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.

Figure 1

Rarefaction curves representing the average number of OTUs (y axis) by the number of reads (x axis).

Figure 2

Relative abundance of predominant bacteria at the phylum (A), class (B) and genus (C) levels. Figure legend: penicillin (PEN), ceftiofur (CEF) and sulfa trimethoprin (TMS) and control group (CON). Day 0: before treatment; Day 5: last day of treatment.

Figure 3

Variation in relative abundance of predominant bacteria in feces of healthy horses treated with antibiotics. Figure legend: A: penicillin; B: ceftiofur; C: sulfa trimethoprin; D: control group. Day 0: before treatment; Day 5: last day of treatment.

Figure 4

Dendrograms representing the similarities between population structure addressed by the Yue and Clayton analysis (A) and community membership addressed by the Classic Jaccard (B). Figure legend: Dendrograms were generated based on phylip-formatted distance matrixes using the UPGMA algorithm. The number after the name of the horse represents the day of sampling and the color of the tree brunch represents the drug used: Penicillin = blue, Ceftiofur = green, TMS = red and Control = black.

Figure 5

Principal coordinate analysis (PCoA) of bacterial communities present in feces of horses treated with antibiotics. Figure legend: Bidimentional representation of the principal coordinate analysis of bacterial communities structure addressed by the Yue and Clayton analysis (A) and bacterial membership addressed by the Classic Jaccard analysis (B) found in feces of healthy horses before (Day 1), after (Day 5) treatment with antibiotics and at Days 14 and 30.