A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts

Luis Víquez-R; Maik Henrich; Vanessa Riegel; Marvin Bader; Kerstin Wilhelm; Marco Heurich; Simone Sommer

doi:10.1186/s42523-024-00315-6

A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts

Anim Microbiome. 2024 May 14;6(1):28. doi: 10.1186/s42523-024-00315-6.

Authors

Luis Víquez-R^{1

2}, Maik Henrich^{3

4}, Vanessa Riegel⁵, Marvin Bader^{5

6}, Kerstin Wilhelm⁵, Marco Heurich^{3

4

7}, Simone Sommer⁸

Affiliations

¹ Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Baden-Württemberg, Germany. luisviquez@gmail.com.
² Department of Biology, Bucknell University, Lewisburg, PA, USA. luisviquez@gmail.com.
³ Department of National Park Monitoring and Animal Management, Bavarian Forest National Park, Grafenau, Bayern, Germany.
⁴ Chair of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Baden-Württemberg, Germany.
⁵ Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Baden-Württemberg, Germany.
⁶ Albert-Ludwigs University, Freiburg, Baden-Württemberg, Germany.
⁷ Institute for Forest and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, NO-34, Norway.
⁸ Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Baden-Württemberg, Germany. Simone.sommer@uni-ulm.de.

Abstract

The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.

Keywords: Roseburia; 16S rRNA sequencing; Artiodactyla; Bavarian national park/Germany; Diet supplementation; Prevotellaceae; Wildlife management; Winter enclosures.