Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes

Georges P. Schmartz, Jacqueline Rehner, Miriam J. Schuff, Leidy-Alejandra G. Molano, Sören L. Becker, Marcin Krawczyk, Azat Tagirdzhanov, Alexey Gurevich, Richard Francke, Rolf Müller, Verena Keller and Andreas Keller ()
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Georges P. Schmartz: Saarland University
Jacqueline Rehner: 66421 Saarland University
Miriam J. Schuff: 66421 Saarland University
Leidy-Alejandra G. Molano: Saarland University
Sören L. Becker: 66421 Saarland University
Marcin Krawczyk: 66421 Saarland University
Azat Tagirdzhanov: Saarland University
Alexey Gurevich: Helmholtz Center for Infection Research
Richard Francke: Zoo Saarbücken
Rolf Müller: Helmholtz Center for Infection Research
Verena Keller: Saarland University
Andreas Keller: Saarland University

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: Abstract Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the ‘One Health’ approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.

Date: 2024
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DOI: 10.1038/s41467-024-52669-9

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