Gut microbiota diversity among humans, elephants, livestock and wild herbivores in Chitwan National Park bears implications for conservation medicine

Abstract

Gut microbiome influences host health and well-being. Co-occurring hosts may exchange disease-causing bacteria belonging to these microbial communities. Therefore, monitoring gut microbiota composition in wildlife and humans is paramount to prevent zoonotic diseases, thus protecting and strengthening public health. We characterized diversity and abundance of the gut microbiome bacterial component across mahouts (captive elephant trainers and handlers), their pachyderms, livestock and wild herbivores in and around Chitwan National Park (Nepal). Firmicutes and Bacteroidota were invariably the dominant phyla. In humans, the relative abundance of Firmicutes was higher, the alpha diversity lower and beta diversity different compared to other host categories. Livestock and wild herbivores displayed similar alpha and beta diversity due to the presence of Proteobacteria, Actinobacteriota and Verrucomicrobiota. Elephants had a higher alpha diversity, and a significant beta diversity compared to other mammals. Our results suggest that taxonomic affiliation and diet niche are the main drivers of gut microbiota composition. Nevertheless, Mycobacterium and other potentially pathogenic bacteria genera were detected in elephants and livestock other than wild herbivores. These findings shed light on microbiota sharing and interlinking in each environment, thereby highlighting the importance of conservation medicine to better our understanding of health in co-occurring host species.

Keywords: Bacterial function; Human–wildlife–livestock–environment interface; Microbiome; Nepal; One Health; Zoonosis.

Fig. 1

Study area and sampling locations. (a) Map of southern Asia evidencing the location of Nepal (yellow shape). (b) Location of Chitwan National Park (green shape) in Nepal. (c) Physical map of Chitwan National Park and its buffer zone evidencing the main rivers. (d) Sampling locations within the park and the buffer zone (see Table S1 for further details). Maps were created in QGIS v3.30.0 (https://www.qgis.org/).

Fig. 2

Phyla composition of gut microbiota across humans (n = 16), livestock (n = 15), captive elephants (n = 39) and wild herbivores (hog deer: n = 2; sambar deer: n = 1; spotted deer: n = 58; wild boar: n = 16; greater one-horned rhino: n = 28). Animal photos (modified) are not to scale; for credits see the Acknowledgements and Appendix S1.

Fig. 3

Sharing of bacterial genera across the gut microbiota of humans (mahouts), livestock, captive elephants and wild herbivores. The 79 genera common to all four host categories represent the following percentages: 54.11% in humans; 32.11% in livestock; 17.4 in captive elephants and 10.75% in wild herbivores. Animal photos (modified) are not to scale; for credits see the Acknowledgements and Appendix S1.

Fig. 4

Alpha diversity based on Faith’s phylogenetic diversity (a) and Shannon diversity metrics (b) (α = 0.05) across different host categories: captive elephants, livestock, humans and wild herbivores (left to right). Animal photos (modified) are not to scale; for credits see the Acknowledgements and Appendix S1.

Fig. 5

Beta diversity based on: (a) Bray–Curtis, (b) Weighted and (c) Unweighted Unifrac distance metrics. Animal photos (modified) are not to scale; for credits see the Acknowledgements and Appendix S1.