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A yellow-bellied marmot being held in the arms of a researcher while they collect a cheek swab from the marmot.
Researchers at the Rocky Mountain Biological Laboratory capture wild marmots with Tomahawk live traps and release the animals promptly after data and sample collection.
Conner Philson

Microbes may be invisible to the naked eye, but they are vital to life on Earth. Gut microbes protect an animal from pathogens and help extract essential nutrients from the food it eats. The gut and brain also converse and influence each other, and the gut microbiome is a key player in this crosstalk.1  Researchers know that social behavior influences the microbiome in wild animals because microbes spread from one animal to another when they interact, but whether an animal’s microbiome affects its social behavior is still largely understudied. Answering these questions could bolster conservation efforts,2 for example by making probiotics for wildlife to promote positive social behaviors.1

In a study recently published in Royal Society Open Science, researchers led by Daniel Blumstein, who studies animal behavior and its applications in wildlife conservation at UCLA, investigated whether the gut microbiome influences sociality in wild yellow-bellied marmots.3

When asked about the motivation behind this work, Conner Philson, Blumstein’s former graduate student who is now a postdoctoral fellow at the University of Exeter, highlighted the limitations of existing microbiome studies. “So much of what we know [about the microbiome] is in lab systems, in captive mice,” said Philson. “There [are] not that many wild systems to capture enough data, to capture enough variance, to ask that question of what is going to be affecting … sociality.” To overcome this, the researchers collaborated with the Rocky Mountain Biological Laboratory (RMBL) marmot project in Colorado, which has been collecting data on marmots since 1962. In 2015, RMBL started collecting fecal microbiome samples and social network data. The researchers combined this information with RMBL’s 60 years of marmot knowledge to guide how they investigated this wild system.

Blumstein’s team extracted DNA from fecal gut microbiome samples of 148 wild marmots living in social groups or colonies based on overlap of used spaces. They also looked at social behaviors, such as how many marmots an individual interacted with, and a marmot’s position in its social group. The researchers then studied how these social behaviors correlated with the gut microbiome to understand whether the microbiome was influencing sociality.

This study is a nice addition to a growing field focused on the influences of social interaction on the microbiome.                                      -Andrew Moeller, Cornell University

The researchers found that the marmot microbiomes were largely homogenous. Wild mammals generally have high microbial diversity in their guts because they pick up different bacteria when interacting with other individuals.4 Blumstein’s team suspected that social marmots had lower microbiome diversity because they were foraging in the same areas, eating the same vegetation, and possibly consuming each other’s feces, causing their microbiomes to homogenize. The researchers also found that marmots in bigger groups had more similar microbiomes compared to those in smaller groups. They speculated that marmots in the same space are even more likely to eat fecal matter.

Despite the homogeneity, Streptococcus bacteria stood out. Marmots that had fewer social interactions had more Streptococcus in their guts. These bacteria can cause disease in animals, so it may be that these marmots were fighting infections and did not have the energy to participate in social interactions.

The researchers could not conclusively say if the microbiome was influencing sociality. “There is just not a lot of variation in the system, but it is the small variances that you can find that are probably the most interesting,” said Madison Pfau, an undergraduate researcher in Blumstein’s laboratory. The group is now looking at those small variances to investigate their relationship with social behavior.

“This study is a nice addition to a growing field focused on the influences of social interaction on the microbiome. The study is interesting in part because it reports a pattern that opposes prior work, that is, the authors found a negative relationship between sociality and microbiome diversity,” Andrew Moeller wrote in an email. Moeller studies symbiosis and host-microbe relationships at Cornell University and was not involved in this study.

Because the microbiome is vital to an animal’s health, there is a call to raise captive animals with the microbiome in mind so that they can thrive when reintroduced into the wild by successfully fighting environmental stressors.2 Ultimately, microbes could hold the answer to saving species from extinction.     


  1. Johnson KV, et al. Sociability in a non-captive macaque population is associated with beneficial gut bacteria. Front Microbiol. 2022;13:1032495.
  2. Trevelline BK, et al. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc Biol Sci. 2019;286(1895):20182448.
  3. Pfau M, et al. The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal. R Soc Open Sci. 2023;10:231305.
  4. Bensch H.M., et al. Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent.  Anim Microbiome. 2023;5(1):9. 

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