title: Ovine rumen papillae biopsy via oral endoscopy; a rapid and repeatable method for serial sampling.
abstract: OBJECTIVE
  To explore and validate the utility of rumen endoscopy for collection of rumen papillae for gene expression measurement.
  
  
  METHODS
  Four adult Coopworth ewes were fasted for either 4 or 24 hours. Animals were sedated, placed in a dorsally recumbent position at 45 degrees with the head upright, and an endoscope inserted via a tube inserted into the mouth. Biopsies of rumen papillae were taken from the ventral surface of the rumen atrium under visual guidance. Two biopsies were collected from one of the animals that had been fasted for 4 hours, and three from one of the animals that had been fasted for 24 hours. Video of the rumen atrium and reticulum was also collected. The animals recovered uneventfully. Biopsies were subsequently used for extraction and sequencing of mRNA.
  
  
  RESULTS
  The ventral surface of the rumen atrium was accessible after 4 hours off pasture, but a larger region was accessible after 24 hours of fasting. Sedation allowed access for endoscope use for around 5 to 10 minutes after which increased saliva flow was noted. Rumen papillae biopsies were easily collected, with samples from a variety of sites collected in the ∼10 minute time window. High quality RNA was obtained for stranded mRNA sequencing. Of the resulting reads, 69-70% mapped uniquely to version 3.1 of the ovine genome, and 48-49% to a known gene. The rumen mRNA profiles were consistent with a previously reported study.
  
  
  CONCLUSIONS
  This method for obtaining rumenal tissue was found to be rapid and resulted in no apparent short or long term effects on the animal. High quality RNA was successfully extracted and amplified from the rumen papillae biopsies, indicating that this technique could be used for future gene expression studies. The use of rumen endoscopy could be extended to collection of a variety of rumen and reticulum anatomical measurements and deposition and retrieval of small sensors from the rumen. Rumen endoscopy offers an attractive and cost effective approach to repeated rumen biopsies compared with serial slaughter or use of cannulated animals.
authors.affiliation: a AgResearch , Invermay Agricultural Centre , Private Bag 50034, Mosgiel , 9053 , New Zealand.
authors.forename: K M
authors.initials: KM
authors.lastname: McRae
authors.affiliation: b Dunedin School of Medicine, Department of Medicine , University of Otago , PO Box 56, Dunedin , 9054 , New Zealand.
authors.forename: M
authors.initials: M
authors.lastname: Schultz
authors.affiliation: a AgResearch , Invermay Agricultural Centre , Private Bag 50034, Mosgiel , 9053 , New Zealand.
authors.forename: C G
authors.initials: CG
authors.lastname: Mackintosh
authors.affiliation: a AgResearch , Invermay Agricultural Centre , Private Bag 50034, Mosgiel , 9053 , New Zealand.
authors.forename: G H
authors.initials: GH
authors.lastname: Shackell
authors.affiliation: a AgResearch , Invermay Agricultural Centre , Private Bag 50034, Mosgiel , 9053 , New Zealand.
authors.forename: M F
authors.initials: MF
authors.lastname: Martinez
authors.affiliation: a AgResearch , Invermay Agricultural Centre , Private Bag 50034, Mosgiel , 9053 , New Zealand.
authors.forename: K J
authors.initials: KJ
authors.lastname: Knowler
authors.affiliation: b Dunedin School of Medicine, Department of Medicine , University of Otago , PO Box 56, Dunedin , 9054 , New Zealand.
authors.forename: M
authors.initials: M
authors.lastname: Williams
authors.affiliation: b Dunedin School of Medicine, Department of Medicine , University of Otago , PO Box 56, Dunedin , 9054 , New Zealand.
authors.forename: C
authors.initials: C
authors.lastname: Ho
authors.affiliation: a AgResearch , Invermay Agricultural Centre , Private Bag 50034, Mosgiel , 9053 , New Zealand.
authors.forename: S N
authors.initials: SN
authors.lastname: Elmes
authors.affiliation: a AgResearch , Invermay Agricultural Centre , Private Bag 50034, Mosgiel , 9053 , New Zealand.
authors.forename: J C
authors.initials: JC
authors.lastname: McEwan
mesh_terms: D000818:Animals; D001706:Biopsy / Q000379:methods / Q000662:veterinary; D016099:Endoscopy, Gastrointestinal / Q000379:methods / Q000662:veterinary*; D005260:Female; D012417:Rumen / Q000473:pathology*; D012756:Sheep
keywords: Rumen; biopsy; endoscopy; gene expression; papillae; sheep