What Do Cities Look Like Under a Microscope?

[upbeat instrumental music]

[Narrator] This is a subway pole,

a turnstile,

a seat.

And this is what's underneath.

We did see some geodermatophilus species,

which can survive on rocks and hot environments.

We've also seen staphylococcus epidermis.

The most common species was a cutibacter acne,

which is something that's a normal skin flora bacteria

that is really just being shed off of our human bodies

into the transit system.

Hello, I am Christopher Mason,

a professor of genomics, physiology, and biophysics

at Weill Cornell Medicine.

[Narrator] Dr. Mason and his team started swabbing

subway stations in 2013.

We set up an app, a tracking system,

developed a protocol,

and we went on and swabbed every single subway station

in triplicate across New York City.

[Narrator] They're looking to discover and categorize

the microbiome found in city subways.

The microbiome is the collection of microorganisms

that are either in, on, or all around you,

and they include bacteria, viruses, fungi, parasites,

really any little organism that you can't quite see

but that has a strong, a really powerful feature

of mediating health and disease.

There are large cities today

where we just don't have a sense of what they look like

or even many environments,

really most of the world's environments,

we don't have a microbial or macroscopic view

of the biology that's there.

[Narrator] So, what do cities actually look like

underneath the microscope?

[bell dinging]

We normally swab at least three services for each city,

which is consistently the turnstiles,

the kiosks, and the benches.

Like, for example, in New York City,

there was geobacillus thermoleovorans,

which is this really hardy microbe that can survive

on rocks and soil and even be desiccated or dried out

and, you know, really it takes a licking

and keeps on ticking.

It goes on fine, like, I think, New Yorkers.

We can see that, you know, these really hardy microbes

have evolved for the harsh surfaces of the cities.

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[bell dinging]

In Naples, we could actually see

a lot of Mediterranean microbes that have already been found

that isolated in the shores of Italy

or in Greece that could pop up in the cities.

But then we could see, you know, other food-related microbes

that would pop up as well.

So, certain kinds of yeast that are associated

even with cooking pizza and sort of baking bread.

We could sometimes pick up more in Naples

than in other cities.

That was kind of interesting to see.

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[bell dinging]

We started sampling before, during, and after

the 2016 Olympics, and we could actually see, you know,

this change because a million people swarmed into Rio

and started to actually add their microbiome to the city.

So we've seen the burst of new species emerging

as there's a mass increase of humans coming into a city.

And so, that disrupted a bit of what the city looks like

at the microbial perspective,

but it also added some diversity to what's present.

So I actually think that the Olympics serve

not only as a gathering for sports and human endeavors,

but also gives this interesting, you know, addition,

like a probiotic to a city, essentially in a way.

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[bell dinging]

Tokyo actually has the greatest amount of novel peptides

or new sort of biology that we've discovered

from any of the cities so far.

And why this is is not entirely clear.

So there's a chance that, you know,

some of the novel biology that we find there

is because it's been so isolated from the rest of the world

at earlier centuries.

And so, you know, that's a hypothesis,

so we have to really test that,

but we're trying to not really blend microbial ecology,

modern genetics, plus history

to get a more comprehensive view

of what's happening in the cities and in their people.

Tokyo also had a range of new phages

or these viruses that attack bacteria

that we didn't see anywhere else in the world,

including some phages that are specific for C. acne

or a very common skin microbe.

So, you know, we can actually see that these ecosystems

on the surface and on the skin of people in these cities

really have their own geography

and their own specificity wherever you are in the world.

[Narrator] While each city

has a unique microbial footprint,

Dr. Mason and his team have identified

a core set of commonalities that cities share.

[bell dinging]

Across all the systems we've analyzed,

there's actually 31 species of bacteria and microbes

that are really consistently found.

We find them in 97% of every swab that we take.

So, on the one hand, there's this core set of microbes

that includes things like cutibacter acne

or geodermatophilus species.

Humans have evolved a tolerance for milk

over the past few 10,000 years

and this even is reflected in the subway.

Some of the species of lactobacillus are showing up,

things that you find in milk or in dairy products,

that we can also see riding on people's hands and skin,

and then show up in the cities.

We've seen a good number of extremophiles in the subway

in particular some that can survive

in say the cooling waters of nuclear power plants,

like deinococcus radiodurans is one

or other bacteria that are known to survive on stone

or survive under high UV light or a lot of radiations.

The subway system and the city's surfaces enrich for

and probably select for these hardier microbes

that can survive on rough surfaces

full of toxins and radiation.

But at the same time, we find that there's a lot of species

that are very unique to one part of the world,

that even give us a forensic capacity to tell, you know,

what city did you come from?

And if you look at your shoe, for example,

we can tell what about 90% certainty

where in the world you came from

just from the microbes that you're carrying with you.

[upbeat instrumental music]

[Narrator] With subways teeming with bacteria,

should commuters start to worry about the microbes

they'll encounter on the subway?

There is some good news in that there is not an avalanche

of pathogens waiting to greet you at the subway systems.

A pathogen is an organism that is known to cause

an infection and a disease.

We seen no evidence of wealth of harmful pathogens,

or really even that many opportunistic pathogens,

in the city centers or transit systems.

But rather we've actually seen

it seemed to be a relatively safe environment.

And even if we look at things like antibiotic resistance

or these antimicrobial resistance genes,

what you'll find in the subway and transit systems

is often less than what you'd find in the soil

or even in your own stomach.

From the first study, my favorite fact then and now

is actually that about half of the DNA that we sequenced

matched no known species.

It had never been seen before.

A new species means that it has to be at least 20% divergent

from anything that's been seen before,

meaning if it was a 100-page book of the genetic code,

at least 20 pages would be completely new

and never been seen before.

But evolution is conservative.

So actually, a lot of pieces of DNA

that we have are bacteria or viruses

get recycled and reused.

[Narrator] Their subway swabs uncovered

over 11,000 new bacteria and viruses.

There was all this unknown life

really under our fingertips.

But then other species we could see

looked like they were bacteria

that were associated more with rats,

or sometimes we'd actually see the rat DNA itself.

Actually, we could see cucumber DNA.

We can see plants and animals.

We can see more plant DNA closer to the parks, for example.

So, we could actually see this entire ecosystem of life

really reflected in the surfaces of the subway.

We've also seen a lot of new CRISPR arrays.

These are basically the bacterial immune systems

that are defending against other viruses,

and they also could serve as a new way to understand

how do the CRISPR systems work,

can you use them for new actually therapies or drugs

or even treatments.

CRISPR is even being used right now for gene therapies.

And so, finding these new bacterial functions

could potentially lead the way towards new medicines.

[Narrator] So, for commuters riding subways

around the world, you might not wanna touch the poles,

turnstiles, and seats like you used to,

but the microbes underneath our fingers serve a purpose.

I would actually think it's okay to grab the subway pole.

If anything, the ecosystem we discovered

shows that there's a very consistent core microbiome

that humans probably have evolved with

and essentially probably could use the exposure

to that environment.

So, instead of being afraid of the subway,

you could even go in with reckless abandon

and grab it with some confidence.

Or at least I do at this point.

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