Metagenomic assessment of the rumen resistome, mobilome and stress response genes in smallholder dairy cattle in Kenya

Smallholder dairy cattle rumen microbiotas are subjected to a wide range of antimicrobials as well as sudden fluctuations in diets. As such, they develop an enormous reservoir of resistant genes, mobilome and stress response genes. However, information on metagenomic reactions to such dietary variations, especially for cattle reared in the tropics, remains largely unexplored. This meta-analysis was conducted to assess if antibiotic and toxic compound resistance genes (ARGs), stress response genes and bacterial phages, prophages and transposable element genes were present, and to what extent, in three dairy cattle genotypes (Friesian, FriesianXJersey crossbreed, Jersey) reared in a farm that practiced judicious use of antimicrobials. Potential bacterial hosts to these genes were also explored. The rumen metagenomes generated from Next Generation Sequencing (NGS) technology were analyzed using MG-RAST. According to the results stress reaction, resistance and mobilome genes were present in similar amounts in all the three genotypes. Cobalt-zinc-cadmium resistance, fluoroquinolone resistance, methicillin resistance in Staphylococci and multidrug resistance efflux pumps were the most abundant resistant genes and were spread across 20, 24, 16 and 21 bacterial classes, respectively. Bacteria in charge of phage integration and excision, phages replication and phage packaging were mostly allocated to the phyla Firmicutes, Bacteroides and Proteobacteria. Within the stress response genes, metagenomic assembly-based host-tracking analysis identified the extended heat shock dnaK gene cluster as the most abundant genes, while Bacteroides and Clostridium were the principal bacterial hosts. The results show that even with proper use of antimicrobials, the cattle rumen contained an immense distribution of responses to stress, ARGs and mobilome genes distributed in a vast assemblage of hosts. There is also a high correlation between these three functional groups. Key words: Resistome, metagenome, MG-RAST, Stress genes, mobilome