Effects of land-use changes and diet on the viral and bacterial load of black-backed jackals and bat-eared foxes in Namibia - a metagenomics approach to understand the ecological and molecular attributes affecting population health in important pathogen reservoirs and vectors.
Evolution, Anthropology
Final Report Abstract
Human encroachment into former natural habitat has a tremendous impact on global ecosystems. Especially in sub-Saharan Africa, wild-lands are vulnerable to conversion into commercially used farmlands promoting the contact of wildlife species with humans and domestic animals. This facilitates the exchange of parasites and pathogens causing obvious disease risks for wildlife, livestock and humans. In this project, we investigated the role of intrinsic and extrinsic factors driving gastrointestinal (GI) microbiome variability in wildlife species, potential effects of anthropogenic land use changes on microbial community pattern and associated metabolic pathways, as well as potential consequences for host health. We applied a next-generation sequencing approach to disentangle ‘normal’ inter-individual variability in microbiome communities from disease promoting disorders in two Namibian carnivores, the cheetah (Acinonyx jubatus) and the black-backed jackals (Canis mesomelas). In order to understand how bacteria are exchanged between wildlife and livestock on farmland, shared by livestock and game, we complemented our approach by sampling sympatric cattle and shared waterholes. In addition, we aimed at improving the research field of GI microbiome ecology and evolution by investigating the usefulness of field-collected fecal samples and different preservation treatments for reliable microbiome investigations. Results revealed that intrinsic factors do add significant variation to bacterial communities which may overrule the impact of extrinsic factors. Although we did not detect an effect of land use on microbiome alpha and beta diversities, analyses of significantly different abundant bacterial OTUs revealed differences between livestock farms and game farms for bacterial genera such as Helicobacter and Clostridium, known to be potentially pathogenic. When we compared the GI microbiomes of cheetahs and black-backed jackals, we found that the bacterial community differentiation increased from the phylum down to the bacterial species-like level (oligotypes). In general, black-backed jackals were hosts for a wider range of bacterial taxa indicating that the size of home ranges is less important in shaping the GI microbiome of a host than the respective diet, foraging behavior and social system. The usefulness of field-collected samples is highly depending on specific sample characteristics and the respective weather conditions at time of sampling. Thus, this study is among the pioneer studies in the field of GI microbiome research in wildlife species and adds valid basal information which is necessary to understand whether GI microbiome variations are within the natural range or deviate to such an extent that they lead to consequences for health. We show that gut microbiome analyses have the potential to become a valuable tool for noninvasive monitoring of wildlife health has further implications for conservation management.
Publications
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(2014) Oligotyping reveals differences between gutmicrobiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level. Frontiers in Microbiology, 5, 526
Menke S, Wasimuddin, Meier M et al.
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(2015) Shifts in the gut microbiome observed in wildlife (Giraffa camelopardalis, Antidorcas marsupialis) fecal samples exposed to natural weather conditions: lessons from time series analyses using next generation sequencing for application in field studies. Methods in Ecology and Evolution, 6, 1080–1087
Menke S, Meier M, Sommer S
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Effects of host traits and land-use changes on the gut microbiota of the Namibian black-backed jackal (Canis mesomelas). FEMS Microbiology Ecology, Volume 93, Issue 11, 1 November 2017, fix123
Menke S, Meier M, Mfune J, Melzheimer J, Wachter B, Sommer S
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Gut microbiomes of free‐ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens. Molecular ecology, 26,20, October 2017, Pages 5515-5527
Wasimuddin, Sebastian Menke, Jörg Melzheimer, Susanne Thalwitzer, Sonja Heinrich, Bettina Wachter, Simone Sommer
