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Li F, Henderson G, Sun X, et al. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches. Front Microbiol. 2016;7:987doi: 10.3389/fmicb.2016.00987.
Li, F., Henderson, G., Sun, X., Cox, F., Janssen, P. H., & Guan, l. e. . L. (2016). Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches. Frontiers in microbiology, 7987. https://doi.org/10.3389/fmicb.2016.00987
Li, Fuyong, et al. "Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches." Frontiers in microbiology vol. 7 (2016): 987. doi: https://doi.org/10.3389/fmicb.2016.00987
Li F, Henderson G, Sun X, Cox F, Janssen PH, Guan le L. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches. Front Microbiol. 2016 Jun 22;7:987. doi: 10.3389/fmicb.2016.00987. eCollection 2016. PMID: 27446027; PMCID: PMC4916217.
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Front Microbiol. 2016 Jun 22;7:987. doi: 10.3389/fmicb.2016.00987. eCollection 2016.

Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches.

Frontiers in microbiology

Fuyong Li, Gemma Henderson, Xu Sun, Faith Cox, Peter H Janssen, Le Luo Guan

Affiliations

  1. Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada.
  2. AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand.

PMID: 27446027 PMCID: PMC4916217 DOI: 10.3389/fmicb.2016.00987

Abstract

Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data.

Keywords: archaea; bacteria; rumen microbiota; targeted amplicon sequencing; total RNA sequencing

References

  1. Appl Environ Microbiol. 2006 Jul;72(7):5069-72 - PubMed
  2. Appl Environ Microbiol. 2014 Sep;80(18):5761-72 - PubMed
  3. Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38 - PubMed
  4. Environ Microbiol. 2011 May;13(5):1138-52 - PubMed
  5. PLoS One. 2012;7(3):e33306 - PubMed
  6. ISME J. 2012 Feb;6(2):343-51 - PubMed
  7. Clin Microbiol Infect. 2013 Apr;19(4):305-13 - PubMed
  8. Appl Environ Microbiol. 1993 May;59(5):1354-60 - PubMed
  9. Cell Metab. 2012 Nov 7;16(5):559-64 - PubMed
  10. PLoS One. 2013 Sep 11;8(9):e74787 - PubMed
  11. J Microbiol Methods. 2007 May;69(2):330-9 - PubMed
  12. Bioinformatics. 2012 Dec 15;28(24):3211-7 - PubMed
  13. Environ Microbiol. 2009 May;11(5):1292-302 - PubMed
  14. PLoS One. 2013;8(3):e58461 - PubMed
  15. PLoS One. 2013;8(2):e47879 - PubMed
  16. J Nutr Biochem. 2016 Feb;28:191-200 - PubMed
  17. Appl Environ Microbiol. 2009 Apr;75(7):1860-6 - PubMed
  18. Antonie Van Leeuwenhoek. 2004 Oct;86(3):263-81 - PubMed
  19. J Microbiol. 2014 May;52(5):355-65 - PubMed
  20. Genome Res. 2003 Nov;13(11):2498-504 - PubMed
  21. PLoS One. 2008 Jun 25;3(6):e2527 - PubMed
  22. PLoS One. 2013 Dec 31;8(12):e83424 - PubMed
  23. ISME J. 2014 Jul;8(7):1464-75 - PubMed
  24. ISME J. 2012 Nov;6(11):2091-106 - PubMed
  25. FEMS Microbiol Ecol. 2015 Aug;91(8):fiv077 - PubMed
  26. Sci Rep. 2015 Oct 09;5:14567 - PubMed
  27. PLoS One. 2014 Apr 10;9(4):e94249 - PubMed
  28. Appl Environ Microbiol. 2007 Jul;73(13):4206-10 - PubMed
  29. Bioinformatics. 2011 Aug 15;27(16):2194-200 - PubMed
  30. FEMS Microbiol Ecol. 2011 May;76(2):311-26 - PubMed
  31. Bioinformatics. 2014 Aug 1;30(15):2114-20 - PubMed
  32. ISME J. 2012 Aug;6(8):1621-4 - PubMed
  33. Environ Microbiol. 2014 Sep;16(9):2659-71 - PubMed
  34. Curr Microbiol. 2009 May;58(5):464-71 - PubMed
  35. Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32 - PubMed
  36. DNA Res. 2014;21(2):115-25 - PubMed
  37. Nat Rev Microbiol. 2007 May;5(5):384-92 - PubMed
  38. Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6 - PubMed
  39. Genome Res. 2011 Mar;21(3):494-504 - PubMed
  40. ISME J. 2014 May;8(5):1101-14 - PubMed
  41. PLoS One. 2014 Sep 24;9(9):e106491 - PubMed
  42. Appl Environ Microbiol. 2007 Aug;73(16):5261-7 - PubMed
  43. Appl Environ Microbiol. 2013 Sep;79(17):5112-20 - PubMed
  44. Appl Environ Microbiol. 2000 Dec;66(12):5488-91 - PubMed
  45. Appl Environ Microbiol. 2012 Feb;78(4):1203-14 - PubMed
  46. Nat Commun. 2016 Jan 26;7:10410 - PubMed
  47. Appl Environ Microbiol. 2008 Jun;74(12):3619-25 - PubMed
  48. Gut. 2016 Feb;65(2):330-9 - PubMed
  49. Environ Microbiol. 2012 Sep;14(9):2577-88 - PubMed
  50. Microbiology. 2000 Jun;146 ( Pt 6):1287-93 - PubMed
  51. Appl Environ Microbiol. 2007 Jul;73(14):4609-18 - PubMed
  52. EcoSal Plus. 2008 Sep;3(1):null - PubMed
  53. BMC Genet. 2012 Jul 02;13:53 - PubMed
  54. Nat Commun. 2013;4:1428 - PubMed
  55. J Appl Microbiol. 2009 Dec 1;107(6):1924-34 - PubMed
  56. ISME J. 2009 Dec;3(12):1365-73 - PubMed
  57. ISME J. 2014 Jul;8(7):1403-17 - PubMed
  58. World J Gastroenterol. 2014 Nov 21;20(43):16062-78 - PubMed
  59. Annu Rev Anim Biosci. 2014 Feb;2:469-86 - PubMed
  60. FEMS Microbiol Ecol. 2011 Sep;77(3):577-89 - PubMed
  61. PLoS Comput Biol. 2012;8(7):e1002606 - PubMed
  62. J Microbiol Methods. 2009 Apr;77(1):8-16 - PubMed
  63. Anaerobe. 2014 Oct;29:85-90 - PubMed
  64. Appl Environ Microbiol. 2009 Dec;75(23):7537-41 - PubMed
  65. Anal Biochem. 1987 Apr;162(1):156-9 - PubMed
  66. J Biomed Biotechnol. 2012;2012:251364 - PubMed
  67. J Dairy Sci. 2012 Sep;95(9):5024-34 - PubMed
  68. Microb Ecol. 2015 Oct;70(3):596-611 - PubMed
  69. Nature. 2006 Aug 17;442(7104):806-9 - PubMed
  70. ISME J. 2013 Nov;7(11):2061-8 - PubMed
  71. J Appl Microbiol. 2013 Sep;115(3):644-53 - PubMed
  72. Ecology. 2007 Oct;88(10):2427-39 - PubMed

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