Costa MC, Weese JS. Understanding the intestinal microbiome in health and disease. Vet Clin North Am Equine Pract. 2018;34:1–12.
Article
CAS
PubMed
Google Scholar
Ursell LK, Metcalf JL, Parfrey LW, Knight R. Defining the human microbiome. Nutr Rev. 2012;70:38–44.
Article
Google Scholar
D’Argenio V, Salvatore F. The role of the gut microbiome in the healthy adult status. Clin Chim Acta. 2015;451:97–102.
Article
PubMed
CAS
Google Scholar
Young VB. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ. 2017;356:j831. https://doi.org/10.1136/bmj.j831.
Argenzio R, Southworth M, Stevens C. Sites of organic acid production and absorption in the equine gastrointestinal tract. Am J Phys. 1974;226:1043–50.
Article
CAS
Google Scholar
Biddle AS, Black SJ, Blanchard JL. An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction. PLoS One. 2013;8:e77599.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dougal K, de la Fuente G, Harris PA, Girdwood SE, Pinloche E, Newbold CJ. Identification of a Core bacterial community within the large intestine of the horse. PLoS One. 2013;8:e77660.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016;8:51.
Article
PubMed
PubMed Central
Google Scholar
Julliand V, Grimm P, HORSE SPECIES SYMPOSIUM. The microbiome of the horse hindgut: history and current knowledge. J Anim Sci. 2016;94:2262–74.
Article
CAS
PubMed
Google Scholar
Blackmore TM, Dugdale A, Argo CM, Curtis G, Pinloche E, Harris PA, et al. Strong stability and host specific bacterial Community in Faeces of ponies. PLoS One. 2013;8:e75079.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoshida N, Yamashita T, Hirata KI. Gut microbiome and cardiovascular diseases. Diseases. 2018;6(3):56. https://doi.org/10.3390/dieases6030056. Accessed 2018 June 29.
Kasselman LJ, Vernice NA, DeLeon J, Reiss AB. The gut microbiome and elevated cardiovascular risk in obesity and autoimmunity. Atherosclerosis. 2018;271:203–13.
Article
CAS
PubMed
Google Scholar
Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci. 2007;104:13780–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One. 2010;5:e9085.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zheng P, Li Z, Zhou Z. Gut microbiome in type 1 diabetes: a comprehensive review. Diabetes Metab Res Rev. 2018;34:e3043. https://doi.org/10.1002/dmrr.3043.
Article
PubMed
PubMed Central
Google Scholar
Aydin O, Nieuwdorp M, Gerdes V. The gut microbiome as a target for the treatment of type 2 diabetes. Curr Diab Rep. 2018;18:55.
Article
PubMed
PubMed Central
CAS
Google Scholar
Scher JU, Abramson SB. The microbiome and rheumatoid arthritis. Nat Rev Rheumatol. 2011;7:569–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zalar B, Haslberger A, Peterlin B. The role of microbiota in depression - a brief review. Psychiatr Danub. 2018;30:136–41.
Article
CAS
PubMed
Google Scholar
Dart A. Gut microbiota bile acid metabolism controls cancer immunosurveillance. Nat Rev Microbiol. 2018;16:453. https://doi.org/10.1038/s41579-018-0053-9.
Article
CAS
PubMed
Google Scholar
Ma C, Han M, Heinrich B, Fu Q, Zhang Q, Sandhu M, et al. Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells. Science. 2018;360(6391):5931. https://doi.org/10.1126/science.aan5931.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gopalakrishnan V, Helmink BA, Spencer CN, Reuben A, Wargo JA. The influence of the gut microbiome on Cancer, immunity, and Cancer immunotherapy. Cancer Cell. 2018;33:570–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kwa M, Plottel CS, Blaser MJ, Adams S. The intestinal microbiome and estrogen receptor-positive female breast Cancer. J Natl Cancer Inst. 2016;108:(8):djw029. https://doi.org/10.1093/jnci/djw029.
Leng J, Proudman C, Darby A, Blow F, Townsend N, Miller A, et al. Exploration of the fecal microbiota and biomarker discovery in equine grass sickness. J Proteome Res. 2018;17:1120–8.
Article
CAS
PubMed
Google Scholar
Garrett LA, Brown R, Poxton IR. A comparative study of the intestinal microbiota of healthy horses and those suffering from equine grass sickness. Vet Microbiol. 2002;87:81–8.
Article
PubMed
Google Scholar
Costa MC, Arroyo LG, Allen-Vercoe E, Stämpfli HR, Kim PT, Sturgeon A, et al. 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:e41484.
Article
CAS
PubMed
PubMed Central
Google Scholar
Milinovich GJ, Burrell PC, Pollitt CC, Klieve AV, Blackall LL, Ouwerkerk D, et al. Microbial ecology of the equine hindgut during oligofructose-induced laminitis. ISME J. 2008;2:1089.
Article
CAS
PubMed
Google Scholar
Willing B, Voros A, Roos S, Jones C, Jansson A, Lindberg JE. Changes in faecal bacteria associated with concentrate and forage-only diets fed to horses in training. Equine Vet J. 2009;41:908–14.
Article
CAS
PubMed
Google Scholar
Dougal K, de la Fuente G, Harris PA, Girdwood SE, Pinloche E, Geor RJ, et al. Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing. PLoS One. 2014;9:e87424.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ericsson AC, Johnson PJ, Lopes MA, Perry SC, Lanter HR. A microbiological map of the healthy equine gastrointestinal tract. PLoS One. 2016;11:e0166523.
Article
PubMed
PubMed Central
CAS
Google Scholar
Costa MC, Silva G, Ramos RV, Staempfli HR, Arroyo LG, Kim P, et al. Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses. Vet J. 2015;205:74–80.
Article
CAS
PubMed
Google Scholar
Costa MC, Weese JS. The equine intestinal microbiome. Anim Health Res Rev. 2012;13:121–8.
Article
PubMed
Google Scholar
Tanabe S, Suzuki T, Wasano Y, Nakajima F, Kawasaki H, Tsuda T, et al. Anti-inflammatory and intestinal barrier-protective activities of commensal lactobacilli and Bifidobacteria in thoroughbreds: role of probiotics in diarrhea prevention in neonatal thoroughbreds. J Equine Sci. 2014;25:37–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schoster A, Weese JS, Guardabassi L. Probiotic use in horses - what is the evidence for their clinical efficacy? J Vet Intern Med. 2014;28:1640–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
O’ Donnell MM, Harris HMB, Ross RP, O'Toole PW. Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals. MicrobiologyOpen. 2017;6:e00509-n/a.
Article
Google Scholar
MM OD, Harris HM, Jeffery IB, Claesson MJ, Younge B, PW OT, et al. The core faecal bacterial microbiome of Irish thoroughbred racehorses. Lett Appl Microbiol. 2013;57:492–501.
Article
Google Scholar
Shade A, Handelsman J. Beyond the Venn diagram: the hunt for a core microbiome. Environ Microbiol. 2012;14:4–12.
Article
CAS
PubMed
Google Scholar
Costa MC, Stampfli 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;11:19.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schoster A, Mosing M, Jalali M, Staempfli HR, Weese JS. Effects of transport, fasting and anaesthesia on the faecal microbiota of healthy adult horses. Equine Vet J. 2016;48:595–602.
Article
CAS
PubMed
Google Scholar
Panek M, Čipčić Paljetak H, Barešić A, Perić M, Matijašić M, Lojkić I, et al. Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies. Sci Rep. 2018;8:5143.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lagier J-C, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P, et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol. 2016;1:16203.
Article
CAS
PubMed
Google Scholar
Lagier J-C, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, et al. Culturing the human microbiota and culturomics. Nat Rev Microbiol. 2018;16:540–50.
Article
CAS
PubMed
Google Scholar
Reuter JA, Spacek DV, Snyder MP. High-throughput sequencing technologies. Mol Cell. 2015;58:586–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lewis RW, Islam AA, Dilla-Ermita CJ, Hulbert SH, Sullivan TS. High-throughput Siderophore screening from environmental samples: plant tissues, bulk soils, and rhizosphere soils. J Vis Exp. 2019;(144). https://doi.org/10.3791/59137.
Quince C, Walker AW, Simpson JT, Loman NJ, Segata N. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. 2017;35:833.
Article
CAS
PubMed
Google Scholar
Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, et al. Optimizing methods and dodging pitfalls in microbiome research. Microbiome. 2017;5:52.
Article
PubMed
PubMed Central
Google Scholar
Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 1993;21:3025–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cao Y, Fanning S, Proos S, Jordan K, Srikumar S. A review on the applications of next generation sequencing technologies as applied to food-related microbiome studies. Front Microbiol. 2017;8(21):1829. https://doi.org/10.3389/fmicb.2017.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids R. 2013;41:D590–D6.
Article
CAS
Google Scholar
Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, et al. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One. 2015;10:e0117617.
Article
PubMed
PubMed Central
CAS
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nature Meth. 2010;7:335–6.
Article
CAS
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Article
CAS
PubMed
Google Scholar
Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol. 2007;45:2761–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Klappenbach JA, Saxman PR, Cole JR, Schmidt TM. Rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 2001;29:181–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vetrovsky T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One. 2013;8:e57923.
Article
CAS
PubMed
PubMed Central
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
Article
CAS
PubMed
Google Scholar
D'Argenio V, Petrillo M, Pasanisi D, Pagliarulo C, Colicchio R, Tala A, et al. The complete 12 Mb genome and transcriptome of Nonomuraea gerenzanensis with new insights into its duplicated "magic" RNA polymerase. Sci Rep. 2016;6:18.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ranjan R, Rani A, Metwally A, McGee HS, Perkins DL. Analysis of the microbiome: advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys R Commun. 2016;469:967–77.
Article
CAS
Google Scholar
Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K. SLIMM: species level identification of microorganisms from metagenomes. PeerJ. 2017;5:e3138.
Article
PubMed
PubMed Central
Google Scholar
Zou Y, Xue W, Luo G, Deng Z, Qin P, Guo R, et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nature Biotech. 2019;37:179–85.
Article
CAS
Google Scholar
D’Argenio V. Human microbiome acquisition and Bioinformatic challenges in metagenomic studies. Int J Mol Sci. 2018;19:383.
Article
PubMed Central
CAS
Google Scholar
Langille MGI, Ravel J, Fricke WF. "Available upon request": not good enough for microbiome data! Microbiome. 2018;6:8.
Article
PubMed
PubMed Central
Google Scholar
Props R, Kerckhof F-M, Rubbens P, De Vrieze J, Hernandez Sanabria E, Waegeman W, et al. Absolute quantification of microbial taxon abundances. ISME J. 2017;11:584–7.
Article
PubMed
Google Scholar
Whittaker RH. Vegetation of the Siskiyou Mountains, Oregon and California. Ecol Monogr. 1960;30:279–338.
Article
Google Scholar
Hubálek Z. Measures of species diversity in ecology: an evaluation. Folia Zool. 2000:241–60.
Simpson EH. Measurement of diversity. Nature. 1949;163:688.
Article
Google Scholar
Good IJ. The population frequencies of species and the estimation of population parameters. Biometrika. 1953;40:237–64.
Article
Google Scholar
Chao A. Nonparametric estimation of the number of classes in a population. Scand J Stat. 1984;11:265–70.
Google Scholar
Ludwig JA, Reynolds JF. Statistical ecology - a primer on methods and computing. New York: Wiley Inc.; 1988.
Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep. 2016;6:19233.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schloss PD, Handelsman J. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol. 2006;72:6773–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lemos LN, Fulthorpe RR, Triplett EW, Roesch LFW. Rethinking microbial diversity analysis in the high throughput sequencing era. J Microbiol Meth. 2011;86:42–51.
Article
CAS
Google Scholar
Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332:970–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dougal K, Harris PA, Edwards A, Pachebat JA, Blackmore TM, Worgan HJ, et al. A comparison of the microbiome and the metabolome of different regions of the equine hindgut. FEMS Microbiol Ecol. 2012;82:642–52.
Article
CAS
PubMed
Google Scholar
Shepherd ML, Swecker WS Jr, Jensen RV, Ponder MA. Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons. FEMS Microbiol Let. 2012;326:62–8.
Article
CAS
Google Scholar
Stewart HL, Pitta D, Indugu N, Vecchiarelli B, Engiles JB, Southwood LL. Characterization of the fecal microbiota of healthy horses. Am J Vet Res. 2018;79:811–9.
Article
CAS
PubMed
Google Scholar
Zhao Y, Li B, Bai D, Huang J, Shiraigo W, Yang L, et al. Comparison of fecal microbiota of Mongolian and thoroughbred horses by high-throughput sequencing of the V4 region of the 16S rRNA gene. Asian-Australas J Anim Sci. 2016;29:1345–52.
Article
CAS
PubMed
Google Scholar
Jensen BB. Methanogenesis in monogastric animals. Environ Monitor Assess. 1996;42:99–112.
Article
CAS
Google Scholar
Joblin KN, Campbell GP, Richardson AJ, Stewart CS. Fermentation of barley straw by anaerobic rumen bacteria and fungi in axenic culture and in co-culture with methanogens. Let Appl Microbiol. 1989;9:195–7.
Article
Google Scholar
Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3:289–306.
Article
PubMed
PubMed Central
Google Scholar
Roshchina VV. New trends and perspectives in the evolution of neurotransmitters in microbial, plant, and animal cells. In: Cham LM, editor. Microbial endocrinology: Interkingdom signaling in infectious disease and health. Imes: Springer International Publishing; 2016. p. 25–77.
Chapter
Google Scholar
Louis P, Hold GL, Flint HJ. The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol. 2014;12:661.
Article
CAS
PubMed
Google Scholar
Cotta M, Forster R. The family Lachnospiraceae, including the genera Butyrivibrio, Lachnospira and Roseburia. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors. The prokaryotes: Vol 4: Bacteria: Firmicutes, cyanobacteria. New York: Springer US; 2006. p. 1002–21.
Google Scholar
Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. The microbiology of butyrate formation in the human colon. FEMS Microbiol Let. 2002;217:133–9.
Article
CAS
Google Scholar
Antharam VC, Li EC, Ishmael A, Sharma A, Mai V, Rand KH, et al. Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol. 2013;51:2884–92.
Article
PubMed
PubMed Central
Google Scholar
Harhangi HR, Freelove ACJ, Ubhayasekera W, van Dinther M, Steenbakkers PJM, Akhmanova A, et al. Cel6A, a major exoglucanase from the cellulosome of the anaerobic fungi Piromyces sp. E2 and Piromyces equi. Biochem Biophys Acta. 2003;1628:30–9.
CAS
PubMed
Google Scholar
Dijkerman R, Op den Camp HJM, van der Drift C, Vogels GD. The role of the cellulolytic high molecular mass (HMM) complex of the anaerobic fungus Piromyces sp. strain E2 in the hydrolysis of microcrystalline cellulose. Arch Microbiol. 1997;167:137–42.
Article
CAS
PubMed
Google Scholar
Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS. Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J. 2010;4:1225.
Article
PubMed
Google Scholar
Cann AJ, Fandrich SE, Heaphy S. Analysis of the virus population present in equine Faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes. 2005;30:151–6.
Article
CAS
PubMed
Google Scholar
Golomidova A, Kulikov E, Isaeva A, Manykin A, Letarov A. The diversity of Coliphages and coliforms in horse feces reveals a complex pattern of ecological interactions. Appl Environ Microbiol. 2007;73:5975–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kulikov EE, Isaeva AS, Rotkina AS, Manykin AA, Letarov AV. Diversity and dynamics of bacteriophages in horse feces. Microbiol. 2007;76:236–42.
Article
CAS
Google Scholar
Ogilvie LA, Jones BV. The human gut virome: a multifaceted majority. Front Microbiol. 2015;6:918.
Article
PubMed
PubMed Central
Google Scholar
Duerkop BA, Clements CV, Rollins D, Rodrigues JL, Hooper LV. A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc Natl Acad Sci. 2012;109:17621–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Modi SR, Lee HH, Spina CS, Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature. 2013;499:219–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kirkpatrick CE, Saik JE. Ciliated protozoa in the colonic wall of horses. J Comp Pathol. 1988;98:205–12.
Article
CAS
PubMed
Google Scholar
Gürelli G, Göçmen B. Intestinal ciliate composition found in the feces of racing horses from Izmir, Turkey. Europ J Protistol. 2012;48:215–26.
Article
Google Scholar
Moore BE, Dehority BA. Effects of diet and hindgut defaunation on diet digestibility and microbial concentrations in the cecum and colon of the horse. J Anim Sci. 1993;71:3350–8.
Article
CAS
PubMed
Google Scholar
Julliand V, de Vaux A, Millet L, Fonty G. Identification of Ruminococcus flavefaciens as the predominant cellulolytic bacterial species of the equine cecum. Appl Environ Microbiol. 1999;65:3738–41.
CAS
PubMed
PubMed Central
Google Scholar
Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, et al. Evaluating the impact of domestication and captivity on the horse gut microbiome. Sci Rep. 2017;7:15497.
Article
PubMed
PubMed Central
CAS
Google Scholar
Costa MC, Stampfli HR, Allen-Vercoe E, Weese JS. Development of the faecal microbiota in foals. Equine Vet J. 2016;48:681–8.
Article
CAS
PubMed
Google Scholar
Almeida ML, Feringer WHJ, Carvalho JR, Rodrigues IM, Jordao LR, Fonseca MG, et al. Intense exercise and aerobic conditioning associated with chromium or L-carnitine supplementation modified the fecal microbiota of fillies. PLoS One. 2016;11:e0167108.
Article
PubMed
PubMed Central
CAS
Google Scholar
Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, et al. The microbiome of uncontacted Amerindians. Sci advance. 2015;1:e1500183.
Google Scholar
Dougal K, Harris PA, Girdwood SE, Creevey CJ, Curtis GC, Barfoot CF, et al. Changes in the Total fecal bacterial population in individual horses maintained on a restricted diet over 6 weeks. Front Microbiol. 2017;8:1502.
Article
PubMed
PubMed Central
Google Scholar
Salem SE, Maddox TW, Berg A, Antczak P, Ketley JM, Williams NJ, et al. Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period. Sci Rep. 2018;8:8510.
Article
PubMed
PubMed Central
CAS
Google Scholar
Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474:1823–36.
Article
CAS
PubMed
Google Scholar
Ze X, Le Mougen F, Duncan SH, Louis P, Flint HJ. Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates. Gut Microbes. 2013;4:236–40.
Article
PubMed
PubMed Central
Google Scholar
Tsoy OV, Ravcheev DA, Čuklina J, Gelfand MS. Nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in Alphaproteobacteria. Front Microbiol. 2016;7. https://doi.org/10.3389/fmicb.2016.01343.
Weese JS, Holcombe SJ, Embertson RM, Kurtz KA, Roessner HA, Jalali M, et al. Changes in the faecal microbiota of mares precede the development of post partum colic. Equine Vet J. 2015;47:641–9.
Article
CAS
PubMed
Google Scholar
Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem. 2011;43:1450–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fuerst JA. The PVC superphylum: exceptions to the bacterial definition? Antonie Van Leeuwenhoek. 2013;104:451–66.
Article
CAS
PubMed
Google Scholar
Fujio-Vejar S, Vasquez Y, Morales P, Magne F, Vera-Wolf P, Ugalde JA, et al. Gut microbiota of healthy Chilean subjects reveals a high abundance of the phylum Verrucomicrobia. Front Microbiol. 2017;8:1221.
Article
PubMed
PubMed Central
Google Scholar
Chakraborti CK. New-found link between microbiota and obesity. World J Gastrointest Pathophysiol. 2015;6:110–9.
Article
PubMed
PubMed Central
Google Scholar
Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci. 2013;110:9066–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Warzecha CM, Coverdale JA, Janecka JE, Leatherwood JL, Pinchak WE, Wickersham TA, et al. Influence of short-term dietary starch inclusion on the equine cecal microbiome. J Animal Sci. 2017;95:5077–90.
Article
CAS
Google Scholar
McConnico RS. Acute Equine Colitis. In: Robinson NE, Sprayberry KA, editors. Current therapy in equine medicine, vol. 6. Missouri: SAUNDERS ELSEVIER; 2009. p. 418.
Google Scholar
Wilson DA. Clinical veterinary advisor: the horse. Missouri: Saunders; 2012.
Google Scholar
Cohen ND, Woods AM. Characteristics and risk factors for failure of horses with acute diarrhea to survive: 122 cases (1990-1996). J Am Vet Med Assoc. 1999;214:382–90.
CAS
PubMed
Google Scholar
Larsen J. Acute colitis in adult horses. A review with emphasis on aetiology and pathogenesis. Vet Q. 1997;19:72–80.
Article
CAS
PubMed
Google Scholar
Rodriguez C, Taminiau B, Brevers B, Avesani V, Van Broeck J, Leroux A, et al. Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission. BMC Microbiol. 2015;15:181.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schoster A, Staempfli HR, Guardabassi LG, Jalali M, Weese JS. Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life. BMC Vet Res. 2017;13:144.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barr BS, Waldridge BM, Morresey PR, Reed SM, Clark C, Belgrave R, et al. Antimicrobial-associated diarrhoea in three equine referral practices. Equine Vet J. 2013;45:154–8.
Article
CAS
PubMed
Google Scholar
Chapman AM. Acute diarrhea in hospitalized horses. Vet Clin North Am Equine Pract. 2009;25:363–80.
Article
PubMed
Google Scholar
Baverud V, Gustafsson A, Franklin A, Aspan A, Gunnarsson A. Clostridium difficile: prevalence in horses and environment, and antimicrobial susceptibility. Equine Vet J. 2003;35:465–71.
Article
CAS
PubMed
Google Scholar
Mahrt CR. Safety of ceftiofur sodium administered intramuscularly in horses. Am J Vet Res. 1992;53:2201–5.
CAS
PubMed
Google Scholar
Davis JLP, Mark G. Prevention and control of infectious diseases - antimicrobial therapy. In: Debra C, Sellon ML, editors. Equine infectious diseases. St. Louis: Elsevier Health Sciences; 2014. p. 571–8.
Chapter
Google Scholar
Haggett EF, Wilson WD. Overview of the use of antimicrobials for the treatment of bacterial infections in horses. Equine Vet Education. 2008;20:433–48.
Article
Google Scholar
Rabold D, Espelage W, Abu Sin M, Eckmanns T, Schneeberg A, Neubauer H, et al. The zoonotic potential of Clostridium difficile from small companion animals and their owners. PLoS One. 2018;13:e0193411.
Article
PubMed
PubMed Central
CAS
Google Scholar
Freeman J, Bauer MP, Baines SD, Corver J, Fawley WN, Goorhuis B, et al. The changing epidemiology of Clostridium difficile infections. Clin Microbiol Rev. 2010;23:529–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Battaglioli EJ, Hale VL, Chen J, Jeraldo P, Ruiz-Mojica C, Schmidt BA, et al. Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea. Sci Transl Med. 2018;10:eaam7019.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ihler CF, Venger JL, Skjerve E. Evaluation of clinical and laboratory variables as prognostic indicators in hospitalised gastrointestinal colic horses. Acta Vet Scand. 2004;45:109–18.
Article
PubMed
PubMed Central
Google Scholar
Fernandes KA, Kittelmann S, Rogers CW, Gee EK, Bolwell CF, Bermingham EN, et al. Faecal microbiota of forage-fed horses in New Zealand and the population dynamics of microbial communities following dietary change. PLoS One. 2014;9:e112846.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hudson JM, Cohen ND, Gibbs PG, Thompson JA. Feeding practices associated with colic in horses. J Am Vet Med Assoc. 2001;219:1419–25.
Article
CAS
PubMed
Google Scholar
Stewart HL, Southwood LL, Indugu N, Vecchiarelli B, Engiles JB, Pitta D. Differences in the equine faecal microbiota between horses presenting to a tertiary referral hospital for colic compared with an elective surgical procedure. Equine Vet J. 2019;51:336–42.
Article
CAS
PubMed
Google Scholar
Al Jassim RAM. Supplementary feeding of horses with processed sorghum grains and oats. Animal Feed Sci Technol. 2006;125:33–44.
Article
Google Scholar
Bailey SR, Baillon ML, Rycroft AN, Harris PA, Elliott J. Identification of equine cecal bacteria producing amines in an in vitro model of carbohydrate overload. Appl Environ Microbiol. 2003;69:2087–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Milinovich GJ, Burrell PC, Pollitt CC, Klieve AV, Blackall LL, Ouwerkerk D, et al. Microbial ecology of the equine hindgut during oligofructose-induced laminitis. ISME J. 2008;2:1089–100.
Article
CAS
PubMed
Google Scholar
Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, et al. The international scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Rev Gastro Hepatol. 2014;11:506.
Article
Google Scholar
Joint Food and Agriculture Organization/World Health Organization Working Group. Guidelines for the evaluation of probiotics in food: report of a joint FAO/WHO working group on drafting guidelines for the evaluation of probiotics in food. London: World Health Organization website; 2002. http://www.who.int/foodsafety/fs_management/en/probiotic_guidelines.pdf
Google Scholar
Schoster A. Probiotic use in equine gastrointestinal disease. Vet Clin North Am Equine Pract. 2018;34:13–24.
Article
PubMed
Google Scholar
Food and Agriculture Organization (FAO). Probiotics in Animal Nutrition. In: Makka HPS, editor. FAO Animal production and Health, vol. 179; 2016. p. 59. http://www.fao.org/3/a-i5933e.pdf.
Google Scholar
Ganguly NK, Bhattacharya SK, Sesikeran B, Nair GB, Ramakrishna BS, Sachdev HPS, et al. ICMR-DBT guidelines for evaluation of probiotics in food. Indian J Med Res. 2011;134:22–5.
PubMed Central
Google Scholar
Schoster A, Guardabassi L, Staempfli HR, Abrahams M, Jalali M, Weese JS. The longitudinal effect of a multi-strain probiotic on the intestinal bacterial microbiota of neonatal foals. Equine Vet J. 2016;48:689–96.
Article
CAS
PubMed
Google Scholar
Desrochers AM, Dolente BA, Roy MF, Boston R, Carlisle S. Efficacy of Saccharomyces boulardii for treatment of horses with acute enterocolitis. J Am Vet Med Assoc. 2005;227:954–9.
Article
PubMed
Google Scholar
Yuyama T, Takai S, Tsubaki S, Kado Y, Morotomi M. Evaluation of a host-specific Lactobacillus probiotic in training-horses and neonatal foals. J Intest Microbiol. 2004;18:101–6.
Google Scholar
Landes AD, Hassel DM, Funk JD, Hill A. Fecal sand clearance is enhanced with a product combining probiotics, prebiotics, and psyllium in clinically Normal horses. J Equine Vet Sci. 2008;28:79–84.
Article
Google Scholar
Institute of Medicine. In: Pray L, Pillsbury L, Tomayko E, editors. The Human Microbiome, Diet, and Health: Workshop Summary. Washington, DC: The National Academies Press; 2013. https://doi.org/10.17226/13522.
Chapter
Google Scholar
Zatorski H, Fichna J. What is the future of the gut microbiota-related treatment? Toward modulation of microbiota in preventive and therapeutic medicine. Front Med. 2014;1. https://doi.org/10.3389/fmed.2014.00019.
Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nature Comm. 2017;8:1784.
Article
CAS
Google Scholar
Brito IL, Alm EJ. Tracking strains in the microbiome: insights from metagenomics and models. Front Microbiol. 2016;7:712.
PubMed
PubMed Central
Google Scholar
Ciesinski L, Guenther S, Pieper R, Kalisch M, Bednorz C, Wieler LH. High dietary zinc feeding promotes persistence of multi-resistant E. coli in the swine gut. PLoS One. 2018;13:e0191660.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bednorz C, Oelgeschlager K, Kinnemann B, Hartmann S, Neumann K, Pieper R, et al. The broader context of antibiotic resistance: zinc feed supplementation of piglets increases the proportion of multi-resistant Escherichia coli in vivo. Int J Med Microbiol. 2013;303:396–403.
Article
CAS
PubMed
Google Scholar
Ingala MR, Simmons NB, Wultsch C, Krampis K, Speer KA, Perkins SL. Comparing microbiome sampling methods in a wild mammal: fecal and intestinal samples record different signals of host ecology, evolution. Front Microbiol. 2018;9:803.
Article
PubMed
PubMed Central
Google Scholar
Walther B, Klein K-S, Barton A-K, Semmler T, Huber C, Merle R, et al. Equine methicillin-resistant sequence type 398 Staphylococcus aureus (MRSA) harbor Mobile genetic elements promoting host adaptation. Front Microbiol. 2018;9:2516.
Article
PubMed
PubMed Central
Google Scholar
Walther B, Klein K-S, Barton A-K, Semmler T, Huber C, Wolf SA, et al. Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Acinetobacter baumannii among horses entering a veterinary teaching hospital: The contemporary "Trojan Horse". PloS one. 2018;13:e0191873.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lagier J-C, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, et al. Culturing the human microbiota and culturomics. Nature Rev Microbiol. 2018;16:540–50.
Article
CAS
Google Scholar
Martínez JL, Coque TM, Baquero F. What is a resistance gene? Ranking risk in resistomes. Nature Rev Microbiol. 2014;13:116.
Article
CAS
Google Scholar
Peterson JW. Bacterial pathogenesis. In: Baron S, editor. Medical microbiology. 4th ed. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Chapter 7. https://www.ncbi.nlm.nih.gov/books/NBK8526/.
Google Scholar
Hubbell SP. The unified neutral theory of biodiversity and biogeography. New Jersey: Princeton University Press; 2001.
Google Scholar
Colwell RK. Biodiversity: concepts, patterns and measurement. New Jersey: Princeton University Press; 2009.
Google Scholar
Tuomisto H. A consistent terminology for quantifying species diversity? Yes, it does exist. Oecologia. 2010;164(4):853–60.
Article
PubMed
Google Scholar
Claesson MJ, Clooney AG, O'Toole PW. A clinicians guide to microbiome analysis. Nature Rev Gastro Hepatol. 2017;14:585.
Article
Google Scholar
Perkins GA, den Bakker HC, Burton AJ, Erb HN, McDonough SP, McDonough PL, et al. Equine Stomachs Harbor an abundant and diverse mucosal microbiota. Appl Environ Microbiol. 2012;78:2522–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Proudman CJ, Hunter JO, Darby AC, Escalona EE, Batty C, Turner C. Characterisation of the faecal metabolome and microbiome of thoroughbred racehorses. Equine Vet J. 2015;47:580–6.
Article
CAS
PubMed
Google Scholar
Hansen NC, Avershina E, Mydland LT, Naesset JA, Austbo D, Moen B, et al. High nutrient availability reduces the diversity and stability of the equine caecal microbiota. Microb Ecol Health Dis. 2015;26:27216.
PubMed
Google Scholar
Daly K, Stewart CS, Flint HJ, Shirazi-Beechey SP. Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiol Ecol. 2001;38:141–51.
Article
CAS
Google Scholar
Quercia S, Freccero F, Castagnetti C, Soverini M, Turroni S, Biagi E, et al. Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals. Equine Vet J. 2019;51:231–7.
Article
CAS
PubMed
Google Scholar
Graham H, Åman P, Theander O, Kolankaya N, Stewart CS. Influence of heat sterilization and ammoniation on straw composition and degradation by pure cultures of cellulolytic rumen bacteria. Ani Feed Sci Technol. 1985;12:195–203.
Article
Google Scholar
Dicks LMT, Botha M, Dicks E, Botes M. The equine gastro-intestinal tract: an overview of the microbiota, disease and treatment. Livestock Sci. 2014;160:69–81.
Article
Google Scholar
Ransom-Jones E, Jones DL, McCarthy AJ, McDonald JE. The Fibrobacteres: an important phylum of cellulose-degrading Bacteria. Microbial Ecol. 2012;63:267–81.
Article
CAS
Google Scholar
Kristoffersen C, Jensen RB, Avershina E, Austbø D, Tauson A-H, Rudi K. Diet-dependent modular dynamic interactions of the equine Cecal microbiota. Microb Environments. 2016;31:378–86.
Article
Google Scholar
Harlow BE, Lawrence LM, Hayes SH, Crum A, Flythe MD. Effect of dietary starch source and concentration on equine fecal microbiota. PLoS One. 2016;11:e0154037.
Article
PubMed
PubMed Central
CAS
Google Scholar
Al Jassim RAM, Scott PT, Trebbin AL, Trott D, Pollitt CC. The genetic diversity of lactic acid producing bacteria in the equine gastrointestinal tract. FEMS Microbiol Let. 2005;248:75–81.
Article
CAS
Google Scholar
Morotomi M, Yuki N, Kado Y, Kushiro A, Shimazaki T, Watanabe K, et al. Lactobacillus equi sp. nov., a predominant intestinal Lactobacillus species of the horse isolated from faeces of healthy horses. Int J Systematic Evolution Microbiol. 2002;52:211–4.
Article
Google Scholar
Morita H, Shiratori C, Murakami M, Takami H, Kato Y, Endo A, et al. Lactobacillus hayakitensis sp. nov., isolated from intestines of healthy thoroughbreds. Int J Systematic Evolution Microbiol. 2007;57:2836–9.
Article
CAS
Google Scholar
Alexander F, Margaret JDM, Oxford AE. Fermentative activities of some members of the Normal Coccal Flora of the Horse's large intestine. J Comp Pathol Therap. 1952;62:252–9.
Article
CAS
Google Scholar
Mach N, Foury A, Kittelmann S, Reigner F, Moroldo M, Ballester M, et al. The effects of weaning methods on gut microbiota composition and horse physiology. Front Physiol. 2017;8:535.
Article
PubMed
PubMed Central
Google Scholar
Julliand V, Riondet C, de Vaux A, Alcaraz G, Fonty G. Comparison of metabolic activities between Piromyces citronii, an equine fungal species, and Piromyces communis, a ruminal species. Anim Feed Sci Technol. 1998;70:161–8.
Article
CAS
Google Scholar
Alexander F, Davies ME, Muir AR. Bacteriophage-like particles in the large intestine of the horse. Res Vet Sci. 1970;11:592–3.
Article
CAS
PubMed
Google Scholar
Daly K, Proudman CJ, Duncan SH, Flint HJ, Dyer J, Shirazi-Beechey SP. Alterations in microbiota and fermentation products in equine large intestine in response to dietary variation and intestinal disease. Br J Nutr. 2012;107:989–95.
Article
CAS
PubMed
Google Scholar
Bordin AI, Suchodolski JS, Markel ME, Weaver KB, Steiner JM, Dowd SE, et al. Effects of Administration of Live or inactivated virulent Rhodococccus equi and age on the fecal microbiome of neonatal foals. PLoS One. 2013;8:e66640.
Article
CAS
PubMed
PubMed Central
Google Scholar
Clark A, Sallé G, Ballan V, Reigner F, Meynadier A, Cortet J, et al. Strongyle infection and gut microbiota: profiling of resistant and susceptible horses over a grazing season. Front Physiol. 2018;9:272.
Article
PubMed
PubMed Central
Google Scholar
Garner HE, Moore JN, Johnson JH, Clark L, Amend JF, Tritschler LG, et al. Changes in the Caecal Flora associated with the onset of laminitis. Equine Vet J. 1978;10:249–52.
Article
CAS
PubMed
Google Scholar
O' Donnell M, Harris H, Jeffery I, Claesson M, Younge B, O' Toole P, Ross R. The core faecal bacterial microbiome of Irish Thoroughbred racehorses. Lett Appl Microbiol. 2013; 57: 492-501. https://doi.org/10.1111/lam.12137.
Article
CAS
PubMed
Google Scholar
Biddle AS, Tomb JF, Fan Z. Microbiome and Blood Analyte Differences Point to Community and Metabolic Signatures in Lean and Obese Horses. Front Vet Sci. 2018;5:225. Published 2018 Sep 20. https://doi.org/10.3389/fvets.2018.00225.
Morrison PK, Newbold CJ, Jones E, et al. The Equine Gastrointestinal Microbiome: Impacts of Age and Obesity. Front Microbiol. 2018;9:3017. Published 2018 Dec 7. https://doi.org/10.3389/fmicb.2018.03017.