Humans pass on gut microbes to wildlife living in cities

Wildlife living in urban environments appear to have picked up some gut bugs from humans that are missing from their rural dwelling relatives, according to a report published today in eLife.

The results of the report, which was conducted in the US, suggest that urbanization affects both humans and wildlife in parallel ways, and that wildlife in cities acquire some of the bacteria that predominate in the microbiomes of urban-living humans.

The communities of microbes living in the gut of a vertebrate – collectively called the microbiome – tend to reflect the evolutionary history of the host organism. Microbiomes are usually similar between hosts of the same species, and dissimilarity of microbiomes between species mirrors the evolutionary distance between the hosts. However, close contact with humans can disrupt these relationships, causing a mismatch between host and microbiota evolutionary history and potentially contributing to disorders in the gut and other systems throughout the body.

“With the influence of humans on ecosystems becoming more pronounced globally, there is a need to better understand the effects of urbanization on global wildlife microbiota,” explains lead author Brian A. Dillard, a PhD student in the Department of Ecology and Evolutionary Biology at Cornell University, Ithaca, New York, US. “Others have shown that urbanization can alter the composition of gut microbiota in diverse species of wildlife, leading to differences between wildlife living in urban and rural settings, but we did not know whether urbanization has similar effects on the microbiota across host species.”

To explore this, Dillard and colleagues compared the gut microbiota of both urban and rural populations of three vertebrate species – crested anoles (a type of lizard), coyotes, and white-crowned sparrows – with the gut microbiota of urban and rural populations of humans. Using newly generated data as well as previously published datasets from public repositories, they analyzed nearly 500 microbiota profiles from faeces collected from 94 anoles, 78 coyotes and 320 adult humans. Samples from anoles were collected from urban and rural areas in Puerto Rico, samples from coyotes were collected from urban or rural areas around Edmonton, Alberta, Canada, and samples from sparrows were collected from urban or rural areas around San Francisco, California, US. Human samples were derived from rural communities in Malawi and Venezuela, urban centres across the US, and urban and rural communities in Tibet and Cameroon.

The samples were genetically sequenced to identify ‘amplicon sequence variants’, which can then be used to classify the microbiota in the sample. Analysis of the samples showed significant differences in gut microbiota within the same species of wildlife populations from different locations. In fact, the anole microbiota profiles changed in a way that reflected their distance from the most urban areas to the most rural, with the urban anoles having a microbiota that was more closely related to the microbiota of humans than was the microbiota of anoles living in rural locations. Similarly, the gut microbiota of urban coyotes was more similar to those of humans than was the microbiota of coyotes from more rural areas.

Next, the team looked at the differences in the abundances of specific microbes between urban and rural settings and whether these differences were shared between wildlife and humans. In every case, bacteria differed in abundance between urban and rural populations in the same way in both wildlife and humans. A group of microbes common in humans, called Bacteroides, accounted for up to 15% of the microbiota in humans from urban environments and was similarly overrepresented in the urban wildlife faecal samples. Bacteroides is one of the groups of microbes that is considered an established indicator of urbanization in humans, and the researchers say it seems likely that humans are the source of these microbes in urban wildlife. 

“The observation that these bacterial lineages found in humans increased in prevalence in urban wildlife is consistent with bacterial spillover from humans into wildlife in cities,” concludes senior author Andrew H. Moeller, Assistant Professor at the Department of Ecology and Evolutionary Biology, Cornell University. “Interspecies transmission of microbes can lead to deleterious effects for the recipient host, although that is not always the case. We still don’t know what effects, if any, the microbes identified are having on urban wildlife. What is clear is that wildlife microbiomes are more similar to human microbiomes in urban environments than they are in rural environments. We also know that changing the microbiome can affect health, so it will be important to investigate what the consequences are for wildlife hosts.”

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