Some metro systems have a reputation  for being clean as a whistle.

Others …I’m looking at you, New York City… have  reputations for being subterranean cesspools. We get it.

With 58 billion annual rides taken, the world’s  subway systems are bound to host some germs,   even in the cleanest trains and stations. And in the dirty ones… it’s frightening to  think about what could be festering in there. But more than a few scientists have studied  the microbial environments of subways,   and they’ve made some fascinating discoveries  about the differences between them.

So hold on tight and stand clear of the closing doors. You’re about to learn what’s riding  along with you on the subway. [♪ INTRO] Listen, microbes are everywhere and  you’re picking up a bunch when you   ride the T or L or the underground  or whatever you want to call it. We know because scientists in Mexico City swabbed   passengers’ hands before and  after they rode the metro.

By the end of a trip, the assortment of microbes  they collected was more diverse than at the start. So you’re picking up quite a variety of germs. And you’re getting them from the  guy down the car picking his nose. …Or maybe from the lady who shared a  section of her newspaper with you instead.

Based purely on vibes, I’d rather  have her bacteria all over me. But based on science, we know that after  a ride, the swabbed passengers’ microbial   milieu ended up looking a lot more  like their fellow commuters’ microbes. And it’s not just a Mexico City thing.

One of the most famous studies  on metropolitan microbes was set   in the New York City subway system: one  of the oldest and busiest in the world. It’s one of only a handful of  systems globally that runs 24/7,   and has a long-standing  reputation for being gross. Yes, I am picking on New York, but  we have a lot of Complexly staff who live in New York, and  so I am saying this with love.

Even the senior author of the New York study  was worried about how gross it might be. He said he was inspired to discover the  microbial underbelly of the City that   Never Sleeps when he caught his young daughter  licking a New York City subway pole and was,   understandably, concerned for her health. So he and his team got to work swabbing  more than a thousand benches, turnstiles,   handrails, and other places in every  single subway station in the Big Apple.

They collected tiny bits of microbial DNA and  then ran it through a process called sequencing. First, you identify the order of A’s,  T’s, G’s, and C’s in parts of that DNA. Then you run that sequence through a database  to see if it matches known organisms.

And they got more than a few matches. I’ll start with the good news: Of the top  10 most common bacterial species they found,   most were bacteria usually  found on skin or in soil. None of them normally cause disease  in humans, although several can cause   infections in people who are already sick  or have had a weakened immune system.

So maybe New York City deserves a little more   credit for their relatively  harmless subway microbiome. But New Yorkers weren’t the  only ones interested in the   microscopic stowaways of their transit systems. Researchers studying the T in Boston  found microbes all over that system, too.

But they noticed that the type of  surface, like a hand grip versus a bench,   was the biggest determinant of what  kind of microbes would be there. Hanging grips close to face  level had more oral microbes,   and seats had more vaginal-associated microbes. And before you raise too much concern  over what goes on in Boston transit,    those researchers pointed out that vaginal-associated  microbes can be transmitted through clothing.

So you can end up with different microbes  from riding with different people and   from coming into contact with different surfaces. But scientists in Shanghai found that microbes   in the air at subway stations  can also vary with the seasons. In their study, about 500 bacterial species were only detected during the springtime and more than 6,000  were only found in the summer.

Meaning: there’s no one subway microbe. Every trip has a different bunch of  microscopic passengers along for the ride. But for the most part, the microbes come from us.

And, importantly, researchers haven’t found a  ton of pathogens, or germs that make you sick. …Although note that I said they  didn’t find a ton of pathogens. It wasn’t unheard of for them to be lurking. But overall, things are looking a lot  less scary for public transit users   than you might have worried about  when we started this episode.

And on top of helping us all sleep easy at night,   these microbes are telling some pretty cool  stories about their specific neighborhoods. But before we can talk about all that,  all science needs funding, including ours. So, here’s an ad.

Thanks for watching this SciShow video! And thanks for supporting us on SciShow by  commenting, sharing, and joining us on Patreon. There’s a lot of online ways to  keep fact-checked information,   like what you find in these videos, around.

And now there’s a way to do that in person too! Complexly, the 501c3 non-profit that  makes SciShow, PBS Eons, Crash Course,   Bizarre Beasts, and more, is  holding our very first benefit! It’s called Something Worth Knowing and  it’s live at the Wilshire Ebell theatre   in Los Angeles California on September 16th, 2026.

This first-ever Complexly in-person  event is a fundraiser to support   our mission of inspiring curiosity and  lowering barriers to knowledge building   …because curiosity builds understanding,  and understanding builds a better world. You can get your ticket at  somethingworthknowing.org. See you there!

In one publication summarizing 60 cities’ worth  of swabbing and sequencing, each city had its own   unique microbial fingerprint determined by which  species were found there and in what amounts. Those researchers identified more than  4,000 different kinds of microbes. And most of them were specific to  less than a quarter of the samples.

That means part of each city’s microbial   fingerprint comes from some  super regional microbes. Each fingerprint was so distinct that a machine   learning algorithm could accurately  identify cities based on microbial data. And that’s even more impressive  when you consider how much of   the cities’ microbiome still overlapped!

More than 97% of the samples contained  the same 31 bacterial species. They might not have been the most  common microbes in each city,   but they did show up in almost every single one. Those 31 bacteria formed what the researchers  call the “core urban microbiome,” shared across   places as diverse as Singapore, Rio de  Janeiro, London, Barcelona, and Denver!

About half of those core microbes are known to  hang out with humans, like some that cause acne,   some that cause dental plaque, and  others that make your feet stink. These include staph and strep, which  might sound scary, but there are lots   of bacteria in those families that  don’t typically make people sick. And even the ones that do usually only  cause problems under specific conditions.

The other half of the core microbes were  bacteria commonly found in the environment. They tend to be harmless to you and me,  but can cause serious infections if, say,   you managed to get some in contact  with a catheter inside your body. …Which is unlikely to happen on the subway. I just had to mention that  they’re not totally harmless.

And then there are the weird ones. The microbe researchers found extremophiles  that live in and around rocks, and can   survive conditions that make other microbes  shake in their tiny boots …if they had them. I’m talking about exposure to heavy  metals, ionizing radiation, and UV light.

And, yes, all of these species tell a story. You know how Sherlock Holmes can see flecks of mud   on someone’s clothes and know  exactly where they’ve been? Now that microbial fingerprints have been  established for so many major cities,   we might have a higher tech version of that.

By sequencing the microbes on  someone's clothes or shoes,   detectives might be able to  figure out where they’ve been! Another helpful hint these microbes give us  is in relation to antimicrobial resistance. When pathogens evolve workarounds to  the chemicals we use to eliminate them,   they can end up becoming superbugs  that are very hard to kill.

This often happens when people misuse  antibiotics, like taking them when you   don’t actually have a bacterial infection  or not finishing your complete course. At that point, you’re just giving a competitive   advantage to bugs with mutations that  allow them to survive the antibiotic. So it’s not great if we find a bunch of   antimicrobial resistance in  our global subway microbiome.

But at least we’d know what we’re up against. And when it comes to knowing  what we’re up against, this   survey of subway microbiomes was super helpful. It identified almost 11,000  viruses that aren’t in databases! …Meaning we may never have seen them before!

We’re learning about a totally  new world of subway microbes. And they could turn out to be good guys  that only infect and kill harmful bacteria. So yes, they uncovered a giant amount  of microbes in our subway systems.

But no, you don’t need to be that worried  about getting sick from riding public transit. Remember, the overwhelming majority of microbes   identified in subway systems are not  microbes known to cause disease in humans,   but rather microbes that are already living  in and on human bodies without making us sick. But for those that do make us sick, a  study published in 2020 across 121 US   cities investigated if riding public transit was  associated with influenza and pneumonia deaths.

Those researchers compared  the death rates from those   causes to the percentage of people  in that city who use public transit. If public transit were a major cause of  disease spread, they figured that cities   with high proportions of transit users  would have the highest number of deaths. But they didn’t.

In fact, New York City, which had the highest rate  of public transit users at 57% of the population   over age 16, was among the 10 cities with the  lowest rate of influenza and pneumonia deaths. Despite the close quarters, the authors  think transmission was lessened by   typical practices like not talking to or  touching strangers when you can help it. And a simulation of an influenza epidemic in New   York City predicted that only 4.4% of all  transmission would happen on the subway,   compared to 30% of transmission  at home and 24.5% at school.

Those are the places you probably  spend more of your time anyway. So nasty viral infections don’t seem to be super  associated with riding the subway in general. But the giant caveat to that statement is that   there’s only so much we can  learn from DNA sequencing.

A DNA sequence alone can’t tell us whether a  microbe was even alive at the time of sampling. After all, DNA is a remarkably stable molecule,   so it can stick around long after  the organism it belongs to is dead. But even if the microbes are alive,  sometimes that’s a good thing too.

Many studies have shown that  exposing children to microbes   early in life is really important  for training a healthy immune system,   and might even prevent issues like  allergies and asthma later on in life. For adults, those microbes can also  become part of a healthy microbiome,   where there is often strength in diversity. So if you, like that researcher’s kid,   licked a subway pole, it seems  pretty unlikely you’d get sick.

But keeping your hands and arms  inside the car and your tongue   inside of your mouth is still probably a  good idea as you zip around the city. [♪ OUTRO]