title: Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs.
abstract: BACKGROUND
  The intestinal tract is a rich and complex environment and its microbiota has been shown to have an important role in health and disease in the host. Several factors can cause disruption of the normal intestinal microbiota, including antimicrobial therapy, which is an important cause of diarrhea in horses. This study aimed to characterize changes in the fecal bacterial populations of healthy horses associated with the administration of frequently used antimicrobial drugs.
  
  
  RESULTS
  Twenty-four adult mares were assigned to receive procaine penicillin intramuscularly (IM), ceftiofur sodium IM, trimethoprim sulfadiazine (TMS) orally or to a control group. Treatment was given for 5 consecutive days and fecal samples were collected before drug administration (Day 1), at the end of treatment (Days 5), and on Days 14 and 30 of the trial. High throughput sequencing of the V4 region of the 16S rRNA gene was performed using an Illumina MiSeq sequencer. Significant changes of population structure and community membership were observed after the use of all drugs. TMS caused the most marked changes on fecal microbiota even at higher taxonomic levels including a significant decrease of richness and diversity. Those changes were mainly due to a drastic decrease of Verrucomicrobia, specifically the "5 genus incertae sedis". Changes in structure and membership caused by antimicrobial administration were specific for each drug and may be predictable. Twenty-five days after the end of treatment, bacterial profiles were more similar to pre-treatment patterns indicating a recovery from changes caused by antimicrobial administration, but differences were still evident, especially regarding community membership.
  
  
  CONCLUSIONS
  The use of systemic antimicrobials leads to changes in the intestinal microbiota, with different and specific responses to different antimicrobials. All antimicrobials tested here had some impact on the microbiota, but TMS significantly reduced bacterial species richness and diversity and had the greatest apparent impact on population structure, specifically targeting members of the Verrucomicrobia phylum.
authors: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada. costamc@gmail.com.
authors: Marcio C
authors: MC
authors: Costa
authors: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Canada. hstaempf@uoguelph.ca.
authors: Henry R
authors: HR
authors: Stämpfli
authors: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Canada. larroyo@uoguelph.ca.
authors: Luis G
authors: LG
authors: Arroyo
authors: Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, Guelph, Canada. eav@uoguelph.ca.
authors: Emma
authors: E
authors: Allen-Vercoe
authors: Department of Clinical Studies, "Universidade Estadual de Londrina", Londrina, Brazil. garbelinirg@uel.br.
authors: Roberta G
authors: RG
authors: Gomes
authors: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada. jsweese@uoguelph.ca.
authors: J Scott
authors: JS
authors: Weese
mesh_terms: D000284:Administration, Oral; D000818:Animals; D000890:Anti-Infective Agents / Q000008:administration & dosage / Q000494:pharmacology*; D002511:Cephalosporins / Q000008:administration & dosage / Q000494:pharmacology; D004269:DNA, Bacterial / Q000235:genetics; D004338:Drug Combinations; D005243:Feces / Q000382:microbiology*; D005260:Female; D006736:Horses / Q000382:microbiology*; D007273:Injections, Intramuscular / Q000662:veterinary; D064307:Microbiota / Q000187:drug effects* / Q000235:genetics; D010402:Penicillin G Procaine / Q000008:administration & dosage / Q000494:pharmacology; D013413:Sulfadoxine / Q000008:administration & dosage / Q000494:pharmacology; D014295:Trimethoprim / Q000008:administration & dosage / Q000494:pharmacology
chemical_list: D000890:Anti-Infective Agents; D002511:Cephalosporins; D004269:DNA, Bacterial; D004338:Drug Combinations; D010402:Penicillin G Procaine; C000301:trimethoprim, sulfadoxine drug combination; C053503:ceftiofur; D013413:Sulfadoxine; D014295:Trimethoprim
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