Molecular Characterization of Abomasal-Related Bacteria in Sheep with Haemonchus contortus Infection

Abstract Haemonchus contortus is an important parasite in sheep and the abuse of anti-helminthics has resulted in a rapid resistance. Little is known about the abomasal microbiota in sheep and the relation to local parasitism. This study aimed to identify bacteria in the abomasum of sheep, through the abomasal content, abomasal mucosa, and adult H. contortus parasites, in high and low parasitism. Eight sheep naturally infected with H. contortus were classified as high (n = 4) and low infection (n = 4). Samples of abomasal contents, abomasal mucosa, and adult H. contortus parasites were collected. Samples were pooled to form six groups, three in each level of parasitism: high infection/abomasal contents (HC), high infection/mucosa (HM), high infection/parasites (HP); low infection/abomasal contents (LC), low infection/mucosa (LM), and low infection/parasites (LP). Molecular identification of bacteria was performed by the amplification and sequencing of the 16S rRNA bacterial gene. A similar distribution of phyla was observed between pools HC/LC and HP/LP. For pools HM/LM, there was a significant difference (p = 0.01) in the proportion of phyla observed. The bacterial phyla predominant for libraries HC/LC were Firmicutes (82% and 62%) and Bacteroidetes (10.4% and 17.6%); for HM/LM, Firmicutes (76.9% and 56%) and Proteobacteria (10.2% and 38.4%); and for HP/LP, Proteobacteria (42.8% and 55%) and Firmicutes (31.6% and 40%). We observed differences about the samples analyzed, suggesting that there are various bacterial communities closely associated with the different materials analyzed, even from the close environment.