Tracking Gut Microbiome Shifts in Zoo-Housed Hamadryas Baboons
Metagenomic sequencing tracks bacterial, fungal, protozoan, and bacteriophage communities in zoo-housed baboons over four months.
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A scientific poster from MiDOG and Oakland Zoo researchers explores how the gut microbiome of zoo-housed Hamadryas baboons changed over four months. Analysis of 31 fecal samples from a population of 14 baboons revealed shifts in bacterial, fungal, protozoan, and bacteriophage communities during a period that included antibiotic and antiparasitic treatment.
The research examines the microbiome across multiple microbial groups, offering a broader view of changes that may be missed when studying bacteria or a single parasite alone. It also highlights the value of collecting samples over time to investigate microbial relationships in zoo-housed primates.
Following the Microbiome Over Four Months
Researchers collected fecal samples from Hamadryas baboons at Oakland Zoo between January and April 2025. All baboons received albendazole for Trichuris trichiura, a whipworm, on January 7, 2025, before sample collection began. The poster also reports monthly cephalexin treatment.
Samples underwent community-wide metagenomic sequencing, with reads classified against a database containing bacterial, fungal, parasite, and viral taxa. The analysis tracked changes in microbial composition across the four-month sampling period.
Whipworm detection required a separate approach. The researchers used enhanced lysis and 18S marker-gene amplification and sequencing to identify T. trichiura, addressing the challenges posed by resilient eggs and low egg counts reported in the samples.
Bacterial and Bacteriophage Communities Shifted Together
The poster reports pronounced changes in the fecal microbiome between January and April. Bacteria belonging to the genus Prevotella dominated the microbiota in March and April. Their expansion correlated with a greater abundance of Prevotella phages—viruses that infect these bacteria.
The researchers proposed that the bacterial shift could be associated with cephalexin exposure. However, the findings do not establish that treatment caused the change. The study provides an observational view of microbial patterns during the sampling period.
Fungal and Protozoan Profiles Changed Over Time
The fungal community was diverse in January, with substantially lower diversity reported during the remainder of the study.
Blastocystis was the most abundant protozoan genus reported. Four strains or subtypes were detected at varying abundances: the poster identifies B. hominis and subtypes 1 and 3 across all sampling months, while subtype 2 appeared in March and April.
Together, these findings show that different components of the gut microbiome can follow different patterns over time. The presence of a microbial organism alone does not establish that it is responsible for disease.
A Broader View of Primate Microbial Communities
For zoo veterinarians and researchers, examining bacteria, fungi, protozoa, and bacteriophages together can help generate questions about microbial interactions, treatment exposure, and changes in gut ecology.
In this study, the parallel changes in Prevotella and its phages illustrate the value of examining more than one microbial group. The separate workflow needed for whipworm identification also demonstrates the importance of matching sample processing and detection methods to the organism being investigated.
These findings describe one zoo-housed population. They do not establish treatment efficacy, demonstrate parasite clearance, or provide diagnostic thresholds for other animals. Clinical interpretation requires the animal’s history, examination findings, and other diagnostic evidence.
Study Authors and Collaborators
The poster was authored by:
- Jenna Archambeau, BSc: MiDOG
- Mark N. Yacoub, PhD: MiDOG
- Kaylie Zapanta, PhD: MiDOG
- Janina A. Krumbeck, PhD: MiDOG
- Andrea Goodnight, DVM, MPH: Oakland Zoo
Explore the study methods, microbial abundance plots, and parasite findings in the full poster.
Poster title: Pioneering Insights into the Cross Kingdom Effect: First Study of Gut Microbiome Shifts in Zoo-Housed Hamadryas Baboons
Authors: Archambeau J, Yacoub MN, Zapanta K, Krumbeck JA, Goodnight A.
Affiliations: MiDOG LLC and Oakland Zoo.
Publication type: Scientific poster.
Study sampling period: January-April 2025.