Metagenomic profiling for gut of indigenous poultry reared under free range system of management reveal prevalence of zoonotic pathogens in chicken, while predominating beneficial microbes in duck

Abstract

Zoonosis is an important phenomenon of disease transmission through livestock and poultry. In the current study, we explored gut metagenomics and identified a heavy percentage of pathogenic microbial loads in small intestine (duodenum) of chicken in comparison to duodenum of duck. Another important observation was that the percentage of pathogenic microbe decreases in large intestine (caecum), thereby reducing the chance of disease transmission through faeces. This may be the reason how indigenous duck and chicken were more hardy and resistant to common avian pathogens, that they have the ability to manage the reduction of the pathogenic microbes ingested through free range grazing with the help of beneficial microbes in caecum. Significant microbial load have been observed for Chlamydia abortus and Nocardia nova, with the every possibilities of transmission from chicken duodenum, so, handling of chicken need to be carried out with utmost care. We observed a remarkable finding that caecum of the gut reveal very less percentage of these pathogenic microbes, rather caecum is dominated by a beneficial microbe. 10 percent of the duck caecum is inhabited by Bacteroides spp (7 percent of Bacteroides sp OF04-15BH and 3 percent of Bacteriodes plebius), while it is almost negligible in chicken. This is the first report of this kind. This may be employed for the isolation and utilization as future probiotics from a ready source. Scavenging by indigenous poultry may serve as a useful tool for reducing pathogens prevailing in the environment.