to shave, or at least trim, before trying to wax an area. Unfortunately, both this researcher and I are dudes, and neither of us knew what we were doing. This is why we need more women in STEM.

2. that’s science talk for “armpit”

3. There are, in fact, two kinds of sweat glands in your body. The eccrine glands, which reside closer to the surface, are responsible for the sweat your body produces to cool itself when you’re overheated. Eccrine sweat is primarily composed of water and electrolytes, and doesn’t tend to smell as much. The apocrine glands, which are seated deeper, are the ones which contain more oils and other substrates for bacterial fermentation. These fire up in response to adrenaline and other stressors, so apocrine sweat is the kind you produce when you’re nervous—and it’s believed that this is a major part of the subliminal milieu of sensory signals that allows animals (or particularly perceptive humans) to sense when a person is afraid.