The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.

The moisture and manure contents of soils at cattle feedlot surfaces vary spatiotemporally and likely are important factors in the persistence of Escherichia coli O157 in these soils. The impacts of water content (0.11-1.50 g H2O g(-1) dry feedlot surface material [FSM]) and manure level (5, 25, and 75% dry manure in dry FSM) on E. coli O157:H7 in feedlot soils were evaluated. Generally, E. coli O157:H7 numbers either persisted or increased at all but the lowest moisture levels examined. Manure content modulated the effect of water on E. coli growth; for example, at water content of 0.43 g H2O g(-1) dry FSM and 25% manure, E. coli O157:H7 increased by 2 log10 colony forming units (CFU) g(-1) dry FSM in 3 d, while at 0.43 g H2O g(-1) dry FSM and 75% manure, populations remained stable over 14 d. Escherichia coli and coliform populations responded similarly. In a second study, the impacts of cycling moisture levels and different drying rates on naturally occurring E. coli O157 in feedlot soils were examined. Low initial levels of E. coli O157 were reduced to below enumerable levels by 21 d, but indigenous E. coli populations persisted at >2.50 log10 CFU g(-1) dry FSM up to 133 d. We conclude that E. coli O157 can persist and may even grow in feedlot soils, over a wide range of water and manure contents. Further investigations are needed to determine if these variables can be manipulated to reduce this pathogen in cattle and the feedlot environment.

Exposure to low pH and organic acids in the bovine gastrointestinal tract may result in the induced acid resistance of Escherichia coli O157:H7 and other pathogens that may subsequently contaminate beef carcasses. The effect of acid adaptation of E. coli O157:H7 on the ability of acetic acid spray washing to reduce populations of this organism on beef carcass tissue was examined. Stationary-phase acid resistance and the ability to induce acid tolerance were determined for a collection of E. coli O157:H7 strains by testing the survival of acid-adapted and unadapted cells in HCl-acidified tryptic soy broth (pH 2.5). Three E. coli O157:H7 strains that were categorized as acid resistant (ATCC 43895) or acid sensitive (ATCC 43890) or that demonstrated inducible acid tolerance (ATCC 43889) were used in spray wash studies. Prerigor beef carcass surface tissue was inoculated with bovine feces containing either acid-adapted or unadapted E. coli O157:H7. The beef tissue was subjected to spray washing treatments with water or 2% acetic acid or left untreated. For strains ATCC 43895 and 43889, larger populations of acid-adapted cells than of unadapted cells remained on beef tissue following 2% acetic acid treatments and these differences remained throughout 14 days of 4°C storage. For both strains, numbers of acid-adapted cells remaining on tissue following 2% acetic acid treatments were similar to numbers of both acid-adapted and unadapted cells remaining on tissue following water treatments. For strain ATCC 43890, there was no difference between populations of acid-adapted and unadapted cells remaining on beef tissue immediately following 2% acetic acid treatments. These data indicate that adaptation to acidic conditions by E. coli O157:H7 can negatively influence the effectiveness of 2% acetic acid spray washing in reducing the numbers of this organism on carcasses.