A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Leimena, Milkha M ^a,b   Ramiro Garcia, Javier ^a,b   Davids, Mark ^a,b   van den Bogert, Bartholomeus ^a,b   Smidt, Hauke ^b   Smid, Eddy J ^a,b   Boekhorst, Jos ^c,d   Zoetendal, Erwin G ^a,b   Schaap, Peter J ^a,b   Kleerebezem, Michiel ^a,b,d  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d NIZO FOOD RESEARCH   (Netherlands)

Author keywords

Bioinformatic pipeline; COG; Human small intestine microbiota; Illumina sequencing; KEGG; Metabolic pathways; Metatranscriptome; Paired end reads; Single end reads

Indexed keywords

COMPLEMENTARY DNA; DNA 16S; MESSENGER RNA; METATRANSCRIPTOME; RIBOSOME DNA; RIBOSOME RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; BIOINFORMATICS; CLOSTRIDIUM; DNA LIBRARY; GENUS; HAEMOPHILUS; HUMAN; INTESTINE FLORA; MICROBIAL COMMUNITY; NONHUMAN; PHYLOGENY; POPULATION ABUNDANCE; PROKARYOTE; PYROSEQUENCING; RELIABILITY; REPRODUCIBILITY; RNA SEQUENCE; SEQUENCE ANALYSIS; SIMULATION; SPECIES DISTRIBUTION; STREPTOCOCCUS; TAXONOMY; TRANSCRIPTOMICS; VALIDITY; VEILLONELLA;

AGED; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; HUMANS; INTESTINE, SMALL; METABOLIC NETWORKS AND PATHWAYS; METAGENOME; MIDDLE AGED; PHYLOGENY; REFERENCE STANDARDS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA;

BACTERIA (MICROORGANISMS);

EID: 84880911975     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-530     Document Type: Article

References (57)

1. van den Bogert B, Leimena MM, de Vos WM, Zoetendal EG, Kleerebezem M. Functional Intestinal Metagenomics. Handbook of Molecular Microbial Ecology. Volume 2 2011, 170-190. Hoboken, New Jersey: Wiley-Blackwell, de Bruin FJ.
2. Maccaferri S, Biagi E, Brigidi P. Metagenomics: key to human gut microbiota. Dig Dis 2011, 29:525-530. 10.1159/000332966, 22179207.
3. Booijink CC, Zoetendal EG, Kleerebezem M, de Vos WM. Microbial communities in the human small intestine: coupling diversity to metagenomics. Future Microbiol 2007, 2:285-295. 10.2217/17460913.2.3.285, 17661703.
4. Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. Isme J 2012, 6:1415-1426. 10.1038/ismej.2011.212, 3379644, 22258098.
5. Gilbert JA, Hughes M. Gene expression profiling: metatranscriptomics. Methods Mol Biol 2011, 733:195-205. 10.1007/978-1-61779-089-8_14, 21431772.
6. Morales SE, Holben WE. Linking bacterial identities and ecosystem processes: can 'omic' analyses be more than the sum of their parts?. FEMS Microbiol Ecol 2011, 75:2-16. 10.1111/j.1574-6941.2010.00938.x, 20662931.
7. Warnecke F, Hess M. A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 2009, 142:91-95. 10.1016/j.jbiotec.2009.03.022, 19480952.
8. Sorek R, Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 2010, 11:9-16.
9. Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A 2009, 106:3976-3981. 10.1073/pnas.0813403106, 2645912, 19234113.
10. Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH. Structure and complexity of a bacterial transcriptome. J Bacteriol 2009, 191:3203-3211. 10.1128/JB.00122-09, 2687165, 19304856.
11. Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG, Kleerebezem M. Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Appl Environ Microbiol 2012, 78:4141-4148. 10.1128/AEM.00470-12, 3370542, 22492454.
12. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 2008, 3:e3042. 10.1371/journal.pone.0003042, 2518522, 18725995.
13. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 2008, 105:3805-3810. 10.1073/pnas.0708897105, 2268829, 18316740.
14. Baldrian P, Kolarik M, Stursova M, Kopecky J, Valaskova V, Vetrovsky T, Zifcakova L, Snajdr J, Ridl J, Vlcek C, Voriskova J. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. Isme J 2012, 6:248-258. 10.1038/ismej.2011.95, 3260513, 21776033.
15. Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 2008, 3:e2527. 10.1371/journal.pone.0002527, 2424134, 18575584.
16. Gosalbes MJ, Durban A, Pignatelli M, Abellan JJ, Jimenez-Hernandez N, Perez-Cobas AE, Latorre A, Moya A. Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 2011, 6:e17447. 10.1371/journal.pone.0017447, 3050895, 21408168.
17. 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, 107:7503-7508. 10.1073/pnas.1002355107, 2867707, 20363958.
18. Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. Isme J 2012, 6:1273-1276. 10.1038/ismej.2011.186, 3379627, 22170427.
19. Xiong X, Frank DN, Robertson CE, Hung SS, Markle J, Canty AJ, McCoy KD, Macpherson AJ, Poussier P, Danska JS, Parkinson J. Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One 2012, 7:e36009. 10.1371/journal.pone.0036009, 3338770, 22558305.
20. Goncalves A, Tikhonov A, Brazma A, Kapushesky M. A pipeline for RNA-seq data processing and quality assessment. Bioinformatics 2011, 27:867-869. 10.1093/bioinformatics/btr012, 3051320, 21233166.
21. Copois V, Bibeau F, Bascoul-Mollevi C, Salvetat N, Chalbos P, Bareil C, Candeil L, Fraslon C, Conseiller E, Granci V, et al. Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J Biotechnol 2007, 127:549-559. 10.1016/j.jbiotec.2006.07.032, 16945445.
22. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 2011, 39:e90. 10.1093/nar/gkr344, 3141275, 21576222.
23. Lee ZMP, Bussema C, Schmidt TM. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 2009, 37:D489-493. 10.1093/nar/gkn689, 2686494, 18948294.
24. Klappenbach JA, Dunbar JM, Schmidt TM. rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 2000, 66:1328-1333. 10.1128/AEM.66.4.1328-1333.2000, 91988, 10742207.
25. Sooknanan R, Pease J, Doyle K. Novel methods for rRNA removal and directional, ligation-free RNA-seq library preparation. Nat Methods 2010, 7:i-ii.
26. Booijink CCGM, El-Aidy S, Rajilic-Stojanovic M, Heilig HGHJ, 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, 12:3213-3227. 10.1111/j.1462-2920.2010.02294.x, 20626454.
27. van den Bogert B, de Vos WM, Zoetendal EG, Kleerebezem M. Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 2011, 77:2071-2080. 10.1128/AEM.02477-10, 3067328, 21257804.
28. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009, 37:D141-145. 10.1093/nar/gkn879, 2686447, 19004872.
29. Ben-Amor K, Heilig H, Smidt H, Vaughan EE, Abee T, de Vos WM. Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis. Appl Environ Microbiol 2005, 71:4679-4689. 10.1128/AEM.71.8.4679-4689.2005, 1183343, 16085863.
30. Peris-Bondia F, Latorre A, Artacho A, Moya A, D'Auria G. The active human gut microbiota differs from the total microbiota. PLoS One 2011, 6:e22448. 10.1371/journal.pone.0022448, 3145646, 21829462.
31. Yomtovian I, Teerakulkittipong N, Lee B, Moult J, Unger R. Composition bias and the origin of ORFan genes. Bioinformatics 2010, 26:996-999. 10.1093/bioinformatics/btq093, 2853687, 20231229.
32. Clancy S. Chemical structure of RNA. Nature Education 2008, 1:1.
33. Westhof E. The amazing world of bacterial structured RNAs. Genome Biol 2010, 11:108. 10.1186/gb-2010-11-3-108, 2864558, 20236470.
34. Peregrin-Alvarez JM, Parkinson J. The global landscape of sequence diversity. Genome Biol 2007, 8:R238. 10.1186/gb-2007-8-11-r238, 2258180, 17996061.
35. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65. 10.1038/nature08821, 20203603.
36. Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, et al. Genomic variation landscape of the human gut microbiome. Nature 2013, 493:45-50. 3536929, 23222524.
37. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
38. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
39. Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, et al. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol 2012, 13:r23. 10.1186/gb-2012-13-3-r23, 3439974, 22455878.
40. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28:33-36. 10.1093/nar/28.1.33, 102395, 10592175.
41. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
42. Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. iPath2.0: interactive pathway explorer. Nucleic Acids Res 2011, 39:W412-415. 10.1093/nar/gkr313, 3125749, 21546551.
43. Zoetendal EG, Booijink CCGM, Klaassens ES, Heilig HGHJ, Kleerebezem M, Smidt H, de Vos WM. Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nat Protoc 2006, 1:954-959. 10.1038/nprot.2006.143, 17406329.
44. Murphy NR, Hellwig RJ. Improved nucleic acid organic extraction through use of a unique gel barrier material. BioTechniques 1996, 21:934-936. 938-939.
45. Suzuki MT, Taylor LT, DeLong EF. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays. Appl Environ Microbiol 2000, 66:4605-4614. 10.1128/AEM.66.11.4605-4614.2000, 92356, 11055900.
46. Kovatcheva-Datchary P, Egert M, Maathuis A, Rajilic-Stojanovic M, de Graaf AA, Smidt H, de Vos WM, Venema K. Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 2009, 11:914-926. 10.1111/j.1462-2920.2008.01815.x, 19128319.
47. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008, 5:235-237. 10.1038/nmeth.1184, 3439997, 18264105.
48. Daims H, Bruhl A, Amann R, Schleifer KH, Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 1999, 22:434-444. 10.1016/S0723-2020(99)80053-8, 10553296.
49. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7:335-336. 10.1038/nmeth.f.303, 3156573, 20383131.
50. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011, 21:494-504. 10.1101/gr.112730.110, 3044863, 21212162.
51. van Veen SQ, Claas EC, Kuijper EJ. High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. J Clin Microbiol 2010, 48:900-907. 10.1128/JCM.02071-09, 2832429, 20053859.
52. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 2009, 48:240-248. 10.1016/j.ymeth.2009.03.001, 19275939.
53. Kopylova E, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 2012, 28:3211-3217. 10.1093/bioinformatics/bts611, 23071270.
54. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007, 35:7188-7196. 10.1093/nar/gkm864, 2175337, 17947321.
55. van den Bogert B, Erkus OE, Boekhorst J, De Goffau M, Smid EJ, Zoetendal EG MK. Diversity of human small intestinal streptococcus and Veillonella populations. FEMS Microbiol Ecol in press.
56. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007, 35:W182-185. 10.1093/nar/gkm321, 1933193, 17526522.
57. Dillies M-A, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform 2012,