Characterization of microbial community structure during Shiga toxin-producing Escherichia coli (STEC) shedding in beef cattle

Abstract Text: A rich microbial community inhabits the gastrointestinal intestinal tract of ruminants, and cattle are a principle reservoir of the pathogen Escherichia coli O157:H7. This food borne pathogen produces shiga toxins that cause worldwide disease with their main route of entry to the environment is through cattle feces. Previous studies have shown that the level and frequency of shiga toxin producing E. coli (STEC) varies widely between individual animals. Some animals shed very high concentrations of the pathogen and therefore may be responsible for a majority of transmission of the STECs among individuals and into the environment. In this study, we hypothesize that dysbiosis of the gut microbiota will result in STEC colonization in beef cattle and subsequent shedding of STEC in beef animals. Using selective microbiological culture methods and molecular methods, STEC high-shedders and low-shedders were identified among 170 beef steers over 3 time periods. Based on shedding numbers 48 high-shedders (>10⁴ STEC cfu/g of feces) and 48 low shedders (<10² cfu/g of feces) were phenotyped for gut microbial composition using 16s rRNA based amplicon sequencing. A total of ~525,000 high-quality DNA sequences generated through 454-pyrosequencing was used to evaluate microbial community composition. Bioinformatic analysis of the sequences from high-shedders and low-shedders indicated significant variations in mricrobiome composition between high and low shedders. It was revealed that members of the phylum Bacteroidetes were more abundant in the low-shedders, while members of the phylum Proteobacteria were more abundant in the high-shedding animals. Furthermore, at the family level, Prevotellaceae were represented more in the low-shedders than in the high-shedders. Further analysis showed that 9 operational taxonomic units (OTUs) were significantly more abundant in low-shedders than in high-shedders. Most of these OTUs represented members of the genus Prevotella. These results provide new insight into bacterial populations that are present in the feces of shedding cattle.

Keywords: STEC, 16S microbial community