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

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.

Exploring gut microbiota diversity in Catharsius molossus: influence of dietary conditions on ecosystem functionality

“…Leveraging amplicon sequencing data, PICRUSt2 analysis was employed for predictive and analytical functional profiling of microbial communities(C. Yang et al, 2023). Employing Wilcoxon rank-sum tests and Metastats analysis, a significance threshold of p-value <0.05 was used for differential significance screening, with the Bonferroni correction applied to the p-values to minimize the potential for false positives (Feng et al, 2023;Neuhäuser, 2015). This methodology was adopted to assess whether significant interspecies diversity exists among groups.…”

Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana).

“…Research has demonstrated that animal immune, digestive and reproductive health are intrinsically linked to the composition and the corresponding functional processes of the hostassociated microbial communities 11 . In the context of elephant microbiome research, focus has been placed on the characterisation of African and Asian elephant intestinal microbiota in an effort to improve the health status and welfare of these animals [12][13][14][15][16][17][18][19] , restore the microbial diversity of captive elephants 12,14,15,17,19,20 , and enhance their diet 13,16,20 . Investigation into the respiratory microbiota of this species may enable broad characterisation of the microbiota of healthy animals, documentation of undescribed microbial diversity, and identi cation of relationships between microbiota and host disease phenotypes.…”