Species-Level Gut Microbiota Analysis after Antibiotic-Induced Dysbiosis in Horses

Abstract

All current studies have used Illumina short-read sequencing to characterize the equine intestinal microbiota. Long-read sequencing can classify bacteria at the species level. The objectives of this study were to characterize the gut microbiota of horses at the species level before and after trimethoprim sulfadiazine (TMS) administration and to compare results with Illumina sequencing. Nine horses received TMS (30 mg/kg) orally for 5 days twice a day to induce dysbiosis. Illumina sequencing of the V4 region or full-length PacBio sequencing of the 16S rRNA gene was performed in fecal samples collected before and after antibiotic administration. The relative abundance and alpha diversity were compared between the two technologies. PacBio failed to classify the equine intestinal microbiota at the species level but confirmed Bacteroidetes as the most abundant bacteria in the feces of the studied horses, followed by Firmicutes and Fibrobacteres. An unknown species of the Bacteroidales order was highly abundant (13%) and deserves further investigation. In conclusion, PacBio was not suitable to classify the equine microbiota species but detected greater richness and less unclassified bacteria. Further efforts in improving current databanks to be used in equine studies are necessary.

Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome

“…Generally, in all animals, irrespective of the type of antimicrobial administered, a decrease in species richness and alpha-diversity is observed [ 45 ], as was also the case in our study. The most profound effects of TMS on the intestinal microbiota were observed immediately after treatment, which is in line with previous reports that also demonstrated a rapid, significant decrease in alpha-diversity [ 5 , 35 , 46 ]. Relative abundance of Kiritimatiellaeota, Fibrobacteres, and Verrucomicrobia decreased significantly, suggesting that TMS has a strong action against bacteria in these phyla.…”

“…Faecal microbiota composition at the phylum level was similar to previously reported in healthy equids from the same geographic area [ 2 ] and other geographic areas [ 35 – 37 ]. Individual variation among the ponies included in our study was limited, potentially as a result of the fact that these ponies were housed under the same circumstances and fed the same diet for > 7 years.…”

“…The decrease of Fibrobacteres (degradation of plant-based cellulose [ 47 ]) and Verrucomicrobia (mucin degradation [ 48 ]) are of interest as they are thought to have a positive effect on equine intestinal health [ 49 , 50 ]. The observed trends were similar in all study subjects, which corresponds to another study reporting the effect of TMS on the equine faecal microbiota to be predictive [ 5 ] but contrast with a recent study reporting high inter-individual variability [ 35 ]. In that last study, the authors did not specify horse characteristics such as age, gender, and breed, which might affect response to treatment [ 35 ].…”

“…In that last study, the authors did not specify horse characteristics such as age, gender, and breed, which might affect response to treatment [ 35 ]. Also, the horses in that study had not received antimicrobials for only 3 months prior to the study, so potential previous antimicrobial administration might still have affected microbiota composition [ 35 ]. However, by using long-read sequencing, the authors of that study observed that species Phascolarctobacterium (phylum Firmicutes) and Subdivision 5 (former phylum Verrucomicrobia, currently Kiritimatiellaeota [ 51 ]) decreased after TMS administration, whereas Paraprevotella (phylum Bacteroidetes) increased [ 35 ].…”

Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity

“…However, earlier studies have largely relied on short-read meta-barcoding analyses of 16S rRNA gene sequences, which are limited in that they fail to provide resolution down to the species or strain level, provide limited insight into population structures or functional repertoires of microbial species and fail to cover viruses and eukaryotes. Thus, despite previous efforts—and drawing on comparisons with the human microbiome, where new species are still being discovered ( Almeida et al, 2019 ; Forster et al, 2019 )—the horse hindgut microbiome presents us with a vast, only superficially explored ( Di Pietro et al, 2021 ) landscape of taxonomic, ecological and functional diversity, certain to encompass important, yet undiscovered roles. Babenko et al (2020) emphasize this with their preliminary exploration of the equine faecal virome, presenting a rich taxonomically diverse viral community which is thought to be essential in shaping microbial ecology.…”