New research can ‘fingerprint’ a city’s ecosystem to better understand the microbes within it

Chris Mason: The microbiome is the collection of all the organisms that you can’t quite see, hence they’re microscopic. And the biome is that entire ecosystem of the bacteria, the viruses, the fungi, even little bits of human DNA that might show up. There are plants, you know, really all the DNA that’s kind of under your fingertips when you ride the subway or get on the bus or really touch any city surface. There’s this whole ecosystem that’s right under our fingers. And we’ve begun to explore it, and just published work on 60 cities around the world.

It’s interesting because every city has its own real unique genetic fingerprint, which is really evident of what you see with your eyes when you travel to a different country, for example. You’ll see different plants and animals. And that’s very evident, of course, by eye. And so, our hypothesis going in was that we would likely see different city signatures, because this is just a really, an echo and mirror of what we observe at a macroscopic level.

And indeed, we did see that, that there are different types of species that really define different cities. So, for example, those by the coast often had more marine-related bacteria and some even contribute towards that sense of the smell of the ocean. When you’re in the city, you can actually see some of that in the bacteria and the viruses that we find. And also, a lot of them are really hearty microbes, ones that can survive on stone or metal. And then a third set though were ones that were pretty universal. You could see like skin-related bacteria for humans. So, you’ll see skin bacteria also show up pretty commonly.

There were three things that happened to me. One is, I ride the subway every day to the lab. So I got curious. The second is, we started doing a lot more sequencing of tumor samples and patient samples for looking for human DNA. But we always found microbial DNA, and I wanted to understand it better in terms of human disease. And the third thing really is I just became a parent, and my daughter one day actually licked a subway pole when she was 3 years old. And I really wanted to know what had happened because, clearly, if you lick a subway pole, it creates this really intense microbial exchange. And I wanted to know more. I’ve also seen people where, like other kids will be riding the subway, might grab a piece of gum and put it in their mouth that they found on the subway. So, there’s weird things that happen when you’re a parent. And I really wanted to understand what was there. And there was no data when we started this study to understand the microbial ecology in mass transit. So, we went to go figure it out.

This is the time to study. So, you know, I want to run towards information rather than away in fear.

Well, I think there’s two big takeaways, I think, from the study. One of them that we described is that there’s this really rich treasure trove of new biology that’s right under our fingertips. We found over 10,000 new viruses, almost 1,000 new kinds of bacteria that, as far as we can tell, are novel, and have not been observed before, and other kinds of species. We also picked up what are called new CRISPR arrays.

These are — you’ve probably heard about CRISPR in the news — it’s the way you can edit DNA. It’s being used in therapeutics and in diagnostics right now. So actually, we’re excited about it. This new biology is not just saying, oh, we found some new species, which itself is interesting I think, all alone. But also, we found that their biology reveals new biochemistry, new functions, really new microbial abilities that we can then use for essentially, potentially new medicines, new therapeutics, even new diagnostics. The second big takeaway, though, is that we also map the antimicrobial resistance, so the antibiotic resistance around the world.

And this shows us where we’ve seen more resistance in different pockets around the world. So, this can help with antimicrobial stewardship. When you basically prescribe antibiotics, you want to make sure you do it in a way that doesn’t increase resistance. But also, the way you stockpile antibiotics could be more tailored to the area in which you live. And so, you could have a better efficient deployment of antibiotics potentially in the future.

What’s intriguing is, we did see a change during the pandemic. So, this infrastructure we’ve built globally lets us track microbes around the world. And that includes SARS-CoV-2, or the virus that causes COVID-19. And we’ve been able to see that hand sanitizer and less people on the subways has created a disruption in that microbiome. Basically, there’s less human RNA, there’s less viral RNA. We did see in some cases, trace amounts of the virus in different cities, but none of them appear to be infectious.

And so, what’s interesting is this ecosystem that we’ve been tracking is now also a viral surveillance network where we can look for kind of an early warning system. And we can already see this past year of hand sanitizer, and people really avoiding mass transit has led to a decrease in the diversity of the organisms in our cities. So, it’s actually dropped down, and we expect, we’re sampling again on an ongoing basis, that we’ll see that that diversity and presence of the human RNA start to pick up again very soon.

It’s not necessarily good or bad. I mean, general biological diversity is a good thing for all ecosystems, including in your body and also in soils and forests. But for urban systems, it’s not as clear yet. It’s probably better to have it be more diverse, but it’s not necessarily bad. We just don’t know enough yet to say if it’s good or bad. We just know it’s changed so far.

You know, we saw evidence of microbes that are not just related to bacteria, but also we could see things that you often would find with dogs. So, basically, we could see evidence of the pets that people have. We could also see that these are bacteria that are often on plants. And so, when you got closer to a park, of course, it looked more like the park at the microbial level. We could see pollen, we could see viruses that are specific for plants. But I think, you know, just the weirdest thing we saw was that there’s these entirely new species, really thousands of new creatures that have been really in front of our face.

And we just have now cataloged them. And I think it’s really extraordinary that they’re there, but then also that we found organisms that are heavily resistant to radiation, UV, or X-rays, and they can survive on hard stone surfaces. So, we found out there’s these hardy microbes that you could even find in cooling waters of nuclear power plants that also can persist just fine on a harsh curb or a surface of a steel railing. And they’re really hardy microbes that can be really tough. And so, I think it’s a bit like the New Yorkers — they’re kind of tough and can take a look and keep on kicking.