FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / BMC Genomics / Metagenomic investigation of potential abortigenic pathogens...
BMC genomics2021; 22(1); 713; doi: 10.1186/s12864-021-08010-5

Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses.

Abstract: Abortion in horses leads to economic and welfare losses to the equine industry. Most cases of equine abortions are sporadic, and the cause is often unknown. This study aimed to detect potential abortigenic pathogens in equine abortion cases in Australia using metagenomic deep sequencing methods. Results: After sequencing and analysis, a total of 68 and 86 phyla were detected in the material originating from 49 equine abortion samples and 8 samples from normal deliveries, respectively. Most phyla were present in both groups, with the exception of Chlamydiae that were only present in abortion samples. Around 2886 genera were present in the abortion samples and samples from normal deliveries at a cut off value of 0.001% of relative abundance. Significant differences in species diversity between aborted and normal tissues was observed. Several potential abortigenic pathogens were identified at a high level of relative abundance in a number of the abortion cases, including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Streptococcus equi subspecies zooepidemicus, Pantoea agglomerans, Acinetobacter lwoffii, Acinetobacter calcoaceticus and Chlamydia psittaci. Conclusions: This work revealed the presence of several potentially abortigenic pathogens in aborted specimens. No novel potential abortigenic agents were detected. The ability to screen samples for multiple pathogens that may not have been specifically targeted broadens the frontiers of diagnostic potential. The future use of metagenomic approaches for diagnostic purposes is likely to be facilitated by further improvements in deep sequencing technologies.
© 2021. The Author(s).
Get Full Text
Publication Date: 2021-10-02 PubMed ID: 34600470PubMed Central: PMC8487468DOI: 10.1186/s12864-021-08010-5Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • 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 focuses on identifying the root cause of horse abortions in Australia using metagenomic deep sequencing. The study found several potentially abortigenic pathogens present in the aborted samples but found no new abortigenic agents.

Research Objective

  • The study sought to investigate potential pathogens causing abortion in horses in Australia. Abortions in horses lead to significant economic and animal welfare losses in the equine industry.

Methodology

  • The research utilizes metagenomic deep sequencing, an advanced method that sequences genetic material from environmental samples to identify and quantify all genes of all members of a population.
  • Materials from 49 equine abortion samples and 8 samples from normal deliveries were analyzed in the study.

Study Findings

  • The study found a total of 68 and 86 detected phyla in the materials from abortion samples and normal deliveries, respectively.
  • Most phyla were found in both groups. However, Chlamydiae were found solely in the abortion samples.
  • There was a significant difference in species diversity between the tissues from aborted and normal deliveries.
  • Several potential abortigenic pathogens were identified in a high abundance in several abortion samples including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Streptococcus equi subspecies zooepidemicus, Pantoea agglomerans, Acinetobacter lwoffii, Acinetobacter calcoaceticus, and Chlamydia psittaci.

Conclusions and Implications

  • The study did not discover any new potential abortigenic agents in the horses.
  • This research expands diagnostic potential by demonstrating the ability to screen samples for multiple pathogens.
  • Findings suggest that the application of metagenomic approaches for diagnostic purposes may be facilitated by further improvements in deep sequencing technologies.
  • The identification of these potential abortigenic pathogens could lead to newer prevention strategies and improved horse health care in the equine industry.

Cite This Article

APA
Akter R, El-Hage CM, Sansom FM, Carrick J, Devlin JM, Legione AR. (2021). Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses. BMC Genomics, 22(1), 713. https://doi.org/10.1186/s12864-021-08010-5

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 22
Issue: 1
Pages: 713
PII: 713

Researcher Affiliations

Akter, Rumana
  • Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia.
  • Department of Medicine (Royal Melbourne Hospital), The University of Melbourne, Parkville, Victoria, 3010, Australia.
El-Hage, Charles M
  • Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia.
Sansom, Fiona M
  • Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia.
Carrick, Joan
  • Equine Specialist Consulting, Scone, New South Wales, 2337, Australia.
Devlin, Joanne M
  • Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia.
Legione, Alistair R
  • Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia. legionea@unimelb.edu.au.

MeSH Terms

  • Acinetobacter
  • Animals
  • Australia
  • Female
  • Fetus
  • Horse Diseases
  • Horses
  • Metagenome
  • Metagenomics
  • Pregnancy

Grant Funding

  • PRJ-011758 / Agrifutures Australia

Conflict of Interest Statement

The authors declare that they have no competing interests.

References

This article includes 87 references
  1. Giles RC, Donahue JM, Hong CB, Tuttle PA, Petrites-Murphy MB, Poonacha KB, Roberts AW, Tramontin RR, Smith B, Swerczek TW. Causes of abortion, stillbirth, and perinatal death in horses: 3,527 cases (1986-1991).. J Am Vet Med Assoc 1993 Oct 15;203(8):1170-5.
    pubmed: 8244867
  2. Hong CB, Donahue JM, Giles RC Jr, Petrites-Murphy MB, Poonacha KB, Roberts AW, Smith BJ, Tramontin RR, Tuttle PA, Swerczek TW. Etiology and pathology of equine placentitis.. J Vet Diagn Invest 1993 Jan;5(1):56-63.
    doi: 10.1177/104063879300500113pubmed: 8466982google scholar: lookup
  3. Hong CB, Donahue JM, Giles RC Jr, Petrites-Murphy MB, Poonacha KB, Roberts AW, Smith BJ, Tramontin RR, Tuttle PA, Swerczek TW. Equine abortion and stillbirth in central Kentucky during 1988 and 1989 foaling seasons.. J Vet Diagn Invest 1993 Oct;5(4):560-6.
    doi: 10.1177/104063879300500410pubmed: 8286455google scholar: lookup
  4. Marenzoni ML, Lepri E, Casagrande Proietti P, Bietta A, Coletti M, Timoney PJ, Passamonti F. Causes of equine abortion, stillbirth and neonatal death in central Italy.. Vet Rec 2012 Mar 10;170(10):262.
    doi: 10.1136/vr.100551pubmed: 22368162google scholar: lookup
  5. Leon A, Richard E, Fortier C, Laugier C, Fortier G, Pronost S. Molecular detection of Coxiella burnetii and Neospora caninum in equine aborted foetuses and neonates.. Prev Vet Med 2012 Apr 1;104(1-2):179-83.
    doi: 10.1016/j.prevetmed.2011.11.001pubmed: 22130310google scholar: lookup
  6. Smith KC, Blunden AS, Whitwell KE, Dunn KA, Wales AD. A survey of equine abortion, stillbirth and neonatal death in the UK from 1988 to 1997.. Equine Vet J 2003 Jul;35(5):496-501.
    doi: 10.2746/042516403775600578pubmed: 12875329google scholar: lookup
  7. Szeredi L, Tenk M, Jánosi S, Pálfi V, Hotzel H, Sachse K, Pospischil A, Bozsó M, Glávits R, Molnár T. A survey of equine abortion and perinatal foal losses in Hungary during a three-year period (1998-2000).. Acta Vet Hung 2008 Sep;56(3):353-67.
    doi: 10.1556/avet.56.2008.3.9pubmed: 18828487google scholar: lookup
  8. Szeredi L, Hotzel H, Sachse K. High prevalence of chlamydial (Chlamydophila psittaci) infection in fetal membranes of aborted equine fetuses.. Vet Res Commun 2005 Mar;29 Suppl 1:37-49.
    doi: 10.1007/s11259-005-0835-1pubmed: 15943064google scholar: lookup
  9. Henning K, Sachse K, Sting R. [Demonstration of Chlamydia from an equine abortion].. Dtsch Tierarztl Wochenschr 2000 Feb;107(2):49-52.
    pubmed: 10743333
  10. Polkinghorne A, Greub G. A new equine and zoonotic threat emerges from an old avian pathogen, Chlamydia psittaci.. Clin Microbiol Infect 2017 Oct;23(10):693-694.
    doi: 10.1016/j.cmi.2017.05.025pubmed: 28583739google scholar: lookup
  11. Jenkins C, Jelocnik M, Micallef ML, Galea F, Taylor-Brown A, Bogema DR, Liu M, O'Rourke B, Chicken C, Carrick J, Polkinghorne A. An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots.. Emerg Microbes Infect 2018 May 16;7(1):88.
    doi: 10.1038/s41426-018-0089-ypmc: PMC5953950pubmed: 29765033google scholar: lookup
  12. Akter R, Stent AW, Sansom FM, Gilkerson JR, Burden C, Devlin JM, Legione AR, El-Hage CM. Chlamydia psittaci: a suspected cause of reproductive loss in three Victorian horses.. Aust Vet J 2020 Nov;98(11):570-573.
    doi: 10.1111/avj.13010pubmed: 32830314google scholar: lookup
  13. Barkallah M, Gharbi Y, Hassena AB, Slima AB, Mallek Z, Gautier M, Greub G, Gdoura R, Fendri I. Survey of infectious etiologies of bovine abortion during mid- to late gestation in dairy herds.. PLoS One 2014;9(3):e91549.
    doi: 10.1371/journal.pone.0091549pmc: PMC3963856pubmed: 24662769google scholar: lookup
  14. Canada N, Meireles CS, Rocha A, da Costa JM, Erickson MW, Dubey JP. Isolation of viable Toxoplasma gondii from naturally infected aborted bovine fetuses.. J Parasitol 2002 Dec;88(6):1247-8.
    doi: 10.1645/0022-3395(2002)088[1247:IOVTGF]2.0.CO;2pubmed: 12537120google scholar: lookup
  15. Tenter AM, Heckeroth AR, Weiss LM. Erratum-Toxoplasma gondii: From animals to humans. Int J Parasitol 2001;31(2):217–220.
    doi: 10.1016/S0020-7519(01)00125-4google scholar: lookup
  16. Akter R, Legione A, Sansom FM, El-Hage CM, Hartley CA, Gilkerson JR, Devlin JM. Detection of Coxiella burnetii and equine herpesvirus 1, but not Leptospira spp. or Toxoplasma gondii, in cases of equine abortion in Australia - a 25 year retrospective study.. PLoS One 2020;15(5):e0233100.
    doi: 10.1371/journal.pone.0233100pmc: PMC7250447pubmed: 32453753google scholar: lookup
  17. Butler C, Werners A, Newton R. In the DEFRA/AHT/BEVA Equine quarterly disease surveillance report. 2011. Surveillance of infectious and non-infectious causes of equine abortion in the UK: 2006–2011.
  18. Laugier C, Foucher N, Sevin C, Leon A, Tapprest J. A 24-year retrospective study of equine abortion in Normandy (France). J Equine Vet Sci 2011;31(3):116–123.
    doi: 10.1016/j.jevs.2010.12.012google scholar: lookup
  19. Vidal S, Kegler K, Posthaus H, Perreten V, Rodriguez-Campos S. Amplicon sequencing of bacterial microbiota in abortion material from cattle.. Vet Res 2017 Oct 10;48(1):64.
    doi: 10.1186/s13567-017-0470-1pmc: PMC5633877pubmed: 29017611google scholar: lookup
  20. Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P. Metagenomics for pathogen detection in public health.. Genome Med 2013;5(9):81.
    doi: 10.1186/gm485pmc: PMC3978900pubmed: 24050114google scholar: lookup
  21. Mokili JL, Dutilh BE, Lim YW, Schneider BS, Taylor T, Haynes MR, Metzgar D, Myers CA, Blair PJ, Nosrat B, Wolfe ND, Rohwer F. Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness.. PLoS One 2013;8(3):e58404.
    doi: 10.1371/journal.pone.0058404pmc: PMC3600855pubmed: 23554892google scholar: lookup
  22. Wan XF, Barnett JL, Cunningham F, Chen S, Yang G, Nash S, Long LP, Ford L, Blackmon S, Zhang Y, Hanson L, He Q. Detection of African swine fever virus-like sequences in ponds in the Mississippi Delta through metagenomic sequencing.. Virus Genes 2013 Jun;46(3):441-6.
    doi: 10.1007/s11262-013-0878-2pmc: PMC5413091pubmed: 23338931google scholar: lookup
  23. Chao A, Gotelli NJ, Hsieh TC, Sander EL, Ma KH, Colwell RK, Ellison AM. Rarefaction and extrapolation with hill numbers: a framework for sampling and estimation in species diversity studies. Ecol Monogr 2014;84(1):45–67.
    doi: 10.1890/13-0133.1google scholar: lookup
  24. Seemann T. Abricate. 2015.
  25. Costa MC, Weese JS. The equine intestinal microbiome.. Anim Health Res Rev 2012 Jun;13(1):121-8.
    doi: 10.1017/S1466252312000035pubmed: 22626511google scholar: lookup
  26. 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
  27. O' Donnell MM, Harris HM, Jeffery IB, Claesson MJ, Younge B, O' Toole PW, Ross RP. The core faecal bacterial microbiome of Irish Thoroughbred racehorses.. Lett Appl Microbiol 2013 Dec;57(6):492-501.
    doi: 10.1111/lam.12137pubmed: 23889584google scholar: lookup
  28. 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.0187044pmc: PMC5665523pubmed: 29091944google scholar: lookup
  29. Xia YW, Cornelius AJ, Donnelly CG, Bicalho RC, Cheong SH, Sones JL. Metagenomic analysis of the equine placental microbiome. Clin Theriogenol 2017;9:452.
  30. Husso A, Jalanka J, Alipour MJ, Huhti P, Kareskoski M, Pessa-Morikawa T. The composition of the perinatal intestinal microbiota in horse. BioRxiv 2019;1:726109.
  31. LA Sathe S, Plummer P. Metagenomic sequencing of the uterine microbial environment during estrus and early pregnancy in mares. Clin Theriogenol 2017;9:453.
  32. Bond SL, Timsit E, Workentine M, Alexander T, Léguillette R. Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone.. BMC Microbiol 2017 Aug 23;17(1):184.
    doi: 10.1186/s12866-017-1092-5pmc: PMC5569571pubmed: 28835202google scholar: lookup
  33. Jones E. Characterization of the equine microbiome during late gestation and the early postpartum period, and at various times during the estrous cycle in mares being bred with raw or extended semen. Masters Thesis: Kansas State University; 2019.
  34. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome.. Sci Transl Med 2014 May 21;6(237):237ra65.
    pmc: PMC4929217pubmed: 24848255doi: 10.1126/scitranslmed.3008599google scholar: lookup
  35. Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, Leite R, Elovitz MA, Parry S, Bushman FD. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota.. Microbiome 2016 Jun 23;4(1):29.
    doi: 10.1186/s40168-016-0172-3pmc: PMC4917942pubmed: 27338728google scholar: lookup
  36. Pelzer E, Gomez-Arango LF, Barrett HL, Nitert MD. Review: Maternal health and the placental microbiome.. Placenta 2017 Jun;54:30-37.
    doi: 10.1016/j.placenta.2016.12.003pubmed: 28034467google scholar: lookup
  37. Stinson LF, Boyce MC, Payne MS, Keelan JA. The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth.. Front Microbiol 2019;10:1124.
    doi: 10.3389/fmicb.2019.01124pmc: PMC6558212pubmed: 31231319google scholar: lookup
  38. Hoffman AM, Viel L, Prescott JF, Rosendal S, Thorsen J. Association of microbiologic flora with clinical, endoscopic, and pulmonary cytologic findings in foals with distal respiratory tract infection.. Am J Vet Res 1993 Oct;54(10):1615-22.
    pubmed: 8250386
  39. Platt H, Atherton JG, Orskov I. Klebsiella and Enterobacter organisms isolated from horses.. J Hyg (Lond) 1976 Dec;77(3):401-8.
    doi: 10.1017/S0022172400055789pmc: PMC2129811pubmed: 794407google scholar: lookup
  40. Szeredi L, Jánosi S, Tenk M. Klebsiella oxytoca as a cause of equine abortion--short communication.. Acta Vet Hung 2008 Jun;56(2):215-20.
    doi: 10.1556/avet.56.2008.2.9pubmed: 18669249google scholar: lookup
  41. Timoney PJ, McArdle JF, Bryne MJ. Abortion and meningitis in a Thoroughbred mare associated with Klebsiella pneumoniae, type 1.. Equine Vet J 1983 Jan;15(1):64-5.
    doi: 10.1111/j.2042-3306.1983.tb01711.xpubmed: 6337834google scholar: lookup
  42. Henker LC, Lorenzett MP, Keller A, Siqueira FM, Driemeier D, Pavarini SP. Fibrinonecrotic Placentitis and Abortion Associated With Pantoea agglomerans Infection in a Mare.. J Equine Vet Sci 2020 Sep;92:103156.
    pubmed: 32797784doi: 10.1016/j.jevs.2020.103156google scholar: lookup
  43. Klemm P. Fimbriae adhesion, genetics, biogenesis, and vaccines. Boca Raton: CRC Press; 1994.
  44. Bloch CA, Stocker BA, Orndorff PE. A key role for type 1 pili in enterobacterial communicability.. Mol Microbiol 1992 Mar;6(6):697-701.
    doi: 10.1111/j.1365-2958.1992.tb01518.xpubmed: 1349417google scholar: lookup
  45. Yamamoto T, Fujita K, Yokota T. Adherence characteristics to human small intestinal mucosa of Escherichia coli isolated from patients with diarrhea or urinary tract infections.. J Infect Dis 1990 Oct;162(4):896-908.
    doi: 10.1093/infdis/162.4.896pubmed: 1976131google scholar: lookup
  46. Connell I, Agace W, Klemm P, Schembri M, Mărild S, Svanborg C. Type 1 fimbrial expression enhances Escherichia coli virulence for the urinary tract.. Proc Natl Acad Sci U S A 1996 Sep 3;93(18):9827-32.
    doi: 10.1073/pnas.93.18.9827pmc: PMC38514pubmed: 8790416google scholar: lookup
  47. Sokurenko EV, Chesnokova V, Doyle RJ, Hasty DL. Diversity of the Escherichia coli type 1 fimbrial lectin. Differential binding to mannosides and uroepithelial cells.. J Biol Chem 1997 Jul 11;272(28):17880-6.
    doi: 10.1074/jbc.272.28.17880pubmed: 9211945google scholar: lookup
  48. Dijkshoorn L, Nemec A, Seifert H. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii.. Nat Rev Microbiol 2007 Dec;5(12):939-51.
    doi: 10.1038/nrmicro1789pubmed: 18007677google scholar: lookup
  49. Mule P, Patil N, Gaikwad S. Urinary tract infections by multidrug resistant Acinetobacter species-a retrospective analysis. J Health Allied Sc 2018;8(03):017–024.
    doi: 10.1055/s-0040-1708758google scholar: lookup
  50. Di Blasio A, Traversa A, Giacometti F, Chiesa F, Piva S, Decastelli L, Dondo A, Gallina S, Zoppi S. Isolation of Arcobacter species and other neglected opportunistic agents from aborted bovine and caprine fetuses.. BMC Vet Res 2019 Jul 24;15(1):257.
    doi: 10.1186/s12917-019-2009-3pmc: PMC6651951pubmed: 31340816google scholar: lookup
  51. He M, Kostadinov S, Gundogan F, Struminsky J, Pinar H, Sung CJ. Pregnancy and Perinatal Outcomes Associated with Acinetobacter baumannii Infection.. AJP Rep 2013 May;3(1):51-6.
    doi: 10.1055/s-0033-1334460pmc: PMC3699149pubmed: 23943711google scholar: lookup
  52. Gibson JA, Eaves LE. Isolation of Acinetobacter calcoaceticus from an aborted equine foetus.. Aust Vet J 1981 Nov;57(11):529-31.
    doi: 10.1111/j.1751-0813.1981.tb05799.xpubmed: 7342938google scholar: lookup
  53. Das AM, Paranjape VL. Acinetobacter calcoaceticus in three cases of late abortion in water buffaloes.. Vet Rec 1986 Feb 22;118(8):214.
    doi: 10.1136/vr.118.8.214pubmed: 3716168google scholar: lookup
  54. Müller S, Janssen T, Wieler LH. Multidrug resistant Acinetobacter baumannii in veterinary medicine--emergence of an underestimated pathogen?. Berl Munch Tierarztl Wochenschr 2014 Nov-Dec;127(11-12):435-46.
    pubmed: 25872253
  55. Chicken C, Begg A, Todhunter K. Cluster of equine abortion in Australia associated with bacterial amnionitis-equine amnionitis and foetal loss-a new condition?. Aust Equine Vet 2005;2005(3):127.
  56. Sánchez-Encinales V, Álvarez-Marín R, Pachón-Ibáñez ME, Fernández-Cuenca F, Pascual A, Garnacho-Montero J, Martínez-Martínez L, Vila J, Tomás MM, Cisneros JM, Bou G, Rodríguez-Baño J, Pachón J, Smani Y. Overproduction of Outer Membrane Protein A by Acinetobacter baumannii as a Risk Factor for Nosocomial Pneumonia, Bacteremia, and Mortality Rate Increase.. J Infect Dis 2017 Mar 15;215(6):966-974.
    pubmed: 28453834doi: 10.1093/infdis/jix010google scholar: lookup
  57. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.. BMC Biol 2014 Nov 12;12:87.
    doi: 10.1186/s12915-014-0087-zpmc: PMC4228153pubmed: 25387460google scholar: lookup
  58. Clothier KA, Villanueva M, Torain A, Hult C, Wallace R. Effects of bacterial contamination of media on the diagnosis of Tritrichomonas foetus by culture and real-time PCR.. Vet Parasitol 2015 Mar 15;208(3-4):143-9.
    doi: 10.1016/j.vetpar.2015.01.006pubmed: 25639514google scholar: lookup
  59. Annavajhala MK, Gomez-Simmonds A, Macesic N, Sullivan SB, Kress A, Khan SD, Giddins MJ, Stump S, Kim GI, Narain R, Verna EC, Uhlemann AC. Colonizing multidrug-resistant bacteria and the longitudinal evolution of the intestinal microbiome after liver transplantation.. Nat Commun 2019 Oct 17;10(1):4715.
    doi: 10.1038/s41467-019-12633-4pmc: PMC6797753pubmed: 31624266google scholar: lookup
  60. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics.. Cell 2013 Sep 26;155(1):27-38.
    doi: 10.1016/j.cell.2013.09.006pmc: PMC3969849pubmed: 24074859google scholar: lookup
  61. Charalampous T, Kay GL, Richardson H, Aydin A, Baldan R, Jeanes C, Rae D, Grundy S, Turner DJ, Wain J, Leggett RM, Livermore DM, O'Grady J. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.. Nat Biotechnol 2019 Jul;37(7):783-792.
    doi: 10.1038/s41587-019-0156-5pubmed: 31235920google scholar: lookup
  62. Ehlers B, Borchers K, Grund C, Frölich K, Ludwig H, Buhk HJ. Detection of new DNA polymerase genes of known and potentially novel herpesviruses by PCR with degenerate and deoxyinosine-substituted primers.. Virus Genes 1999;18(3):211-20.
    doi: 10.1023/A:1008064118057pubmed: 10456789google scholar: lookup
  63. Robertson T, Bibby S, O'Rourke D, Belfiore T, Lambie H, Noormohammadi AH. Characterization of Chlamydiaceae species using PCR and high resolution melt curve analysis of the 16S rRNA gene.. J Appl Microbiol 2009 Dec 1;107(6):2017-28.
    doi: 10.1111/j.1365-2672.2009.04388.xpubmed: 19583801google scholar: lookup
  64. Jaton K, Peter O, Raoult D, Tissot JD, Greub G. Development of a high throughput PCR to detect Coxiella burnetii and its application in a diagnostic laboratory over a 7-year period.. New Microbes New Infect 2013 Oct;1(1):6-12.
    doi: 10.1002/2052-2975.8pmc: PMC4184484pubmed: 25356317google scholar: lookup
  65. Stoddard RA, Gee JE, Wilkins PP, McCaustland K, Hoffmaster AR. Detection of pathogenic Leptospira spp. through TaqMan polymerase chain reaction targeting the LipL32 gene.. Diagn Microbiol Infect Dis 2009 Jul;64(3):247-55.
    doi: 10.1016/j.diagmicrobio.2009.03.014pubmed: 19395218google scholar: lookup
  66. Lélu M, Villena I, Dardé ML, Aubert D, Geers R, Dupuis E, Marnef F, Poulle ML, Gotteland C, Dumètre A, Gilot-Fromont E. Quantitative estimation of the viability of Toxoplasma gondii oocysts in soil.. Appl Environ Microbiol 2012 Aug;78(15):5127-32.
    doi: 10.1128/AEM.00246-12pmc: PMC3416395pubmed: 22582074google scholar: lookup
  67. Andrews S. FastQC. 2010.
  68. Krueger F. TrimGalore. 2019.
  69. Janečka JE, Davis BW, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen MK, Stout TAE, Brashear W, Li G, Johnson CD, Metz RP, Zadjali AMA, Love CC, Varner DD, Bellott DW, Murphy WJ, Chowdhary BP, Raudsepp T. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes.. Nat Commun 2018 Jul 27;9(1):2945.
    doi: 10.1038/s41467-018-05290-6pmc: PMC6063916pubmed: 30054462google scholar: lookup
  70. Li H. Minimap2: pairwise alignment for nucleotide sequences.. Bioinformatics 2018 Sep 15;34(18):3094-3100.
    doi: 10.1093/bioinformatics/bty191pmc: PMC6137996pubmed: 29750242google scholar: lookup
  71. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools.. Bioinformatics 2009 Aug 15;25(16):2078-9.
    doi: 10.1093/bioinformatics/btp352pmc: PMC2723002pubmed: 19505943google scholar: lookup
  72. . Database resources of the National Center for Biotechnology Information.. Nucleic Acids Res 2018 Jan 4;46(D1):D8-D13.
    pmc: PMC5753372pubmed: 29140470doi: 10.1093/nar/gkx1095google scholar: lookup
  73. Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences.. Genome Res 2016 Dec;26(12):1721-1729.
    doi: 10.1101/gr.210641.116pmc: PMC5131823pubmed: 27852649google scholar: lookup
  74. Meade B, Lafayette L, Sauter G, Tosello D. Spartan HPC-cloud hybrid: delivering performance and flexibility. Univ Melbourne 2017;10:49.
  75. Breitwieser FP, Salzberg SL. Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification.. Bioinformatics 2020 Feb 15;36(4):1303-1304.
    doi: 10.1093/bioinformatics/btz715pmc: PMC8215911pubmed: 31553437google scholar: lookup
  76. Hsieh TC, Ma KH, Chao A. iNEXT: an R package for rarefaction and extrapolation of species diversity (hill numbers). Methods Ecol Evol 2016;7(12):1451–1456.
    doi: 10.1111/2041-210X.12613google scholar: lookup
  77. Patil I. Visualizations with statistical details: the ‘ggstatsplot’ approach. PsyArxiv 2018.
  78. Holm S. A simple sequentially Rejective multiple test procedure. Scand J Stat 1979;6(2):65–70.
  79. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D. Vegan: community ecology package. R package version 2.4–3 Vienna: R Foundation for Statistical Computing; 2016.
  80. Anderson MJ, Millar RB. Spatial variation and effects of habitat on temperate reef fish assemblages in northeastern New Zealand. J Exp Mar Biol Ecol 2004;305(2):191–221.
    doi: 10.1016/j.jembe.2003.12.011google scholar: lookup
  81. McArdle BH, Anderson MJ. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 2001;82(1):290–297.
    doi: 10.1890/0012-9658(2001)082[0290:FMMTCD]2.0.CO;2google scholar: lookup
  82. Martí JM. Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.. PLoS Comput Biol 2019 Apr;15(4):e1006967.
    doi: 10.1371/journal.pcbi.1006967pmc: PMC6472834pubmed: 30958827google scholar: lookup
  83. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2.. Nat Methods 2012 Mar 4;9(4):357-9.
    doi: 10.1038/nmeth.1923pmc: PMC3322381pubmed: 22388286google scholar: lookup
  84. Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.. Genome Med 2014;6(11):90.
    doi: 10.1186/s13073-014-0090-6pmc: PMC4237778pubmed: 25422674google scholar: lookup
  85. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q. VFDB: a reference database for bacterial virulence factors.. Nucleic Acids Res 2005 Jan 1;33(Database issue):D325-8.
    pmc: PMC539962pubmed: 15608208doi: 10.1093/nar/gki008google scholar: lookup
  86. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, Rolain JM. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes.. Antimicrob Agents Chemother 2014;58(1):212-20.
    doi: 10.1128/AAC.01310-13pmc: PMC3910750pubmed: 24145532google scholar: lookup
  87. Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.. Bioinformatics 2015 May 15;31(10):1674-6.
    doi: 10.1093/bioinformatics/btv033pubmed: 25609793google scholar: lookup

Citations

This article has been cited 3 times.
  1. Jin Y, Li W, Ba X, Li Y, Wang Y, Zhang H, Li Z, Zhou J. Gut microbiota changes in horses with Chlamydia.. BMC Microbiol 2023 Sep 2;23(1):246.
    doi: 10.1186/s12866-023-02986-8pubmed: 37660043google scholar: lookup
  2. White RT, Anstey SI, Kasimov V, Jenkins C, Devlin J, El-Hage C, Pannekoek Y, Legione AR, Jelocnik M. One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia.. Microb Genom 2022 Oct;8(10).
    doi: 10.1099/mgen.0.000888pubmed: 36269227google scholar: lookup
  3. Wen X, Luo S, Lv D, Jia C, Zhou X, Zhai Q, Xi L, Yang C. Variations in the fecal microbiota and their functions of Thoroughbred, Mongolian, and Hybrid horses.. Front Vet Sci 2022;9:920080.
    doi: 10.3389/fvets.2022.920080pubmed: 35968025google scholar: lookup
Subscribe to our newsletter
Join 99,344 horse owners like you who receive our email updates on horse health and nutrition.