Changes in bacterial community composition of Escherichia coli O157:H7 super-shedding cattle occur in the lower intestine

Escherichia coli O157:H7 is a foodborne pathogen hosted by ruminant animals. Cattle are considered as the primary reservoir but highly variable shedding patterns have been observed between animals. Super-shedders, namely individuals shedding >104 CFU/g of feces, appeared to be potential good targets for mitigation strategies aiming at reducing the incidence and spread of this pathogen in the feedlot/farm environment. However, the mechanisms leading to the super-shedding condition are poorly understood. In a recent study using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), the composition of the fecal bacterial community was found to be significantly different between super-shedder and non-shedder animals. Here, we used the same approach to depict changes in the bacterial communities at several locations along the digestive tract (from the duodenum to the rectal-anal junction) of 10 animals exhibiting contrasted shedding patterns. Almost one million 16SrRNA pyrotags were produced with an average of 11,401 sequences per sample. The bacterial community composition was similar between animals across the upper part of the intestine, from the duodenum to the distal jejeunum, but started to be significantly different from the cecum and remained stable along the large intestine. Interestingly, Escherichia coli O157:H7 was detected by multiplex PCR only for the super-shedder animal in the lower intestine, from the cecum to the rectal-anal junction. This finding reinforced the link between Escherichia coli O157:H7 colonization in cattle and the microbial diversity inhabiting the digestive tract of these animals.