title: Assessment of the Fecal Microbiota in Beef Calves.
abstract: BACKGROUND
  There is increasing interest in the fecal microbiota, but study in calves has been limited.
  
  
  OBJECTIVE
  To evaluate the fecal microbiota of beef calves and cows on different farms, and to preliminarily explore the impact of antimicrobial exposure.
  
  
  METHODS
  A total of 172 animals, 156 (91%) calves and 16 (9.3%) cows, were enrolled from 5 cow-calf farms.
  
  
  METHODS
  The fecal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V4 region) amplicons.
  
  
  RESULTS
  There were significant differences in the relative abundances of numerous phyla between calves on different farms. Farms could be separated into 2 groups: 1 (farms B and C) dominated by Firmicutes and 1 (farms A, D, and E) with predominance of Proteobacteria and Actinobacteria. Richness (median 2,974 versus 1,477, P = .008), diversity (51.4 versus 29.1, P = .0029), and evenness (0.73 versus 0.68, P = .006) were higher in cows. Over-represented operational taxonomic units (OTUs) in cows tended to be from the classes Bacilli and Bacteroidia, whereas Clostridia and Actinobacteria were most prominently over-represented in calves. There were differences in community membership (P = .028) and structure (P = .029) in calves that had a history of antimicrobial exposure compared those that did not. Eight (89%) over-represented OTUs in the untreated group were Firmicutes (7 from the order Clostridiales), compared to only 3 (38%) (2 Clostridiales) in the untreated group.
  
  
  CONCLUSIONS
  Interfarm variation should be investigated to determine the causes and potential implications for health and production. Antimicrobial exposure may have an impact on the fecal microbiota at individual and farm levels.
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
authors.forename: J S
authors.initials: JS
authors.lastname: Weese
authors.affiliation: Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
authors.forename: M
authors.initials: M
authors.lastname: Jelinski
mesh_terms: D000818:Animals; D000831:Animals, Newborn; D002417:Cattle; D002418:Cattle Diseases / Q000382:microbiology*; D005243:Feces / Q000382:microbiology*; D005260:Female; D000069196:Gastrointestinal Microbiome; D006090:Gram-Negative Bacteria / Q000302:isolation & purification; D006094:Gram-Positive Bacteria / Q000302:isolation & purification; D008297:Male; D008460:Meat; D009864:Ontario
keywords: Antimicrobial; Bacteriology; Bovine; Gastrointestinal