title: Changes in the faecal microbiota of mares precede the development of post partum colic.
abstract: BACKGROUND
  Disruptions in the gastrointestinal microbiota may trigger development of post partum colic.
  
  
  OBJECTIVE
  To determine the effects of the periparturient period on the faecal microbiome and identify associations between the faecal microbiota and post partum colic.
  
  
  METHODS
  Longitudinal case-control study.
  
  
  METHODS
  Pre- and post partum faecal samples were collected from mares on 3 farms in central Kentucky. Next generation sequencing of the V4 region of the 16S rRNA gene was performed on samples from 13 mares that developed colic, 13 mares that did not display colic and 5 nonpregnant controls.
  
  
  RESULTS
  There were 4,523,727 sequences from 85 samples evaluated (mean ± s.d. 53,220 ± 29,160, range 8442-122,535). Twenty-five phyla were identified, although only Firmicutes, Verrucomicrobia, Actinobacteria and Proteobacteria were present at a relative abundance of 1% or greater. The faecal microbiota of late-term mares differed from nonpregnant mares, with differences in microbial community membership and structure but not the relative abundance of major phyla. There was limited impact of foaling and the post partum period on the faecal microbiome. Faecal samples obtained from mares prior to episodes of colic had significantly higher relative abundance of Proteobacteria (8.2%, P = 0.0006) compared with samples from mares that did not display colic (3.7%). All samples with a relative abundance of Firmicutes of ≤50% preceded colic, as did 6/7 (86%) samples with >4% Proteobacteria. Differences in microbiota membership and structure were also present between mares that developed large colon volvulus and matched controls that did not have colic. Sixty-one indicator operational taxon units were identified for the control (vs. volvulus) samples, and these were dominated by Lachnospiraceae (n = 38) and Ruminococcaceae (n = 8).
  
  
  CONCLUSIONS
  Foaling had minimal effects on the mares' faecal microbiota. Numerous differences in the faecal microbiota preceded colic. Associations between Firmicutes (particularly Lachnospiraceae and Ruminococcaceae) and Proteobacteria and development of colic could lead to measures to predict and prevent colic. The Summary is available in Chinese - see Supporting information.
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Ontario, Canada.
authors.forename: J S
authors.initials: JS
authors.lastname: Weese
authors.affiliation: Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, USA.
authors.forename: S J
authors.initials: SJ
authors.lastname: Holcombe
authors.affiliation: Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, USA.
authors.forename: R M
authors.initials: RM
authors.lastname: Embertson
authors.affiliation: Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, USA.
authors.forename: K A
authors.initials: KA
authors.lastname: Kurtz
authors.affiliation: Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, USA.
authors.forename: H A
authors.initials: HA
authors.lastname: Roessner
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Ontario, Canada.
authors.forename: M
authors.initials: M
authors.lastname: Jalali
authors.affiliation: Rood and Riddle Equine Hospital, Lexington, Kentucky, USA.
authors.forename: S E
authors.initials: SE
authors.lastname: Wismer
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D016022:Case-Control Studies; D003085:Colic / Q000382:microbiology / Q000662:veterinary*; D005243:Feces / Q000382:microbiology*; D005260:Female; D006734:Horse Diseases; D006736:Horses; D010802:Phylogeny; D049590:Postpartum Period; D011247:Pregnancy; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Firmicutes; Proteobacteria; colic; faecal microbiome; horse; post partum