{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T06:25:53Z","timestamp":1791440753408,"version":"4.3.3"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T00:00:00Z","timestamp":1770076800000},"content-version":"vor","delay-in-days":1616,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2021,7,16]],"date-time":"2021-07-16T00:00:00Z","timestamp":1626393600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Donley Family"},{"name":"The Paula and Michael Gaughan Fund"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2021,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The fecal microbiome of healthy horses may be influenced by signalment, diet, environmental factors, and disease.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To assess the effects of age, breed, sex, geographic location, season, diet, and colitis caused by antibiotic use (antimicrobial-associated diarrhea [AAD]) and Salmonella infection on fecal microbiota.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Animals<\/jats:title>\n                    <jats:p>Healthy horses (n\u00a0=\u00a080) were sampled from nonhospital environments across multiple geographical locations in the United States. Horses with AAD (n\u00a0=\u00a014) were defined as those that developed diarrhea secondary to antimicrobial use. Horses with Salmonella infection (n\u00a0=\u00a012) were presented with spontaneous onset of colitis and subsequently tested positive on Salmonella quantitative polymerase chain reaction. All horses were &amp;gt;1\u2009year of age and stratified by a dietary scale that included forages (pasture and hay) and concentrates grouped by percentage of fiber and amount.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Illumina sequencing of 16S rRNA genes was performed on fecal DNA.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Healthy horses fed higher amounts of grain clustered separately from those fed lower amounts of grain (analysis of similarities [ANOSIM], R\u00a0=\u00a00.356-0.385, Q\u00a0=\u00a00.002). Horses with AAD and Salmonella had decreased richness and evenness compared to healthy horses (P\u2009&amp;lt;\u2009.05). Univariable analysis of the 3 groups identified increases in Bacteroidetes (Q\u00a0=\u00a00.002) and Protebacteria (Q\u00a0=\u00a00.001) and decreases in Verrucomicrobia (Q\u00a0=\u00a00.001) in AAD horses whereas Salmonella horses had less Firmicutes (Q\u00a0=\u00a00.001) when compared to healthy horses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions and Clinical Importance<\/jats:title>\n                    <jats:p>Although the amount of grain in the diet had some impact on the fecal microbiome, colitis had a significantly larger influence. Horses with ADD have a more severe dysbiosis than do horses with Salmonella.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/jvim.16206","type":"journal-article","created":{"date-parts":[[2021,7,16]],"date-time":"2021-07-16T03:46:12Z","timestamp":1626407172000},"page":"2437-2448","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["The effects of signalment, diet, geographic location, season, and colitis associated with antimicrobial use or\n                    <i>Salmonella<\/i>\n                    infection on the fecal microbiome of horses"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2354-5903","authenticated-orcid":false,"given":"Carolyn E.","family":"Arnold","sequence":"first","affiliation":[{"name":"College of Veterinary Medicine & Biomedical Sciences, Texas A&M University Department of Large Animal Clinical Sciences, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7758-2609","authenticated-orcid":false,"given":"Rachel","family":"Pilla","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine & Biomedical Sciences, Texas A&M University Department of Small Animal Clinical Sciences, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Keith","family":"Chaffin","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine & Biomedical Sciences, Texas A&M University Department of Large Animal Clinical Sciences, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica L.","family":"Leatherwood","sequence":"additional","affiliation":[{"name":"Texas A&M University Department of Animal Science, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tryon A.","family":"Wickersham","sequence":"additional","affiliation":[{"name":"Texas A&M University Department of Animal Science, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Todd R.","family":"Callaway","sequence":"additional","affiliation":[{"name":"University of Georgia Department of Animal and Dairy Science, , Athens, Georgia,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara D.","family":"Lawhon","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine & Biomedical Sciences, Texas A&M University Department of Veterinary Pathobiology, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5107-4577","authenticated-orcid":false,"given":"Jonathan A.","family":"Lidbury","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine & Biomedical Sciences, Texas A&M University Department of Small Animal Clinical Sciences, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3336-2086","authenticated-orcid":false,"given":"Joerg M.","family":"Steiner","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine & Biomedical Sciences, Texas A&M University Department of Small Animal Clinical Sciences, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2176-6932","authenticated-orcid":false,"given":"Jan S.","family":"Suchodolski","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine & Biomedical Sciences, Texas A&M University Department of Small Animal Clinical Sciences, , College Station, Texas,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,9,1]]},"reference":[{"key":"2026020303470572900_jvim16206-bib-0001","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1056\/NEJMra1600266","article-title":"The human intestinal microbiome in health and disease","volume":"375","author":"Lynch","year":"2016","journal-title":"N Engl J Med"},{"key":"2026020303470572900_jvim16206-bib-0002","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s40168-017-0296-0","article-title":"(Dis)Trust your gut: the gut microbiome in age-related inflammation, health, and disease","volume":"5","author":"Buford","year":"2017","journal-title":"Microbiome"},{"key":"2026020303470572900_jvim16206-bib-0003","doi-asserted-by":"crossref","first-page":"16489","DOI":"10.3748\/wjg.v20.i44.16489","article-title":"Microbiota alterations in acute and chronic gastrointestinal inflammation of cats and dogs","volume":"20","author":"Honneffer","year":"2014","journal-title":"World J Gastroenterol"},{"key":"2026020303470572900_jvim16206-bib-0004","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.tvjl.2016.04.011","article-title":"Diagnosis and interpretation of intestinal dysbiosis in dogs and cats","volume":"215","author":"Suchodolski","year":"2016","journal-title":"Vet J"},{"key":"2026020303470572900_jvim16206-bib-0005","doi-asserted-by":"crossref","DOI":"10.1093\/femsec\/fix136","article-title":"A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy","volume":"93","author":"AlShawaqfeh","year":"2017","journal-title":"FEMS Microbiol Ecol"},{"key":"2026020303470572900_jvim16206-bib-0006","doi-asserted-by":"crossref","first-page":"67","DOI":"10.2460\/javma.2001.219.67","article-title":"Estimate of the national incidence of and operation-level risk factors for colic among horses in the United States, spring 1998 to spring 1999","volume":"219","author":"Traub-Dargatz","year":"2001","journal-title":"J Am Vet Med Assoc"},{"key":"2026020303470572900_jvim16206-bib-0007","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.tvjl.2015.03.018","article-title":"Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses","volume":"205","author":"Costa","year":"2015","journal-title":"Vet J"},{"key":"2026020303470572900_jvim16206-bib-0008","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.5713\/ajas.15.0587","article-title":"Comparison of fecal microbiota of Mongolian and Thoroughbred horses by high-throughput sequencing of the V4 Region of the 16S rRNA gene","volume":"29","author":"Zhao","year":"2016","journal-title":"Asian-Australas J Anim Sci"},{"key":"2026020303470572900_jvim16206-bib-0009","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.jevs.2017.03.013","article-title":"Development of an ethogram for evaluating riding horses","volume":"52","author":"Collins","year":"2017","journal-title":"J Equine Vet Sci"},{"key":"2026020303470572900_jvim16206-bib-0010","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cveq.2017.11.005","article-title":"Understanding the intestinal microbiome in health and disease","volume":"34","author":"Costa","year":"2018","journal-title":"Vet Clin North Am Equine Pract"},{"key":"2026020303470572900_jvim16206-bib-0011","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1111\/lam.12137","article-title":"The core faecal bacterial microbiome of Irish Thoroughbred racehorses","volume":"57","author":"O'Donnell","year":"2013","journal-title":"Lett Appl Microbiol"},{"key":"2026020303470572900_jvim16206-bib-0012","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1111\/jbg.12441","article-title":"Inter-breed diversity and temporal dynamics of the faecal microbiota in healthy horses","volume":"137","author":"Massacci","year":"2020","journal-title":"J Anim Breed Genet"},{"key":"2026020303470572900_jvim16206-bib-0013","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0087424","article-title":"Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing","volume":"9","author":"Dougal","year":"2014","journal-title":"PLoS One"},{"key":"2026020303470572900_jvim16206-bib-0014","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1111\/evj.12361","article-title":"Changes in the faecal microbiota of mares precede the development of post partum colic","volume":"47","author":"Weese","year":"2015","journal-title":"Equine Vet J"},{"key":"2026020303470572900_jvim16206-bib-0015","doi-asserted-by":"crossref","first-page":"1736","DOI":"10.2527\/jas.2012-5720","article-title":"Effect of transportation on fecal bacterial communities and fermentative activities in horses: impact of Saccharomyces cerevisiae CNCM I-1077 supplementation","volume":"91","author":"Faubladier","year":"2013","journal-title":"J Anim Sci"},{"key":"2026020303470572900_jvim16206-bib-0016","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0167108","article-title":"Intense exercise and aerobic conditioning associated with chromium or L-carnitine supplementation modified the fecal microbiota of fillies","volume":"11","author":"Almeida","year":"2016","journal-title":"PLoS One"},{"key":"2026020303470572900_jvim16206-bib-0017","doi-asserted-by":"crossref","first-page":"119","DOI":"10.3920\/CEP160015","article-title":"Exercise training-induced changes in the gut microbiota of Standardbred racehorses","volume":"12","author":"Janabi","year":"2016","journal-title":"Comp Exerc Physiol"},{"key":"2026020303470572900_jvim16206-bib-0018","doi-asserted-by":"crossref","first-page":"13","DOI":"10.3920\/CEP160030","article-title":"The effects of acute strenuous exercise on the faecal microbiota in Standardbred racehorses","volume":"13","author":"Janabi","year":"2017","journal-title":"Comp Exerc Physiol"},{"key":"2026020303470572900_jvim16206-bib-0019","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1111\/evj.12479","article-title":"Effects of transport, fasting and anaesthesia on the faecal microbiota of healthy adult horses","volume":"48","author":"Schoster","year":"2016","journal-title":"Equine Vet J"},{"key":"2026020303470572900_jvim16206-bib-0020","first-page":"351","article-title":"Feed restriction enhances the depressive effects of erythromycin on equine hindgut microbial metabolism in vitro","volume":"125","author":"Kuhn","year":"2012","journal-title":"Berl Munch Tierarztl Wochenschr"},{"key":"2026020303470572900_jvim16206-bib-0021","doi-asserted-by":"crossref","first-page":"8510","DOI":"10.1038\/s41598-018-26930-3","article-title":"Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period","volume":"8","author":"Salem","year":"2018","journal-title":"Sci Rep"},{"key":"2026020303470572900_jvim16206-bib-0022","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-15375-9","article-title":"Evaluating the impact of domestication and captivity on the horse gut microbiome","volume":"7","author":"Metcalf","year":"2017","journal-title":"Sci Rep"},{"key":"2026020303470572900_jvim16206-bib-0023","doi-asserted-by":"crossref","first-page":"908","DOI":"10.2746\/042516409X447806","article-title":"Changes in faecal bacteria associated with concentrate and forage-only diets fed to horses in training","volume":"41","author":"Willing","year":"2009","journal-title":"Equine Vet J"},{"key":"2026020303470572900_jvim16206-bib-0024","doi-asserted-by":"crossref","first-page":"5077","DOI":"10.2527\/jas2017.1754","article-title":"Influence of short-term dietary starch inclusion on the equine cecal microbiome","volume":"95","author":"Warzecha","year":"2017","journal-title":"J Anim Sci"},{"key":"2026020303470572900_jvim16206-bib-0025","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.vetmic.2013.05.003","article-title":"Diarrhea-associated pathogens, lactobacilli and cellulolytic bacteria in equine feces: responses to antibiotic challenge","volume":"166","author":"Harlow","year":"2013","journal-title":"Vet Microbiol"},{"key":"2026020303470572900_jvim16206-bib-0026","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s12917-015-0335-7","article-title":"Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs","volume":"11","author":"Costa","year":"2015","journal-title":"BMC Vet Res"},{"key":"2026020303470572900_jvim16206-bib-0027","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1111\/evj.13010","article-title":"Differences in the equine faecal microbiota between horses presenting to a tertiary referral hospital for colic compared with an elective surgical procedure","volume":"51","author":"Stewart","year":"2019","journal-title":"Equine Vet J"},{"key":"2026020303470572900_jvim16206-bib-0028","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1111\/evj.13010","article-title":"Differences in the equine faecal microbiota between horses presenting to a tertiary referral hospital for colic compared to an elective surgical procedure","volume":"51","author":"Stewart","year":"2018","journal-title":"Equine Vet J"},{"key":"2026020303470572900_jvim16206-bib-0029","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1038\/nature25973","article-title":"Environment dominates over host genetics in shaping human gut microbiota","volume":"555","author":"Rothschild","year":"2018","journal-title":"Nature"},{"key":"2026020303470572900_jvim16206-bib-0030","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.chom.2019.05.005","article-title":"Daily sampling reveals personalized diet-microbiome associations in humans","volume":"25","author":"Johnson","year":"2019","journal-title":"Cell Host Microbe"},{"key":"2026020303470572900_jvim16206-bib-0031","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0201279","article-title":"The fecal microbiome and metabolome differs between dogs fed bones and raw food (BARF) diets and dogs fed commercial diets","volume":"13","author":"Schmidt","year":"2018","journal-title":"PLoS One"},{"key":"2026020303470572900_jvim16206-bib-0032","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.2460\/ajvr.2002.63.1265","article-title":"Detection of Salmonella spp in fecal specimens by use of real-time polymerase chain reaction assay","volume":"63","author":"Kurowski","year":"2002","journal-title":"Am J Vet Res"},{"key":"2026020303470572900_jvim16206-bib-0033","doi-asserted-by":"crossref","first-page":"129","DOI":"10.3354\/ame01753","article-title":"Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton","volume":"75","author":"Apprill","year":"2015","journal-title":"Aquat Microb Ecol"},{"key":"2026020303470572900_jvim16206-bib-0034","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1111\/1462-2920.13023","article-title":"Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples","volume":"18","author":"Parada","year":"2016","journal-title":"Environ Microbiol"},{"key":"2026020303470572900_jvim16206-bib-0035","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026020303470572900_jvim16206-bib-0036","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-55691-w","article-title":"Characterization of the fecal microbiome in cats with inflammatory bowel disease or alimentary small cell lymphoma","volume":"9","author":"Marsilio","year":"2019","journal-title":"Sci Rep"},{"key":"2026020303470572900_jvim16206-bib-0037","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1007\/s12975-019-00760-5","article-title":"Reproductive senescence and ischemic stroke remodel the gut microbiome and modulate the effects of estrogen treatment in female rats","volume":"11","author":"Park","year":"2019","journal-title":"Transl Stroke Res"},{"key":"2026020303470572900_jvim16206-bib-0038","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat Methods"},{"key":"2026020303470572900_jvim16206-bib-0039","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat Methods"},{"key":"2026020303470572900_jvim16206-bib-0040","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00021-16","article-title":"Preservation methods differ in fecal microbiome stability, affecting suitability for field studies","volume":"1","author":"Song","year":"2016","journal-title":"mSystems"},{"key":"2026020303470572900_jvim16206-bib-0041","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0230148","article-title":"The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea","volume":"15","author":"McKinney","year":"2020","journal-title":"PLoS One"},{"key":"2026020303470572900_jvim16206-bib-0042","article-title":"How and why men and women differ in their microbiomes: medical ecology and network analyses of the microgenderome","volume":"6","author":"Ma","year":"2019","journal-title":"Adv Sci (Weinh)"},{"key":"2026020303470572900_jvim16206-bib-0043","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-54039-8","article-title":"High-starch diets alter equine faecal microbiota and increase behavioural reactivity","volume":"9","author":"Bulmer","year":"2019","journal-title":"Sci Rep"}],"container-title":["Journal of Veterinary Internal Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jvim.16206","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/jvim.16206","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/jvim\/article-pdf\/35\/5\/2437\/66673202\/jvim16206.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jvim\/article-pdf\/35\/5\/2437\/66673202\/jvim16206.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T08:47:28Z","timestamp":1770108448000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jvim\/article\/35\/5\/2437\/8448723"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,1]]},"references-count":43,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,9,1]]}},"URL":"https:\/\/doi.org\/10.1111\/jvim.16206","relation":{},"ISSN":["1939-1676"],"issn-type":[{"value":"1939-1676","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,9]]},"published":{"date-parts":[[2021,9,1]]},"assertion":[{"value":"2020-07-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-06-18","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-07-16","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}