16SrRNA-based bacterial community profiling of Haemonchus contortus infecting Dohne Merino sheep using next generation sequencing

Abstract

Gastrointestinal parasitism causes major economic losses in most livestock species including small ruminants’ production throughout the world. The control of gastrointestinal nematode (GIN) parasites is mostly based on administration of anthelmintic drugs. Unfortunately, the extensive use of anthelmintic drugs leads to the evolution of drug resistance in GIN parasites. Hence, alternative control measures are needed to effectively control GIN parasites. A novel approach based on biocontrol using GIN parasites symbiotic microbiota has been suggested to limit the use of chemical based treatments. In the present study, Illumina MiSeq sequencing technology was exploited to study the bacterial communities associated with the adult Haemonchus contortus worms and that of its predilection site, the abomasum, with the long-term goal of manipulating them to control these GIN parasites. The abomasum contents and adult H. contortus were collected from the 7 abomasum of 10 slaughtered Dohne Merino sheep collected from Wauldby farm. Adult male H. contortus specimens were identified and distinguished from females using morphological analysis (i.e., body length, colour, spicules and valval morphology). The bacterial community of both the adult H. contortus worms and the abomasum were determined with the aid of Illumina Miseq platform and metagenomics analysis. High bacterial diversity was observed from the adult H. contortus and the abomasum content samples. A total of 26 bacterial phyla were found in both the adult H. contortus worms and the abomasum, with Firmicutes (45%), Bacteroidetes (26%) and Actinobacteria (7%) being the most abundant phyla present in the abomasum content. Proteobacteria (94%), Firmicutes (3%) and Bacteroidetes (1%) were the most abundant phyla in the adult female H. contortus and for adult male H. contortus the most abundant phyla were Proteobacteria (57%), Firmicutes (24%) and Bacteroidetes (8%). The present study also elucidated the core genera Succiniclasticum (5%), Rikenellaceae RC9 gut group (4%) and Candidatus Saccharimonas (4%) which were the most predominant assigned genera in the abomasum. The predominant assigned genera of the adult female H. contortus were Escherichia-Shigella (28%), Vibrio (11%) and Halomonas (6%). The dominant genera assigned in the adult male H. contortus were Vibrio (15%), Escherichia-Shigella (8%) and Halomonas (8%). Moreover, our results revealed the bacterial genera including Lysinibacillus which can produce nematicidal volatile compounds with activities against nematodes. This study has pioneered detection of bacterial genera of medical and veterinary significance by metagenomics in the abomasum content of the Dohne Merino sheep and adult male and female H. contortus in South Africa. Overall, the present study provides insight into the bacterial community composition in the adult male and female H. contortus worms and the abomasum which is highly diverse and needs to be studied further to exploit the complex interactions of different GIN parasites microbiota with the host, which has, and will continue to offer considerable potential for better understanding a wide-variety of devastating animal diseases.