Advertisement

Exploration of Microbial Cells: The Storehouse of Bio-wealth Through Metagenomics and Metatranscriptomics

  • Ravi Ranjan
  • Asha Rani
  • Rajesh Kumar

Abstract

Microbes are omnipresent, most abundant, versatile, have been studied exhaustively, and used historically for the human welfare. This enormous diversity of microbes serves as tiny cellular factories and has been used to generate “bio” energy, gas, fuel, and polymers and in waste management. However, to date majority of these microbes remain unexplored and thus remain unexploited for bioprospecting. Recent advancements in molecular biology techniques, next-generation high-throughput sequencing, and bioinformatics have aided to circumvent this caveat by providing insights in the genomes and biological process of these microbes. These recent developments in scientific research have advantages but also present the researchers with economic and computational challenges, but none the less it has led to tremendous discoveries compared to decades ago. In this review, we focus on the technological advancements and the recent studies using metagenomics and metatranscriptomics for exploration of “microbial cell factories” – the storehouse of biological wealth.

Keywords

Hydrogen Production Biogas Plant Multiple Displacement Amplification Lignocellulolytic Enzyme Biogas Reactor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors would like to sincerely thank Dr. V. C. Kalia, Chief Scientist, Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India, for helpful and constructive comments that greatly contributed to improving the final version of the chapter. The motivation behind this review stems from the Ph.D., research undertaken at IGIB and Delhi University by RR, AR, and RK.

References

  1. Agarwal L, Purohit HJ (2013) Genome sequence of Rhizobium lupini HPC(L) isolated from saline desert soil, Kutch (Gujarat). Genome Announc 1:00071-12. doi: 10.1128/genomeA.00071-12 CrossRefGoogle Scholar
  2. Ai H, Zhang J, Yang M, Yu P, Li S, Zhu M, Dong H, Wang S, Wang J (2014) Draft genome sequence of an anaerobic, thermophilic bacterium, Thermoanaerobacterium aotearoense SCUT27, isolated from a hot spring in China. Genome Announc 2:00041-14. doi: 10.1128/genomeA.00041-14 CrossRefGoogle Scholar
  3. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31:533–538. doi: 10.1038/nbt.2579 PubMedCrossRefGoogle Scholar
  4. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169PubMedCentralPubMedGoogle Scholar
  5. Angly FE, Willner D, Prieto-Davo A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C et al (2009) The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol 5, e1000593. doi: 10.1371/journal.pcbi.1000593 PubMedCentralPubMedCrossRefGoogle Scholar
  6. Arndt D, Xia J, Liu Y, Zhou Y, Guo AC, Cruz JA, Sinelnikov I, Budwill K, Nesbo CL, Wishart DS (2012) METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res 40:W88–W95. doi: 10.1093/nar/gks497 PubMedCentralPubMedCrossRefGoogle Scholar
  7. Benowitz S (2014) Nanopore DNA sequencing: new approaches to an old challenge. National Human Genome Research Institute. Report number: 27555651. www.genome.gov/27555651
  8. Bowers J, Mitchell J, Beer E, Buzby PR, Causey M, Efcavitch JW, Jarosz M, Krzymanska-Olejnik E, Kung L, Lipson D et al (2009) Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 6:593–595. doi: 10.1038/nmeth.1354 PubMedCentralPubMedCrossRefGoogle Scholar
  9. Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X et al (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26:1146–1153. doi: 10.1038/nbt.1495 PubMedCentralPubMedCrossRefGoogle Scholar
  10. Bharadwaj Sv V, Shrivastav A, Dubey S, Ghosh T, Paliwal C, Maurya R, Mishra S (2015) Draft genome sequence of Halomonas hydrothermalis MTCC 5445, isolated from the west coast of India. Genome Announc 3:01419-14. doi: 10.1128/genomeA.01419-14 CrossRefGoogle Scholar
  11. Carnevali P, Baccash J, Halpern AL, Nazarenko I, Nilsen GB, Pant KP, Ebert JC, Brownley A, Morenzoni M, Karpinchyk V et al (2011) Computational techniques for human genome resequencing using mated gapped reads. J Comput Biol 19:279–292. doi: 10.1089/cmb.2011.0201 PubMedCrossRefGoogle Scholar
  12. Carvalhais LC, Schenk PM (2013) Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities. Methods Enzymol 531:251–267. doi: 10.1016/B978-0-12-407863-5.00013-7 PubMedCrossRefGoogle Scholar
  13. Carvalhais LC, Dennis PG, Tyson GW, Schenk PM (2012) Application of metatranscriptomics to soil environments. J Microbiol Methods 91:246–251. doi: 10.1016/j.mimet.2012.08.011 PubMedCrossRefGoogle Scholar
  14. Ciranna A, Larjo A, Kivisto A, Santala V, Roos C, Karp M (2013) Draft genome sequence of the hydrogen- and ethanol-producing anaerobic alkalithermophilic bacterium Caloramator celer. Genome Announc 1:00471-13. doi: 10.1128/genomeA.00471-13 CrossRefGoogle Scholar
  15. Claassen S, du Toit E, Kaba M, Moodley C, Zar HJ, Nicol MP (2013) A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J Microbiol Methods 94:103–110. doi: 10.1016/j.mimet.2013.05.008 PubMedCrossRefGoogle Scholar
  16. Cole J, Wang Q, Cardenas E, Fish J, Chai B, Farris R, Kulam-Syed-Mohideen A, McGarrell D, Marsh T, Garrity G et al (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145. doi: 10.1093/nar/gkn879 PubMedCentralPubMedCrossRefGoogle Scholar
  17. Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99:10494–10499. doi: 10.1073/pnas.142680199 PubMedCentralPubMedCrossRefGoogle Scholar
  18. de Bourcy CF, De Vlaminck I, Kanbar JN, Wang J, Gawad C, Quake SR (2014) A quantitative comparison of single-cell whole genome amplification methods. PLoS ONE 9, e105585. doi: 10.1371/journal.pone.0105585 PubMedCentralPubMedCrossRefGoogle Scholar
  19. Deutscher MP (2006) Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Res 34:659–666. doi: 10.1093/nar/gkj472 PubMedCentralPubMedCrossRefGoogle Scholar
  20. Dineen SM, Aranda R, Anders DL, Robertson JM (2010) An evaluation of commercial DNA extraction kits for the isolation of bacterial spore DNA from soil. J Appl Microbiol 109:1886–1896. doi: 10.1111/j.1365-2672.2010.04816.x PubMedCrossRefGoogle Scholar
  21. Ding JY, Chiang PW, Hong MJ, Dyall-Smith M, Tang SL (2014) Complete genome sequence of the extremely halophilic archaeon Haloarcula hispanica strain N601. Genome Announc 2:00178-14. doi: 10.1128/genomeA.00178-14 Google Scholar
  22. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G et al (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327:78–81. doi: 10.1126/science.1181498 PubMedCrossRefGoogle Scholar
  23. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138. doi: 10.1126/science.1162986 PubMedCrossRefGoogle Scholar
  24. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512. doi: 10.1126/science.7542800 PubMedCrossRefGoogle Scholar
  25. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM et al (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397–403. doi: 10.1126/science.270.5235.397 PubMedCrossRefGoogle Scholar
  26. Gerlach W, Junemann S, Tille F, Goesmann A, Stoye J (2009) WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 10:430. doi: 10.1186/1471-2105-10-430 PubMedCentralPubMedCrossRefGoogle Scholar
  27. Gifford S, Satinsky B, Moran M (2014) Quantitative microbial metatranscriptomics. In: Paulsen IT, Holmes AJ (eds) Environmental microbiology. Humana Press, Totowa, pp 213–229CrossRefGoogle Scholar
  28. Gilbert JA, Hughes M (2011) Gene expression profiling: metatranscriptomics. Methods Mol Biol 733:195–205. doi: 10.1007/978-1-61779-089-8_14 PubMedCrossRefGoogle Scholar
  29. Gilbert J, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3, e3042. doi: 10.1371/journal.pone.0003042 PubMedCentralPubMedCrossRefGoogle Scholar
  30. Gulder TA, Moore BS (2009) Chasing the treasures of the sea – bacterial marine natural products. Curr Opin Microbiol 12:252–260. doi: 10.1016/j.mib.2009.05.002 PubMedCentralPubMedCrossRefGoogle Scholar
  31. Guy AT, Piggot TJ, Khalid S (2012) Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study. Biophys J 103:1028–1036. doi: 10.1016/j.bpj.2012.08.012 PubMedCentralPubMedCrossRefGoogle Scholar
  32. Hammer O, Haper D, Ryan P (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9Google Scholar
  33. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685. doi: 10.1128/MMBR.68.4.669-685.2004 PubMedCentralPubMedCrossRefGoogle Scholar
  34. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249. doi: 10.1016/S1074-5521(98)90108-9 PubMedCrossRefGoogle Scholar
  35. He S, Ivanova N, Kirton E, Allgaier M, Bergin C, Scheffrahn R, Kyrpides N, Warnecke F, Tringe S, Hugenholtz P (2013) Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS ONE 8, e61126. doi: 10.1371/journal.pone.0061126 PubMedCentralPubMedCrossRefGoogle Scholar
  36. Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P (2014) Library construction for next-generation sequencing: overviews and challenges. Biotechniques 56:61–77. doi: 10.2144/000114133 PubMedCentralPubMedGoogle Scholar
  37. Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207–214. doi: 10.1038/nature11234 CrossRefGoogle Scholar
  38. Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E et al (2014) EBI metagenomics-a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Res 42:D600–D606. doi: 10.1093/nar/gkt961 PubMedCentralPubMedCrossRefGoogle Scholar
  39. Huson DH, Weber N (2013) Microbial community analysis using MEGAN. Methods Enzymol 531:465–485. doi: 10.1016/B978-0-12-407863-5.00021-6 PubMedCrossRefGoogle Scholar
  40. Kalia VC (2014) Microbes, antimicrobials and resistance: the battle goes on. Indian J Microbiol 54:1–2. doi: 10.1007/s12088-013-0443-7 PubMedCentralPubMedCrossRefGoogle Scholar
  41. Kalia VC, Purohit HJ (2008) Microbial diversity and genomics in aid of bioenergy. J Ind Microbiol Biotechnol 35:403–419. doi: 10.1007/s10295-007-0300-y PubMedCrossRefGoogle Scholar
  42. Kalia VC, Chauhan A, Bhattacharyya G, Rashmi (2003a) Genomic databases yield novel bioplastic producers. Nat Biotechnol 21:845–846. doi: 10.1038/nbt0803-845 PubMedCrossRefGoogle Scholar
  43. Kalia VC, Lal S, Ghai R, Mandal M, Chauhan A (2003b) Mining genomic databases to identify novel hydrogen producers. Trends Biotechnol 21:152–156. doi: 10.1016/s0167-7799(03)00028-3 PubMedCrossRefGoogle Scholar
  44. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42:D199–D205. doi: 10.1093/nar/gkt1076 PubMedCentralPubMedCrossRefGoogle Scholar
  45. Kaplarevic M, Murray AE, Cary SC, Gao GR (2008) EnGenIUS-environmental genome informational utility system. J Bioinform Comput Biol 6:1193–1211. doi: 10.1142/S0219720008003850 PubMedCrossRefGoogle Scholar
  46. Kellenberger E (2001) Exploring the unknown. The silent revolution of microbiology. EMBO Rep 2:5–7. doi: 10.1093/embo-reports/kve014 PubMedCentralPubMedCrossRefGoogle Scholar
  47. King C, Scott-Horton T (2008) Pyrosequencing: a simple method for accurate genotyping. J Vis Exp 11:630. doi: 10.3791/630 PubMedGoogle Scholar
  48. Kivisto A, Larjo A, Ciranna A, Santala V, Roos C, Karp M (2013) Genome sequence of Halanaerobium saccharolyticum subsp. saccharolyticum strain DSM 6643T, a halophilic hydrogen-producing bacterium. Genome Announc 1:e00187-13. doi: 10.1128/genomeA.00187-13 PubMedCentralPubMedCrossRefGoogle Scholar
  49. Kliman HJ (2014) Comment on ‘the placenta harbors a unique microbiome’. Sci Transl Med 6:254le4. doi: 10.1126/scitranslmed.3009864 PubMedCrossRefGoogle Scholar
  50. Koch C, Muller S, Harms H, Harnisch F (2014) Microbiomes in bioenergy production: from analysis to management. Curr Opin Biotechnol 27:65–72. doi: 10.1016/j.copbio.2013.11.006 PubMedCrossRefGoogle Scholar
  51. Kolek J, Sedlar K, Provaznik I, Patakova P (2014) Draft genome sequence of Clostridium pasteurianum NRRL B-598, a potential butanol or hydrogen producer. Genome Announc 2:e00192-14. doi: 10.1128/genomeA.00192-14 PubMedCentralPubMedCrossRefGoogle Scholar
  52. Koren O, Spor A, Felin J, Fak F, Stombaugh J, Tremaroli V, Behre CJ, Knight R, Fagerberg B, Ley RE et al (2011) Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A 108:4592–4598. doi: 10.1073/pnas.1011383107 PubMedCentralPubMedCrossRefGoogle Scholar
  53. Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 36:2230–2239. doi: 10.1093/nar/gkn038 PubMedCentralPubMedCrossRefGoogle Scholar
  54. Kuck P, Struck TH (2014) BaCoCa-a heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions. Mol Phylogenet Evol 70:94–98. doi: 10.1016/j.ympev.2013.09.011 PubMedCrossRefGoogle Scholar
  55. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R (2012a) Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 13:47–58. doi: 10.1038/nrg3129 CrossRefGoogle Scholar
  56. Kuczynski J, Stombaugh J, Walters WA, Gonzalez A, Caporaso JG, Knight R (2012b) Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics Chapter 1:Unit 1E.5. doi: 10.1002/9780471729259.mc01e05s27 Google Scholar
  57. Kuhad RC, Gupta R, Singh A (2011) Microbial cellulases and their industrial applications. Enzyme Res 2011:280696. doi: 10.4061/2011/280696 PubMedCentralPubMedCrossRefGoogle Scholar
  58. Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J et al (2012) MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS ONE 7, e47656. doi: 10.1371/journal.pone.0047656 PubMedCentralPubMedCrossRefGoogle Scholar
  59. Kumar T, Singh M, Purohit HJ, Kalia VC (2009) Potential of Bacillus sp. to produce polyhydroxybutyrate from biowaste. J Appl Microbiol 106:2017–2023. doi: 10.1111/j.1365-2672.2009.04160.x PubMedCrossRefGoogle Scholar
  60. Kumar P, Patel SK, Lee JK, Kalia VC (2013) Extending the limits of Bacillus for novel biotechnological applications. Biotechnol Adv 31:1543–1561. doi: 10.1016/j.biotechadv.2013.08.007 PubMedCrossRefGoogle Scholar
  61. Kumar P, Pant DC, Mehariya S, Sharma R, Kansal A, Kalia VC (2014a) Ecobiotechnological strategy to enhance efficiency of bioconversion of wastes into hydrogen and methane. Indian J Microbiol 54:262–267. doi: 10.1007/s12088-014-0467-7 PubMedCentralPubMedCrossRefGoogle Scholar
  62. Kumar P, Singh M, Mehariya S, Patel SK, Lee JK, Kalia VC (2014b) Ecobiotechnological approach for exploiting the abilities of Bacillus to produce co-polymer of polyhydroxyalkanoate. Indian J Microbiol 54:151–157. doi: 10.1007/s12088-014-0457-9 PubMedCentralPubMedCrossRefGoogle Scholar
  63. Ladoukakis E, Kolisis FN, Chatziioannou AA (2014) Integrative workflows for metagenomic analysis. Front Cell Dev Biol 2:70. doi: 10.3389/fcell.2014.00070 PubMedCentralPubMedCrossRefGoogle Scholar
  64. Lal S, Ramachandran U, Zhang X, Munir R, Sparling R, Levin DB (2013a) Draft genome sequence of the cellulolytic, mesophilic, anaerobic bacterium Clostridium termitidis strain CT1112 (DSM 5398). Genome Announc 1:e00281-13. doi: 10.1128/genomeA.00281-13 PubMedCentralPubMedGoogle Scholar
  65. Lal S, Ramachandran U, Zhang X, Sparling R, Levin DB (2013b) Draft genome sequence of the hydrogen- and ethanol-producing bacterium Clostridium intestinale strain URNW. Genome Announc 1:e00871-13. doi: 10.1128/genomeA.00871-13 PubMedCentralPubMedGoogle Scholar
  66. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R et al (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821. doi: 10.1038/nbt.2676 PubMedCentralPubMedCrossRefGoogle Scholar
  67. Larsson A (2014) AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30:3276–3278. doi: 10.1093/bioinformatics/btu531 PubMedCentralPubMedCrossRefGoogle Scholar
  68. Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey A, Nova IC, Craig JM, Langford KW, Samson JM, Daza R et al (2014) Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol 32:829–833. doi: 10.1038/nbt.2950 PubMedCentralPubMedCrossRefGoogle Scholar
  69. Latif H, Zeidan AA, Nielsen AT, Zengler K (2014) Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms. Curr Opin Biotechnol 27:79–87. doi: 10.1016/j.copbio.2013.12.001 PubMedCrossRefGoogle Scholar
  70. Leonardo FC, da Cunha AF, da Silva MJ, Carazzolle MF, Costa-Leonardo AM, Costa FF, Pereira GA (2011) Analysis of the workers head transcriptome of the asian subterranean termite, Coptotermes gestroi. Bull Entomol Res 101:383–391. doi: 10.1017/s0007485310000556 PubMedCrossRefGoogle Scholar
  71. Li A, Chu Y, Wang X, Ren L, Yu J, Liu X, Yan J, Zhang L, Wu S, Li S (2013) A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol Biofuels 6:3. doi: 10.1186/1754-6834-6-3 PubMedCentralPubMedCrossRefGoogle Scholar
  72. Li H, Zhou S, Johnson T, Vercruysse K, Ropelewski AJ, Thannhauser TW (2014) Draft genome sequence of new Bacillus cereus strain tsu1. Genome Announc 2:e01294-14. doi: 10.1128/genomeA.01294-14 PubMedCentralPubMedCrossRefGoogle Scholar
  73. Licciardello G, Bella P, Devescovi G, Strano CP, Sarris PF, Catara AF, Venturi V, Catara V (2014) Draft genome sequence of Pseudomonas mediterranea strain CFBP 5447T, a producer of filmable medium-chain-length polyhydroxyalkanoates. Genome Announc 2:e01260-14. doi: 10.1128/genomeA.01260-14 PubMedCentralPubMedCrossRefGoogle Scholar
  74. Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schaberle TF, Hughes DE, Epstein S et al (2015) A new antibiotic kills pathogens without detectable resistance. Nature 517:455–459. doi: 10.1038/nature14098 PubMedCrossRefGoogle Scholar
  75. Lingner T, Asshauer KP, Schreiber F, Meinicke P (2011) CoMet-a web server for comparative functional profiling of metagenomes. Nucleic Acids Res 39:W518–W523. doi: 10.1093/nar/gkr388 PubMedCentralPubMedCrossRefGoogle Scholar
  76. Luo C, Rodriguez RL, Konstantinidis KT (2013) A user’s guide to quantitative and comparative analysis of metagenomic datasets. Methods Enzymol 531:525–547. doi: 10.1016/B978-0-12-407863-5.00023-X PubMedCrossRefGoogle Scholar
  77. MacDonald NJ, Parks DH, Beiko RG (2012) Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res 40, e111. doi: 10.1093/nar/gks335 PubMedCentralPubMedCrossRefGoogle Scholar
  78. Madigan MT, Clark DP, Stahl D, Martinko JM (2010) Brock biology of microorganisms, 13th edn. Benjamin Cummings, San FranciscoGoogle Scholar
  79. Mahmoudi N, Slater GF, Fulthorpe RR (2011) Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils. Can J Microbiol 57:623–628. doi: 10.1139/w11-049 PubMedCrossRefGoogle Scholar
  80. Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P et al (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40:D115–D122. doi: 10.1093/nar/gkr1044 PubMedCentralPubMedCrossRefGoogle Scholar
  81. Martinez V, Hormigo D, Del Cerro C, Gomez de Santos P, Garcia-Hidalgo J, Arroyo M, Prieto A, Garcia JL, de la Mata I (2014) Genome sequence of Streptomyces exfoliatus DSMZ 41693, a source of poly(3-hydroxyalkanoate)-degrading enzymes. Genome Announc 2:e01272-13. doi: 10.1128/genomeA.01272-13 PubMedCentralPubMedCrossRefGoogle Scholar
  82. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618. doi: 10.1038/ismej.2011.139 PubMedCentralPubMedCrossRefGoogle Scholar
  83. Mettel C, Kim Y, Shrestha PM, Liesack W (2010) Extraction of mRNA from soil. Appl Environ Microbiol 76:5995–6000. doi: 10.1128/AEM.03047-09 PubMedCentralPubMedCrossRefGoogle Scholar
  84. Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11:31–46. doi: 10.1038/nrg2626 PubMedCrossRefGoogle Scholar
  85. Meyer F, Paarmann D, D’Souza M, Olson R, Glass E, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A et al (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi: 10.1186/1471-2105-9-386 PubMedCentralPubMedCrossRefGoogle Scholar
  86. Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH (2011) Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics 12(Suppl 1):S21. doi: 10.1186/1471-2105-12-s1-s21 PubMedCentralPubMedCrossRefGoogle Scholar
  87. Motley ST, Picuri JM, Crowder CD, Minich JJ, Hofstadler SA, Eshoo MW (2014) Improved multiple displacement amplification (iMDA) and ultraclean reagents. BMC Genomics 15:443. doi: 10.1186/1471-2164-15-443 PubMedCentralPubMedCrossRefGoogle Scholar
  88. Ni M, Leung DYC, Leung MKH (2007) A review on reforming bio-ethanol for hydrogen production. Int J Hydrogen Energy 32:3238–3247. doi: 10.1016/j.ijhydene.2007.04.038 CrossRefGoogle Scholar
  89. Nilakanta H, Drews KL, Firrell S, Foulkes MA, Jablonski KA (2014) A review of software for analyzing molecular sequences. BMC Res Notes 7:830. doi: 10.1186/1756-0500-7-830 PubMedCentralPubMedCrossRefGoogle Scholar
  90. Noar JD, Bruno-Barcena JM (2013) Complete genome sequences of Azotobacter vinelandii wild-type strain CA and tungsten-tolerant mutant strain CA6. Genome Announc 1:e00313-13. doi: 10.1128/genomeA.00313-13 PubMedCentralPubMedCrossRefGoogle Scholar
  91. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R et al (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691–5702. doi: 10.1093/nar/gki866 PubMedCentralPubMedCrossRefGoogle Scholar
  92. Parkinson NJ, Maslau S, Ferneyhough B, Zhang G, Gregory L, Buck D, Ragoussis J, Ponting CP, Fischer MD (2012) Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res 22:125–133. doi: 10.1101/gr.124016.111 PubMedCentralPubMedCrossRefGoogle Scholar
  93. Pace N, Stahl D, Lane D, Olsen G (1986) The analysis of natural microbial populations by ribosomal RNA sequences. In: Marshall KC (ed) Advances in microbial ecology. Springer US, New York, pp 1–55CrossRefGoogle Scholar
  94. Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30:3123–3124. doi: 10.1093/bioinformatics/btu494 PubMedCentralPubMedCrossRefGoogle Scholar
  95. Patel SK, Kalia VC (2013) Integrative biological hydrogen production: an overview. Indian J Microbiol 53:3–10. doi: 10.1007/s12088-012-0287-6 PubMedCentralPubMedCrossRefGoogle Scholar
  96. Patel SK, Singh M, Kalia VC (2011) Hydrogen and polyhydroxybutyrate producing abilities of Bacillus spp. from glucose in two stage system. Indian J Microbiol 51:418–423. doi: 10.1007/s12088-011-0236-9 PubMedCentralPubMedCrossRefGoogle Scholar
  97. Patel SK, Kumar P, Singh M, Lee JK, Kalia VC (2015) Integrative approach to produce hydrogen and polyhydroxybutyrate from biowaste using defined bacterial cultures. Bioresour Technol 176:136–141. doi: 10.1016/j.biortech.2014.11.029 PubMedCrossRefGoogle Scholar
  98. Pignatelli M, Moya A, Tamames J (2009) EnvDB, a database for describing the environmental distribution of prokaryotic taxa. Environ Microbiol Rep 1:191–197. doi: 10.1111/j.1758-2229.2009.00030.x PubMedCrossRefGoogle Scholar
  99. Pyne ME, Utturkar S, Brown SD, Moo-Young M, Chung DA, Chou CP (2014) Improved draft genome sequence of Clostridium pasteurianum strain ATCC 6013 (DSM 525) using a hybrid next-generation sequencing approach. Genome Announc 2:e00790-14. doi: 10.1128/genomeA.00790-14 PubMedCentralPubMedCrossRefGoogle Scholar
  100. Rajilic-Stojanovic M, de Vos WM (2014) The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 38:996–1047. doi: 10.1111/1574-6976.12075 PubMedCentralPubMedCrossRefGoogle Scholar
  101. Rani A (2008) Studies for identification, distribution and diversity of microbes through 16S rDNA sequences. Ph.D. thesis, University of Delhi, Delhi, IndiaGoogle Scholar
  102. Ranjan R (2008) Functional metagenomics to identify novel genes for biocatalysts. Ph.D. thesis, University of Delhi, Delhi, IndiaGoogle Scholar
  103. Ranjan R, Grover A, Kapardar RK, Sharma R (2005) Isolation of novel lipolytic genes from uncultured bacteria of pond water. Biochem Biophys Res Commun 335:57–65. doi: 10.1016/j.bbrc.2005.07.046 PubMedCrossRefGoogle Scholar
  104. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394. doi: 10.1146/annurev.micro.57.030502.090759 PubMedCrossRefGoogle Scholar
  105. Ross DE, Marshall CW, May HD, Norman RS (2015) Draft genome sequence of Sulfurospirillum sp. strain MES, reconstructed from the metagenome of a microbial electrosynthesis system. Genome Announc 3:e01336-14. doi: 10.1128/genomeA.01336-14 PubMedCentralPubMedCrossRefGoogle Scholar
  106. Sanders JG, Beinart RA, Stewart FJ, Delong EF, Girguis PR (2013) Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts. ISME J 7:1556–1567. doi: 10.1038/ismej.2013.45 PubMedCentralPubMedCrossRefGoogle Scholar
  107. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467PubMedCentralPubMedCrossRefGoogle Scholar
  108. Schadt EE, Turner S, Kasarskis A (2010) A window into third-generation sequencers. Hum Mol Genet 19:R227–R240. doi: 10.1093/hmg/ddq416 PubMedCrossRefGoogle Scholar
  109. Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68:686–691. doi: 10.1128/MMBR.68.4.686-691.2004 PubMedCentralPubMedCrossRefGoogle Scholar
  110. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506. doi:10.1128/AEM.71.3.1501-1506.2005PubMedCentralPubMedCrossRefGoogle Scholar
  111. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. doi: 10.1128/aem.01541-09 PubMedCentralPubMedCrossRefGoogle Scholar
  112. Schomburg I, Chang A, Placzek S, Sohngen C, Rother M, Lang M, Munaretto C, Ulas S, Stelzer M, Grote A et al (2013) BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res 41:D764–D772. doi: 10.1093/nar/gks1049 PubMedCentralPubMedCrossRefGoogle Scholar
  113. Schommer NN, Gallo RL (2013) Structure and function of the human skin microbiome. Trends Microbiol 21:660–668. doi: 10.1016/j.tim.2013.10.001 PubMedCentralPubMedCrossRefGoogle Scholar
  114. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5, e75. doi: 10.1371/journal.pbio.0050075 PubMedCentralPubMedCrossRefGoogle Scholar
  115. Sharma R, Ranjan R, Kapardar RK, Grover A (2005) ‘Unculturable’ bacterial diversity: an untapped resource. Curr Sci 89:72–77Google Scholar
  116. Sharma VK, Kumar N, Prakash T, Taylor TD (2010) MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. Nucleic Acids Res 38:D468–D472. doi: 10.1093/nar/gkp1001 PubMedCentralPubMedCrossRefGoogle Scholar
  117. Simmons C, Reddy A, D’haeseleer P, Khudyakov J, Billis K, Pati A, Simmons B, Singer S, Thelen M, VanderGheynst J (2014) Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol Biofuels 7:495. doi: 10.1186/s13068-014-0180-0 PubMedCentralPubMedCrossRefGoogle Scholar
  118. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 15:121–132. doi: 10.1038/nrg3642 PubMedCrossRefGoogle Scholar
  119. Singh M, Patel SK, Kalia VC (2009) Bacillus subtilis as potential producer for polyhydroxyalkanoates. Microb Cell Fact 8:38. doi: 10.1186/1475-2859-8-38 PubMedCentralPubMedCrossRefGoogle Scholar
  120. Singh M, Kumar P, Patel SK, Kalia VC (2013) Production of polyhydroxyalkanoate co-polymer by Bacillus thuringiensis. Indian J Microbiol 53:77–83. doi: 10.1007/s12088-012-0294-7 PubMedCentralPubMedCrossRefGoogle Scholar
  121. Soares I, Tavora Z, Patera R, Baroni S (2012) Microorganism-produced enzymes in the food industry. In: Valdez DB (ed) Food industry, scientific, health and social aspects of the food industry. InTech, RijekaGoogle Scholar
  122. Solaiman DY, Catara V, Greco S (2005) Poly(hydroxyalkanoate) synthase genotype and PHA production of Pseudomonas corrugata and P. mediterranea. J Ind Microbiol Biotechnol 32:75–82. doi: 10.1007/s10295-005-0205-6 PubMedCrossRefGoogle Scholar
  123. Solli L, Havelsrud O, Horn S, Rike A (2014) A metagenomic study of the microbial communities in four parallel biogas reactors. Biotechnol Biofuels 7:146. doi: 10.1186/s13068-014-0146-2 PubMedCentralPubMedCrossRefGoogle Scholar
  124. Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321–346. doi: 10.1146/annurev.mi.39.100185.001541 PubMedCrossRefGoogle Scholar
  125. Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160. doi: 10.1128/jb.00345-12 PubMedCentralPubMedCrossRefGoogle Scholar
  126. Streit WR, Schmitz RA (2004) Metagenomics-the key to the uncultured microbes. Curr Opin Microbiol 7:492–498. doi: 10.1016/j.mib.2004.08.002 PubMedCrossRefGoogle Scholar
  127. Su H, Zhang T, Bao M, Jiang Y, Wang Y, Tan T (2014) Genome sequence of a promising hydrogen-producing facultative anaerobic bacterium, Brevundimonas naejangsanensis strain B1. Genome Announc 2:e00542-14. doi: 10.1128/genomeA.00542-14 PubMedCentralPubMedCrossRefGoogle Scholar
  128. Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K, Tamaki H, Tanaka M, Nakatsu CH, Kamagata Y (2014) A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Appl Environ Microbiol 80:7659–7666. doi: 10.1128/aem.02741-14 PubMedCentralPubMedCrossRefGoogle Scholar
  129. Tariq MA, Kim HJ, Jejelowo O, Pourmand N (2011) Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res 39, e120. doi: 10.1093/nar/gkr547 PubMedCentralPubMedCrossRefGoogle Scholar
  130. Thomas T, Gilbert J, Meyer F (2012) Metagenomics – a guide from sampling to data analysis. Microb Inform Exp 2:3. doi: 10.1186/2042-5783-2-3 PubMedCentralPubMedCrossRefGoogle Scholar
  131. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43. doi: 10.1038/nature02340 PubMedCrossRefGoogle Scholar
  132. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74. doi: 10.1126/science.1093857 PubMedCrossRefGoogle Scholar
  133. Vermelho AB, Supuran CT, Guisan JM (2012) Microbial enzyme: applications in industry and in bioremediation. Enzyme Res 2012:980681. doi: 10.1155/2012/980681 PubMedCentralPubMedCrossRefGoogle Scholar
  134. Vester J, Glaring M, Stougaard P (2015) Improved cultivation and metagenomics as new tools for bioprospecting in cold environments. Extremophiles 19:17–29. doi: 10.1007/s00792-014-0704-3 PubMedCentralPubMedCrossRefGoogle Scholar
  135. Vishnivetskaya TA, Layton AC, Lau MCY, Chauhan A, Cheng KR, Meyers AJ, Murphy JR, Rogers AW, Saarunya GS, Williams DE et al (2014) Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiol Ecol 87:217–230. doi: 10.1111/1574-6941.12219 PubMedCrossRefGoogle Scholar
  136. Wang Y, Hayatsu M, Fujii T (2012) Extraction of bacterial RNA from soil: challenges and solutions. Microbes Environ 27:111–121. doi: 10.1264/jsme2.ME11304 PubMedCentralPubMedCrossRefGoogle Scholar
  137. Wang Y, Zhang R, Zheng Q, Jiao N (2014) Draft genome sequences of two marine phototrophic bacteria, Erythrobacter longus strain DSM 6997 and Erythrobacter litoralis strain DSM 8509. Genome Announc 2:e00677-14. doi:10.1128/genomeA.00677-14PubMedCentralPubMedCrossRefGoogle Scholar
  138. Ward BB (2002) How many species of prokaryotes are there? Proc Natl Acad Sci U S A 99:10234–10236. doi: 10.1073/pnas.162359199 PubMedCentralPubMedCrossRefGoogle Scholar
  139. Warnecke F, Hess M (2009) A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 142:91–95. doi: 10.1016/j.jbiotec.2009.03.022 PubMedCrossRefGoogle Scholar
  140. Weiland P (2010) Biogas production: current state and perspectives. Appl Microbiol Biotechnol 85:849–860. doi: 10.1007/s00253-009-2246-7 PubMedCrossRefGoogle Scholar
  141. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578–6583PubMedCentralPubMedCrossRefGoogle Scholar
  142. Williams PG (2009) Panning for chemical gold: marine bacteria as a source of new therapeutics. Trends Biotechnol 27:45–52. doi: 10.1016/j.tibtech.2008.10.005 PubMedCrossRefGoogle Scholar
  143. Wirth R, Kovacs E, Maroti G, Bagi Z, Rakhely G, Kovacs KL (2012) Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing. Biotechnol Biofuels 5:41. doi: 10.1186/1754-6834-5-41 PubMedCentralPubMedCrossRefGoogle Scholar
  144. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271. doi:0146-0749/87/020221-51$02.00/0Google Scholar
  145. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74:5088–5090. doi: 10.1073/pnas.74.11.5088 PubMedCentralPubMedCrossRefGoogle Scholar
  146. Wong YM, Juan JC, Gan HM, Austin CM (2014a) Draft genome sequence of Clostridium bifermentans strain WYM, a promising biohydrogen producer isolated from landfill leachate sludge. Genome Announc 2:e00077-14. doi: 10.1128/genomeA.00077-14 PubMedCentralPubMedCrossRefGoogle Scholar
  147. Wong YM, Juan JC, Gan HM, Austin CM (2014b) Draft genome sequence of Clostridium perfringens strain JJC, a highly efficient hydrogen producer isolated from landfill leachate sludge. Genome Announc 2:e00064-14. doi: 10.1128/genomeA.00064-14 PubMedCentralPubMedCrossRefGoogle Scholar
  148. Wong YM, Juan JC, Ting A, Wu TY, Gan HM, Austin CM (2014c) Draft genome sequence of Clostridium sp. strain Ade.TY, a new biohydrogen- and biochemical-producing bacterium isolated from landfill leachate sludge. Genome Announc 2:e00078-14. doi: 10.1128/genomeA.00078-14 PubMedCentralPubMedCrossRefGoogle Scholar
  149. Wooley JC, Ye Y (2009) Metagenomics: facts and artifacts, and computational challenges. J Comput Sci Technol 25:71–81. doi: 10.1007/s11390-010-9306-4 PubMedCentralPubMedCrossRefGoogle Scholar
  150. Wu S, Zhu Z, Fu L, Niu B, Li W (2011) WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12:444. doi: 10.1186/1471-2164-12-444 PubMedCentralPubMedCrossRefGoogle Scholar
  151. Xia X (2013) DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol 30:1720–1728. doi: 10.1093/molbev/mst064 PubMedCentralPubMedCrossRefGoogle Scholar
  152. Zakrzewski M, Goesmann A, Jaenicke S, Junemann S, Eikmeyer F, Szczepanowski R, Al-Soud W, Sorensen S, Puhler A, Schluter A (2012) Profiling the metabolically active community from a production scale biogas plant by means of high throughput metatranscriptome sequencing. J Biotechnol 158:248–258. doi: 10.1016/j.jbiotec.2012.01.020 PubMedCrossRefGoogle Scholar
  153. Zhang T, Bao M, Wang Y, Su H, Tan T (2014) Genome sequence of Bacillus cereus strain A1, an efficient starch-utilizing producer of hydrogen. Genome Announc 2:e00494-14. doi: 10.1128/genomeA.00494-14 PubMedCentralPubMedCrossRefGoogle Scholar
  154. Zoetendal EG, Booijink CC, Klaassens ES, Heilig HG, Kleerebezem M, Smidt H, de Vos WM (2006) Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nat Protoc 1:954–959. doi: 10.1038/nprot.2006.143 PubMedCrossRefGoogle Scholar
  155. Zong C, Lu S, Chapman AR, Xie XS (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338:1622–1626. doi: 10.1126/science.1229164 PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer India 2015

Authors and Affiliations

  1. 1.Department of MedicineUniversity of IllinoisChicagoUSA
  2. 2.Department of Botany, Hindu CollegeUniversity of DelhiDelhiIndia

Personalised recommendations