Birds, bats and bacteria


Extensive study questions microbial co-evolution across species.


Evolving to fly may have had an unexpected effect on the likes of the Kenyan fruit bat (Epomophorus wahlbergi).

Holly Lutz.

By Natalie Parletta

Collecting poo samples from nearly 900 different species of invertebrates might seem daunting – and messy – for some, but not for an international group of scientists from more than two dozen institutions.

Their study, published in the journal mBio, has upended current thinking about microbial similarities between related species by revealing that, unlike other mammals, bats have unpredictable gut bacteria much like birds.

This suggests that evolving to fly may have a dramatic impact on the gut microbiome, raising questions about how evolution impacts microbial communities.

Research has established that gut microbes co-evolved with mammals – including humans – over millions of years and are intimately connected to diet and wellbeing.

But the new study implies that mammals’ reliance on their microscopic friends may be unique, according to co-first author Se Jin Song, from the University of California San Diego.

“This represents a paradigm shift in how we think about animals and the relationships they have with their microbes,” he says.

Initially, Song and colleagues expected to find that all mammals would have similarly close relationships with their gut microbiome – termed phylosymbiosis – enabling the types and quantities of their microbial communities to be predicted.

“What was shocking,” he says, “was that we didn’t find that birds and bats share a similar microbiome per se, but rather that both lack a specific relationship with microbes.”

While all mammals showed clear patterns of bacteria in closely related groups, those found in flying birds and bats were virtually unpredictable.

“It’s almost like they’re just picking up whatever’s around them and they don’t really need their microbes to help them in ways that we do,” says co-author Holly Lutz from UC San Diego and Chicago’s Field Museum.

Micro-organisms might, therefore, have less importance for supporting healthy digestion in bats and birds, possibly an adaptive response to taking flight.

“If you’re carrying a lot of bacteria in your gut, it can be pretty heavy and may take resources away from you,” Lutz explains.

“So if you’re an animal that has really high energetic demands, say because you’re flying, you may not be able to afford to carry all those bacteria around, and you may not be able to afford to feed them or deal with them.”

The study was a collaboration between scientists, museum collections and zoos from around the globe, and Lutz even scraped samples from African bats in remote Ugandan and Kenyan caves.

The samples were gathered from 315 mammalian, 491 bird and 86 other vertebrate species using the Earth Microbiome Project standard methods.

They were processed using high throughput genetic sequencing; DNA was extracted from individual cells to enable microbial communities to be identified and compared across species.

By learning more about the microbiomes of different animals, the researchers hope to understand more about our own; in this case species that don’t rely on their gut bacteria could provide unique insights.

“If we are ever putting ourselves in some kind of extreme situation where we’re disrupting our microbiome,” says Lutz, “there is something that we can learn from animals that don’t need their microbiomes as much.”

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Natalie Parletta is a freelance science writer based in Adelaide and an adjunct senior research fellow with the University of South Australia.
  1. https://mbio.asm.org/content/11/1/e02901-19
  2. https://www.frontiersin.org/articles/10.3389/fpubh.2018.00235/full
  3. http://www.earthmicrobiome.org/
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