What Can Gut Microbes Tell Us About Animal Evolution?

What’s the question? How do mammals and their gut microbes evolve together, and what can microbial communities reveal about the movement and history of animal populations?

The big picture: Mammals and their gut microbes have evolved in close association, and those relationships can influence health, adaptation and survival. Understanding how these partnerships are maintained—or disrupted—could inform research in ecology, conservation and precision medicine.

NEON Biorepository samples used:  

Researchers used small mammal samples from the NEON Biorepository:

• Fecal samples from deer mice (Peromyscus) for sequencing the gut microbiome
• DNA extracts from the same mice to confirm species identity

Researcher(s): Dr. Taichi Suzuki, Assistant Professor, Health Through Microbiomes Faculty, Arizona State University (Suzuki Lab). Study led by Dr. Danielle M. Blumstein with Aishwarya Patel, Dr. Gabriele Schiro, and Dr. Suzuki.  

What they did and what they learned:

Dr. Danielle M. Blumstein (postdoctoral researcher) and her colleagues in the Suzuki Lab analyzed paired fecal and host DNA samples from deer mice in the Peromyscus maniculatus species complex collected from 13 populations across the contiguous United States. The research team used full-length 16S rRNA long-read sequencing to characterize the gut microbiome, while the host DNA helped confirm the identity of each animal. The team then compared microbial communities across locations to see how geographic distance and major landscape features influenced microbiome composition.

“NEON gives us access not only to samples, but also to the standardized metadata that make those samples scientifically useful. That combination allows us to ask questions across geographic scales that would be very difficult to study on our own.” – Dr. Taichi Suzuki, Arizona State University  

As expected, mice living farther apart tended to have more dissimilar gut microbiomes. However, the Mississippi River created a much stronger divide than distance alone could explain: mice on opposite sides of the river had distinctly different microbial communities. The researchers also found that some bacterial lineages appeared more restricted by the river than others, suggesting that microbes differ in how easily they move through the environment or between hosts.

The study is part of the Suzuki Lab’s broader investigation into host-microbial coevolution: how mammals and their gut microbes evolve together and how those microbes are passed between individuals and populations. It suggests that gut microbes can preserve evidence of a host population’s history and movement across a landscape. The team is also exploring what happens when long-standing host-microbe relationships are disrupted or lost. By identifying which microbes are most closely tied to their hosts and determining how they affect health and biological traits, the researchers hope to generate insights relevant to biodiversity conservation, disease research and precision medicine.  

Suzuki’s lab is extending that same idea to human health by asking whether some microbes are so closely tied to our evolutionary history that losing them creates a biological mismatch. By examining whether those changes correlate with inflammatory, metabolic or disease markers, the researchers hope to determine whether microbial ancestry should be considered alongside human genetics in precision medicine.

Taichi credited Laura Steger, NEON Biorepository Environmental and Zoological Collections Manager, who helped identify and select the paired samples and supported the technical planning, along with his colleagues at the ASU College of Health Solutions, the Biodesign Center for Health Through Microbiomes and members of his lab.

Read the study: Beyond distance-decay: The Mississippi River shapes gut microbiome communities in the Peromyscus maniculatus species complex (preprint: bioRxiv)