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Animal microbiome2020; 2(1); 6; doi: 10.1186/s42523-020-0023-1

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species.

Abstract: Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world's domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra). Results: Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant. Conclusions: Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.
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Publication Date: 2020-02-12 PubMed ID: 33499982PubMed Central: PMC7807809DOI: 10.1186/s42523-020-0023-1Google Scholar: Lookup
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  • 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.

The research examines the diversity in the gut bacteria, fungi, and archaea present in different equine (horse family) species – including horses, donkeys, zebras, and horse-donkey hybrids. The study finds that despite some differences in microbial community composition, there exists a common core of microbes shared across all equine species.

Study Objectives and Approach

  • The primary aim of the study was to broaden our understanding of equine gut microbiota, focusing not just on horses and ponies, but across diverse (sub)species such as donkeys, zebras, and horse-donkey hybrids.
  • The study explored both bacterial and non-bacterial organisms, including anaerobic fungi and methanogenic archaea, both of which are important for the degradation of dietary fiber.
  • Scientists used fecal samples from these animals to determine the core taxa (major groups of species) shared by all equine types.

Key Findings

  • The fecal microbial concentrations and community compositions differed among the horse, donkey, zebra, and horse-donkey hybrids. Donkeys were found to have the most distinctive gut microbiota, while horses and zebras showed no notable differences.
  • Despite these variations, a common core of eight OTUs (operational taxonomic units – a way to classify groups of closely related individuals) and 16 genus-level groups was found in all the fecal samples.
  • This core constitutes a much larger proportion of the equine gut microbiota than was previously known. The core taxa are predominantly bacteria belonging to the Kiritimatiellaeota and Spirochaetes phyla.
  • Archaea and anaerobic fungi were found in all animals, but no core taxon was detected for them, despite their presence in many samples.

Implications and Conclusions

  • While the study observed differences between equine types, it identified a substantial core microbiota across all equines studied. This common core is mainly a few predominant bacterial taxa.
  • Most of these bacterial taxa have not been cultured in the lab, highlighting a gap in our understanding of their function. Resolving this gap would provide invaluable insights into the microbial functions that underpin the equine gut ecosystem.

Cite This Article

APA
Edwards JE, Shetty SA, van den Berg P, Burden F, van Doorn DA, Pellikaan WF, Dijkstra J, Smidt H. (2020). Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species. Anim Microbiome, 2(1), 6. https://doi.org/10.1186/s42523-020-0023-1

Publication

Animal microbiome
ISSN: 2524-4671
NlmUniqueID: 101759457
Country: England
Language: English
Volume: 2
Issue: 1
Pages: 6
PII: 6

Researcher Affiliations

Edwards, J E
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, Netherlands. joanee2002@hotmail.com.
Shetty, S A
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, Netherlands.
van den Berg, P
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, Netherlands.
Burden, F
  • The Donkey Sanctuary, Sidmouth, Devon, EX10 ONU, UK.
van Doorn, D A
  • Division of Nutrition, Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CM, Netherlands.
  • Department of Equine Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, Netherlands.
Pellikaan, W F
  • Animal Nutrition Group, Wageningen University & Research, Wageningen, 6708 WD, Netherlands.
Dijkstra, J
  • Animal Nutrition Group, Wageningen University & Research, Wageningen, 6708 WD, Netherlands.
Smidt, H
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, Netherlands. hauke.smidt@wur.nl.

Grant Funding

  • 706899 / H2020 Marie Sku0142odowska-Curie Actions

Conflict of Interest Statement

The authors declare that they have no competing interests.

References

This article includes 74 references
  1. Steelman SM, Chowdhary BP, Dowd S, Suchodolski J, Janečka JE. Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis.. BMC Vet Res 2012 Nov 27;8:231.
    doi: 10.1186/1746-6148-8-231pmc: PMC3538718pubmed: 23186268google scholar: lookup
  2. 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 Lett 2012 Jan;326(1):62-8.
    doi: 10.1111/j.1574-6968.2011.02434.xpubmed: 22092776google scholar: lookup
  3. 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.
    doi: 10.1371/journal.pone.0041484pmc: PMC3409227pubmed: 22859989google scholar: lookup
  4. 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.
    doi: 10.1186/s12917-015-0335-7pmc: PMC4323147pubmed: 25644524google scholar: lookup
  5. Rodriguez C, Taminiau B, Brévers B, Avesani V, Van Broeck J, Leroux A, Gallot M, Bruwier A, Amory H, Delmée M, Daube G. Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission.. BMC Microbiol 2015 Sep 16;15:181.
    doi: 10.1186/s12866-015-0514-5pmc: PMC4573688pubmed: 26377067google scholar: lookup
  6. Fernandes KA, Kittelmann S, Rogers CW, Gee EK, Bolwell CF, Bermingham EN, Thomas DG. Faecal microbiota of forage-fed horses in New Zealand and the population dynamics of microbial communities following dietary change.. PLoS One 2014;9(11):e112846.
    doi: 10.1371/journal.pone.0112846pmc: PMC4226576pubmed: 25383707google scholar: lookup
  7. Morrison PK, Newbold CJ, Jones E, Worgan HJ, Grove-White DH, Dugdale AH, Barfoot C, Harris PA, Argo CM. The Equine Gastrointestinal Microbiome: Impacts of Age and Obesity.. Front Microbiol 2018;9:3017.
    doi: 10.3389/fmicb.2018.03017pmc: PMC6293011pubmed: 30581426google scholar: lookup
  8. 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(10):e77660.
    doi: 10.1371/journal.pone.0077660pmc: PMC3812009pubmed: 24204908google scholar: lookup
  9. 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.
    doi: 10.1016/j.tvjl.2015.03.018pubmed: 25975855google scholar: lookup
  10. Dougal K, de la Fuente G, Harris PA, Girdwood SE, Pinloche E, Geor RJ, Nielsen BD, Schott HC 2nd, Elzinga S, Newbold CJ. 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(2):e87424.
    doi: 10.1371/journal.pone.0087424pmc: PMC3913607pubmed: 24504261google scholar: lookup
  11. Dougal K, Harris PA, Girdwood SE, Creevey CJ, Curtis GC, Barfoot CF, Argo CM, Newbold CJ. Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks.. Front Microbiol 2017;8:1502.
    doi: 10.3389/fmicb.2017.01502pmc: PMC5554519pubmed: 28848517google scholar: lookup
  12. Blackmore TM, Dugdale A, Argo CM, Curtis G, Pinloche E, Harris PA, Worgan HJ, Girdwood SE, Dougal K, Newbold CJ, McEwan NR. Strong stability and host specific bacterial community in faeces of ponies.. PLoS One 2013;8(9):e75079.
    doi: 10.1371/journal.pone.0075079pmc: PMC3770578pubmed: 24040388google scholar: lookup
  13. Shetty SA, Hugenholtz F, Lahti L, Smidt H, de Vos WM. Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies.. FEMS Microbiol Rev 2017 Mar 1;41(2):182-199.
    doi: 10.1093/femsre/fuw045pmc: PMC5399919pubmed: 28364729google scholar: lookup
  14. Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning.. Nat Rev Microbiol 2018 Sep;16(9):567-576.
    doi: 10.1038/s41579-018-0024-1pubmed: 29789680google scholar: lookup
  15. Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. Speciation with gene flow in equids despite extensive chromosomal plasticity.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):18655-60.
    doi: 10.1073/pnas.1412627111pmc: PMC4284605pubmed: 25453089google scholar: lookup
  16. FAOSTAT. 2016. http://faostat.fao.org/. Accessed 23 Nov 2016.
  17. Cí·¯ord D, Pearson RA, Archibald RF, Muirhead R. Digestibility and gastro-intestinal transit time of diets containing different proportions of alfalfa and oat straw given to thoroughbreds, Shetland ponies, Highland ponies and donkeys. Anim Sci 1995;61:407–417.
    doi: 10.1017/S1357729800013953google scholar: lookup
  18. Smith DG, Pearson RA. A review of the factors affecting the survival of donkeys in semi-arid regions of sub-Saharan Africa.. Trop Anim Health Prod 2005 Nov;37 Suppl 1:1-19.
    doi: 10.1007/s11250-005-9002-5pubmed: 16335068google scholar: lookup
  19. Julliand V, Grimm P. HORSE SPECIES SYMPOSIUM: The microbiome of the horse hindgut: History and current knowledge.. J Anim Sci 2016 Jun;94(6):2262-74.
    doi: 10.2527/jas.2015-0198pubmed: 27285903google scholar: lookup
  20. Lee SS, Ha JK, Cheng K. Relative contributions of bacteria, protozoa, and fungi to in vitro degradation of orchard grass cell walls and their interactions.. Appl Environ Microbiol 2000 Sep;66(9):3807-13.
    doi: 10.1128/AEM.66.9.3807-3813.2000pmc: PMC92224pubmed: 10966394google scholar: lookup
  21. Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef N, Dagar SS, Fliegerova K, Griffith GW, Forster R, Tsang A, McAllister T, Elshahed MS. Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential.. FEMS Microbiol Ecol 2014 Oct;90(1):1-17.
    doi: 10.1111/1574-6941.12383pubmed: 25046344google scholar: lookup
  22. Solomon KV, Haitjema CH, Henske JK, Gilmore SP, Borges-Rivera D, Lipzen A, Brewer HM, Purvine SO, Wright AT, Theodorou MK, Grigoriev IV, Regev A, Thompson DA, O'Malley MA. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes.. Science 2016 Mar 11;351(6278):1192-5.
    doi: 10.1126/science.aad1431pmc: PMC5098331pubmed: 26912365google scholar: lookup
  23. Cheng YF, Edwards JE, Allison GG, Zhu WY, Theodorou MK. Diversity and activity of enriched ruminal cultures of anaerobic fungi and methanogens grown together on lignocellulose in consecutive batch culture.. Bioresour Technol 2009 Oct;100(20):4821-8.
    doi: 10.1016/j.biortech.2009.04.031pubmed: 19467591google scholar: lookup
  24. 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 Dec;71(12):3350-8.
    doi: 10.2527/1993.71123350xpubmed: 8294287google scholar: lookup
  25. 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 Oct;4(10):1225-35.
    doi: 10.1038/ismej.2010.49pubmed: 20410935google scholar: lookup
  26. 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;70:161–168.
    doi: 10.1016/S0377-8401(97)00043-6google scholar: lookup
  27. Lwin KO, Matsui H. Comparative analysis of the methanogen diversity in horse and pony by using mcrA gene and archaeal 16s rRNA gene clone libraries.. Archaea 2014;2014:483574.
    doi: 10.1155/2014/483574pmc: PMC3941164pubmed: 24678264google scholar: lookup
  28. Dougal K, Harris PA, Edwards A, Pachebat JA, Blackmore TM, Worgan HJ, Newbold CJ. A comparison of the microbiome and the metabolome of different regions of the equine hindgut.. FEMS Microbiol Ecol 2012 Dec;82(3):642-52.
    doi: 10.1111/j.1574-6941.2012.01441.xpubmed: 22757649google scholar: lookup
  29. Koetschan C, Kittelmann S, Lu J, Al-Halbouni D, Jarvis GN, Müller T, Wolf M, Janssen PH. Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota).. PLoS One 2014;9(3):e91928.
    doi: 10.1371/journal.pone.0091928pmc: PMC3963862pubmed: 24663345google scholar: lookup
  30. Gordon GL, Phillips MW. The role of anaerobic gut fungi in ruminants.. Nutr Res Rev 1998 Jun;11(1):133-68.
    doi: 10.1079/NRR19980009pubmed: 19087463google scholar: lookup
  31. Mountfort DO, Asher RA, Bauchop T. Fermentation of Cellulose to Methane and Carbon Dioxide by a Rumen Anaerobic Fungus in a Triculture with Methanobrevibacter sp. Strain RA1 and Methanosarcina barkeri.. Appl Environ Microbiol 1982 Jul;44(1):128-34.
    doi: 10.1128/AEM.44.1.128-134.1982pmc: PMC241979pubmed: 16346048google scholar: lookup
  32. 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;38:141–151.
    doi: 10.1111/j.1574-6941.2001.tb00892.xgoogle scholar: lookup
  33. Hugenholtz P, Goebel BM, Pace NR. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity.. J Bacteriol 1998 Sep;180(18):4765-74.
    doi: 10.1128/JB.180.18.4765-4774.1998pmc: PMC107498pubmed: 9733676google scholar: lookup
  34. Spring S, Bunk B, Spröer C, Schumann P, Rohde M, Tindall BJ, Klenk HP. Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum.. ISME J 2016 Dec;10(12):2801-2816.
    doi: 10.1038/ismej.2016.84pmc: PMC5148204pubmed: 27300277google scholar: lookup
  35. van Vliet DM, Palakawong Na Ayudthaya S, Diop S, Villanueva L, Stams AJM, Sánchez-Andrea I. Anaerobic Degradation of Sulfated Polysaccharides by Two Novel Kiritimatiellales Strains Isolated From Black Sea Sediment.. Front Microbiol 2019;10:253.
    doi: 10.3389/fmicb.2019.00253pmc: PMC6388578pubmed: 30833937google scholar: lookup
  36. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.. Nucleic Acids Res 2013 Jan;41(Database issue):D590-6.
    doi: 10.1093/nar/gks1219pmc: PMC3531112pubmed: 23193283google scholar: lookup
  37. Dojka MA, Hugenholtz P, Haack SK, Pace NR. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation.. Appl Environ Microbiol 1998 Oct;64(10):3869-77.
    doi: 10.1128/AEM.64.10.3869-3877.1998pmc: PMC106571pubmed: 9758812google scholar: lookup
  38. Stanton TB, Canale-Parola E. Treponema bryantii sp. nov., a rumen spirochete that interacts with cellulolytic bacteria.. Arch Microbiol 1980 Sep;127(2):145-56.
    doi: 10.1007/BF00428018pubmed: 7425785google scholar: lookup
  39. Cwyk WM, Canale-Parola E. Treponema succinifaciens sp. nov., an anaerobic spirochete from the swine intestine.. Arch Microbiol 1979 Sep;122(3):231-9.
    doi: 10.1007/BF00411285pubmed: 120726google scholar: lookup
  40. Nakazawa F, Poco SE, Sato M, Ikeda T, Kalfas S, Sundqvist G, Hoshino E. Taxonomic characterization of Mogibacterium diversum sp. nov. and Mogibacterium neglectum sp. nov., isolated from human oral cavities.. Int J Syst Evol Microbiol 2002 Jan;52(Pt 1):115-122.
    doi: 10.1099/00207713-52-1-115pubmed: 11837293google scholar: lookup
  41. Nakazawa F, Sato M, Poco SE, Hashimura T, Ikeda T, Kalfas S, Sundqvist G, Hoshino E. Description of Mogibacterium pumilum gen. nov., sp. nov. and Mogibacterium vescum gen. nov., sp. nov., and reclassification of Eubacterium timidum (Holdeman et al. 1980) as Mogibacterium timidum gen. nov., comb. nov.. Int J Syst Evol Microbiol 2000 Mar;50 Pt 2:679-688.
    doi: 10.1099/00207713-50-2-679pubmed: 10758875google scholar: lookup
  42. Freier TA, Beitz DC, Li L, Hartman PA. Characterization of Eubacterium coprostanoligenes sp. nov., a cholesterol-reducing anaerobe.. Int J Syst Bacteriol 1994 Jan;44(1):137-42.
    doi: 10.1099/00207713-44-1-137pubmed: 8123557google scholar: lookup
  43. Del Dot T, Osawa R, Stackebrandt E. Phascolarctobacterium faecium gen. Nov, spec. Nov., a novel taxon of the Sporomusa group of Bacteria. Syst Appl Microbiol 1993;16:380–384.
    doi: 10.1016/S0723-2020(11)80269-9google scholar: lookup
  44. Watanabe Y, Nagai F, Morotomi M. Characterization of Phascolarctobacterium succinatutens sp. nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces.. Appl Environ Microbiol 2012 Jan;78(2):511-8.
    doi: 10.1128/AEM.06035-11pmc: PMC3255759pubmed: 22081579google scholar: lookup
  45. Zellner G, Stackebrandt E, Messner P, Tindall BJ, Conway de Macario E, Kneifel H, Sleytr UB, Winter J. Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum, Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov.. Arch Microbiol 1989;151(5):381-90.
    doi: 10.1007/BF00416595pubmed: 2742452google scholar: lookup
  46. Leadbetter JR, Breznak JA. Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes.. Appl Environ Microbiol 1996 Oct;62(10):3620-31.
    doi: 10.1128/AEM.62.10.3620-3631.1996pmc: PMC168169pubmed: 8837417google scholar: lookup
  47. Henderson G, Cox F, Ganesh S, Jonker A, Young W, Janssen PH. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range.. Sci Rep 2015 Oct 9;5:14567.
    doi: 10.1038/srep14567pmc: PMC4598811pubmed: 26449758google scholar: lookup
  48. Orpin CG. Isolation of cellulolytic phycomycete fungi from the caecum of the horse.. J Gen Microbiol 1981 Apr;123(2):287-96.
    doi: 10.1099/00221287-123-2-287pubmed: 7033458google scholar: lookup
  49. Freelove AC, Bolam DN, White P, Hazlewood GP, Gilbert HJ. A novel carbohydrate-binding protein is a component of the plant cell wall-degrading complex of Piromyces equi.. J Biol Chem 2001 Nov 16;276(46):43010-7.
    doi: 10.1074/jbc.M107143200pubmed: 11560933google scholar: lookup
  50. Gaillard-Martinie B, Breton A, Dusser M, Julliand V. Piromyces citronii sp. nov., a strictly anaerobic fungus from the equine caecum: a morphological, metabolic, and ultrastructural study. FEMS Microbiol Lett 1995;130:321–326.
    doi: 10.1111/j.1574-6968.1995.tb07738.xgoogle scholar: lookup
  51. Li J, Heath IB, Bauchop T. Piromyces mae and Piromyces dumbonica, two new species of uniflagellate anaerobic chytridiomycete fungi from the hindgut of the horse and elephant. Can J Bot 1990;68:1021–1033.
    doi: 10.1139/b90-129google scholar: lookup
  52. Gold JJ, Heath IB, Bauchop T. Ultrastructural description of a new chytrid genus of caecum anaerobe, Caecomyces equi gen. nov., sp. nov., assigned to the Neocallimasticaceae.. Biosystems 1988;21(3-4):403-15.
    doi: 10.1016/0303-2647(88)90039-1pubmed: 3395694google scholar: lookup
  53. Callaghan TM, Podmirseg SM, Hohlweck D, Edwards JE, Puniya AK, Dagar SS. Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces. MycoKeys 2015;9:11–28.
    doi: 10.3897/mycokeys.9.9032google scholar: lookup
  54. Mura E, Edwards J, Kittelmann S, Kaerger K, Voigt K, Mrázek J, Moniello G, Fliegerova K. Anaerobic fungal communities differ along the horse digestive tract.. Fungal Biol 2019 Mar;123(3):240-246.
    doi: 10.1016/j.funbio.2018.12.004pubmed: 30798879google scholar: lookup
  55. Fliegerova K, Mura E, Mrázek J, Moniello G. A comparison of microbial profiles of different regions of the equine hindgut. Livest Sci 2016;190:18–19.
    doi: 10.1016/j.livsci.2016.05.015google scholar: lookup
  56. Julliand V, Grimm P. The impact of diet on the hindgut microbiome. J Equine Vet Sci 2017;52:23–28.
    doi: 10.1016/j.jevs.2017.03.002google scholar: lookup
  57. van Lingen HJ, Edwards JE, Vaidya JD, van Gastelen S, Saccenti E, van den Bogert B, Bannink A, Smidt H, Plugge CM, Dijkstra J. Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen.. Front Microbiol 2017;8:425.
    pmc: PMC5355475pubmed: 28367142doi: 10.3389/fmicb.2017.00425google scholar: lookup
  58. Edwards JE, Kingston-Smith AH, Jimenez HR, Huws SA, Skøt KP, Griffith GW, McEwan NR, Theodorou MK. Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen.. FEMS Microbiol Ecol 2008 Dec;66(3):537-45.
    doi: 10.1111/j.1574-6941.2008.00563.xpubmed: 18673390google scholar: lookup
  59. Dollhofer V, Callaghan TM, Griffith GW, Lebuhn M, Bauer J. Presence and transcriptional activity of anaerobic fungi in agricultural biogas plants.. Bioresour Technol 2017 Jul;235:131-139.
    doi: 10.1016/j.biortech.2017.03.116pubmed: 28365340google scholar: lookup
  60. Ramiro-Garcia J, Hermes GDA, Giatsis C, Sipkema D, Zoetendal EG, Schaap PJ, Smidt H. NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes.. F1000Res 2016;5:1791.
    doi: 10.12688/f1000research.9227.1pmc: PMC6419982pubmed: 30918626google scholar: lookup
  61. Edwards JE, Hermes GDA, Kittelmann S, Nijsse B, Smidt H. Assessment of the Accuracy of Anaerobic Fungal ITS1 Based Barcoded Amplicon Sequencing for Community Composition Analysis. .
  62. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2013.
  63. Neuwirth E. RColorBrewer: ColorBrewer Palettes. R package version 1.1–2. 2014.
  64. Milton Bache S, Wickham H. magrittr: A Forward-Pipe Operator for R. R package version 1.5. 2014.
  65. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.. PLoS One 2013;8(4):e61217.
    doi: 10.1371/journal.pone.0061217pmc: PMC3632530pubmed: 23630581google scholar: lookup
  66. Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. Picante: R tools for integrating phylogenies and ecology.. Bioinformatics 2010 Jun 1;26(11):1463-4.
    doi: 10.1093/bioinformatics/btq166pubmed: 20395285google scholar: lookup
  67. Pinheiro J, Bates D, DebRoy S, Sarkar D, R Core Team. _nlme: Linear and Nonlinear Mixed Effects Models_. R package version 3.1–131. 2017.
  68. Oksanen J, Guillaume Blanchet F, Friendly M, Kindt R, Legendre P, McGlinn D. vegan: Community Ecology Package. R package version 2.5–3. 2018.
  69. Deepayan S. Lattice: multivariate data visualization with R. New York: Springer; 2008.
  70. Simpson GL. permute: Functions for Generating Restricted Permutations of Data. 2016.
  71. Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language.. Bioinformatics 2004 Jan 22;20(2):289-90.
    doi: 10.1093/bioinformatics/btg412pubmed: 14734327google scholar: lookup
  72. Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2016.
  73. Kassambara A. ggpubr: “ggplot2” Based Publication Ready Plots. R package version 0.2.
  74. Šmilauer P, Leps J. Multivariate analysis of ecological data using Canoco 5. Second Edition. New York: Cambridge University Press; 2014.

Citations

This article has been cited 39 times.
  1. Lu H, Zhang W, Sun S, Mei Y, Zhao G, Yang K. Effect of Supplementary Feeding on Milk Volume, Milk Composition, Blood Biochemical Index, and Fecal Microflora Diversity in Grazing Yili Mares. Animals (Basel) 2023 Jul 26;13(15).
    doi: 10.3390/ani13152415pubmed: 37570224google scholar: lookup
  2. Zhang Z, Huang B, Gao X, Shi X, Wang X, Wang T, Wang Y, Liu G, Wang C. Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning. Front Microbiol 2023;14:1105330.
    doi: 10.3389/fmicb.2023.1105330pubmed: 36778861google scholar: lookup
  3. Wunderlich G, Bull M, Ross T, Rose M, Chapman B. Understanding the microbial fibre degrading communities & processes in the equine gut. Anim Microbiome 2023 Jan 12;5(1):3.
    doi: 10.1186/s42523-022-00224-6pubmed: 36635784google scholar: lookup
  4. Li C, Li X, Guo R, Ni W, Liu K, Liu Z, Dai J, Xu Y, Abduriyim S, Wu Z, Zeng Y, Lei B, Zhang Y, Wang Y, Zeng W, Zhang Q, Chen C, Qiao J, Liu C, Hu S. Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse. Microbiome 2023 Jan 12;11(1):7.
    doi: 10.1186/s40168-022-01448-zpubmed: 36631912google scholar: lookup
  5. Chaucheyras-Durand F, Sacy A, Karges K, Apper E. Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens. Microorganisms 2022 Dec 19;10(12).
    doi: 10.3390/microorganisms10122517pubmed: 36557769google scholar: lookup
  6. Żak-Bochenek A, Bajzert J, Sambor D, Siwińska N, Szponar B, Łaczmański Ł, Żebrowska P, Czajkowska A, Karczewski M, Chełmońska-Soyta A. Homeostasis of the Intestinal Mucosa in Healthy Horses-Correlation between the Fecal Microbiome, Secretory Immunoglobulin A and Fecal Egg Count. Animals (Basel) 2022 Nov 10;12(22).
    doi: 10.3390/ani12223094pubmed: 36428322google scholar: lookup
  7. Wenner BA, Park T, Mitchell K, Kvidera SK, Griswold KE, Horst EA, Baumgard LH. Effect of zinc source (zinc sulfate or zinc hydroxychloride) on relative abundance of fecal Treponema spp. in lactating dairy cows. JDS Commun 2022 Sep;3(5):334-338.
    doi: 10.3168/jdsc.2022-0238pubmed: 36340900google scholar: lookup
  8. Wang X, Wu X, Shang Y, Gao Y, Li Y, Wei Q, Dong Y, Mei X, Zhou S, Sun G, Liu L, Lige B, Zhang Z, Zhang H. High-Altitude Drives the Convergent Evolution of Alpha Diversity and Indicator Microbiota in the Gut Microbiomes of Ungulates. Front Microbiol 2022;13:953234.
    doi: 10.3389/fmicb.2022.953234pubmed: 35875556google scholar: lookup
  9. Tang L, Gao Y, Yan L, Jia H, Chu H, Ma X, He L, Wang X, Li K, Hu D, Zhang D. Comparative Analysis of Microbiome Metagenomics in Reintroduced Wild Horses and Resident Asiatic Wild Asses in the Gobi Desert Steppe. Microorganisms 2022 Jun 7;10(6).
    doi: 10.3390/microorganisms10061166pubmed: 35744684google scholar: lookup
  10. 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.
    doi: 10.7717/peerj.13084pubmed: 35345588google scholar: lookup
  11. Zhang Z, Wang Y, Huang B, Zhu M, Wang C. The Fibrolytic Enzyme Profiles and the Composition of Fungal Communities in Donkey Cecum-Colon Ecosystem. Animals (Basel) 2022 Feb 9;12(4).
    doi: 10.3390/ani12040412pubmed: 35203120google scholar: lookup
  12. Laustsen L, Edwards JE, Hermes GDA, Lúthersson N, van Doorn DA, Okrathok S, Kujawa TJ, Smidt H. Free Faecal Water: Analysis of Horse Faecal Microbiota and the Impact of Faecal Microbial Transplantation on Symptom Severity. Animals (Basel) 2021 Sep 23;11(10).
    doi: 10.3390/ani11102776pubmed: 34679798google scholar: lookup
  13. Filek K, Trotta A, Gračan R, Di Bello A, Corrente M, Bosak S. Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta). Anim Microbiome 2021 Sep 3;3(1):59.
    doi: 10.1186/s42523-021-00120-5pubmed: 34479653google scholar: lookup
  14. Johnson ACB, Biddle AS. A Standard Scale to Measure Equine Keeper Status and the Effect of Metabolic Tendency on Gut Microbiome Structure. Animals (Basel) 2021 Jul 1;11(7).
    doi: 10.3390/ani11071975pubmed: 34359102google scholar: lookup
  15. Yanez-Montalvo A, Gaona O, Águila B, Arias-Domínguez N, Falcón LI, Pérez-Flores J. Tapirus bairdii-Associated Fecal Microbiome from a Critical Conservation Area: Calakmul, México. Curr Microbiol 2021 Jul;78(7):2648-2659.
    doi: 10.1007/s00284-021-02531-8pubmed: 33990869google scholar: lookup
  16. Rojas CA, Ramírez-Barahona S, Holekamp KE, Theis KR. Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales. Anim Microbiome 2021 Apr 23;3(1):33.
    doi: 10.1186/s42523-021-00094-4pubmed: 33892813google scholar: lookup
  17. Wimmer-Scherr C, Taminiau B, Renaud B, van Loon G, Palmers K, Votion D, Amory H, Daube G, Cesarini C. Comparison of Fecal Microbiota of Horses Suffering from Atypical Myopathy and Healthy Co-Grazers. Animals (Basel) 2021 Feb 15;11(2).
    doi: 10.3390/ani11020506pubmed: 33672034google scholar: lookup
  18. McAdams ZL, Campbell EJ, Dorfmeyer RA, Turner G, Shaffer S, Ford T, Lawson J, Terry J, Raju M, Coghill L, Cresci L, Lascola K, Pridgen T, Blikslager A, Barrell E, Banse H, Paul L, Gillen A, Nott S, VandeCandelaere M, van Galen G, Townsend KS, Martin LM, Johnson PJ, Ericsson AC. A novel dataset of 2,362 equine fecal microbiomes from veterinary teaching hospitals across three countries reveals effects of geography and disease. Anim Microbiome 2025 Dec 3;7(1):124.
    doi: 10.1186/s42523-025-00493-xpubmed: 41339959google scholar: lookup
  19. Yano R, Moriyama T, Arai H, Scheftgen AJ, Suen G, Nishida T, Handa M, Fukuma N. Correlation of hindgut microbiome and fermentation properties with a history of gas and/or impaction colic in Japanese draft horses. J Equine Sci 2025;36(3):93-102.
    doi: 10.1294/jes.36.93pubmed: 40980339google scholar: lookup
  20. Gilyazova I, Korytina G, Kochetova O, Savelieva O, Mikhaylova E, Vershinina Z, Chumakova A, Markelov V, Abdeeva G, Karunas A, Khusnutdinova E, Gusev O. Advances in Genomics and Postgenomics in Poultry Science: Current Achievements and Future Directions. Int J Mol Sci 2025 Aug 26;26(17).
    doi: 10.3390/ijms26178285pubmed: 40943207google scholar: lookup
  21. Li Y, Zhou H, Yu J, Dong B, Li H, Zhang C, Zhang G, Guo C. Dietary protein sources in concentrate supplementation influence growth performance by manipulating gut microbiota and serum metabolites in suckling Donkey foals. Anim Microbiome 2025 Aug 26;7(1):91.
    doi: 10.1186/s42523-025-00457-1pubmed: 40859348google scholar: lookup
  22. Arnalot L, Pascal G, Cauquil L, Vanbergue E, Foucras G, Zened A. The bacterial faecal microbiota shifts during the transition period in dairy cows. Anim Microbiome 2025 Jul 24;7(1):79.
    doi: 10.1186/s42523-025-00443-7pubmed: 40708057google scholar: lookup
  23. Wang Y, Shi M, Wu J, Han X, Li M, Wu Y, Jiang Y, Zhang H, Liu S, Hu D. Variations in Intestinal Microbiota Among Three Species in the Cervidae Family Under the Same Feeding Conditions. Vet Sci 2025 May 3;12(5).
    doi: 10.3390/vetsci12050438pubmed: 40431531google scholar: lookup
  24. Li C, Li X, Liu K, Xu J, Yu J, Liu Z, Mach N, Ni W, Liu C, Zhou P, Wang L, Hu S. Multiomic analysis of different horse breeds reveals that gut microbial butyrate enhances racehorse athletic performance. NPJ Biofilms Microbiomes 2025 May 24;11(1):87.
    doi: 10.1038/s41522-025-00730-wpubmed: 40410196google scholar: lookup
  25. Kinoshita Y, Niwa H, Ueno T. Minimal disruption of equine gut microbiota by intravenous cephalothin treatment. J Vet Med Sci 2025 Jun 1;87(6):690-696.
    doi: 10.1292/jvms.25-0105pubmed: 40254462google scholar: lookup
  26. Deng X, Li H, Wu A, He J, Mao X, Dai Z, Tian G, Cai J, Tang J, Luo Y. Composition, Influencing Factors, and Effects on Host Nutrient Metabolism of Fungi in Gastrointestinal Tract of Monogastric Animals. Animals (Basel) 2025 Mar 1;15(5).
    doi: 10.3390/ani15050710pubmed: 40075993google scholar: lookup
  27. Żak-Bochenek A, Żebrowska-Różańska P, Bajzert J, Łaczmański Ł, Szponar B, Siwińska N, Gładysz K, Sikorska K, Chełmońska-Soyta A. Investigating the potential immunomodulatory effects of commercial oral probiotic supplements on equine gastrointestinal tract barrier function. Front Immunol 2024;15:1487664.
    doi: 10.3389/fimmu.2024.1487664pubmed: 39906737google scholar: lookup
  28. Kou X, Ma Q, Liu Y, Khan MZ, Wu B, Chen W, Liu X, Wang C, Li Y. Exploring the Effect of Gastrointestinal Prevotella on Growth Performance Traits in Livestock Animals. Animals (Basel) 2024 Jul 2;14(13).
    doi: 10.3390/ani14131965pubmed: 38998077google scholar: lookup
  29. Mikkelsen D, McGowan AM, Gibson JS, Lanyon JM, Horsman S, Seddon JM. Faecal bacterial communities differ amongst discrete foraging populations of dugongs along the east Australian coast. FEMS Microbiol Ecol 2024 May 14;100(6).
    doi: 10.1093/femsec/fiae051pubmed: 38658192google scholar: lookup
  30. Shen H, Wang T, Dong W, Sun G, Liu J, Peng N, Zhao S. Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties. Microbiome 2024 Feb 12;12(1):25.
    doi: 10.1186/s40168-023-01745-1pubmed: 38347598google scholar: lookup
  31. Kauter A, Brombach J, Lübke-Becker A, Kannapin D, Bang C, Franzenburg S, Stoeckle SD, Mellmann A, Scherff N, Köck R, Guenther S, Wieler LH, Gehlen H, Semmler T, Wolf SA, Walther B. Antibiotic prophylaxis and hospitalization of horses subjected to median laparotomy: gut microbiota trajectories and abundance increase of Escherichia. Front Microbiol 2023;14:1228845.
    doi: 10.3389/fmicb.2023.1228845pubmed: 38075913google scholar: lookup
  32. Pohlin F, Frei C, Meyer LCR, Roch FF, Quijada NM, Conrady B, Neubauer V, Hofmeyr M, Cooper D, Stalder G, Wetzels SU. Capture and transport of white rhinoceroses (Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis. Conserv Physiol 2023;11(1):coad089.
    doi: 10.1093/conphys/coad089pubmed: 38026796google scholar: lookup
  33. Klinsawat W, Uthaipaisanwong P, Jenjaroenpun P, Sripiboon S, Wongsurawat T, Kusonmano K. Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing. Sci Rep 2023 Oct 17;13(1):17685.
    doi: 10.1038/s41598-023-44981-zpubmed: 37848699google scholar: lookup
  34. Ward AB, Harris PA, Argo CM, Watson C, Neacsu M, Russell WR, Ribeiro A, Collie-Duguid E, Heidari Z, Morrison PK. Homemade Nucleic Acid Preservation Buffer Proves Effective in Preserving the Equine Faecal Microbiota over Time at Ambient Temperatures. Animals (Basel) 2023 Oct 5;13(19).
    doi: 10.3390/ani13193107pubmed: 37835713google scholar: lookup
  35. Beckers KF, Gomes VCL, Crissman KR, Liu CC, Schulz CJ, Childers GW, Sones JL. Metagenetic Analysis of the Pregnant Microbiome in Horses. Animals (Basel) 2023 Jun 15;13(12).
    doi: 10.3390/ani13121999pubmed: 37370509google scholar: lookup
  36. Baniel A, Amato KR, Beehner JC, Bergman TJ, Mercer A, Perlman RF, Petrullo L, Reitsema L, Sams S, Lu A, Snyder-Mackler N. Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas. Microbiome 2021 Jan 23;9(1):26.
    doi: 10.1186/s40168-020-00977-9pubmed: 33485388google scholar: lookup
  37. 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.
    doi: 10.1371/journal.pone.0244381pubmed: 33444319google scholar: lookup
  38. Tassone S, Fortina R, Valle E, Cavallarin L, Raspa F, Boggero S, Bergero D, Giammarino M, Renna M. Comparison of In Vivo and In Vitro Digestibility in Donkeys. Animals (Basel) 2020 Nov 12;10(11).
    doi: 10.3390/ani10112100pubmed: 33198168google scholar: lookup
  39. Hess M, Paul SS, Puniya AK, van der Giezen M, Shaw C, Edwards JE, Fliegerová K. Anaerobic Fungi: Past, Present, and Future. Front Microbiol 2020;11:584893.
    doi: 10.3389/fmicb.2020.584893pubmed: 33193229google scholar: lookup
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