title: Development of the faecal microbiota in foals.
abstract: BACKGROUND
  The intestinal microbiota is a complex polymicrobial ecosystem that exerts extremely important roles in the development and maintenance of health. Recently, as new sequencing technologies have become more available, there has been a revolution in the understanding of the equine intestinal microbiota. However, studies characterising the pioneer intestinal bacteria colonising foals and its development over time are still limited.
  
  
  OBJECTIVE
  The objectives of this study were to characterise the intestinal bacterial colonisation of newborn foals and to follow individual animals over time until age 9 months.
  
  
  METHODS
  Longitudinal study.
  
  
  METHODS
  Eleven pregnant mares from one farm were enrolled and faecal samples were collected longitudinally from mares and foals during their first day post partum and again periodically until foals were age 9 months. The V4 region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform.
  
  
  RESULTS
  Newborn foals had a rich and diverse bacterial community, which was mainly comprised of the Firmicutes phylum with several low abundant genera being unique at this age. Foals aged 2-30 days had significantly decreased diversity compared to older animals, with the majority of organisms classified as Akkermansia spp. After 60 days of life, the intestinal microbiota structure tended to remain stable, but differences in community membership were still present between 9-month-old animals and mature mares. Several differences at the phylum level were observed between different ages, including a higher abundance of Fibrobacteres after weaning.
  
  
  CONCLUSIONS
  The intestinal microbiota of the equine newborn is already complex by the first day of life. Microbiota adaptation occurs during the first month and the microbiota of foals older than 60 days resemble the mother's microbiota, although differences in community membership are still present.
authors.affiliation: Department of Pathobiology, University of Guelph, Canada. costamc@gmail.com.
authors.forename: M C
authors.identifier: http://orcid.org/0000-0001-5067-7501
authors.initials: MC
authors.lastname: Costa
authors.affiliation: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Canada.
authors.forename: H R
authors.initials: HR
authors.lastname: Stämpfli
authors.affiliation: Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, Canada.
authors.forename: E
authors.initials: E
authors.lastname: Allen-Vercoe
authors.affiliation: Department of Pathobiology, University of Guelph, Canada.
authors.forename: J S
authors.initials: JS
authors.lastname: Weese
mesh_terms: D000375:Aging; D000818:Animals; D000831:Animals, Newborn; D001419:Bacteria / Q000145:classification*; D005243:Feces / Q000382:microbiology*; D005260:Female; D006736:Horses / Q000254:growth & development / Q000382:microbiology*; D011247:Pregnancy
keywords: 16S rRNA gene; distal gut; foal heat diarrhoea; horse; intestinal bacteria; microbiome