Skip to main content
SpringerLink
Log in

Advancements in Microbial Genome Sequencing and Microbial Community Characterization

  • Chapter
  • First Online:
Microbial Genomics in Sustainable Agroecosystems

Abstract

The microorganism play an essential role in various metabolic activity associated with health, obesity, immune system, complex carbohydrate, nitrogen, sulfur, and xenobiotic metabolism etc. The identification of microorganism involved in such process is becoming possible with the sequencing of 16S rRNA amplicon and responsible gene through molecular cloning and then sequencing. The first-generation sequencing extensively facilitated the molecular characterization of microorganism and functional gene with expense of high cost with low throughput. The advent of next-generation sequencing technology enables the high-scale full-length 16S rRNA molecular characterization and genome sequencing with reduced time and cost with high yield. The present article describes available genomes in public database and the role of next- and third-generation sequencing technology contribution to the growth of genome and metagenome sequencing and its associated projects, their taxonomy, and functional characterization through bioinformatic analysis. This chapter also provides an overview on the metagenomic sequencing and functional characterization of three important ecological niches, viz., rumen, soil, and human gut. The massive advancement in high-throughput sequencing technology and bioinformatic analysis enabled robust genome and metagenome characterization in short time with reduced budget.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S et al (2012) A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One 7:e36466

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Adessi C, Matton G, Ayala G, Turcatti G, Mermod JJ, Mayer P, Kawashima E (2000) Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res 28(20):E87

    Google Scholar 

  • Arabidopsis Genome I (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bennett GM, Moran NA (2013) Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect. Genome Biol Evol 5:1675–1688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486

    Article  CAS  PubMed  Google Scholar 

  • Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD et al (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453–1462

    Article  CAS  PubMed  Google Scholar 

  • Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60

    Article  CAS  PubMed  Google Scholar 

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao Y, Fanning S, Proos S, Jordan K, Srikumar S (2017) A review on the applications of next generation sequencing technologies as applied to food-related microbiome studies. Front Microbiol 8:1829

    Article  PubMed  PubMed Central  Google Scholar 

  • Cho I, Blaser MJ (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13:260–270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, Harris HM, Coakley M et al (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488:178–184

    Article  CAS  PubMed  Google Scholar 

  • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Conlon MA, Bird AR (2014) The impact of diet and lifestyle on gut microbiota and human health. Nutrients 7:17–44

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cook H, Ussery DW (2013) Sigma factors in a thousand E. coli genomes. Environ Microbiol 15:3121–3129

    Article  CAS  PubMed  Google Scholar 

  • Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJ (2011) Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genet 4:22

    CAS  Google Scholar 

  • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6:e280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dicksved J, Halfvarson J, Rosenquist M, Jarnerot G, Tysk C, Apajalahti J, Engstrand L, Jansson JK (2008) Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J 2:716–727

    Article  CAS  PubMed  Google Scholar 

  • Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C et al (2008) Functional metagenomic profiling of nine biomes. Nature 452:629–632

    Article  CAS  PubMed  Google Scholar 

  • Dube AN, Moyo F, Dhlamini Z (2015) Metagenome sequencing of the greater kudu (Tragelaphus strepsiceros) rumen microbiome. Genome Announc 3

    Google Scholar 

  • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461

    Article  CAS  PubMed  Google Scholar 

  • Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    Article  CAS  PubMed  Google Scholar 

  • Ekblom R, Wolf JB (2014) A field guide to whole-genome sequencing, assembly and annotation. Evol Appl 7:1026–1042

    Article  PubMed  PubMed Central  Google Scholar 

  • Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G (2006) BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 34(3):e22

    Google Scholar 

  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512

    Article  CAS  PubMed  Google Scholar 

  • Forde BM, O’Toole PW (2013) Next-generation sequencing technologies and their impact on microbial genomics. Brief Funct Genomics 12:440–453

    Article  CAS  PubMed  Google Scholar 

  • Francke C, Siezen RJ, Teusink B (2005) Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol 13:550–558

    Article  CAS  PubMed  Google Scholar 

  • Gilbert JA, Jansson JK, Knight R (2014) The Earth Microbiome project: successes and aspirations. BMC Biol 12:69

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goffeau A (1998) The yeast genome. Pathol Biol (Paris) 46:96–97

    CAS  Google Scholar 

  • Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351

    Article  CAS  PubMed  Google Scholar 

  • Han K, Li ZF, Peng R, Zhu LP, Zhou T, Wang LG, Li SG, Zhang XB et al (2013) Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Sci Rep 3:2101

    Article  PubMed  PubMed Central  Google Scholar 

  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hartman WH, Ye R, Horwath WR, Tringe SG (2017) A genomic perspective on stoichiometric regulation of soil carbon cycling. ISME J 11:2652–2665

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Howe A, Yang F, Williams RJ, Meyer F, Hofmockel KS (2016) Identification of the core set of carbon-associated genes in a bioenergy grassland soil. PLoS One 11:e0166578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Human Microbiome Project Consortium (2012a) A framework for human microbiome research. Nature 486:215–221

    Article  CAS  Google Scholar 

  • Human Microbiome Project Consortium (2012b) Structure, function and diversity of the healthy human microbiome. Nature 486:207–214

    Article  CAS  Google Scholar 

  • Huse SM, Ye Y, Zhou Y, Fodor AA (2012) A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One 7:e34242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ju J, Kim DH, Bi L, Meng Q, Bai X, Li Z, Li X, Marma MS et al (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci U S A 103:19635–19640

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Judge K, Harris SR, Reuter S, Parkhill J, Peacock SJ (2015) Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes. J Antimicrob Chemother 70:2775–2778

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol Biol 1399:207–233

    Article  CAS  PubMed  Google Scholar 

  • Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (2012) Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res 40:e9

    Article  CAS  PubMed  Google Scholar 

  • Kolbert CP, Persing DH (1999) Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Curr Opin Microbiol 2:299–305

    Article  CAS  PubMed  Google Scholar 

  • Kuczynski J, Stombaugh J, Walters WA, Gonzalez A, Caporaso JG, Knight R (2011) Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics Chapter 10:Unit 10 17

    Google Scholar 

  • Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P et al (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249–256

    Article  CAS  PubMed  Google Scholar 

  • Lamelas A, Gosalbes MJ, Manzano-Marin A, Pereto J, Moya A, Latorre A (2011) Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont. PLoS Genet 7:e1002357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Land ML, Hyatt D, Jun S-R, Kora GH, Hauser LJ, Lukjancenko O, Ussery DW (2014) Quality scores for 32,000 genomes. Stand Genomic Sci 9:20

    Article  PubMed  PubMed Central  Google Scholar 

  • Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey A, Nova IC, Craig JM, Langford KW et al (2014) Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol 32:829–833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration (2011) The sequence read archive. Nucleic Acids Res 39:D19–D21

    Article  CAS  PubMed  Google Scholar 

  • Li E, Hamm CM, Gulati AS, Sartor RB, Chen H, Wu X, Zhang T, Rohlf FJ et al (2012a) Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One 7:e26284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li RW, Connor EE, Li C, Baldwin Vi RL, Sparks ME (2012b) Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environ Microbiol 14:129–139

    Article  CAS  PubMed  Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18

    Article  PubMed  PubMed Central  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    Article  PubMed  PubMed Central  Google Scholar 

  • McCutcheon JP, Moran NA (2011) Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10:13–26

    Article  CAS  PubMed  Google Scholar 

  • Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A, Qureshi M, Salazar GA, Pesseat S et al (2018) EBI metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. Nucleic Acids Res 46:D726–D735

    Article  CAS  PubMed  Google Scholar 

  • Morgan XC, Segata N, Huttenhower C (2013) Biodiversity and functional genomics in the human microbiome. Trends Genet 29:51–58

    Article  CAS  PubMed  Google Scholar 

  • Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Katta HY, Mojica A, Chen IA, Kyrpides NC et al (2018) Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Res 47:D649–D659

    Article  CAS  PubMed Central  Google Scholar 

  • Namiki T, Hachiya T, Tanaka H, Sakakibara Y (2012) MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 40:e155

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nannipieri P (2014) Soil as a biological system and omics approaches. EQA – Int J Environ Qual 13:61

    Google Scholar 

  • Nathani NM, Patel AK, Mootapally CS, Reddy B, Shah SV, Lunagaria PM, Kothari RK, Joshi CG (2015) Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis). BMC Genomics 16:1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegard A, Heulin T et al (2016) Back to the future of soil metagenomics. Front Microbiol 7:73

    Article  PubMed  PubMed Central  Google Scholar 

  • Patel V, Patel AK, Parmar NR, Patel AB, Reddy B, Joshi CG (2014) Characterization of the rumen microbiome of Indian Kankrej cattle (Bos indicus) adapted to different forage diet. Appl Microbiol Biotechnol 98:9749–9761

    Article  CAS  PubMed  Google Scholar 

  • Peng Y, Leung HC, Yiu SM, Chin FY (2011) Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 27:i94–i101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peng Y, Leung HC, Yiu SM, Chin FY (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–1428

    Article  CAS  PubMed  Google Scholar 

  • Pennisi E (2010) Genomics. Semiconductors inspire new sequencing technologies. Science 327:1190

    Article  CAS  PubMed  Google Scholar 

  • Pfreundt U, Kopf M, Belkin N, Berman-Frank I, Hess WR (2014) The primary transcriptome of the marine diazotroph Trichodesmium erythraeum IMS101. Sci Rep 4:6187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pitta DW, Kumar S, Veiccharelli B, Parmar N, Reddy B, Joshi CG (2014a) Bacterial diversity associated with feeding dry forage at different dietary concentrations in the rumen contents of Mehshana buffalo (Bubalus bubalis) using 16S pyrotags. Anaerobe 25:31–41

    Article  CAS  PubMed  Google Scholar 

  • Pitta DW, Parmar N, Patel AK, Indugu N, Kumar S, Prajapathi KB, Patel AB, Reddy B et al (2014b) Bacterial diversity dynamics associated with different diets and different primer pairs in the rumen of Kankrej cattle. PLoS One 9:e111710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pop M (2009) Genome assembly reborn: recent computational challenges. Brief Bioinform 10:354–366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T (2011) Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599–609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pylro VS, Roesch LF, Ortega JM, do Amaral AM, Totola MR, Hirsch PR, Rosado AS, Goes-Neto A et al (2014) Brazilian microbiome project: revealing the unexplored microbial diversity--challenges and prospects. Microb Ecol 67:237–241

    Article  PubMed  Google Scholar 

  • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:W116–W120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ran L, Larsson J, Vigil-Stenman T, Nylander JA, Ininbergs K, Zheng WW, Lapidus A, Lowry S et al (2010) Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. PLoS One 5:e11486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reddy B, Dubey SK (2018) River Ganges water as reservoir of microbes with antibiotic and metal ion resistance genes: high throughput metagenomic approach. Environ Pollut 246:443–451

    Article  CAS  PubMed  Google Scholar 

  • Reddy B, Singh KM, Patel AK, Antony A, Panchasara HJ, Joshi CG (2014) Insights into resistome and stress responses genes in Bubalus bubalis rumen through metagenomic analysis. Mol Biol Rep 41:6405–6417

    Article  CAS  PubMed  Google Scholar 

  • Rho M, Tang H, Ye Y (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 38:e191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, Connor R, Fiorini N et al (2018) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res

    Google Scholar 

  • Schloss PD, Handelsman J (2005) Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol 6:229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh KM, Reddy B, Patel AK, Panchasara H, Parmar N, Patel AB, Shah TM, Bhatt VD et al (2014a) Metagenomic analysis of buffalo rumen microbiome: effect of roughage diet on dormancy and sporulation genes. Meta Gene 2:252–268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh KM, Reddy B, Patel D, Patel AK, Parmar N, Patel A, Patel JB, Joshi CG (2014b) High potential source for biomass degradation enzyme discovery and environmental aspects revealed through metagenomics of Indian buffalo rumen. Biomed Res Int 2014:267189

    CAS  PubMed  PubMed Central  Google Scholar 

  • Singh KM, Jisha TK, Reddy B, Parmar N, Patel A, Patel AK, Joshi CG (2015a) Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S rRNA gene pyrosequencing. Mol Biol Rep 42:95–103

    Article  CAS  PubMed  Google Scholar 

  • Singh KM, Patel AK, Shah RK, Reddy B, Joshi CG (2015b) Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen. J Appl Genet 56:411–426

    Article  CAS  PubMed  Google Scholar 

  • Stanke M, Morgenstern B (2005) AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res 33:W465–W467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. BioTechniques 28(1102):1104

    Google Scholar 

  • Swerdlow H, Gesteland R (1990) Capillary gel electrophoresis for rapid, high resolution DNA sequencing. Nucleic Acids Res 18:1415–1419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5:93–121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A et al (2017) A communal catalogue reveals Earth's multiscale microbial diversity. Nature 551:457–463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Torsvik V, Sørheim R, Goksøyr J (1996) Total bacterial diversity in soil and sediment communities—a review. J Ind Microbiol 17:170–178

    CAS  Google Scholar 

  • Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M et al (2001) The sequence of the human genome. Science 291:1304–1351

    Article  CAS  PubMed  Google Scholar 

  • Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, van Elsas JD, Bailey MJ, Nalin R et al (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7:252

    Article  CAS  Google Scholar 

  • Vos M, Velicer GJ (2006) Genetic population structure of the soil bacterium Myxococcus xanthus at the centimeter scale. Appl Environ Microbiol 72:3615–3625

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Westbrook A, Ramsdell J, Schuelke T, Normington L, Bergeron RD, Thomas WK, MacManes MD (2017) PALADIN: protein alignment for functional profiling whole metagenome shotgun data. Bioinformatics 33:1473–1478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Widmer F, Shaffer BT, Porteous LA, Seidler RJ (1999) Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon cascade mountain range. Appl Environ Microbiol 65:374–380

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu H, Fang Y, Yu J, Zhang Z (2014) The quest for a unified view of bacterial land colonization. ISME J 8:1358–1369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu J (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15:1713–1731

    Article  CAS  PubMed  Google Scholar 

  • Xue PP, Carrillo Y, Pino V, Minasny B, McBratney AB (2018) Soil properties drive microbial community structure in a large scale transect in south eastern Australia. Sci Rep 8:11725

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yassour M, Vatanen T, Siljander H, Hamalainen AM, Harkonen T, Ryhanen SJ, Franzosa EA, Vlamakis H et al (2016) Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med, 8:343ra381

    Google Scholar 

  • Ye Y, Choi JH, Tang H (2011) RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics 12:159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zani S, Mellon MT, Collier JL, Zehr JP (2000) Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl Environ Microbiol 66:3119–3124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu W, Lomsadze A, Borodovsky M (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38:e132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA (2013) The MaSuRCA genome assembler. Bioinformatics 29:2669–2677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India

    Bhaskar Reddy

Authors
  1. Bhaskar Reddy
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bhaskar Reddy .

Editor information

Editors and Affiliations

  1. Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, India

    Vijay Tripathi

  2. Department of Forestry, North Eastern Regional Institute of Science and Technology (Deemed To Be University-MHRD), Itanagar, Arunachal Pradesh, India

    Pradeep Kumar

  3. Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, India

    Pooja Tripathi

  4. Department of Botany, Kamla Nehru P.G. College, Raebareli, Uttar Pradesh, India

    Amit Kishore

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Reddy, B. (2019). Advancements in Microbial Genome Sequencing and Microbial Community Characterization. In: Tripathi, V., Kumar, P., Tripathi, P., Kishore, A. (eds) Microbial Genomics in Sustainable Agroecosystems. Springer, Singapore. https://doi.org/10.1007/978-981-13-8739-5_5

Download citation

Publish with us

Policies and ethics

Search

Navigation