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.
Publication Date: 2021-09-30 PubMed ID: 34679880PubMed Central: PMC8533001DOI: 10.3390/ani11102859Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
Summary
This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.
This research studied the impact of an antibiotic, trimethoprim sulfadiazine, on the gut microbiota of horses using two types of sequencing technologies, Illumina short-read and PacBio long-read. The findings suggest PacBio technology was not effective at classifying bacterial species but showed more diversity and less undefined bacteria.
Objectives of the Study
- The study aimed to understand the impact of antibiotic-induced dysbiosis on the gut microbiota of horses.
- The focus was to use two sequencing technologies, Illumina short-read and PacBio long-read sequencing, to classify bacteria at the species level.
- Trimethoprim sulfadiazine (TMS), an antibiotic, was used to induce dysbiosis, an imbalance or disruption in the gut microbiota, in the horses.
Methodology
- The study included nine horses that were administrated an oral dose of TMS for five days to stimulate dysbiosis.
- Fecal samples were obtained from the horses before and after the antibiotic administration.
- These samples were then processed using both Illumina and PacBio sequencing technologies for comparison purposes.
Results
- PacBio sequencing failed to successfully classify the intestinal microbiota of the horses at species level, unlike Illumina sequencing.
- PacBio sequencing confirmed that Bacteroidetes was the most prevalent bacteria present in the horse feces. This was followed by Firmicutes and Fibrobacteres.
- An unidentified Bacteroidales species was found to be highly abundant (13%) in the horse feces, indicating a need for further investigation.
- The results did show that PacBio sequencing detected a greater amount of diversity (richness) in the microbiota, and less unclassified bacteria compared to Illumina sequencing.
Conclusion
- The study concluded that PacBio sequencing was not as effective as Illumina for classifying bacteria at the species level in the horse intestinal microbiota.
- PacBio sequencing proved beneficial in showing greater biodiversity and fewer unclassified bacteria.
- The findings suggest a requirement for further developments in current databases to improve bacterial classification in future equine studies.
Cite This Article
APA
Di Pietro R, Arroyo LG, Leclere M, Costa MC.
(2021).
Species-Level Gut Microbiota Analysis after Antibiotic-Induced Dysbiosis in Horses.
Animals (Basel), 11(10), 2859.
https://doi.org/10.3390/ani11102859 Publication
Researcher Affiliations
- Department of Biomedical Sciences, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada.
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada.
- Department of Clinical Sciences, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada.
- Department of Biomedical Sciences, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada.
Grant Funding
- 054224 / Equine Guelph
- 04514-2018 / Natural Sciences and Engineering Research Council
Conflict of Interest Statement
The authors declare no conflict of interest.
References
This article includes 33 references
- Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system.. Science 2016 Apr 29;352(6285):539-44.
- den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism.. J Lipid Res 2013 Sep;54(9):2325-40.
- Bäumler AJ, Sperandio V. Interactions between the microbiota and pathogenic bacteria in the gut.. Nature 2016 Jul 7;535(7610):85-93.
- Glinsky MJ, Smith RM, Spires HR, Davis CL. Measurement of volatile fatty acid production rates in the cecum of the pony.. J Anim Sci 1976 Jun;42(6):1465-70.
- Costa MC, Arroyo LG, Allen-Vercoe E, Stämpfli HR, Kim PT, Sturgeon A, Weese JS. Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene.. PLoS One 2012;7(7):e41484.
- McKinney CA, Bedenice D, Pacheco AP, Oliveira BCM, Paradis MR, Mazan M, Widmer G. Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea.. PLoS One 2021;16(1):e0244381.
- Stewart HL, Pitta D, Indugu N, Vecchiarelli B, Hennessy ML, Engiles JB, Southwood LL. Changes in the faecal bacterial microbiota during hospitalisation of horses with colic and the effect of different causes of colic.. Equine Vet J 2021 Nov;53(6):1119-1131.
- Costa MC, Stämpfli HR, Arroyo LG, Allen-Vercoe E, Gomes RG, Weese JS. Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs.. BMC Vet Res 2015 Feb 3;11:19.
- Arnold C, Pilla R, Chaffin K, Lidbury J, Steiner J, Suchodolski J. Alterations in the Fecal Microbiome and Metabolome of Horses with Antimicrobial-Associated Diarrhea Compared to Antibiotic-Treated and Non-Treated Healthy Case Controls.. Animals (Basel) 2021 Jun 17;11(6).
- Volkova A, Ruggles K, Schulfer A, Gao Z, Ginsberg SD, Blaser MJ. Effects of early-life penicillin exposure on the gut microbiome and frontal cortex and amygdala gene expression.. iScience 2021 Jul 23;24(7):102797.
- Arnold CE, Isaiah A, Pilla R, Lidbury J, Coverdale JS, Callaway TR, Lawhon SD, Steiner J, Suchodolski JS. The cecal and fecal microbiomes and metabolomes of horses before and after metronidazole administration.. PLoS One 2020;15(5):e0232905.
- Stewart EJ. Growing unculturable bacteria.. J Bacteriol 2012 Aug;194(16):4151-60.
- Costa MC, Weese JS. Understanding the Intestinal Microbiome in Health and Disease.. Vet Clin North Am Equine Pract 2018 Apr;34(1):1-12.
- Costa M, Weese JS. Methods and basic concepts for microbiota assessment.. Vet J 2019 Jul;249:10-15.
- Rhoads A, Au KF. PacBio Sequencing and Its Applications.. Genomics Proteomics Bioinformatics 2015 Oct;13(5):278-89.
- Whon TW, Chung WH, Lim MY, Song EJ, Kim PS, Hyun DW, Shin NR, Bae JW, Nam YD. The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces.. Sci Data 2018 Apr 24;5:180068.
- Graf J, Ledala N, Caimano MJ, Jackson E, Gratalo D, Fasulo D, Driscoll MD, Coleman S, Matson AP. High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon.. mBio 2021 Feb 16;12(1).
- Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.. mSystems 2016 Jan-Feb;1(1).
- Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data.. Nat Methods 2016 Jul;13(7):581-3.
- Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.. Appl Environ Microbiol 2009 Dec;75(23):7537-41.
- Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.. Appl Environ Microbiol 2013 Sep;79(17):5112-20.
- Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation.. Genome Biol 2011 Jun 24;12(6):R60.
- Sadowsky MJ, Staley C, Heiner C, Hall R, Kelly CR, Brandt L, Khoruts A. Analysis of gut microbiota - An ever changing landscape.. Gut Microbes 2017 May 4;8(3):268-275.
- Zhang M, Dang N, Ren D, Zhao F, Lv R, Ma T, Bao Q, Menghe B, Liu W. Comparison of Bacterial Microbiota in Raw Mare's Milk and Koumiss Using PacBio Single Molecule Real-Time Sequencing Technology.. Front Microbiol 2020;11:581610.
- Lau JT, Whelan FJ, Herath I, Lee CH, Collins SM, Bercik P, Surette MG. Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling.. Genome Med 2016 Jul 1;8(1):72.
- Leclere M, Costa MC. Fecal microbiota in horses with asthma.. J Vet Intern Med 2020 Mar;34(2):996-1006.
- Collinet A, Grimm P, Julliand S, Julliand V. Multidimensional Approach for Investigating the Effects of an Antibiotic-Probiotic Combination on the Equine Hindgut Ecosystem and Microbial Fibrolysis.. Front Microbiol 2021;12:646294.
- Harlow BE, Lawrence LM, Flythe MD. Diarrhea-associated pathogens, lactobacilli and cellulolytic bacteria in equine feces: responses to antibiotic challenge.. Vet Microbiol 2013 Sep 27;166(1-2):225-32.
- Freccero F, Lanci A, Mariella J, Viciani E, Quercia S, Castagnetti A, Castagnetti C. Changes in the Fecal Microbiota Associated with a Broad-Spectrum Antimicrobial Administration in Hospitalized Neonatal Foals with Probiotics Supplementation.. Animals (Basel) 2021 Aug 2;11(8).
- Cheung SG, Goldenthal AR, Uhlemann AC, Mann JJ, Miller JM, Sublette ME. Systematic Review of Gut Microbiota and Major Depression.. Front Psychiatry 2019;10:34.
- Iglesias-Vázquez L, Van Ginkel Riba G, Arija V, Canals J. Composition of Gut Microbiota in Children with Autism Spectrum Disorder: A Systematic Review and Meta-Analysis.. Nutrients 2020 Mar 17;12(3).
- Costa MC, Silva G, Ramos RV, Staempfli HR, Arroyo LG, Kim P, Weese JS. Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses.. Vet J 2015 Jul;205(1):74-80.
- Morotomi M, Nagai F, Sakon H, Tanaka R. Paraprevotella clara gen. nov., sp. nov. and Paraprevotella xylaniphila sp. nov., members of the family 'Prevotellaceae' isolated from human faeces.. Int J Syst Evol Microbiol 2009 Aug;59(Pt 8):1895-900.
Citations
This article has been cited 6 times.- Di Pietro R, Arroyo LG, Leclere M, Costa M. Effects of concentrated fecal microbiota transplant on the equine fecal microbiota after antibiotic-induced dysbiosis.. Can J Vet Res 2023 Apr;87(2):85-96.
- Arantes JA, Borges AS, Zakia LS, Surette MG, Weese JS, Costa MC, Arroyo LG. Effect of dietary iron supplementation on the equine fecal microbiome.. Can J Vet Res 2023 Apr;87(2):97-104.
- Theelen MJP, Luiken REC, Wagenaar JA, Sloet van Oldruitenborgh-Oosterbaan MM, Rossen JWA, Schaafstra FJWC, van Doorn DA, Zomer AL. Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome.. Microbiome 2023 Feb 27;11(1):33.
- Liepman RS, Swink JM, Habing GG, Boyaka PN, Caddey B, Costa M, Gomez DE, Toribio RE. Effects of Intravenous Antimicrobial Drugs on the Equine Fecal Microbiome.. Animals (Basel) 2022 Apr 13;12(8).
- Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ. Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity.. PeerJ 2022;10:e13084.
- Simões J, Batista M, Tilley P. The Immune Mechanisms of Severe Equine Asthma-Current Understanding and What Is Missing.. Animals (Basel) 2022 Mar 16;12(6).
Use Nutrition Calculator
Check if your horse's diet meets their nutrition requirements with our easy-to-use tool Check your horse's diet with our easy-to-use tool
Talk to a Nutritionist
Discuss your horse's feeding plan with our experts over a free phone consultation Discuss your horse's diet over a phone consultation
Submit Diet Evaluation
Get a customized feeding plan for your horse formulated by our equine nutritionists Get a custom feeding plan formulated by our nutritionists
