New Study Maps the Eastern Indigo Snake Microbiome Through Shotgun Metagenomics
A newly published study in PLOS ONE provides the first in-depth shotgun metagenomic characterization of the cloacal microbiome in Eastern Indigo Snakes (Drymarchon couperi), a federally threatened species native to the southeastern United States.
The research examines how captivity and Cryptosporidium serpentis infection may be associated with differences in the microbial communities found in these snakes. The findings establish an important foundation for future research into reptile health, infectious disease, captive management, and wildlife conservation.
Comparing Wild and Captive Eastern Indigo Snakes
Researchers analyzed cloacal samples from 80 Eastern Indigo Snakes across three study groups:
- 30 captive snakes positive for C. serpentis
- 30 captive snakes negative for C. serpentis
- 20 wild or free-ranging snakes
Cloacal swabs offered a minimally invasive method for investigating microbial composition while reducing the stress and risks associated with direct gastrointestinal sampling.
The samples underwent shotgun metagenomic sequencing to characterize bacteria, fungi, protozoa, nematodes, and bacteriophages. This broad approach allowed researchers to evaluate the wider microbial community rather than focusing on a single pathogen or microbial group.
Wild Snakes Showed Greater Microbial Diversity
Wild snakes exhibited significantly greater overall microbial diversity than captive snakes. They also showed greater fungal, protozoan, and nematode diversity.
Overall microbial diversity did not differ significantly between captive snakes that were positive or negative for C. serpentis. However, several individual microbial taxa were significantly enriched in infected snakes, including Trichosporon asahii and Edwardsiella tarda.
These findings identify microbial associations that warrant further investigation but do not establish that the enriched organisms caused infection or related clinical signs. Captivity, diet, environmental exposure, and health status may all contribute to differences in reptile microbial communities.
Much of the Reptile Microbiome Remains Unknown
Approximately 96–99% of the metagenomic signatures detected across the samples could not be classified using currently available genomic reference databases.
This substantial unclassified fraction highlights the microbial “dark matter” that remains unexplored in reptiles and other understudied species. Expanding genomic reference databases will be essential for improving the detection, identification, and interpretation of microorganisms associated with exotic animals and wildlife.
Supporting Reptile Health and Conservation
Captive breeding, head-starting, and reintroduction programs are important components of Eastern Indigo Snake conservation. Understanding how microbial communities differ between wild and captive snakes may help researchers explore the effects of diet, environment, disease, and husbandry on long-term health and reintroduction outcomes.
The study establishes baseline data that may support future investigations into microbiota-host interactions, gastric cryptosporidiosis, captive care, and conservation management.
Study Authors and Collaborators
The study was authored by:
- Christopher Roger Brown, Department of Comparative Medicine, Tulane University
- Mark Nikolaus Yacoub, MiDOG Animal Diagnostics
- James E. Bogan, Central Florida Zoo and Botanical Gardens’ Orianne Center for Indigo Conservation
- Matthew D. Buehler, Department of Biological Sciences and Auburn University Museum of Natural History
- Michelle Lea Hoffman, Central Florida Zoo and Botanical Gardens’ Orianne Center for Indigo Conservation
- Janina Alessandra Krumbeck, MiDOG Animal Diagnostics
- Zachary J. Loughman, Department of Biological Sciences, West Liberty University
MiDOG researchers Mark Nikolaus Yacoub and Dr. Janina Alessandra Krumbeck contributed to the investigation, metagenomic data analysis, and interpretation. Samples were sent to MiDOG for DNA extraction and shotgun metagenomic sequencing.
Read the Published Study
“Cloacal microbiome variation in wild and captive Eastern Indigo Snakes (Drymarchon couperi) with and without Cryptosporidium serpentis infection” was published in PLOS ONE on July 9, 2026.