Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Xiong, Xuejian ^a   Frank, Daniel N ^b   Robertson, Charles E ^c   Hung, Stacy S ^a,d   Markle, Janet ^a,d   Canty, Angelo J ^e   McCoy, Kathy D ^f   Macpherson, Andrew J ^f   Poussier, Philippe ^d   Danska, Jayne S ^a,d,g   Parkinson, John ^a,d  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b UNIVERSITY OF COLORADO   (United States)

^c UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF TORONTO   (Canada)

^e MCMASTER UNIVERSITY   (Canada)

^f UNIVERSITY OF BERN   (Switzerland)

^g UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; ESCHERICHIA COLI PROTEIN; MESSENGER RNA; PEPTIDE; TRANSCRIPTOME;

ANIMAL EXPERIMENT; ARTICLE; BACTERIAL COLONIZATION; BACTEROIDES; CLOSTRIDIUM; CONTROLLED STUDY; FEASIBILITY STUDY; HIGH THROUGHPUT SEQUENCING; HOST PATHOGEN INTERACTION; INTESTINE FLORA; METATRANSCRIPTOMICS; MICROBIAL COMMUNITY; MOLECULAR PHYLOGENY; MOUSE; NONHUMAN; NONOBESE DIABETIC MOUSE; OPEN READING FRAME; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; ANIMAL; BACTERIAL GENE; ESCHERICHIA COLI; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; INTESTINE; METABOLISM; METAGENOMICS; METHODOLOGY; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; SMALL RIBOSOMAL SUBUNIT;

ANIMALIA; BACTERIA (MICROORGANISMS); BACTEROIDES; CLOSTRIDIUM; ESCHERICHIA COLI;

ANIMALS; BASE SEQUENCE; DATABASES, GENETIC; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE REGULATORY NETWORKS; GENES, BACTERIAL; INTESTINES; METAGENOMICS; MICE; MICE, INBRED NOD; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; PEPTIDES; PHYLOGENY; PROTEIN INTERACTION MAPS; RIBOSOME SUBUNITS, SMALL, EUKARYOTIC; RNA, MESSENGER; RNA, RIBOSOMAL; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84860477454     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036009     Document Type: Article

References (69)

1. Schloss PD, Handelsman J, (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14: 303-310.
2. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185: 6220-6223.
3. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
4. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16.
5. Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A 107: 7503-7508.
6. Gilbert JA, Field D, Swift P, Thomas S, Cummings D, et al. (2010) The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation. PLoS ONE 5: e15545.
7. Poroyko V, White JR, Wang M, Donovan S, Alverdy J, et al. (2010) Gut microbial gene expression in mother-fed and formula-fed piglets. PLoS One 5: e12459.
8. Booijink CC, Boekhorst J, Zoetendal EG, Smidt H, Kleerebezem M, et al. (2010) Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol 76: 5533-5540.
9. Weckx S, Allemeersch J, Van der Meulen R, Vrancken G, Huys G, et al. (2011) Metatranscriptome analysis for insight into whole-ecosystem gene expression during spontaneous wheat and spelt sourdough fermentations. Appl Environ Microbiol 77: 618-626.
10. Nam YD, Chang HW, Kim KH, Roh SW, Bae JW, (2009) Metatranscriptome analysis of lactic acid bacteria during kimchi fermentation with genome-probing microarrays. Int J Food Microbiol 130: 140-146.
11. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, et al. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 105: 3805-3810.
12. Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3: e3042.
13. Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA, (2009) Analyzing gene expression from marine microbial communities using environmental transcriptomics. J Vis Exp.
14. Shi Y, Tyson GW, DeLong EF, (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459: 266-269.
15. Marchetti A, Schruth DM, Durkin CA, Parker MS, Kodner RB, et al. (2012) Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proc Natl Acad Sci U S A 109: E317-325.
16. Radax R, Rattei T, Lanzen A, Bayer C, Rapp HT, et al. (2012) Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community. Environ Microbiol.
17. Valles SM, Oi DH, Yu F, Tan XX, Buss EA, (2012) Metatranscriptomics and Pyrosequencing Facilitate Discovery of Potential Viral Natural Enemies of the Invasive Caribbean Crazy Ant, Nylanderia pubens. PLoS ONE 7: e31828.
18. Rowley JW, Oler AJ, Tolley ND, Hunter BN, Low EN, et al. (2011) Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes. Blood 118: e101-111.
19. Xiong Y, Chen X, Chen Z, Wang X, Shi S, et al. (2010) RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet 42: 1043-1047.
20. Stewart FJ, Ulloa O, DeLong EF, (2012) Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol 14: 23-40.
21. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
22. Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proceedings of the National Academy of Sciences 107: 7503-7508.
23. Tatusov RL, Koonin EV, Lipman DJ, (1997) A genomic perspective on protein families. Science 278: 631-637.
24. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
25. The Gene Ontology Consortium (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38: D331-335.
26. Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, et al. (2011) Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics 12 (Suppl 1): S21.
27. Letunic I, Yamada T, Kanehisa M, Bork P, (2008) iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci 33: 101-103.
28. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: D354-357.
29. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
30. Frank DN, Pace NR, (2008) Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol 24: 4-10.
31. Peterson DA, Frank DN, Pace NR, Gordon JI, (2008) Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe 3: 417-427.
32. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, et al. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104: 13780-13785.
33. Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, et al. (2007) Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum. ISME J 1: 403-418.
34. Giongo A, Gano KA, Crabb DB, Mukherjee N, Novelo LL, et al. Toward defining the autoimmune microbiome for type 1 diabetes. ISME J 5: 82-91.
35. Dewhirst FE, Chien CC, Paster BJ, Ericson RL, Orcutt RP, et al. (1999) Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl Environ Microbiol 65: 3287-3292.
36. Robertson BR, O'Rourke JL, Neilan BA, Vandamme P, On SL, et al. (2005) Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents. Int J Syst Evol Microbiol 55: 1199-1204.
37. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
38. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R, (2005) The microbial pan-genome. Curr Opin Genet Dev 15: 589-594.
39. Peregrin-Alvarez JM, Parkinson J, (2007) The global landscape of sequence diversity. Genome Biol 8: R238.
40. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 102: 13950-13955.
41. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
42. Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA, (2010) Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. Isme J 5: 461-472.
43. Tatusov RL, Galperin MY, Natale DA, Koonin EV, (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: 33-36.
44. Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC, (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21: 1552-1560.
45. Green ML, Karp PD, (2006) The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res 34: 3687-3697.
46. Peregrin-Alvarez JM, Sanford C, Parkinson J, (2009) The conservation and evolutionary modularity of metabolism. Genome Biol 10: R63.
47. Hahn MW, Kern AD, (2005) Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein-Interaction Networks. Molecular Biology and Evolution 22: 803-806.
48. Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-537.
49. Parrish JR, Yu J, Liu G, Hines JA, Chan JE, et al. (2007) A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol 8: R130.
50. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, et al. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35: D358-362.
51. Yellaboina S, Goyal K, Mande SC, (2007) Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data. Genome Res 17: 527-535.
52. Hu P, Janga SC, Babu M, Diaz-Mejia JJ, Butland G, et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7: e96.
53. Peregrin-Alvarez JM, Xiong X, Su C, Parkinson J, (2009) The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol 5: e1000523.
54. Remm M, Storm CEV, Sonnhammer ELL, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 314: 1041-1052.
55. Stewart F, Sharma A, Bryant J, Eppley J, DeLong E, (2011) Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biology 12: R26.
56. Cheang MC, Chia SK, Voduc D, Gao D, Leung S, et al. (2009) Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst 101: 736-750.
57. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
58. Smith K, McCoy KD, Macpherson AJ, (2007) Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol 19: 59-69.
59. Bennett WE Jr, Gonzalez-Rivera R, Shaikh N, Magrini V, Boykin M, et al. (2009) A method for isolating and analyzing human mRNA from newborn stool. J Immunol Methods 349: 56-60.
60. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
61. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, et al. (2008) The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31: 241-250.
62. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
63. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
64. van Dongen S, (2000) Graph clustering by flow simulation: University of Utrecht.
65. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
66. Bairoch A, Apweiler R, (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28: 45-48.
67. Hung SS, Wasmuth J, Sanford C, Parkinson J, (2010) DETECT-a density estimation tool for enzyme classification and its application to Plasmodium falciparum. Bioinformatics 26: 1690-1698.
68. Peregrín-Alvarez J, Sanford C, Parkinson J, (2009) The conservation and evolutionary modularity of metabolism. Genome Biol 10: R63.
69. Remm M, Storm CE, Sonnhammer EL, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.