title: Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission.
abstract: BACKGROUND
  The equine faecal microbiota is very complex and remains largely unknown, while interspecies interactions have an important contribution to animal health. Clostridium difficile has been identified as an important cause of diarrhoea in horses. This study provides further information on the nature of the bacterial communities present in horses developing an episode of diarrhoea. The prevalence of C. difficile in hospitalised horses at the time of admission is also reported.
  
  
  RESULTS
  Bacterial diversity of the gut microbiota in diarrhoea is lower than that in non-diarrhoeic horses in terms of species richness (p-value <0.002) and in population evenness (p-value: 0.02). Statistical differences for Actinobacillus, Porphyromonas, RC9 group, Roseburia and Ruminococcaceae were revealed. Fusobacteria was found in horses with diarrhoea but not in any of the horses with non-diarrheic faeces. In contrast, Akkermansia was among the three predominant taxa in all of the horses studied. The overall prevalence of C. difficile in the total samples of hospitalised horses at admission was 3.7 % (5/134), with five different PCR-ribotypes identified, including PCR-ribotype 014. Two colonised horses displayed a decreased bacterial species richness compared to the remaining subjects studied, which shared the same Bacteroides genus. However, none of the positive animals had diarrhoea at the moment of sampling.
  
  
  CONCLUSIONS
  The abundance of some taxa in the faecal microbiota of diarrhoeic horses can be a result of microbiome dysbiosis, and therefore a cause of intestinal disease, or some of these taxa may act as equine enteric pathogens. Clostridium difficile colonisation seems to be transient in all of the horses studied, without overgrowth to trigger infection. A large proportion of the sequences were unclassified, showing the complexity of horses' faecal microbiota.
authors.affiliation: Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium. c.rodriguez@ulg.ac.be.
authors.forename: Cristina
authors.initials: C
authors.lastname: Rodriguez
authors.affiliation: Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium. bernard.taminiau@ulg.ac.be.
authors.forename: Bernard
authors.initials: B
authors.lastname: Taminiau
authors.affiliation: Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium. bastien.brevers@student.hepl.be.
authors.forename: Bastien
authors.initials: B
authors.lastname: Brévers
authors.affiliation: Microbiology Unit, Catholic University of Louvain, Brussels, Belgium. veronique.avesani@uclouvain.be.
authors.forename: Véronique
authors.initials: V
authors.lastname: Avesani
authors.affiliation: Microbiology Unit, Catholic University of Louvain, Brussels, Belgium. johan.vanbroeck@uclouvain.be.
authors.forename: Johan
authors.initials: J
authors.lastname: Van Broeck
authors.affiliation: Equine Teaching Hospital, Clinical Department of Companion Animals and Equids, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium. aurelia.leroux@ulg.ac.be.
authors.forename: Aurélia
authors.initials: A
authors.lastname: Leroux
authors.affiliation: Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium. marjonneur@hotmail.com.
authors.forename: Marjorie
authors.initials: M
authors.lastname: Gallot
authors.affiliation: Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium. bruwierantoine@hotmail.com.
authors.forename: Antoine
authors.initials: A
authors.lastname: Bruwier
authors.affiliation: Equine Teaching Hospital, Clinical Department of Companion Animals and Equids, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium. helene.amory@ulg.ac.be.
authors.forename: Hélene
authors.initials: H
authors.lastname: Amory
authors.affiliation: Microbiology Unit, Catholic University of Louvain, Brussels, Belgium. michel.delmee@uclouvain.be.
authors.forename: Michel
authors.initials: M
authors.lastname: Delmée
authors.affiliation: Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium. georges.daube@ulg.ac.be.
authors.forename: Georges
authors.initials: G
authors.lastname: Daube
mesh_terms: D000818:Animals; D002353:Carrier State / Q000453:epidemiology / Q000382:microbiology / Q000662:veterinary*; D016360:Clostridioides difficile / Q000302:isolation & purification*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D003967:Diarrhea / Q000453:epidemiology / Q000382:microbiology / Q000662:veterinary*; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome; D006734:Horse Diseases / Q000453:epidemiology* / Q000382:microbiology*; D006736:Horses / Q000382:microbiology*; D006762:Hospitals, Animal; D008969:Molecular Sequence Data; D010802:Phylogeny; D015995:Prevalence; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S