Analysis of the gut microbiome sheds insights into breed resilience and the challenges of antimicrobial resistance in Dohne merino sheep.

Abstract

This study focused on analysing the gut microbiome of Dohne Merino, one of South Africa’s leading sheep breeds, that is also reared in Australia, New Zealand, and other European countries. Dohne Merino is of high economic importance in South Africa as it maintains livelihoods in many small rural communities. In South Africa, sheep and other livestock are exposed to multiple diseases and parasites. The efforts to manage these diseases and infections while keeping high productivity have led to an increased usage of antimicrobials in agriculture. This has resulted in high prevalence of antimicrobial resistance (AMR), that is a primary global concern demanding surveillance and action. Some sheep breeds and populations are known to be resilient to diseases, harsh production, and environmental conditions and have low AMR prevalence, which could be due to the defense provided by their gut microbiome. Studying the gut microbiome is essential because the gut microbiome contributes to animal nutrition and health. The study investigated the gut microbial environment of South African Dohne merino sheep. Metagenomic sequencing of the rumen, reticulum, omasum, and abomasum of six mature Dohne Merino ewes that were raised on open pasture was performed. Illumina HiSeq2500 was used to generate a total of 15million reads of 150bp illumina base pairs. The members of the microbial population were fully characterised, and the resistome of the gut was analysed. The microbial population was studied at phylum, class, order, genus, and species level, with bacteria being the most abundant and diverse domain. Other present domains included archaea and viruses. Majority of the microbial population was Bacteroides (53,9%) and Firmicutes (25,4%). Two illness-related bacterial phyla were also identified, Actinobacteria and Cyanobacteria. Identified archaea belonged to the phyla Candidatus Asgardarchaeota, Candidatus Thermoplasmatota, and Euryarchaeota. The observed viral population was very diverse with a total of 5 realms, 8 kingdoms,13 phyla, and 21 classes. Many of the viruses were dsDNA phages belonging to the Duplodnaviria realm. Disease-linked RNA viruses belonging to the Riboviria realm were also observed. Riboviria members have been associated with diseases such as influenzae, rabies and the corona virus. The relationships between microbiome composition and AMR prevalence across the four gut compartments were assessed. A total of 12 AMR genes were identified in the gut and were found to confer resistance to 15 antimicrobials. The observed antimicrobial resistance profiles were low compared to those reported for other breeds and species implying breed resilience of the Dohne Merino sheep. The analysis of the resistance profiles within the compartments revealed that, the higher the diversity, the lower the prevalence of AMR. The overall high diversity of the gut microbiome is the probable cause of breed resilience in Dohne Merino sheep. Additionally, the observed AMR high prevalence with no clinical symptoms of AMR in the animals is also indicative of breed resilience. More studies that will investigate the relationships between the gut microbiome and AMR prevalence are required and the knowledge generated can then be applied to overcome the challenges of AMR in livestock species.