title: Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves.
abstract: BACKGROUND
  Neonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population-based studies of cattle have investigated how the microbiota is impacted during diarrhea.
  
  
  OBJECTIVE
  To characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.
  
  
  METHODS
  Fifteen diarrheic calves between the ages of 1 and 30 days and 15 age-matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).
  
  
  RESULTS
  Significant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.
  
  
  CONCLUSIONS
  The fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
authors.forename: D E
authors.identifier: http://orcid.org/0000-0001-7495-4868
authors.initials: DE
authors.lastname: Gomez
authors.affiliation: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
authors.forename: L G
authors.initials: LG
authors.lastname: Arroyo
authors.affiliation: Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.
authors.forename: M C
authors.initials: MC
authors.lastname: Costa
authors.affiliation: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
authors.forename: L
authors.initials: L
authors.lastname: Viel
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
authors.forename: J S
authors.initials: JS
authors.lastname: Weese
mesh_terms: D000818:Animals; D016022:Case-Control Studies; D002417:Cattle; D002418:Cattle Diseases / Q000382:microbiology*; D003967:Diarrhea / Q000382:microbiology / Q000662:veterinary*; D005243:Feces / Q000382:microbiology*; D005260:Female; D064307:Microbiota / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 
  Escherichia coli
  ; Bacterial species; Bifidobacterium; Epidemiology; Infectious diseases; LEfSe; Microbiology; PICRUSt