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Home / Equine Research Bank / Curr Issues Mol Biol / RNA Sequencing of Sperm from Healthy Cattle and Horses Revea...
Current issues in molecular biology2024; 46(9); 10430-10443; doi: 10.3390/cimb46090620

RNA Sequencing of Sperm from Healthy Cattle and Horses Reveals the Presence of a Large Bacterial Population.

Abstract: RNA molecules within ejaculated sperm can be characterized through whole-transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses, using RNA sequencing (RNA-seq) technology. Through processing of transcriptomic data derived from bovine and equine sperm cell preparations, low mapping rates to the reference genomes were observed, mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples, which led to a reduced sequencing depth of RNAs of interest. To explore the presence of bacteria, we aligned the unmapped reads to a complete database of bacterial genomes and identified bacteria-associated transcripts which were characterized. This analysis examines the limitations associated with sperm transcriptome profiling by reporting the nature of the RNA sequences among which bacterial RNA was found. These findings can aid researchers in understanding spermatozoal RNA-seq data and pave the way for the identification of molecular markers of sperm performance.
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Publication Date: 2024-09-19 PubMed ID: 39329972PubMed Central: PMC11430805DOI: 10.3390/cimb46090620Google 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 investigates the nature of RNA sequences found within the sperm of healthy cattle and horses. By using RNA sequencing technology, the researchers found that a significant proportion of the RNA comes from bacteria, which may help to explain some difficulties interpreting sperm RNA sequencing results.

Research Methodology

  • The research focused on understanding the nature of RNA sequences present in the sperm of livestock species – cattle and horses. For this, the researchers employed RNA sequencing technology, which allows for the profiling of sperm transcriptomes.
  • The transcriptomic data derived from these sperm cell preparations were processed and compared against the reference genomes of the respective species.
  • The process revealed a low mapping rate to the reference genomes. This mapping process aims to align the individual RNA sequences against a known reference genome, allowing researchers to identify the nature and source of the RNA sequences.

Main Findings

  • The low mapping rates to the reference genomes were primarily due to the presence of ribosomal RNA and bacteria in sperm samples, reducing the sequencing depth of the RNAs of interest.
  • To better understand the presence of bacteria, the researchers realigned the initially unmapped reads against a comprehensive database of bacterial genomes.
  • The realignment process revealed the presence of bacteria-associated transcripts within the sperm samples. These RNA sequences were characterized, offering an explanation for the initial low mapping results.

Implications

  • This unexpected presence of bacteria-associated RNA within the sperm samples may contribute to the limitations faced in sperm transcriptome profiling. The presence of bacterial RNA within the total RNA pool can distort results and make identifying functional transcripts challenging.
  • The researchers’ findings shed light on the complexities of interpreting spermatozoal RNA sequencing data and can lead to a better understanding of sperm performance at the molecular level.
  • This knowledge can aid future investigations in the field to account for the likely presence of bacteria-derived RNA in their samples and could potentially spur more targeted research into the implications of bacteria within reproductive processes.

Cite This Article

APA
Navarrete-López P, Asselstine V, Maroto M, Lombó M, Cánovas Á, Gutiérrez-Adán A. (2024). RNA Sequencing of Sperm from Healthy Cattle and Horses Reveals the Presence of a Large Bacterial Population. Curr Issues Mol Biol, 46(9), 10430-10443. https://doi.org/10.3390/cimb46090620

Publication

Current issues in molecular biology
ISSN: 1467-3045
NlmUniqueID: 100931761
Country: Switzerland
Language: English
Volume: 46
Issue: 9
Pages: 10430-10443

Researcher Affiliations

Navarrete-López, Paula
  • Department of Animal Reproduction, INIA-CSIC, 28040 Madrid, Spain.
Asselstine, Victoria
  • Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada.
Maroto, María
  • Department of Animal Reproduction, INIA-CSIC, 28040 Madrid, Spain.
Lombó, Marta
  • Department of Animal Reproduction, INIA-CSIC, 28040 Madrid, Spain.
Cánovas, Ángela
  • Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada.
Gutiérrez-Adán, Alfonso
  • Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada.

Grant Funding

  • PID2021-122507OB-I00 / MCIN
  • PRE2019-088813 / MICINN

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.

References

This article includes 47 references
  1. Krawetz SA. Paternal contribution: New insights and future challenges.. Nat. Rev. Genet. 2005;6:633–642.
    doi: 10.1038/nrg1654pubmed: 16136654google scholar: lookup
  2. Jodar M, Selvaraju S, Sendler E, Diamond MP, Krawetz SA, Network RM. The presence, role and clinical use of spermatozoal RNAs.. Hum. Reprod. Update. 2013;19:604–624.
    doi: 10.1093/humupd/dmt031pmc: PMC3796946pubmed: 23856356google scholar: lookup
  3. Ostermeier GC, Miller D, Huntriss JD, Diamond MP, Krawetz SA. Reproductive biology: Delivering spermatozoan RNA to the oocyte.. Nature 2004;429:154.
    doi: 10.1038/429154apubmed: 15141202google scholar: lookup
  4. Johnson GD, Sendler E, Lalancette C, Hauser R, Diamond MP, Krawetz SA. Cleavage of rRNA ensures translational cessation in sperm at fertilization.. Mol. Hum. Reprod. 2011;17:721–726.
    doi: 10.1093/molehr/gar054pmc: PMC3212859pubmed: 21831882google scholar: lookup
  5. Mao S, Sendler E, Goodrich RJ, Hauser R, Krawetz SA. A comparison of sperm RNA-seq methods.. Syst. Biol. Reprod. Med. 2014;60:308–315.
    doi: 10.3109/19396368.2014.944318pmc: PMC4435722pubmed: 25077492google scholar: lookup
  6. Sendler E, Johnson GD, Mao S, Goodrich RJ, Diamond MP, Hauser R, Krawetz SA. Stability, delivery and functions of human sperm RNAs at fertilization.. Nucleic Acids Res. 2013;41:4104–4117.
    doi: 10.1093/nar/gkt132pmc: PMC3627604pubmed: 23471003google scholar: lookup
  7. Corral-Vazquez C, Blanco J, Aiese Cigliano R, Sarrate Z, Rivera-Egea R, Vidal F, Garrido N, Daub C, Anton E. The RNA content of human sperm reflects prior events in spermatogenesis and potential post-fertilization effects.. Mol. Hum. Reprod. 2021;27:gaab035.
    doi: 10.1093/molehr/gaab035pubmed: 33950245google scholar: lookup
  8. Selvaraju S, Parthipan S, Somashekar L, Kolte AP, Krishnan Binsila B, Arangasamy A, Ravindra JP. Occurrence and functional significance of the transcriptome in bovine (Bos taurus) spermatozoa.. Sci. Rep. 2017;7:42392.
    doi: 10.1038/srep42392pmc: PMC5343582pubmed: 28276431google scholar: lookup
  9. Card CJ, Krieger KE, Kaproth M, Sartini BL. Oligo-dT selected spermatozoal transcript profiles differ among higher and lower fertility dairy sires.. Anim. Reprod. Sci. 2017;177:105–123.
    doi: 10.1016/j.anireprosci.2016.12.011pubmed: 28081858google scholar: lookup
  10. Prakash MA, Kumaresan A, Sinha MK, Kamaraj E, Mohanty TK, Datta TK, Morrell JM. RNA-Seq analysis reveals functionally relevant coding and non-coding RNAs in crossbred bull spermatozoa.. Anim. Reprod. Sci. 2020;222:106621.
    doi: 10.1016/j.anireprosci.2020.106621pmc: PMC7607363pubmed: 33069132google scholar: lookup
  11. Gòdia M, Ramayo-Caldas Y, Zingaretti LM, Darwich L, López S, Rodríguez-Gil JE, Yeste M, Sánchez A, Clop A. A pilot RNA-seq study in 40 pietrain ejaculates to characterize the porcine sperm microbiome.. Theriogenology 2020;157:525–533.
    doi: 10.1016/j.theriogenology.2020.08.001pubmed: 32971422google scholar: lookup
  12. Fraser L, Brym P, Pareek CS, Mogielnicka-Brzozowska M, Paukszto Ł, Jastrzębski JP, Wasilewska-Sakowska K, Mańkowska A, Sobiech P, Żukowski K. Transcriptome analysis of boar spermatozoa with different freezability using RNA-Seq.. Theriogenology 2020;142:400–413.
    doi: 10.1016/j.theriogenology.2019.11.001pubmed: 31711689google scholar: lookup
  13. Ureña I, González C, Ramón M, Gòdia M, Clop A, Calvo JH, Carabaño MJ, Serrano M. Exploring the ovine sperm transcriptome by RNAseq techniques. I Effect of seasonal conditions on transcripts abundance.. PLoS ONE 2022;17:e0264978.
    doi: 10.1371/journal.pone.0264978pmc: PMC8920283pubmed: 35286314google scholar: lookup
  14. Das PJ, McCarthy F, Vishnoi M, Paria N, Gresham C, Li G, Kachroo P, Sudderth AK, Teague S, Love CC. Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq.. PLoS ONE 2013;8:e56535.
    doi: 10.1371/journal.pone.0056535pmc: PMC3569414pubmed: 23409192google scholar: lookup
  15. Bianchi E, Stermer A, Boekelheide K, Sigman M, Hall SJ, Reyes G, Dere E, Hwang K. High-quality human and rat spermatozoal RNA isolation for functional genomic studies.. Andrology 2018;6:374–383.
    doi: 10.1111/andr.12471pmc: PMC6309170pubmed: 29470852google scholar: lookup
  16. Swanson GM, Moskovtsev S, Librach C, Pilsner JR, Goodrich R, Krawetz SA. What human sperm RNA-Seq tells us about the microbiome.. J. Assist. Reprod. Genet. 2020;37:359–368.
    doi: 10.1007/s10815-019-01672-xpmc: PMC7056791pubmed: 31902104google scholar: lookup
  17. Reese ST, Franco GA, Poole RK, Hood R, Fernandez Montero L, Oliveira Filho RV, Cooke RF, Pohler KG. Pregnancy loss in beef cattle: A meta-analysis.. Anim. Reprod. Sci. 2020;212:106251.
    doi: 10.1016/j.anireprosci.2019.106251pubmed: 31864492google scholar: lookup
  18. Koziol JH, Sheets T, Wickware CL, Johnson TA. Composition and diversity of the seminal microbiota in bulls and its association with semen parameters.. Theriogenology 2022;182:17–25.
    doi: 10.1016/j.theriogenology.2022.01.029pubmed: 35123307google scholar: lookup
  19. Hou D, Zhou X, Zhong X, Settles ML, Herring J, Wang L, Abdo Z, Forney LJ, Xu C. Microbiota of the seminal fluid from healthy and infertile men.. Fertil. Steril. 2013;100:1261–1269.
    doi: 10.1016/j.fertnstert.2013.07.1991pmc: PMC3888793pubmed: 23993888google scholar: lookup
  20. Weng S-L, Chiu C-M, Lin F-M, Huang W-C, Liang C, Yang T, Yang T-L, Liu C-Y, Wu W-Y, Chang Y-A. Bacterial Communities in Semen from Men of Infertile Couples: Metagenomic Sequencing Reveals Relationships of Seminal Microbiota to Semen Quality.. PLoS ONE 2014;9:e110152.
    doi: 10.1371/journal.pone.0110152pmc: PMC4207690pubmed: 25340531google scholar: lookup
  21. Vilvanathan S, Kandasamy B, Jayachandran AL, Sathiyanarayanan S, Tanjore Singaravelu V, Krishnamurthy V, Elangovan V. Bacteriospermia and Its Impact on Basic Semen Parameters among Infertile Men.. Interdiscip. Perspect. Infect. Dis. 2016;2016:2614692.
    doi: 10.1155/2016/2614692pmc: PMC4736773pubmed: 26880908google scholar: lookup
  22. Givens MD, Marley MS. Pathogens that cause infertility of bulls or transmission via semen.. Theriogenology 2008;70:504–507.
    doi: 10.1016/j.theriogenology.2008.05.033pubmed: 18501958google scholar: lookup
  23. Villegas J, Schulz M, Soto L, Sanchez R. Bacteria induce expression of apoptosis in human spermatozoa.. Apoptosis 2005;10:105–110.
    doi: 10.1007/s10495-005-6065-8pubmed: 15711926google scholar: lookup
  24. Tvrdá E, Ďuračka M, Benko F, Lukáč N. Bacteriospermia—A formidable player in male subfertility.. Open Life Sci. 2022;17:1001–1029.
    doi: 10.1515/biol-2022-0097pmc: PMC9386612pubmed: 36060647google scholar: lookup
  25. Ruiz-Díaz S, Oseguera-López I, De La Cuesta-Díaz D, García-López B, Serres C, Sanchez-Calabuig MJ, Gutiérrez-Adán A, Perez-Cerezales S. The Presence of D-Penicillamine during the In Vitro Capacitation of Stallion Spermatozoa Prolongs Hyperactive-Like Motility and Allows for Sperm Selection by Thermotaxis.. Animals 2020;10:1467.
    doi: 10.3390/ani10091467pmc: PMC7552178pubmed: 32825582google scholar: lookup
  26. Muiño R, Peña AI, Rodríguez A, Tamargo C, Hidalgo CO. Effects of cryopreservation on the motile sperm subpopulations in semen from Asturiana de los Valles bulls.. Theriogenology 2009;72:860–868.
    doi: 10.1016/j.theriogenology.2009.06.009pubmed: 19640577google scholar: lookup
  27. Santos CS, Silva AR. Current and alternative trends in antibacterial agents used in mammalian semen technology.. Anim. Reprod. 2020;17:e20190111.
    doi: 10.21451/1984-3143-AR2019-0111pmc: PMC7212743pubmed: 32399069google scholar: lookup
  28. Pérez-Cerezales S, Laguna-Barraza R, de Castro AC, Sánchez-Calabuig MJ, Cano-Oliva E, de Castro-Pita FJ, Montoro-Buils L, Pericuesta E, Fernández-González R, Gutiérrez-Adán A. Sperm selection by thermotaxis improves ICSI outcome in mice.. Sci. Rep. 2018;8:2902.
    doi: 10.1038/s41598-018-21335-8pmc: PMC5811574pubmed: 29440764google scholar: lookup
  29. Horiuchi K, Perez-Cerezales S, Papasaikas P, Ramos-Ibeas P, López-Cardona AP, Laguna-Barraza R, Fonseca Balvís N, Pericuesta E, Fernández-González R, Planells B. Impaired Spermatogenesis, Muscle, and Erythrocyte Function in U12 Intron Splicing-Defective Zrsr1 Mutant Mice.. Cell Rep. 2018;23:143–155.
    doi: 10.1016/j.celrep.2018.03.028pubmed: 29617656google scholar: lookup
  30. Gómez-Redondo I, Ramos-Ibeas P, Pericuesta E, Fernández-González R, Laguna-Barraza R, Gutiérrez-Adán A. Minor Splicing Factors Zrsr1 and Zrsr2 are essential for early embryo development and 2-cell-like conversion.. Int. J. Mol. Sci. 2020;21:4115.
    doi: 10.3390/ijms21114115pmc: PMC7312986pubmed: 32527007google scholar: lookup
  31. Michailidou K, Lindström S, Dennis J, Beesley J, Hui S, Kar S, Lemaçon A, Soucy P, Glubb D, Rostamianfar A. Association analysis identifies 65 new breast cancer risk loci.. Nature 2017;551:92–94.
    doi: 10.1038/nature24284pmc: PMC5798588pubmed: 29059683google scholar: lookup
  32. Cánovas A, Reverter A, DeAtley KL, Ashley RL, Colgrave ML, Fortes MR, Islas-Trejo A, Lehnert S, Porto-Neto L, Rincón G. Multi-tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle.. PLoS ONE 2014;9:e102551.
    doi: 10.1371/journal.pone.0102551pmc: PMC4105537pubmed: 25048735google scholar: lookup
  33. Fortes MR, Nguyen LT, Weller MM, Cánovas A, Islas-Trejo A, Porto-Neto LR, Reverter A, Lehnert SA, Boe-Hansen GB, Thomas MG. Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers.. J. Anim. Sci. 2016;94:3693–3702.
    doi: 10.2527/jas.2016-0471pubmed: 27898892google scholar: lookup
  34. Cánovas A, Rincón G, Bevilacqua C, Islas-Trejo A, Brenaut P, Hovey RC, Boutinaud M, Morgenthaler C, VanKlompenberg MK, Martin P. Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing.. Sci. Rep. 2014;4:5297.
    doi: 10.1038/srep05297pmc: PMC5381611pubmed: 25001089google scholar: lookup
  35. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2.. Nat. Methods. 2012;9:357–359.
    doi: 10.1038/nmeth.1923pmc: PMC3322381pubmed: 22388286google scholar: lookup
  36. Asselstine V, Medrano JF, Cánovas A. Identification of novel alternative splicing associated with mastitis disease in Holstein dairy cows using large gap read mapping.. BMC Genom. 2022;23:222.
    doi: 10.1186/s12864-022-08430-xpmc: PMC8934477pubmed: 35305573google scholar: lookup
  37. Klohonatz KM, Coleman SJ, Islas-Trejo AD, Medrano JF, Hess AM, Kalbfleisch T, Thomas MG, Bouma GJ, Bruemmer JE. Coding RNA Sequencing of Equine Endometrium during Maternal Recognition of Pregnancy.. Genes 2019;10:749.
    doi: 10.3390/genes10100749pmc: PMC6826732pubmed: 31557877google scholar: lookup
  38. Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2.. Genome Biol. 2019;20:257.
    doi: 10.1186/s13059-019-1891-0pmc: PMC6883579pubmed: 31779668google scholar: lookup
  39. Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: Estimating species abundance in metagenomics data.. PeerJ Comput. Sci. 2017;3:e104.
    doi: 10.7717/peerj-cs.104google scholar: lookup
  40. Al-Kass Z, Guo Y, Vinnere Pettersson O, Niazi A, Morrell JM. Metagenomic analysis of bacteria in stallion semen.. Anim. Reprod. Sci. 2020;221:106568.
    doi: 10.1016/j.anireprosci.2020.106568pubmed: 32861118google scholar: lookup
  41. Quiñones-Pérez C, Hidalgo M, Ortiz I, Crespo F, Vega-Pla JL. Characterization of the seminal bacterial microbiome of healthy, fertile stallions using next-generation sequencing.. Anim. Reprod. 2021;18:e20200052.
    doi: 10.1590/1984-3143-ar2020-0052pmc: PMC8356074pubmed: 34394753google scholar: lookup
  42. Marčeková P, Mad’ar M, Styková E, Kačírová J, Sondorová M, Mudroň P, Žert Z. The Presence of Treponema spp. in Equine Hoof Canker Biopsies and Skin Samples from Bovine Digital Dermatitis Lesions.. Microorganisms 2021;9:2190.
    doi: 10.3390/microorganisms9112190pmc: PMC8625648pubmed: 34835315google scholar: lookup
  43. Cojkic A, Niazi A, Guo Y, Hallap T, Padrik P, Morrell JM. Identification of Bull Semen Microbiome by 16S Sequencing and Possible Relationships with Fertility.. Microorganisms 2021;9:2431.
    doi: 10.3390/microorganisms9122431pmc: PMC8705814pubmed: 34946031google scholar: lookup
  44. Wolff H, Panhans A, Stolz W, Meurer M. Adherence of Escherichia coli to sperm: A mannose mediated phenomenon leading to agglutination of sperm and E. coli.. Fertil. Steril. 1993;60:154–158.
    doi: 10.1016/S0015-0282(16)56054-3pubmed: 8513934google scholar: lookup
  45. Zuleta-González MC, Zapata-Salazar ME, Guerrero-Hurtado LS, Puerta-Suárez J, Cardona-Maya WD. Klebsiella pneumoniae and Streptococcus agalactiae: Passengers in the sperm travel.. Arch. Esp. Urol. 2019;72:939–947.
    pubmed: 31697255
  46. Marchiani S, Baccani I, Tamburrino L, Mattiuz G, Nicolò S, Bonaiuto C, Panico C, Vignozzi L, Antonelli A, Rossolini GM. Effects of common Gram-negative pathogens causing male genitourinary-tract infections on human sperm functions.. Sci. Rep. 2021;11:19177.
    doi: 10.1038/s41598-021-98710-5pmc: PMC8478950pubmed: 34584150google scholar: lookup
  47. Al-Kass Z, Eriksson E, Bagge E, Wallgren M, Morrell JM. Microbiota of semen from stallions in Sweden identified by MALDI-TOF.. Vet. Anim. Sci. 2020;10:100143.
    doi: 10.1016/j.vas.2020.100143pmc: PMC7593612pubmed: 33145452google scholar: lookup

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