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This ongoing study compares the gut microbial community composition between shedding steers high in shiga toxin-producing E. coli (STEC) counts and low-shedding steers. Shedders were identified among 170 beef animals over three time periods using selective microbiological culture media. The isolated bacterial cultures were confirmed to be STEC using PCR, 16s rRNA sequencing and a shiga toxin immunoassay. The most abundant strains found in the cattle feces were those belonging to the serogroups O111 (40.3%) and O157:H7 (37.3%), with O103 (8.3%), O26 (6.0%), O83 (4.5%), and O55 (3.0%) being detected in much lower numbers . Out of the 52 animals which were identified as super-shedders of STECs which were selected for microbial community analysis, 61.54% shed STEC in at least two of the three sampling time points. Currently, work is being carried out to evaluate the microbial community composition of the identified STEC high-shedding and low-shedding cattle populations using 454-pyrosequencing.

Campylobacter has been established as one of the most common foodborne pathogens, and is a major cause of gastroenteritis throughout the world. The consumption of poultry is most often cited as the mode of transmission to humans. In this study, the genetic diversity of Campylobacters in the farm environment and their association with poultry is investigated over time. From November 2000 to August 2001, Campylobacter isolates were collected over four seasons from environmental samples taken from an Iowa poultry farm. Macrorestriction analysis of genomic DNA by pulsed field gel electrophoresis (PFGE) was used to characterize the isolates and their antibiotic resistance was determined using the E Test method. PFGE analysis of Sma1-digested DNA from all the isolates yielded between 5–11 fragments that ranged in size from ∼46 to 521 kb. 84% of the isolates were assigned to one macrorestriction profile and they were distributed throughout the house though all seasons. PFGE analysis of Kpn1-digested DNA from a selection of isolates yielded between 5–9 fragments that ranged in size from ∼50 to ∼450 kb. The dominant strains in the environment were identified as Campylobacter coli. C. jejuni was isolated from the environment only in the winter, and had a PFGE profile similar to C. jejuni strains recovered from the chicken ceca. The majority of the isolates displayed no antibiotic resistance to nalidixic acid, ciprofloxacin, enrofloxacin, tetracycline, erythromycin, or ampicillin. However, some of the summer isolates showed low-level resistance to tetracycline. Campylobacter has been reported to have a tendency for rapid genetic change and to possess an unstable genome. However, this study identified a strain of Campylobacter coli that remained stable for several months in the poultry environment.