Migrating Birds Change Their Scenery—and Their Gut Bacteria

A new study using birds killed in window collisions finds avian microbiomes, unlike those of mammals including humans, vary as they travel, changing with the surrounding environments.
A close up portrait of a small, streaky, brown and white bird looking at the camera.
Veery, one of four closely related species of thrushes included in the study. Photo: Frank Lehman/Audubon Photography Awards

Migrating birds impress us with the immensity of their feats, from miles flown to days (even months!) without rest. But migration is also a matter of the very small—in fact, the microscopic. Recent research reveals a new, more minuscule mystery of migration: As birds travel throughout the year, the bacteria in their guts is constantly changing, a sharp contrast to the relatively stable bacterial communities, or microbiomes, found inside mammals including humans.

“It’s really local habitat that influences their microbiome,” says Heather Skeen, lead author of the study recently published in Molecular Ecology. “They stop somewhere to rest and refuel, and they’re immediately inundated with local microbes.”

Beneath (and among) their feathers, every bird is teeming with life. The microbial community inside a bird’s digestive tract is especially vibrant, home to bacteria, parasites, and even fungi, though what these microbes actually do for their avian hosts remains largely unknown. While previous research has shown that birds—and bats—have more variable microbiomes than most mammals, the new study takes these findings a step further. The bacterial community in birds’ intestines doesn’t just look different in the spring versus the fall, or breeding season versus non-breeding season—it changes continually. And unlike seasonal plumage, birds' microbiomes don’t seem to follow a predictable cycle. That means the bacteria in a bird’s guts at any given time may just be “a snapshot,” says Skeen, who conducted the research as a PhD student at the University of Chicago.

To collect the “snapshots” she analyzed, Skeen turned to a unique resource: birds that died after colliding with buildings in Chicago. During spring and fall migration, volunteers patrol the sidewalks and bring any dead birds they find to the Field Museum of Natural History. Associate curator of birds Shannon Hackett, co-author of the new paper, says the museum’s window-strike collection was initially started not with a clear research purpose, but “through a desire that no bird give its life in vain.” Though their deaths were preventable, the birds can at least contribute to our understanding of their lives.

Working closely with volunteers and collaborators, Skeen sampled the intestinal contents of close to 700 birds over a period of three years, a process which involved squeezing out the contents of the recently deceased birds’ intestines—“My volunteer called them pre-poop,” she says—onto specialized filter paper that preserves DNA. Molecular analysis of the samples revealed nearly 27,000 types of bacteria. Surprisingly, Skeen and her team found that, more than the age, sex, or even species of the bird sampled, the factor with the greatest impact on the birds’ microbiome was simply time. The microbes in the birds’ guts come and go, Skeen says. “They pass through. They’re transient.”

The study included four closely related species of thrushes: Hermit Thrush, Swainson’s Thrush, Grey-cheeked Thrush, and Veery. Skeen chose them mainly because they are abundant, well-studied, and, “unfortunately, a lot of thrushes do hit windows.”

But Skeen also has a personal connection to these species. Ten years ago, when she was first getting her feet wet as a field researcher, Skeen traveled to Peru. She was overwhelmed by the colorful tanagers, motmots, and other neotropical birds, when suddenly a “kind of drab” little brown bird appeared. Skeen realized it was a Swainson’s Thrush, a bird that perhaps just a month or two earlier had traveled through North America. “It was very strange seeing these birds in the middle of the Amazon when I'm normally seeing them along the lake shore in Chicago,” she says. “I understood the concept of migration, but actually seeing it in practice, your mind goes blank for a second while you consider the improbability of these birds being able to travel that far.”

Studying migratory birds—let alone their inner microbes—is inherently challenging given the vast distances they travel, says evolutionary biologist Sarah Hird, who was not involved in the study. Hird, who works on bird microbiomes at the University of Connecticut, where Skeen is now a postdoctoral researcher, appreciates the connections the new study makes between the “amazing feat” of migration and microbiomes, which likely perform key functions for birds, even if scientists have yet to determine them. “Linking those two big important features of birds is just fascinating,” Hird says.

Research in humans has shown our microbiome helps us maintain a robust immune system and fend off disease. But somehow, even though birds seem to lack a stable microbial community, “they still can function,” says Marcella Baiz, an avian microbiome researcher at Penn State University who was not involved with the study. Scientists are still puzzling over what that means, but one thing it might indicate, Baiz says, is “functional redundancy.” There could be many kinds of bacteria that fill the same role in birds’ guts, switching off with each other over time like relay runners.

Skeen is considering the same idea: “Maybe there’s five different bacteria that help digest insects,” or protect against pathogens, or any of the functions we’ve learned the microbiome performs in humans, she proposes. “Can we find similar processes in birds?” But, she acknowledges, “That’s a big next step,” which will require determining the function of thousands of kinds of bacteria found in birds’ guts. “I will retire very frustrated that there are still a million unanswered questions,” Skeen says.
Hackett is more optimistic: “You have to start somewhere.” Her view of what they’ve learned is distinctly philosophical. Although our microbiomes function quite differently, in a way migratory birds are just like us, shaped by our surroundings and the choices we make, the actions we take. “When you go somewhere, you change because of the experiences you have. I view these birds in the same way,” she says. The bird who heads south in the fall is not the same bird who flies back in the spring. “They change with each trip back and forth. They change based on what they interact with in any environment that they stop in,” Hackett says. “These interconnections are just so profound.”