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PloS one2014; 9(2); e87424; doi: 10.1371/journal.pone.0087424

Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing.

Abstract: Faecal samples were collected from seventeen animals, each fed three different diets (high fibre, high fibre with a starch rich supplement and high fibre with an oil rich supplement). DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the faecal microbiome of the horse. The effect of age was also considered by comparing mature (8 horses aged 5-12) versus elderly horses (9 horses aged 19-28). A reduction in diversity was found in the elderly horse group. Significant differences between diets were found at an OTU level (52 OTUs at corrected Q<0.1). The majority of differences found were related to the Firmucutes phylum (37) with some changes in Bacteroidetes (6), Proteobacteria (3), Actinobacteria (2) and Spirochaetes (1). For the forage only diet,with no added starch or oil, we found 30/2934 OTUs (accounting for 15.9% of sequences) present in all horses. However the core (i.e. present in all horses) associated with the oil rich supplemented diet was somewhat smaller (25/3029 OTUs, 10.3% ) and the core associated with the starch rich supplemented diet was even smaller (15/2884 OTUs, 5.4% ). The core associated with samples across all three diets was extremely small (6/5689 OTUs accounting for only 2.3% of sequences) and dominated by the order Clostridiales, with the most abundant family being Lachnospiraceae. In conclusion, forage based diets plus starch or oil rich complementary feeds were associated with differences in the faecal bacterial community compared with the forage alone. Further, as observed in people, ageing is associated with a reduction in bacterial diversity. However there was no change in the bacterial community structure in these healthy animals associated with age.
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Publication Date: 2014-02-04 PubMed ID: 24504261PubMed Central: PMC3913607DOI: 10.1371/journal.pone.0087424Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research article explores the composition of the faecal bacterial community in horses, with particular attention paid to the effects of diet and age on the diversity of the microbiome. The findings highlight significant differences in bacterial species represented in the gut microbiome due to different diets and also show a reduction in diversity with aging.

Research Methodology

  • The researchers conducted their study on a sample size of seventeen horses, divided into two primary age groups: mature (5-12 years) and elderly (19-28 years).
  • The animals were fed three types of diet: a high fibre diet, a high fibre diet with a starch-rich supplement, and a high fibre diet with an oil-rich supplement.
  • Faecal samples were collected from the horses to extract DNA, with the focus on the V1-V2 regions of 16SrDNA. This particular region is crucial for the identification and classification of bacterial species and is often used in microbiota research.

Study Findings

  • The study revealed a decrease in bacterial diversity in the elderly group of horses, mirroring similar observations made in human studies.
  • A total of 52 operational taxonomic units (OTUs), which are used to categorise bacteria based on DNA sequence similarity, displayed significant differences across the three diets. The majority of these differences were associated with the Firmucutes phylum.
  • The number of OTUs that were present in all horses (termed the ‘core’) varied between diet groups. While 30 distinct OTUs were observed across all horses on the forage-only diet, the count dropped to 25 and 15 OTUs for the oil and starch-supplemented diets, respectively.
  • Across all three diets, only six OTUs were consistently present, making up a minor portion (2.3%) of sequences. These were predominantly from the order Clostridiales, with the family Lachnospiraceae being the most abundant.

Conclusions

  • The study concludes that the addition of oil-rich or starch-rich supplements to high fibre diets can significantly alter the faecal bacterial community in horses.
  • This finding supports the theory that diet plays an important role in shaping the gut microbiome. However, the specific impact of such dietary changes on the horse’s health was not addressed in this study and would require further research.
  • Ageing was found to be related to a decrease in bacterial diversity, which aligns with previous studies on humans and other animals. This does not, however, indicate a significant change in the bacterial community structure with age in healthy horses.

Cite This Article

APA
Dougal K, de la Fuente G, Harris PA, Girdwood SE, Pinloche E, Geor RJ, Nielsen BD, Schott HC, Elzinga S, Newbold CJ. (2014). 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, 9(2), e87424. https://doi.org/10.1371/journal.pone.0087424

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 9
Issue: 2
Pages: e87424
PII: e87424

Researcher Affiliations

Dougal, Kirsty
  • Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
de la Fuente, Gabriel
  • Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
Harris, Patricia A
  • Equine Studies Group, WALTHAM Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom.
Girdwood, Susan E
  • Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
Pinloche, Eric
  • Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
Geor, Raymond J
  • Michigan State University, Department of Animal Science, East Lansing, Michigan, United States of America.
Nielsen, Brian D
  • Michigan State University, Department of Animal Science, East Lansing, Michigan, United States of America.
Schott, Harold C
  • Michigan State University, Department of Animal Science, East Lansing, Michigan, United States of America.
Elzinga, Sarah
  • Michigan State University, Department of Animal Science, East Lansing, Michigan, United States of America.
Newbold, C Jamie
  • Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.

MeSH Terms

  • Aging / physiology
  • Animals
  • Bacteria / drug effects
  • Biodiversity
  • Dietary Fats, Unsaturated / pharmacology
  • Dietary Fiber / pharmacology
  • Feces / microbiology
  • Feeding Behavior / drug effects
  • Horses
  • Phylogeny
  • Sequence Analysis, DNA / methods
  • Starch / pharmacology

Conflict of Interest Statement

Patricia A. Harris is employed by one of the funders of this research (WALTHAM Centre for Pet Nutrition, Melton Mowbray, Leicestershire. LE14 4RT). The authors confirm that this does not alter their adherence to all the PLOS ONE policies on sharing data and materials.

References

This article includes 66 references
  1. Argenzio RA, Southworth M, Stevens CE. Sites of organic acid production and absorption in the equine gastrointestinal tract.. Am J Physiol 1974 May;226(5):1043-50.
    pubmed: 4824856doi: 10.1152/ajplegacy.1974.226.5.1043google scholar: lookup
  2. 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.
    pmc: PMC3409227pubmed: 22859989doi: 10.1371/journal.pone.0041484google scholar: lookup
  3. 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.
    pubmed: 22092776doi: 10.1111/j.1574-6968.2011.02434.xgoogle scholar: lookup
  4. 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.
    pmc: PMC3538718pubmed: 23186268doi: 10.1186/1746-6148-8-231google scholar: lookup
  5. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. Evolution of mammals and their gut microbes.. Science 2008 Jun 20;320(5883):1647-51.
    pmc: PMC2649005pubmed: 18497261doi: 10.1126/science.1155725google scholar: lookup
  6. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.. Proc Natl Acad Sci U S A 2010 Aug 17;107(33):14691-6.
    pmc: PMC2930426pubmed: 20679230doi: 10.1073/pnas.1005963107google scholar: lookup
  7. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes.. Science 2011 Oct 7;334(6052):105-8.
    pmc: PMC3368382pubmed: 21885731doi: 10.1126/science.1208344google scholar: lookup
  8. Zhang C, Zhang M, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G, Chen Y, Zhao L. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice.. ISME J 2010 Feb;4(2):232-41.
    pubmed: 19865183doi: 10.1038/ismej.2009.112google scholar: lookup
  9. Goodson J, Tyznik WJ, Cline JH, Dehority BA. Effects of an abrupt diet change from hay to concentrate on microbial numbers and physical environment in the cecum of the pony.. Appl Environ Microbiol 1988 Aug;54(8):1946-50.
    pmc: PMC202784pubmed: 3178206doi: 10.1128/aem.54.8.1946-1950.1988google scholar: lookup
  10. de Fombelle A, Julliand V, Drogoul C, Jacotot E. Feeding and microbial disorders in horse: 1 Effects of an abrupt incorporation of two levels of barley in a hay diet on microbial profile and activites. J Equine Vet Sci 21: 439–445.
  11. Milinovich GJ, Burrell PC, Pollitt CC, Klieve AV, Blackall LL, Ouwerkerk D, Woodland E, Trott DJ. Microbial ecology of the equine hindgut during oligofructose-induced laminitis.. ISME J 2008 Nov;2(11):1089-100.
    pubmed: 18580970doi: 10.1038/ismej.2008.67google scholar: lookup
  12. Medina B, Girard ID, Jacotot E, Julliand V. Effect of a preparation of Saccharomyces cerevisiae on microbial profiles and fermentation patterns in the large intestine of horses fed a high fiber or a high starch diet.. J Anim Sci 2002 Oct;80(10):2600-9.
    pubmed: 12413082doi: 10.2527/2002.80102600xgoogle scholar: lookup
  13. de Fombelle A, Varloud M, Goachet A-G, Jocotot E, Philippeau C. Characterization of the microbial and biochemical profile of the different segments of the digestive tract in horses given two distinct diets. J Anim Sci 77 293–304.
  14. Willing B, Vörös 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 Dec;41(9):908-14.
    pubmed: 20383990doi: 10.2746/042516409x447806google scholar: lookup
  15. 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 Apr;107(7):989-95.
    pubmed: 21816118doi: 10.1017/s0007114511003825google scholar: lookup
  16. Woodmansey EJ, McMurdo ME, Macfarlane GT, Macfarlane S. Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects.. Appl Environ Microbiol 2004 Oct;70(10):6113-22.
    pmc: PMC522128pubmed: 15466557doi: 10.1128/aem.70.10.6113-6122.2004google scholar: lookup
  17. Biagi E, Nylund L, Candela M, Ostan R, Bucci L, Pini E, Nikkïla J, Monti D, Satokari R, Franceschi C, Brigidi P, De Vos W. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians.. PLoS One 2010 May 17;5(5):e10667.
    pmc: PMC2871786pubmed: 20498852doi: 10.1371/journal.pone.0010667google scholar: lookup
  18. Rajilić-Stojanović M, Heilig HG, Molenaar D, Kajander K, Surakka A, Smidt H, de Vos WM. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults.. Environ Microbiol 2009 Jul;11(7):1736-51.
    pmc: PMC2784037pubmed: 19508560doi: 10.1111/j.1462-2920.2009.01900.xgoogle scholar: lookup
  19. Mariat D, Firmesse O, Levenez F, Guimarăes V, Sokol H, Doré J, Corthier G, Furet JP. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age.. BMC Microbiol 2009 Jun 9;9:123.
    pmc: PMC2702274pubmed: 19508720doi: 10.1186/1471-2180-9-123google scholar: lookup
  20. Mueller S, Saunier K, Hanisch C, Norin E, Alm L, Midtvedt T, Cresci A, Silvi S, Orpianesi C, Verdenelli MC, Clavel T, Koebnick C, Zunft HJ, Doré J, Blaut M. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study.. Appl Environ Microbiol 2006 Feb;72(2):1027-33.
    pmc: PMC1392899pubmed: 16461645doi: 10.1128/aem.72.2.1027-1033.2006google scholar: lookup
  21. Henneke DR, Potter GD, Kreider JL, Yeates BF. Relationship between condition score, physical measurements and body fat percentage in mares.. Equine Vet J 1983 Oct;15(4):371-2.
    pubmed: 6641685doi: 10.1111/j.2042-3306.1983.tb01826.xgoogle scholar: lookup
  22. Skrivanová E, Worgan HJ, Pinloche E, Marounek M, Newbold CJ, McEwan NR. Changes in the bacterial population of the caecum and stomach of the rabbit in response to addition of dietary caprylic acid.. Vet Microbiol 2010 Aug 26;144(3-4):334-9.
    pubmed: 20181443doi: 10.1016/j.vetmic.2010.01.013google scholar: lookup
  23. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis.. Nucleic Acids Res 2007;35(18):e120.
    pmc: PMC2094085pubmed: 17881377doi: 10.1093/nar/gkm541google scholar: lookup
  24. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.. Appl Environ Microbiol 2009 Dec;75(23):7537-41.
    pmc: PMC2786419pubmed: 19801464doi: 10.1128/aem.01541-09google scholar: lookup
  25. Li W, Fu L, Niu B, Wu S, Wooley J. Ultrafast clustering algorithms for metagenomic sequence analysis.. Brief Bioinform 2012 Nov;13(6):656-68.
    pmc: PMC3504929pubmed: 22772836doi: 10.1093/bib/bbs035google scholar: lookup
  26. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.. Appl Environ Microbiol 2007 Aug;73(16):5261-7.
    pmc: PMC1950982pubmed: 17586664doi: 10.1128/aem.00062-07google scholar: lookup
  27. Gihring TM, Green SJ, Schadt CW. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes.. Environ Microbiol 2012 Feb;14(2):285-90.
    pubmed: 21923700doi: 10.1111/j.1462-2920.2011.02550.xgoogle scholar: lookup
  28. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc SeriesB Stat Methodol 57: 289–300.
  29. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments.. Bioinformatics 2009 May 15;25(10):1335-7.
    pmc: PMC2732312pubmed: 19307242doi: 10.1093/bioinformatics/btp157google scholar: lookup
  30. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.. Mol Biol Evol 2011 Oct;28(10):2731-9.
    pmc: PMC3203626pubmed: 21546353doi: 10.1093/molbev/msr121google scholar: lookup
  31. Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.. Nucleic Acids Res 2011 Jul;39(Web Server issue):W475-8.
    pmc: PMC3125724pubmed: 21470960doi: 10.1093/nar/gkr201google scholar: lookup
  32. Shirazi-Beechey SP. Molecular insights into dietary induced colic in the horse.. Equine Vet J 2008 Jun;40(4):414-21.
    pubmed: 18487108doi: 10.2746/042516408x314075google scholar: lookup
  33. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora.. Science 2005 Jun 10;308(5728):1635-8.
    pmc: PMC1395357pubmed: 15831718doi: 10.1126/science.1110591google scholar: lookup
  34. Durbán A, Abellán JJ, Jiménez-Hernández N, Ponce M, Ponce J, Sala T, D'Auria G, Latorre A, Moya A. Assessing gut microbial diversity from feces and rectal mucosa.. Microb Ecol 2011 Jan;61(1):123-33.
    pubmed: 20734040doi: 10.1007/s00248-010-9738-ygoogle scholar: lookup
  35. 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.
    pubmed: 22757649doi: 10.1111/j.1574-6941.2012.01441.xgoogle scholar: lookup
  36. 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.
    pmc: PMC3812009pubmed: 24204908doi: 10.1371/journal.pone.0077660google scholar: lookup
  37. Varoud M, de Fombelle A, Goachet AG, Drogoul C, Julliand V. Partial and total apparent digestibility of dietary carbohydrates in horses as affected by the diet. Anim Sci 79: 61–71.
  38. Yamano H, Koike S, Kobayashi Y, Hata H. Phylogenetic analysis of hindgut microbiota in Hokkaido native horses compared to light horses. Anim Sci J 79: 234–242.
  39. Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.. Proc Natl Acad Sci U S A 2010 Apr 20;107(16):7503-8.
    pmc: PMC2867707pubmed: 20363958doi: 10.1073/pnas.1002355107google scholar: lookup
  40. Sekelja M, Berget I, Næs T, Rudi K. Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach.. ISME J 2011 Mar;5(3):519-31.
    pmc: PMC3105728pubmed: 20740026doi: 10.1038/ismej.2010.129google scholar: lookup
  41. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing.. Nature 2010 Mar 4;464(7285):59-65.
    pmc: PMC3779803pubmed: 20203603doi: 10.1038/nature08821google scholar: lookup
  42. Jalanka-Tuovinen J, Salonen A, Nikkilä J, Immonen O, Kekkonen R, Lahti L, Palva A, de Vos WM. Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms.. PLoS One 2011;6(7):e23035.
    pmc: PMC3145776pubmed: 21829582doi: 10.1371/journal.pone.0023035google scholar: lookup
  43. Jami E, Mizrahi I. Composition and similarity of bovine rumen microbiota across individual animals.. PLoS One 2012;7(3):e33306.
    pmc: PMC3303817pubmed: 22432013doi: 10.1371/journal.pone.0033306google scholar: lookup
  44. Zaura E, Keijser BJ, Huse SM, Crielaard W. Defining the healthy "core microbiome" of oral microbial communities.. BMC Microbiol 2009 Dec 15;9:259.
    pmc: PMC2805672pubmed: 20003481doi: 10.1186/1471-2180-9-259google scholar: lookup
  45. Sturgeon A, Stull JW, Costa MC, Weese JS. Metagenomic analysis of the canine oral cavity as revealed by high-throughput pyrosequencing of the 16S rRNA gene.. Vet Microbiol 2013 Mar 23;162(2-4):891-898.
    pubmed: 23228621doi: 10.1016/j.vetmic.2012.11.018google scholar: lookup
  46. Lowe BA, Marsh TL, Isaacs-Cosgrove N, Kirkwood RN, Kiupel M, Mulks MH. Defining the "core microbiome" of the microbial communities in the tonsils of healthy pigs.. BMC Microbiol 2012 Feb 7;12:20.
    pmc: PMC3297519pubmed: 22313693doi: 10.1186/1471-2180-12-20google scholar: lookup
  47. Booijink CC, El-Aidy S, Rajilić-Stojanović M, Heilig HG, Troost FJ, Smidt H, Kleerebezem M, De Vos WM, Zoetendal EG. High temporal and inter-individual variation detected in the human ileal microbiota.. Environ Microbiol 2010 Dec;12(12):3213-27.
    pubmed: 20626454doi: 10.1111/j.1462-2920.2010.02294.xgoogle scholar: lookup
  48. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-Tamayo R, Paslier DL, Nalin R, Dore J, Leclerc M. Towards the human intestinal microbiota phylogenetic core.. Environ Microbiol 2009 Oct;11(10):2574-84.
    pubmed: 19601958doi: 10.1111/j.1462-2920.2009.01982.xgoogle scholar: lookup
  49. Durso LM, Harhay GP, Smith TP, Bono JL, Desantis TZ, Harhay DM, Andersen GL, Keen JE, Laegreid WW, Clawson ML. Animal-to-animal variation in fecal microbial diversity among beef cattle.. Appl Environ Microbiol 2010 Jul;76(14):4858-62.
    pmc: PMC2901724pubmed: 20472731doi: 10.1128/aem.00207-10google scholar: lookup
  50. Petri RM, Schwaiger T, Penner GB, Beauchemin KA, Forster RJ, McKinnon JJ, McAllister TA. Changes in the rumen epimural bacterial diversity of beef cattle as affected by diet and induced ruminal acidosis.. Appl Environ Microbiol 2013 Jun;79(12):3744-55.
    pmc: PMC3675914pubmed: 23584771doi: 10.1128/aem.03983-12google scholar: lookup
  51. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine.. Cell 2006 Feb 24;124(4):837-48.
    pubmed: 16497592doi: 10.1016/j.cell.2006.02.017google scholar: lookup
  52. Cotta M, Forster R. The family Lachnospiraceae, including the genera Butyrivibrio, Lachnospira and Roseburia. Prokaryotes 4: 1002–1021.
  53. Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. The microbiology of butyrate formation in the human colon.. FEMS Microbiol Lett 2002 Dec 17;217(2):133-9.
    pubmed: 12480096doi: 10.1111/j.1574-6968.2002.tb11467.xgoogle scholar: lookup
  54. Brown CT, Davis-Richardson AG, Giongo A, Gano KA, Crabb DB, Mukherjee N, Casella G, Drew JC, Ilonen J, Knip M, Hyöty H, Veijola R, Simell T, Simell O, Neu J, Wasserfall CH, Schatz D, Atkinson MA, Triplett EW. Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes.. PLoS One 2011;6(10):e25792.
    pmc: PMC3197175pubmed: 22043294doi: 10.1371/journal.pone.0025792google scholar: lookup
  55. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota.. PLoS Biol 2007 Jul;5(7):e177.
    pmc: PMC1896187pubmed: 17594176doi: 10.1371/journal.pbio.0050177google scholar: lookup
  56. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.. PLoS Biol 2008 Nov 18;6(11):e280.
    pmc: PMC2586385pubmed: 19018661doi: 10.1371/journal.pbio.0060280google scholar: lookup
  57. Hopkins MJ, Macfarlane GT. Changes in predominant bacterial populations in human faeces with age and with Clostridium difficile infection.. J Med Microbiol 2002 May;51(5):448-454.
    pubmed: 11990498doi: 10.1099/0022-1317-51-5-448google scholar: lookup
  58. Morley JE. The aging gut: physiology.. Clin Geriatr Med 2007 Nov;23(4):757-67, v-vi.
    pubmed: 17923336doi: 10.1016/j.cger.2007.06.002google scholar: lookup
  59. Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O'Connor M, Harnedy N, O'Connor K, Henry C, O'Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O'Toole PW. Composition, variability, and temporal stability of the intestinal microbiota of the elderly.. Proc Natl Acad Sci U S A 2011 Mar 15;108 Suppl 1(Suppl 1):4586-91.
    pmc: PMC3063589pubmed: 20571116doi: 10.1073/pnas.1000097107google scholar: lookup
  60. Zwielehner J, Liszt K, Handschur M, Lassl C, Lapin A, Haslberger AG. Combined PCR-DGGE fingerprinting and quantitative-PCR indicates shifts in fecal population sizes and diversity of Bacteroides, bifidobacteria and Clostridium cluster IV in institutionalized elderly.. Exp Gerontol 2009 Jun-Jul;44(6-7):440-6.
    pubmed: 19376217doi: 10.1016/j.exger.2009.04.002google scholar: lookup
  61. Elzinga S, Nielsen B, Scott H, Rapson J, Robison C. Effect of age on digestibility of various feedstuffs in horses. J Equine Vet Sci 31: 268–269.
  62. Zened A, Combes S, Cauquil L, Mariette J, Klopp C, Bouchez O, Troegeler-Meynadier A, Enjalbert F. Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets.. FEMS Microbiol Ecol 2013 Feb;83(2):504-14.
    pubmed: 22974422doi: 10.1111/1574-6941.12011google scholar: lookup
  63. Zhang C, Zhang M, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G, Chen Y, Zhao L. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice.. ISME J 2010 Feb;4(2):232-41.
    pubmed: 19865183doi: 10.1038/ismej.2009.112google scholar: lookup
  64. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, Brown D, Stares MD, Scott P, Bergerat A, Louis P, McIntosh F, Johnstone AM, Lobley GE, Parkhill J, Flint HJ. Dominant and diet-responsive groups of bacteria within the human colonic microbiota.. ISME J 2011 Feb;5(2):220-30.
    pmc: PMC3105703pubmed: 20686513doi: 10.1038/ismej.2010.118google scholar: lookup
  65. O'Herrin SM, Kenealy WR. Glucose and carbon dioxide metabolism by Succinivibrio dextrinosolvens.. Appl Environ Microbiol 1993 Mar;59(3):748-55.
    pmc: PMC202185pubmed: 8481001doi: 10.1128/aem.59.3.748-755.1993google scholar: lookup
  66. Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton IL. Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse.. PLoS One 2012;7(3):e32962.
    pmc: PMC3299707pubmed: 22427917doi: 10.1371/journal.pone.0032962google scholar: lookup

Citations

This article has been cited 75 times.
  1. Lee J, Kang YJ, Kim YK, Choi JY, Shin SM, Shin MC. Exploring the Influence of Growth-Associated Host Genetics on the Initial Gut Microbiota in Horses. Genes (Basel) 2023 Jun 27;14(7).
    doi: 10.3390/genes14071354pubmed: 37510259google scholar: lookup
  2. Burnham CM, McKenney EA, van Heugten KA, Minter LJ, Trivedi S. Effects of age, seasonality, and reproductive status on the gut microbiome of Southern White Rhinoceros (Ceratotherium simum simum) at the North Carolina zoo. Anim Microbiome 2023 May 5;5(1):27.
    doi: 10.1186/s42523-023-00249-5pubmed: 37147724google scholar: lookup
  3. Weinert-Nelson JR, Biddle AS, Sampath H, Williams CA. Fecal Microbiota, Forage Nutrients, and Metabolic Responses of Horses Grazing Warm- and Cool-Season Grass Pastures. Animals (Basel) 2023 Feb 22;13(5).
    doi: 10.3390/ani13050790pubmed: 36899650google scholar: lookup
  4. 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
  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. Bustamante CC, de Paula VB, Rabelo IP, Fernandes CC, Kishi LT, Canola PA, Lemos EGM, Valadão CAA. Effects of Starch Overload and Cecal Buffering on Fecal Microbiota of Horses. Animals (Basel) 2022 Dec 6;12(23).
    doi: 10.3390/ani12233435pubmed: 36496956google scholar: lookup
  7. Bedenice D, Resnick-Sousa J, Bookbinder L, Trautwein V, Creasey HN, Widmer G. The association between fecal microbiota, age and endoparasitism in adult alpacas. PLoS One 2022;17(8):e0272556.
    doi: 10.1371/journal.pone.0272556pubmed: 36006927google scholar: lookup
  8. Li QS, Wang R, Ma ZY, Zhang XM, Jiao JZ, Zhang ZG, Ungerfeld EM, Yi KL, Zhang BZ, Long L, Long Y, Tao Y, Huang T, Greening C, Tan ZL, Wang M. Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants. ISME J 2022 Nov;16(11):2535-2546.
    doi: 10.1038/s41396-022-01294-9pubmed: 35931768google scholar: lookup
  9. Lucassen A, Hankel J, Finkler-Schade C, Osbelt L, Strowig T, Visscher C, Schuberth HJ. Feeding a Saccharomyces cerevisiae Fermentation Product (Olimond BB) Does Not Alter the Fecal Microbiota of Thoroughbred Racehorses. Animals (Basel) 2022 Jun 8;12(12).
    doi: 10.3390/ani12121496pubmed: 35739833google scholar: lookup
  10. Weinert-Nelson JR, Biddle AS, Williams CA. Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems. Anim Microbiome 2022 Jun 21;4(1):41.
    doi: 10.1186/s42523-022-00192-xpubmed: 35729677google scholar: lookup
  11. Lara F, Castro R, Thomson P. Changes in the gut microbiome and colic in horses: Are they causes or consequences?. Open Vet J 2022 Mar-Apr;12(2):242-249.
    doi: 10.5455/OVJ.2022.v12.i2.12pubmed: 35603065google scholar: lookup
  12. Raspa F, Vervuert I, Capucchio MT, Colombino E, Bergero D, Forte C, Greppi M, Cavallarin L, Giribaldi M, Antoniazzi S, Cavallini D, Valvassori E, Valle E. A high-starch vs. high-fibre diet: effects on the gut environment of the different intestinal compartments of the horse digestive tract. BMC Vet Res 2022 May 19;18(1):187.
    doi: 10.1186/s12917-022-03289-2pubmed: 35590319google scholar: lookup
  13. Potter SJ, Bamford NJ, Baskerville CL, Harris PA, Bailey SR. Comparison of Feed Digestibility between Ponies, Standardbreds and Andalusian Horses Fed Three Different Diets. Vet Sci 2021 Dec 31;9(1).
    doi: 10.3390/vetsci9010015pubmed: 35051099google scholar: lookup
  14. da Silva CA, Bentin LAT, Dias CP, Callegari MA, Facina VB, Dias FTF, Passos A, da Silva Martins CC, Costa MC. Impact of zinc oxide, benzoic acid and probiotics on the performance and cecal microbiota of piglets. Anim Microbiome 2021 Dec 20;3(1):86.
    doi: 10.1186/s42523-021-00151-ypubmed: 34930490google scholar: lookup
  15. Fernandes KA, Rogers CW, Gee EK, Kittelmann S, Bolwell CF, Bermingham EN, Biggs PJ, Thomas DG. Resilience of Faecal Microbiota in Stabled Thoroughbred Horses Following Abrupt Dietary Transition between Freshly Cut Pasture and Three Forage-Based Diets. Animals (Basel) 2021 Sep 6;11(9).
    doi: 10.3390/ani11092611pubmed: 34573577google scholar: lookup
  16. Zhu Y, Wang X, Liu B, Yi Z, Zhao Y, Deng L, Holyoak R, Li J. The Effect of Ryegrass Silage Feeding on Equine Fecal Microbiota and Blood Metabolite Profile. Front Microbiol 2021;12:715709.
    doi: 10.3389/fmicb.2021.715709pubmed: 34497595google scholar: lookup
  17. Fernandes KA, Gee EK, Rogers CW, Kittelmann S, Biggs PJ, Bermingham EN, Bolwell CF, Thomas DG. Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand. Animals (Basel) 2021 Aug 4;11(8).
    doi: 10.3390/ani11082300pubmed: 34438757google scholar: lookup
  18. 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
  19. Arnold CE, Pilla R, Chaffin MK, Leatherwood JL, Wickersham TA, Callaway TR, Lawhon SD, Lidbury JA, Steiner JM, Suchodolski JS. The effects of signalment, diet, geographic location, season, and colitis associated with antimicrobial use or Salmonella infection on the fecal microbiome of horses. J Vet Intern Med 2021 Sep;35(5):2437-2448.
    doi: 10.1111/jvim.16206pubmed: 34268795google scholar: lookup
  20. Theelen MJP, Luiken REC, Wagenaar JA, Sloet van Oldruitenborgh-Oosterbaan MM, Rossen JWA, Zomer AL. The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors. Animals (Basel) 2021 Jun 12;11(6).
    doi: 10.3390/ani11061762pubmed: 34204691google scholar: lookup
  21. Arnold C, Pilla R, Chaffin K, Lidbury J, Steiner J, Suchodolski J. Alterations in the Fecal Microbiome and Metabolome of Horses with Antimicrobial-Associated Diarrhea Compared to Antibiotic-Treated and Non-Treated Healthy Case Controls. Animals (Basel) 2021 Jun 17;11(6).
    doi: 10.3390/ani11061807pubmed: 34204371google scholar: lookup
  22. Zhu Y, Wang X, Deng L, Chen S, Zhu C, Li J. Effects of Pasture Grass, Silage, and Hay Diet on Equine Fecal Microbiota. Animals (Basel) 2021 May 7;11(5).
    doi: 10.3390/ani11051330pubmed: 34066969google scholar: lookup
  23. Collinet A, Grimm P, Julliand S, Julliand V. Sequential Modulation of the Equine Fecal Microbiota and Fibrolytic Capacity Following Two Consecutive Abrupt Dietary Changes and Bacterial Supplementation. Animals (Basel) 2021 Apr 29;11(5).
    doi: 10.3390/ani11051278pubmed: 33946811google scholar: lookup
  24. Slater R, Frau A, Hodgkinson J, Archer D, Probert C. A Comparison of the Colonic Microbiome and Volatile Organic Compound Metabolome of Anoplocephala perfoliata Infected and Non-Infected Horses: A Pilot Study. Animals (Basel) 2021 Mar 9;11(3).
    doi: 10.3390/ani11030755pubmed: 33803473google scholar: lookup
  25. 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
  26. Reed KJ, Kunz IGZ, Scare JA, Nielsen MK, Turk PJ, Coleman RJ, Coleman SJ. The pelvic flexure separates distinct microbial communities in the equine hindgut. Sci Rep 2021 Feb 22;11(1):4332.
    doi: 10.1038/s41598-021-83783-zpubmed: 33619300google scholar: lookup
  27. Edwards JE, Shetty SA, van den Berg P, Burden F, van Doorn DA, Pellikaan WF, Dijkstra J, Smidt H. Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species. Anim Microbiome 2020 Feb 12;2(1):6.
    doi: 10.1186/s42523-020-0023-1pubmed: 33499982google scholar: lookup
  28. Kauter A, Epping L, Semmler T, Antao EM, Kannapin D, Stoeckle SD, Gehlen H, Lübke-Becker A, Günther S, Wieler LH, Walther B. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Anim Microbiome 2019 Nov 13;1(1):14.
    doi: 10.1186/s42523-019-0013-3pubmed: 33499951google scholar: lookup
  29. Edwards JE, Schennink A, Burden F, Long S, van Doorn DA, Pellikaan WF, Dijkstra J, Saccenti E, Smidt H. Domesticated equine species and their derived hybrids differ in their fecal microbiota. Anim Microbiome 2020 Mar 16;2(1):8.
    doi: 10.1186/s42523-020-00027-7pubmed: 33499942google scholar: lookup
  30. Rolinec M, Medo J, Gábor M, Miluchová M, Bíro D, Šimko M, Juráček M, Hanušovský O, Schubertová Z, Gálik B. The Effect of Coconut Oil Addition to Feed of Pigs on Rectal Microbial Diversity and Bacterial Abundance. Animals (Basel) 2020 Sep 29;10(10).
    doi: 10.3390/ani10101764pubmed: 33003372google scholar: lookup
  31. Morrison PK, Newbold CJ, Jones E, Worgan HJ, Grove-White DH, Dugdale AH, Barfoot C, Harris PA, Argo CM. Effect of age and the individual on the gastrointestinal bacteriome of ponies fed a high-starch diet. PLoS One 2020;15(5):e0232689.
    doi: 10.1371/journal.pone.0232689pubmed: 32384105google scholar: lookup
  32. Mullen KR, Yasuda K, Divers TJ, Weese JS. Equine faecal microbiota transplant: Current knowledge, proposed guidelines and future directions. Equine Vet Educ 2018 Mar;30(3):151-160.
    doi: 10.1111/eve.12559pubmed: 32313396google scholar: lookup
  33. Tang L, Li Y, Srivathsan A, Gao Y, Li K, Hu D, Zhang D. Gut Microbiomes of Endangered Przewalski's Horse Populations in Short- and Long-Term Captivity: Implication for Species Reintroduction Based on the Soft-Release Strategy. Front Microbiol 2020;11:363.
    doi: 10.3389/fmicb.2020.00363pubmed: 32226419google scholar: lookup
  34. Langner K, Blaue D, Schedlbauer C, Starzonek J, Julliand V, Vervuert I. Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme. PLoS One 2020;15(3):e0230015.
    doi: 10.1371/journal.pone.0230015pubmed: 32191712google scholar: lookup
  35. McKinney CA, Oliveira BCM, Bedenice D, Paradis MR, Mazan M, Sage S, Sanchez A, Widmer G. The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea. PLoS One 2020;15(3):e0230148.
    doi: 10.1371/journal.pone.0230148pubmed: 32155205google scholar: lookup
  36. 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 weight-loss. BMC Vet Res 2020 Mar 4;16(1):78.
    doi: 10.1186/s12917-020-02295-6pubmed: 32131835google scholar: lookup
  37. Bulmer LS, Murray JA, Burns NM, Garber A, Wemelsfelder F, McEwan NR, Hastie PM. High-starch diets alter equine faecal microbiota and increase behavioural reactivity. Sci Rep 2019 Dec 9;9(1):18621.
    doi: 10.1038/s41598-019-54039-8pubmed: 31819069google scholar: lookup
  38. Li Y, Zhang K, Liu Y, Li K, Hu D, Wronski T. Community Composition and Diversity of Intestinal Microbiota in Captive and Reintroduced Przewalski's Horse (Equus ferus przewalskii). Front Microbiol 2019;10:1821.
    doi: 10.3389/fmicb.2019.01821pubmed: 31440229google scholar: lookup
  39. Glatter M, Borewicz K, van den Bogert B, Wensch-Dorendorf M, Bochnia M, Greef JM, Bachmann M, Smidt H, Breves G, Zeyner A. Modification of the equine gastrointestinal microbiota by Jerusalem artichoke meal supplementation. PLoS One 2019;14(8):e0220553.
    doi: 10.1371/journal.pone.0220553pubmed: 31393892google scholar: lookup
  40. Peachey LE, Castro C, Molena RA, Jenkins TP, Griffin JL, Cantacessi C. Dysbiosis associated with acute helminth infections in herbivorous youngstock - observations and implications. Sci Rep 2019 Jul 31;9(1):11121.
    doi: 10.1038/s41598-019-47204-6pubmed: 31366962google scholar: lookup
  41. Raspa F, Cavallarin L, McLean AK, Bergero D, Valle E. A Review of the Appropriate Nutrition Welfare Criteria of Dairy Donkeys: Nutritional Requirements, Farm Management Requirements and Animal-Based Indicators. Animals (Basel) 2019 Jun 1;9(6).
    doi: 10.3390/ani9060315pubmed: 31159459google scholar: lookup
  42. Poelaert KCK, Van Cleemput J, Laval K, Descamps S, Favoreel HW, Nauwynck HJ. Beyond Gut Instinct: Metabolic Short-Chain Fatty Acids Moderate the Pathogenesis of Alphaherpesviruses. Front Microbiol 2019;10:723.
    doi: 10.3389/fmicb.2019.00723pubmed: 31024501google scholar: lookup
  43. Coleman MC, Whitfield-Cargile CM, Madrigal RG, Cohen ND. Comparison of the microbiome, metabolome, and lipidome of obese and non-obese horses. PLoS One 2019;14(4):e0215918.
    doi: 10.1371/journal.pone.0215918pubmed: 31013335google scholar: lookup
  44. Zhu C, Faillace V, Laus F, Bazzano M, Laghi L. Characterization of trotter horses urine metabolome by means of proton nuclear magnetic resonance spectroscopy. Metabolomics 2018 Aug 3;14(8):106.
    doi: 10.1007/s11306-018-1403-3pubmed: 30830366google scholar: lookup
  45. 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.2018.03017pubmed: 30581426google scholar: lookup
  46. 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.
    doi: 10.3389/fvets.2018.00225pubmed: 30294603google scholar: lookup
  47. Salem SE, Maddox TW, Berg A, Antczak P, Ketley JM, Williams NJ, Archer DC. Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period. Sci Rep 2018 May 31;8(1):8510.
    doi: 10.1038/s41598-018-26930-3pubmed: 29855517google scholar: lookup
  48. Jenkins EK, DeChant MT, Perry EB. When the Nose Doesn't Know: Canine Olfactory Function Associated With Health, Management, and Potential Links to Microbiota. Front Vet Sci 2018;5:56.
    doi: 10.3389/fvets.2018.00056pubmed: 29651421google scholar: lookup
  49. Peachey LE, Molena RA, Jenkins TP, Di Cesare A, Traversa D, Hodgkinson JE, Cantacessi C. The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins. Int J Parasitol 2018 May;48(6):403-412.
    doi: 10.1016/j.ijpara.2017.11.003pubmed: 29432771google scholar: lookup
  50. Beckers KF, Schulz CJ, Childers GW. Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples. PLoS One 2017;12(11):e0187044.
    doi: 10.1371/journal.pone.0187044pubmed: 29091944google scholar: lookup
  51. Xu Q, Yuan X, Gu T, Li Y, Dai W, Shen X, Song Y, Zhang Y, Zhao W, Chang G, Chen G. Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets. PLoS One 2017;12(10):e0185590.
    doi: 10.1371/journal.pone.0185590pubmed: 28972993google scholar: lookup
  52. 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.2017.01502pubmed: 28848517google scholar: lookup
  53. Gong H, Wang B, Shi Y, Shi Y, Xiao X, Cao P, Tao L, Wang Y, Zhou L. Composition and abundance of microbiota in the pharynx in patients with laryngeal carcinoma and vocal cord polyps. J Microbiol 2017 Aug;55(8):648-654.
    doi: 10.1007/s12275-017-6636-8pubmed: 28752291google scholar: lookup
  54. Wei Z, Hu X, Li X, Zhang Y, Jiang L, Li J, Guan Z, Cai Y, Liao X. The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China. PLoS One 2017;12(4):e0174411.
    doi: 10.1371/journal.pone.0174411pubmed: 28379996google scholar: lookup
  55. Harlow BE, Lawrence LM, Harris PA, Aiken GE, Flythe MD. Exogenous lactobacilli mitigate microbial changes associated with grain fermentation (corn, oats, and wheat) by equine fecal microflora ex vivo. PLoS One 2017;12(3):e0174059.
    doi: 10.1371/journal.pone.0174059pubmed: 28358885google scholar: lookup
  56. Crowley EJ, King JM, Wilkinson T, Worgan HJ, Huson KM, Rose MT, McEwan NR. Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing. PLoS One 2017;12(2):e0165779.
    doi: 10.1371/journal.pone.0165779pubmed: 28182658google scholar: lookup
  57. Huang XF, Chaparro JM, Reardon KF, Judd TM, Vivanco JM. Supplementing Blends of Sugars, Amino Acids, and Secondary Metabolites to the Diet of Termites (Reticulitermes flavipes) Drive Distinct Gut Bacterial Communities. Microb Ecol 2016 Oct;72(3):497-502.
    doi: 10.1007/s00248-016-0792-ypubmed: 27338261google scholar: lookup
  58. 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(4):e0154037.
    doi: 10.1371/journal.pone.0154037pubmed: 27128793google scholar: lookup
  59. Zhao Y, Li B, Bai D, Huang J, Shiraigo W, Yang L, Zhao Q, Ren X, Wu J, Bao W, Dugarjaviin M. 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 Sep;29(9):1345-52.
    doi: 10.5713/ajas.15.0587pubmed: 26954132google scholar: lookup
  60. Lu Y, Hugenholtz P, Batstone DJ. Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community. PLoS One 2015;10(11):e0142720.
    doi: 10.1371/journal.pone.0142720pubmed: 26560873google scholar: lookup
  61. Pajarillo EA, Chae JP, Balolong MP, Kim HB, Seo KS, Kang DK. Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing. Asian-Australas J Anim Sci 2015 Apr;28(4):584-91.
    doi: 10.5713/ajas.14.0651pubmed: 25656184google scholar: lookup
  62. Schoster A, Weese JS, Guardabassi L. Probiotic use in horses - what is the evidence for their clinical efficacy?. J Vet Intern Med 2014 Nov-Dec;28(6):1640-52.
    doi: 10.1111/jvim.12451pubmed: 25231539google scholar: lookup
  63. Wei J, Wei L, Ullah A, Geng M, Zhang X, Wang C, Khan MZ, Wang C, Zhang Z. Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions. Animals (Basel) 2025 Oct 10;15(20).
    doi: 10.3390/ani15202938pubmed: 41153865google scholar: lookup
  64. Qin X, Xi L, Zhao L, Han J, Qu H, Xu Y, Weng W. Exploring the distinctive characteristics of gut microbiota across different horse breeds and ages using metataxonomics. Front Cell Infect Microbiol 2025;15:1590839.
    doi: 10.3389/fcimb.2025.1590839pubmed: 40692682google scholar: lookup
  65. Al-Ansari AS, Duggan V, Mulcahy G, Yin X, Brennan L, Cotter PD, Patel SH, O'Donovan CM, Crispie F, Walshe N. Faecal microbiota and serum metabolome association with equine metabolic syndrome in connemara ponies. BMC Vet Res 2025 Jul 1;21(1):411.
    doi: 10.1186/s12917-025-04853-2pubmed: 40598279google scholar: lookup
  66. Curadi MC, Vallone F, Tenuzzo M, Gazzano A, Gazzano V, Macchioni F, Vannini C. Effect of Management System on Fecal Microbiota in Arabian Horses: Preliminary Results. Vet Sci 2025 Mar 28;12(4).
    doi: 10.3390/vetsci12040309pubmed: 40284811google scholar: lookup
  67. Zhang W, Guo R, Sulayman A, Sun Y, Liu S. Research Progress on Influencing Factors of Gastrointestinal Microbial Diversity in Equine. Vet Med Sci 2025 May;11(3):e70271.
    doi: 10.1002/vms3.70271pubmed: 40145999google scholar: lookup
  68. Wang W, Gibson J, Horsman S, Mikkelsen D, Bertin FR. Characterization and comparison of fecal microbiota in horses with pituitary pars intermedia dysfunction and age-matched controls. J Vet Intern Med 2025 Jan-Feb;39(1):e17288.
    doi: 10.1111/jvim.17288pubmed: 39853825google scholar: lookup
  69. Brandi LA, Nunes AT, Faleiros CA, Poleti MD, Oliveira ECM, Schmidt NT, Sousa RLM, Fukumasu H, Balieiro JCC, Brandi RA. Dietary Energy Sources Affect Cecal and Fecal Microbiota of Healthy Horses. Animals (Basel) 2024 Dec 3;14(23).
    doi: 10.3390/ani14233494pubmed: 39682460google scholar: lookup
  70. Baraille M, Buttet M, Grimm P, Milojevic V, Julliand S, Julliand V. Changes of faecal bacterial communities and microbial fibrolytic activity in horses aged from 6 to 30 years old. PLoS One 2024;19(6):e0303029.
    doi: 10.1371/journal.pone.0303029pubmed: 38829841google scholar: lookup
  71. Raspa F, Chessa S, Bergero D, Sacchi P, Ferrocino I, Cocolin L, Corvaglia MR, Moretti R, Cavallini D, Valle E. Microbiota characterization throughout the digestive tract of horses fed a high-fiber vs. a high-starch diet. Front Vet Sci 2024;11:1386135.
    doi: 10.3389/fvets.2024.1386135pubmed: 38807937google scholar: lookup
  72. Mady EA, Osuga H, Toyama H, El-Husseiny HM, Inoue R, Murase H, Yamamoto Y, Nagaoka K. Relationship between the components of mare breast milk and foal gut microbiome: shaping gut microbiome development after birth. Vet Q 2024 Dec;44(1):1-9.
    doi: 10.1080/01652176.2024.2349948pubmed: 38733121google scholar: lookup
  73. Boucher L, Leduc L, Leclère M, Costa MC. Current Understanding of Equine Gut Dysbiosis and Microbiota Manipulation Techniques: Comparison with Current Knowledge in Other Species. Animals (Basel) 2024 Feb 28;14(5).
    doi: 10.3390/ani14050758pubmed: 38473143google scholar: lookup
  74. Guo Y, Yin G, Hui F, Guo X, Shi B, Zhao Y, Yan S. Effects of dietary energy level on antioxidant capability, immune function and rectal microbiota in late gestation donkeys. Front Microbiol 2024;15:1308171.
    doi: 10.3389/fmicb.2024.1308171pubmed: 38414765google scholar: lookup
  75. Plancade S, Clark A, Philippe C, Helbling JC, Moisan MP, Esquerré D, Le Moyec L, Robert C, Barrey E, Mach N. Unraveling the effects of the gut microbiota composition and function on horse endurance physiology. Sci Rep 2019 Jul 3;9(1):9620.
    doi: 10.1038/s41598-019-46118-7pubmed: 31270376google scholar: lookup
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