Date Published: January 31, 2017
Publisher: Public Library of Science
Author(s): Rahat Zaheer, Eric Dugat-Bony, Devon Holman, Elodie Cousteix, Yong Xu, Krysty Munns, Lorna J. Selinger, Rutn Barbieri, Trevor Alexander, Tim A. McAllister, L. Brent Selinger, Hauke Smidt.
Escherichia coli O157:H7 is a foodborne pathogen that colonizes ruminants. Cattle are considered the primary reservoir of E. coli O157:H7 with super-shedders, defined as individuals excreting > 104E. coli O157:H7 CFU g-1 feces. The mechanisms leading to the super-shedding condition are largely unknown. Here, we used 16S rRNA gene pyrosequencing to examine the composition of the fecal bacterial community in order to investigate changes in the bacterial microbiota at several locations along the digestive tract (from the duodenum to the rectal-anal junction) in 5 steers previously identified as super-shedders and 5 non-shedders. The overall bacterial community structure did not differ by E. coli O157:H7 shedding status; but several differences in the relative abundance of taxa and OTUs were noted between the two groups. The genus Prevotella was most enriched in the non-shedders while the genus Ruminococcus and the Bacteroidetes phylum were notably enriched in the super-shedders. There was greater bacterial diversity and richness in samples collected from the lower- as compared to the upper gastrointestinal tract (GI). The spiral colon was the only GI location that differed in terms of bacterial diversity between super-shedders and non-shedders. These findings reinforced linkages between E. coli O157:H7 colonization in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders.
Escherichia coli O157:H7 is the serotype responsible for the majority of human enterohemorrhagic E. coli (EHEC) infections in most industrial countries . Cattle are considered the primary reservoir of this pathogen although other animals may be carriers . A number of epidemiological studies have shown that up to 30% of feedlot cattle shed E. coli O157:H7 in their feces [3, 4, 5, 6]. Due to public health concerns and the role of cattle in disseminating E. coli O157:H7, this microorganism has a significant negative impact on the beef production industry.
Changes in bacterial community structure along the GI tract has been well documented in humans [39, 40, 41] and more recently in other animals such as cats , horses  and dairy cows  using fingerprinting methods or 16S rRNA gene clone libraries. These studies highlight a clear longitudinal effect on dominant bacterial populations along the digestive tract of mammals. de Oliveira et al.,  reported for the first time the use of pyrosequencing to characterize these changes along the entire gastrointestinal tract of one steer, from the rumen to the feces. The GI tract microbiota of dairy cattle has also recently been described based on high-throughput sequencing of the 16S rRNA gene . In the present study, we used a similar approach to characterize changes in bacterial diversity across eight adjacent intestinal sections of ten feedlot steers, from the duodenum to the rectal-anal junction.