Comparison of the gut microbiome and resistome in captive African and Asian elephants on the same diet

Xin Feng; Rong Hua; Wanying Zhang; Yuhang Liu; Caiyu Luo; Tonghao Li; Xiaolin Chen; Hui Zhu; Youcong Wang; Yan Lu

doi:10.3389/fvets.2023.986382

Comparison of the gut microbiome and resistome in captive African and Asian elephants on the same diet

Front Vet Sci. 2023 Feb 16:10:986382. doi: 10.3389/fvets.2023.986382. eCollection 2023.

Authors

Xin Feng¹, Rong Hua², Wanying Zhang¹, Yuhang Liu¹, Caiyu Luo¹, Tonghao Li¹, Xiaolin Chen¹, Hui Zhu¹, Youcong Wang¹, Yan Lu²

Affiliations

¹ School of Life Science and Engineering, Foshan University, Foshan, China.
² Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.

Abstract

Elephants are endangered species and threatened with extinction. They are monogastric herbivorous, hindgut fermenters and their digestive strategy requires them to consume large amounts of low quality forage. The gut microbiome is important to their metabolism, immune regulation, and ecological adaptation. Our study investigated the structure and function of the gut microbiota as well as the antibiotic resistance genes (ARGs) in captive African and Asian elephants on the same diet. Results showed that captive African and Asian elephants had distinct gut bacterial composition. MetaStats analysis showed that the relative abundance of Spirochaetes (FDR = 0.00) and Verrucomicrobia (FDR = 0.01) at the phylum level as well as Spirochaetaceae (FDR = 0.01) and Akkermansiaceae (FDR = 0.02) at the family level varied between captive African and Asian elephants. Among the top ten functional subcategories at level 2 (57 seed pathway) of Kyoto Encyclopedia of Genes and Genomes (KEGG) database, the relative gene abundance of cellular community-prokaryotes, membrane transport, and carbohydrate metabolism in African elephants were significantly lower than those in Asian elephants (0.98 vs. 1.03%, FDR = 0.04; 1.25 vs. 1.43%, FDR = 0.03; 3.39 vs. 3.63%; FDR = 0.02). Among the top ten functional subcategories at level 2 (CAZy family) of CAZy database, MetaStats analysis showed that African elephants had higher relative gene abundance of Glycoside Hydrolases family 28 (GH 28) compared to Asian elephants (0.10 vs. 0.08%, FDR = 0.03). Regarding the antibiotic resistance genes carried by gut microbes, MetaStats analysis showed that African elephants had significantly higher relative abundance of vanO (FDR = 0.00), tetQ (FDR = 0.04), and efrA (FDR = 0.04) than Asian elephants encoding resistance for glycopeptide, tetracycline, and macrolide/rifamycin/fluoroquinolone antibiotic, respectively. In conclusion, captive African and Asian elephants on the same diet have distinct gut microbial communities. Our findings established the ground work for future research on improving gut health of captive elephants.

Keywords: captivity; diet; elephant; microbiome; resistome.

Grants and funding

The financial support from Guangdong Basic and Applied Basic Research Foundation (2019A1515110780), Discipline Construction Program of Foshan University (CGZ0400162), the research start-up fund for Postdoctoral Fellows from Foshan City (BKS209059), the Scientific research start-up fund for high-level talents of Foshan University (Gg07145), the National Natural Science Foundation of China (Grant No. 31902228), the Scientific Research Foundation in the Higher Education Institutions of Educational Commission of Guangdong Province (2017GCZX006), Guangdong Province Modern Agriculture Poultry Industry technology system innovation team construction project (2020KJ128), Guangdong Science and Technology Innovation Strategy Special Fund (DZX20192520309), and Special Foundation for Key Research Area of Educational Commission of Guangdong Province (2019KZDZX2006) were acknowledged.