Urban Wildlife Shares Human Microbiome

What happens to the bacteria we carry when people and animals share the same space?
16 September 2022

Interview with 

Andy Moeller, Cornell University


A coyote


When people live together, inevitably they share things, and that also goes for the microbes - dubbed the microbiome - that live on them and in them. But what happens when people and animals share the same space? Do they trade bugs too? As he explains to Chris Smith, that’s what Cornell’s Andy Moeller has been trying to find out…

Andy - One of the major ways we're impacting wildlife is through urbanisation, the spread of cities over the landscape. And we set out to answer this question of whether urbanisation and close contact with humans is actually leading to the spread of microbes from humans into wildlife.

Chris - Usually when this happens and there's a jump from wild animals into humans, the outcomes are not good. And one product of that is things like monkeypox, which is causing a headache around the world at the moment, and COVID possibly. So are we talking about pathological spread: us giving animals things that make them unwell, or are we talking about a more innocuous thing where I happen to coexist with an animal and some of the bugs that live on me and in me become incorporated into the microbiome of that animal too?

Andy - That is the key question, I think. Anytime, a microbe from one host transmits into another host species where these are two lineages, the microbe and the new host, that have never interacted before many times you can have very negative effects on the new recipient host. We don't know, in this case, if the bacteria that we find shared between humans and cities and wildlife in cities are deleterious or harmful for the wildlife, but there are reasons to at least speculate that receiving a microbe from a distantly-related host could end up being bad for the recipient.

Chris - How did you study it then?

Andy - What we did is we went out and sampled faecal samples. So we took faeces from wildlife, living in multiple different populations and multiple parts of the world living either in cities or in rural areas, more natural areas. And we simply asked, did the wildlife living in cities share more microbes with humans than the wildlife living in rural areas. And we found, over and over again, this increased sharing between urban wildlife and humans compared to the levels of sharing that we observed between rural wildlife and humans. And so the inference from that was that wildlife seemed to have actually acquired some of these human microbes.

Chris - Is it the interaction and proximity to humans, or is it that for instance, I eat a chicken and that does something to my microbiome; I Chuck the chicken bone in the bin and along comes "Mr. Fox". He raids my bin and eats the chicken bone, and the chicken has the same impact on his microbiome as it did on mine. Do we know whether that is the, the process or is it that I leave some of my microbiome on my chicken, "Mr. Fox" comes along and he picks up my microbiome directly?

Andy - That's a great point. So we can't definitively distinguish between those two alternative explanations. So I should back up, I've sort of been favouring the transmission explanation, but it is possible that there's parallel selective pressures. For example, like you mentioned, due to diet or some other shared environmental factor that leads to the same bacteria being selected for in both wildlife and humans and cities. I think that explanation, although possible, is less likely. It's a little more complicated, less simple of an explanation than there's this sort of cloud of human-derived microbes that's floating around us everywhere we go - our trash and so on, our waste - and that the wildlife in cities are likely just picking up microbes from time to time from humans.

Chris - Is there any evidence that it might be impacting the health of those animals? Because researchers in Australia did a similar sort of study looking at seagulls in the last few years. And they were concerned to see that seagulls, probably playing around in sewage outfalls, were picking up antibiotic-resistant forms of microbes - human forms - but they weren't necessarily becoming unwell in the process, they were just acting as vectors and they were spreading these things around. Do we have any insights, or what does that instinct tell us, these acquisitions or human microbiome makeups might be doing to these animals?

Andy - Yes. So our study finds this very significant pattern of increased sharing of microbes and urban settings, but we don't investigate or, or have any data to speak to the health effects on the wildlife of having microbes that are also found in humans. It is important to note, however that some of the microbes that we see in the urban wildlife that are missing from their rural counterparts belong to bacterial groups known to cause disease in humans. For example, very close relatives of Clostridium difficile. We see close relatives of that bug showing up in some of the wildlife.

Chris - So while there, there may not be direct or visible obvious health impacts on these recipient animals, it may almost end up with us parking some of our pathogens among that community, which may then in some way, continue to evolve or amplify, but ultimately might find their way back into us again?

Andy - Exactly right. It is a possibility. If multiple species of mammal and other vertebrates are able to harbour these lineages of bacterial pathogens, you're completely right, it could actually help maintain genetic diversity in that pathogen and potentially allow it to evolve in ways that it wouldn't have been able to evolve if it didn't have those reservoirs and wildlife.

Chris - Has anyone done the equivalent experiment in humans though, and you compare urban dwellers versus rural dwellers, do you also see sort of sharing - more sharing - of an urban microbiome in the people, and might that have an impact as well?

Andy - We do actually, if, when we just look at the humans, for instance, living in urban settings, their microbiomes tend to be more self-similar than humans from rural populations. So we see kind of this parallelism in convergence, in, in urban settings, among humans and also among humans and, and wildlife species

Chris - And turning it around then how do we know that what we are calling a human microbiome associated with urban living has gone into an animal. Could it not be that the animals give it to the human city-dwellers?

Andy - Right? So in that case, we can show that the microbes underlying this increased similarity between wildlife and human microbiomes and cities are also found in rural humans, but they're not found in rural wildlife. And so that observation tells us that these are more likely human-specific microbes or human-derived microbes than microbes that were already present in the wildlife before they moved into cities.


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