Abstract
Microbes are integral part of our environment. They have enormous industrial and medicinal applications. Even they play a crucial role during digestion where they are present in the form of gut flora. Genomic sequences are a prerequisite for molecular taxonomic characterization of novel microbes, and traditional microbiology is dependent on clone cultures for DNA extraction of a specific microbe population. As a result vast varieties of species are missed since most of the microbes cannot be cultured in laboratory conditions. Metagenomics skips the requirement of culturing the microbes in lab as it studies genetic material which is directly taken from environmental samples.
Microorganisms are of great significance due to their applications in health, agriculture, and industry. Direct DNA sequencing of environmental samples has given opportunity to gather information about the microorganisms that were unexplored so far. Screening of useful bacteria that survive in different environmental conditions like heavily polluted soil, disease-affected tissues or cells, oil-contaminated water bodies, heavy metal-contaminated fields, etc. can be done easily by combining environmental and metagenomics approaches. The data obtained from environmental sample sequencing may be of great use in discovery of new drugs and antibiotics, new bacterial species, plant growth promoters, bioremediation as well as in many other industrial applications. The number of metagenomic studies has increased significantly in recent years, and it is believed that this trend will continue its pace due to huge applicability. This chapter also provides significant elaborations about methodology and tools, experimental design strategies, online resources, and databases applicable in metagenomic data analysis.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Abarenkov K, Henrik Nilsson R, Larsson KH, Alexander IJ, Eberhardt U, Erland S et al (2010) The UNITE database for molecular identification of fungi: recent updates and future perspectives. New Phytol 186:281–285. https://doi.org/10.1111/j.1469-8137.2009.03160.x
Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple Rrn operons. J Bacteriol 186:2629–2635. https://doi.org/10.1128/JB.186.9.2629-2635.2004
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(6):533–538. https://doi.org/10.1038/nbt.2579
Alexander M (1994) Biodegradation and bioremediation. Academic, San Diego. https://doi.org/10.12691/ijebb-2-2-1
Alvarez TM, Paiva JH, Ruiz DM, Cairo JPLF, Pereira IO, Paixão DAA, de Almeida RF, Tonoli CCC, Ruller R, Santos CR, Squina FM, Murakami MT (2013) Structure and function of a novel Cellulase 5 from sugarcane soil metagenome. PLoS 8(12):1–9. https://doi.org/10.1371/journal.pone.0083635
Ambrose HE, Granerod J, Clewley JP, Davies NWS, Keir G, Cunningham R, Zuckerman M, Mutton KJ, Ward KN, Ijaz S, Crowcroft NS, Brown DWG (2011) Diagnostic strategy used to establish etiologies of encephalitis in a prospective cohort of patients in England. J Clin Microbiol 49(10):3576–3583
Anupam R, Denial M, Debarati P, Suresh K, Ol F, Mandal SM (2013) Purification, biochemical characterization and self-assembled structure of a fengycin-like antifungal peptide from Bacillus thuringiensis strain SM1. Front Microbiol 4:332. https://doi.org/10.3389/fmicb.2013.00332
Arrial RT, Togawa RC, Brigido M (2009) Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinform 10(1):239
Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P (2010) Smash community: a metagenomic annotation and analysis tool. Bioinformatics 26(23):2977–2978. https://doi.org/10.1093/bioinformatics/btq536
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M (2009) ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 25(15):1968–1969. https://doi.org/10.1093/bioinformatics/btp347
Atlas RM, Hazen TC (2011) Oil biodegradation and bioremediation: a tale of the two worst spills in U.S. history. Environ Sci Technol 45(16):6709–6715
Ball AP, Bartlett JG, Craig WA, Drusano GL, Felmingham D, Garau JA, Klugman KP, Low DE, Mandell LA, Rubinstein E, Tillotson GS (2013) Future trends in antimicrobial chemotherapy: expert opinion on the 43 ICAAC. J Chemother 16(5):419–436
Berry AE, Chiocchini C, Selby T, Sosio M, Wellington EM (2003) Isolation of high molecular weight DNA from soil for cloning into BAC vectors. FEMS Microbiol Lett 223:15–20. https://doi.org/10.1016/S0378-1097(03)00248-9
Bertelli C, Greub G (2013) Rapid bacterial genome sequencing: methods and applications in clinical microbiology. Clin Microbiol Infect 19(9):803–813
Bowen DLK, Gerlach R, Peyton BM, Fields MW (2013) Archaeal and bacterial communities in three alkaline hot springs in heart Lake Geyser Basin, Yellowstone National Park. Front Microbiol 4:330. https://doi.org/10.3389/fmicb.2013.00330
Boyette CD, Walker HL, Abbas HK (2002) Biological control of kudzu (Pueraria lobata) with an isolate of Myrothecium verrucaria. Biocontrol Sci Tech 12(1):75–82
Brennan Y, Callen WN, Christoffersen L, Dupree P, Goubet F, Healey S, Hernández M, Keller M, Li K, Palackal N, Sittenfeld A, Tamayo G, Wells S, Hazlewood GP, Mathur EJ, Short JM, Robertson DE, Steer BA (2004) Unusual microbial xylanases from insect guts. Appl Environ Microbiol 70(6):3609–3617. https://doi.org/10.1128/AEM.70.6.3609-3617.2004
Bulgarelli D, Schlaeppi K, Spaepen S, Ver Loren Van Themaat E, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838. https://doi.org/10.1146/annurev-arplant-050312-120106
Bzhalava D, Dillner J (2013) Bioinformatics for viral metagenomics. J Data Min Genomics Proteomics 4:3. https://doi.org/10.4172/2153-0602.1000134
Cameotra SS, Bollag JM (2003) Biosurfactant-enhanced bioremediation of polycyclic aromatic hydrocarbons. Crit Rev Environ Sci Technol 33(2):111–126. https://doi.org/10.1080/10643380390814505
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303
Cardenas F, Emilio A, de Castro-Alvarez M-S, Jose-Maria S-M, Manuel V, Elson Steve W, Jose-Vicente S (2001) Screening and catalytic activity in organic synthesis of novel fungal and yeast lipases. J Mol Catal B Enzym 14:111–123. https://doi.org/10.1016/S1381-1177(00)00244-7
Chakraborty R, Wu CH, Hazen TC (2012) Systems biology approach to bioremediation. Curr Opin Biotechnol 23:483–490
Cho I, Blaser MJ (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13:260–270
Christakopoulos P, Katapodis P, Kalogeris E, Kekos D, Macris BJ, Stamatis H, Skaltsa H (2001) Antimicrobial activity of acidic xylooligosaccharides produced by family 10 and 11 endoxylanases. Int J Biol Macromol 31(4–5):171–175. https://doi.org/10.1016/S0141-8130(02)00079-X
Čivljak R, Giannella M, Di Bella S, Petrosillo N (2014) Could chloramphenicol be used against ESKAPE pathogens? Are view of in vitro data in the literature from the 21st century. Expert Rev Anti-Infect Ther 12(2):249–264. https://doi.org/10.1586/14787210.2014.878647
Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, Harris HMB, Coakley M, Lakshminarayanan B, O’Sullivan O, Fitzgerald GF, Deane J, O’Connor M, Harnedy N, O’Connor K, O’Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi JR, Fitzgerald AP, Shanahan F, Hill C, Ross RP, O’Toole PW (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488(7410):178–184
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ et al (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145. https://doi.org/10.1093/nar/gkn879
Cooke SJ, Birnie-Gauvin K, Lennox RJ, Taylor JJ, Rytwinski T, Rummer JL, Franklin CE, Bennett JR, Haddaway NR (2017) How experimental biology and ecology can support evidence-based decision-making in conservation: avoiding pitfalls and enabling application. Conserv Physiol 5(1):cox043
Coppotelli BM, Ibarrolaza A, Dias RL, Del Panno MT, Berthe-Corti L, Morelli IS (2010) Study of the degradation activity and the strategies to promote the bioavailability of phenanthrene by Sphingomonas paucimobilis strain 20006FA. Microb Ecol 59(2):266–276. https://doi.org/10.1007/s00248-009-9563-3
de Souza CE, e Silva Cardoso MH, Sousa DA, Viana JC, de Oliveira-Júnior NG, Miranda V, Franco OL (2014) The use of versatile plant antimicrobial peptides in agribusiness and human health. Peptides 55:65–78. https://doi.org/10.1016/j.peptides.2014.02.003
Delong EF (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3(6):459–469
Deluca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G (2012) RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28(11):1530–1532. https://doi.org/10.1093/bioinformatics/bts196
Desantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072. https://doi.org/10.1128/AEM.03006-05
Duan CJ, Xian L, Zhao GC, Feng Y, Pang H, Bai XL, Tang JL, Ma QS, Feng JX (2009) Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens. J Appl Microbiol 107(1):245–256. https://doi.org/10.1111/j.1365-2672.2009.04202.x
Eddouaouda K, Mnif S, Badis A, Younes SB, Cherif S, Ferhat S, Mhiri N, Chamkha M, Sayadi S (2012) Characterization of a novel biosurfactant produced by Staphylococcus sp. strain 1E with potential application on hydrocarbon bioremediation. J Basic Microbiol 52(4):408–418. https://doi.org/10.1002/jobm.201100268
Edwards et al (2012) Real time metagenomics: using k-mers to annotate metagenomes. Bioinformatics 28(24):3316–3317. https://doi.org/10.1093/bioinformatics/bts599
Felczykowska A, Krajewska A, Zielińska S, Łoś JM (2015) Sampling, metadata and DNA extraction important steps in metagenomic studies. Acta Biochim Pol 62(1):151–160. https://doi.org/10.18388/abp.2014_916
Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, Wang D, Holmes EC (2008) Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 4(2):e1000011
Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, Dantas G (2012) The shared antibiotic resistome of soil bacteria and human pathogens. Science 337(6098):1107–1111. https://doi.org/10.1126/science.1220761
Gerlach W, Stoye J (2011) Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res 39(14):e91. https://doi.org/10.1093/nar/gkr225
Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J (2002) Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68(9):4301–4306. https://doi.org/10.1128/AEM.68.9.4301-4306.2002
Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F (2010) Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc 2010(1):pdb.prot5368. https://doi.org/10.1101/pdb.prot5368
Goll J, Rusch DB, Tanenbaumdm TM, Li K, Methé B, Yooseph S (2010) METAREP: JCVI metagenomics reports–an open source tool for high-performance comparative metagenomics. Bioinformatics 26(20):2631–2632. https://doi.org/10.1093/bioinformatics/btq455
Gottfried A, Singhal N, Elliot R, Swift S (2010) The role of salicylate and biosurfactant in inducing phenanthrene degradation in batch soil slurries. Appl Microbiol Biotechnol 86(5):1563–1571. https://doi.org/10.1007/s00253-010-2453-2
Greninger AL, Chen EC, Sittler T, Scheinerman A, Roubinian N, Guixia Y, Kim E, Pillai DR, Guyard C, Mazzulli T, Isa P, Arias CF, Hackett J, Schochetman G, Miller S, Tang P, Chiu CY, Tripp R (2010) A metagenomic analysis of pandemic influenza a (2009 H1N1) infection in patients from North America. PLoS One 5(10):e13381
Gutierrez T, Singleton DR, Berry D, Yang T, Aitken MD, Teske A (2013) Hydrocarbon-degrading bacteria enriched by the Deepwater horizon oil spill identified by cultivation and DNA-SIP. ISME J 7(11):2091–2104
Haddad NI (2008) Isolation and characterization of a biosurfactant producing strain, Brevibacillus brevis HOB1. J Ind Microbiol Biotechnol 35(12):1597–1604. https://doi.org/10.1007/s10295-008-0403-0
Hajer R, Nuno S, Patrícia P, Carmen T, Susana C, Gilberto I (2014) Potential impact of antimicrobial resistance in wild life, environment and human health. Front Microbiol 5(23). https://doi.org/10.3389/fmicb.2014.00023
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685. https://doi.org/10.1128/MMBR.68.4.669-685.2004
Hassan M, Kjos M, Nes IF, Diep DB, Lotfipour F (2012) Natural antimicrobial peptides from bacteria: characteristics and potential applications to fight against antibiotic resistance. J Appl Microbiol 113(4):723–736. https://doi.org/10.1111/j.1365-2672.2012.05338.x
Hazen TC, Prince RC, Mahmoudi N (2016) Marine oil biodegradation. Environ Sci Technol 50(5):2121–2129
Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D’Haeseleer P, Holman H-YN, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU (2010) Deep-Sea oil plume enriches indigenous oil-degrading Bacteria. Science 330(6001):204–208
Hettich RL, Pan C, Chourey K, Giannone RJ (2013) Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem 85(9):4203–4214
Hoff KJ, Lingner T, Meinicke P, Tech M (2009) Orphelia: predicting genes in metagenomic sequencing reads. Nucleic Acids Res 37(Web Server issue):W101–W105. https://doi.org/10.1093/nar/gkp327
Hosokawa T, Kaiwa N, Matsuura Y, Kikuchi Y, Fukatsu T (2015) Infection prevalence of Sodalis symbionts among stinkbugs. Zool Lett 1(1)
Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT (2014) Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A 111(13):4904–4909. https://doi.org/10.1073/pnas.1402564111
Hugenholtz P, Pace NR (1996) Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol 14(190–197):10025–10021. https://doi.org/10.1016/0167-7799(96)
Hultberg M, Bergstrand KJ, Khalil S, Alsanius B (2008) Characterization of biosurfactant-producing strains of fluorescent pseudomonads in a soilless cultivation system. Antonie Van Leeuwenhoek 94(2):329–334. https://doi.org/10.1007/s10482-008-9250-2
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21(9):1552–1560. https://doi.org/10.1101/gr.120618.111
Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, Brown J, Becker CA, Fleshner PR, Dubinsky M, Rotter JI, Wang HL, McGovern DPB, Brown GD, Underhill DM (2012) Interactions between commensal fungi and the C-type Lectin receptor dectin-1 influence colitis. Science 336(6086):1314–1317
Jacobsen CS, Rasmussen OF (1992) Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation–exchange resine. Appl Environ Microbiol 58:2458–2462
Jacques RJS, Bento FM, de Oliveira CFA (2007) Biodegradação de hidrocarbonetos aromáticos policíclicos. Cienc Nat 29(1):7–24
Jean C, Peter C, Don G, Herman G, Gyssens Inge C, Stephan H, Vincent J, Levy Stuart B, Doye Babacar N, Didier P, Rosana R, Seto Wing H, van der Meer Jos WM, Andreas V (2011) Society’s failure to protect a precious resource: antibiotics. Lancet 378:369–371. https://doi.org/10.1016/S0140-6736(11)60401-7
Jeong YS, Na HB, Kim SK, Kim YH, Kwon EJ, Kim J, Yun HD, Lee JK, Kim H (2012) Characterization of xyn10J, a novel family 10 xylanase from a compost metagenomic library. Appl Biochem Biotechnol 166(5):1328–1339. https://doi.org/10.1007/s12010-011-9520-8
Kang S-W, Kim Y-B, Shin J-D, Kim E-K (2010) Enhanced biodegradation of hydrocarbons in soil by microbial biosurfactant, sophorolipid. Appl Biochem Biotechnol 160(3):780–790
Kamal Kumar B, Balakrishnan H, Rele MV (2004) Compatibility of alkaline xylanases from an alkaliphilic Bacillus NCL (87-6-10) with commercial detergents and proteases. J Ind Microbiol Biotechnol 31(2):83–87. https://doi.org/10.1007/s10295-004-0119-8
Kashyap R, Monika, Subudhi E (2014) A novel thermoalkaliphilic xylanase from Gordonia sp. is salt, solvent and surfactant tolerant. J Basic Microbiol 54:1342–1349. https://doi.org/10.1002/jobm.201400097
Katapodis P, Vardakas M, Kalogeris E, Kekos D, Bj M, Christakopoulos P (2003) Enzymic production of a feruloylated oligosaccharide with antioxidant activity from wheat flour arabinoxylan. Eur J Nutr 42(1):55–60. https://doi.org/10.1007/s00394-003-0400-z
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(1):e9. https://doi.org/10.1093/nar/gkr1067
Kerepesi C, Bánky D, Grolmusz V (2014) Amphora net: the web server implementation of the AMPHORA2metagenomicworkflowsuite. Gene 533:538–540. https://doi.org/10.1016/j.gene.2013.10.015
Kim PI, Bai H, Bai D, Chae H, Chung S, Kim Y, Park R, Chi YT (2004) Purification and characterization of a lipopeptide produced by Bacillus thuringiensis CMB26. J Appl Microbiol 97:942–949. https://doi.org/10.1111/j.1365-2672.2004.02356.x
Kim PI, Ryu J, Kim YH, Chi YT (2010) Production of biosurfactant lipopeptides Iturin A, fengycin and surfactin A from Bacillus subtilis CMB32 for control of Colletotrichum gloeosporioides. J Microbiol Biotechnol 20(1):138–145. https://doi.org/10.4014/jmb.0905.05007
Kim SK, Kim YC, Lee S, Kim JC, Yun MY, Kim IS (2011) Insecticidal activity of rhamnolipid isolated from Pseudomonas sp. EP-3 against green peach aphid (Myzus persicae). J Agric Food Chem 59(3):934–938. https://doi.org/10.1021/jf104027x
Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H et al (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62(Pt 3):716–721. https://doi.org/10.1093/nar/gkr1067
King GM, Kostka JE, Hazen TC, Sobecky PA (2015) Microbial responses to the oil spill: from coastal wetlands to the deep sea. Annu Rev Mar Sci 7(1):377–401
Kirk O, Borchert TV, Fuglsang CC (2002) Industrial enzyme applications. Curr Opin Biotechnol 13(4):345–351. https://doi.org/10.1016/S0958-1669(02)00328-2
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41(1):e1–e1
Krzyzanowska DM, Potrykus M, Golanowska M, Polonis K, Gwizdek-Wisniewska A, Lojkowska E, Jafra S (2012) Rhizosphere bacteria as potential biocontrol agents against soft rot caused by various Pectobacterium and Dickeya spp. strains. J Plant Pathol 94(2):367–378. https://doi.org/10.4454/JPP.FA.2012.042
LaMontagne MG, Michel FC, Holden PA, Reddy CA (2002) Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. J Microbiol Methods 49(3):255–264
Lee CC, Kibblewhite-Accinelli RE, Wagschal K, Robertson GH, Wong DW (2006) Cloning and characterization of a cold-active xylanase enzyme from an environmental DNA library. Extremophiles 10(4):295–300. https://doi.org/10.1007/s00792-005-0499-3
Leng J, Zhong X, Zhu RJ, Yang SL, Gou X, Mao HM (2011) Assessment of protozoa in Yunnan yellow cattle rumen based on the 18S rRNA sequences. Mol Biol Rep 38(1):577–585
Li W (2009) Comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinf 10(1):359. https://doi.org/10.1186/1471-2105-10-359
Lim HK, Chung EJ, Kim JC, Choi GJ, Jang KS, Chung YR, Cho KY, Lee SW (2005) Characterization of a forest soil metagenome clone that confers indirubin and indigo production on Escherichia coli. Appl Environ Microbiol 71(12):7768–7777. https://doi.org/10.1128/AEM.71.12.7768-7777.2005
Links MG, Dumonceaux TJ, Hemmingsen SM, Hill JE, Neufeld J (2012) The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS One 7(11):e49755
Lindgreen S, Adair KL, Gardner PP (2016) An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep 6:19233. https://doi.org/10.1038/srep19233
Lingner T, Asshauer KP, Schreiber F, Meinicke P (2011) CoMet–a web server for comparative functional profiling of metagenomes. Nucleic Acids Res 39(Web Server issue):W518–W523. https://doi.org/10.1093/nar/gkr388
Liu B, Gibbons T, Ghodsi M, Pop M (2010a) MetaPhyler: taxonomic profiling for metagenomic sequences, Bioinformatics and Biomedicine (BIBM). In 2010 IEEE International Conference; IEEE: pp 95100. https://doi.org/10.1109/BIBM.2010.5706544
Liu WW, Yin R, Lin XG, Zhang J, Chen XM, Li XZ, Yang T (2010b) Interaction of biosurfactant-microorganism to enhance phytoremediation of aged polycyclic aromatic hydrocarbons (PAHS) contaminated soils with alfalfa (Medicago sativa L.). Huan Jing Ke Xue 31(4):1079–1084. https://www.ncbi.nlm.nih.gov/pubmed/20527195
Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ-M, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ (2013) A culture-independent sequence-based Metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309(14):1502
Lorenz P, Liebeton K, Niehaus F, Eck J (2002) Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Curr Opin Biotechnol 13(6):572–577. https://doi.org/10.1016/S0958-1669(02)00345-2
Lovley DR (2003) Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol 1(1):35–44
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S et al (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90. https://doi.org/10.1038/nature11237
MacNeil IA, Tiong CL, Minor C, August PR, Grossman TH, Loiacono KA, . Lynch BA, Phillips T, Narula S, Sundaramoorthi R, . Tyler A, Aldredge T, Long H., Gilman M, Holt D, and Osburne MS (2001) Expression and isolation of antimicrobial small molecules from soil DNA libraries. J Mol Microbiol Biotechnol. Vol. 3(2): 301–308. https://www.ncbi.nlm.nih.gov/pubmed/11321587
Marcos MS, Lozada M, Dionisi HM (2006) Aromatic hydrocarbon degradation genes from chronically polluted Subantarctic marine sediments. Lett Appl Microbiol 49(5):602–608. https://doi.org/10.1111/j.1472-765X.2009.02711.x
Mason OU, Hazen TC, Borglin S, Chain PSG, Dubinsky EA, Fortney JL, Han J, Holman H-YN, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe SG, Woyke T, Zhou J, Rubin EM, Jansson JK (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 6(9):1715–1727
Markowitz VM, Chen IA, Chu K, Szeto K, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A et al (2012) IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 40(Database issue):D123–D129. https://doi.org/10.1093/nar/gkr975
McCliment EA, Voglesonger KM, O’Day PA, Dunn EE, Holloway JR, Cary SC (2006) Colonization of nascent, deep-sea hydrothermal vents by a novel archaeal and Nanoarchaeal assemblage. Environ Microbiol 8:114–125. https://doi.org/10.1111/j.1462-2920.2005.00874.x
McGarvey KM, Konstantin Q, Stanley F (2012) Wide variation in antibiotic resistance protein identified by functional metagenomic screening of a soil DNA library. Appl Environ Microbiol 78(6):1708–1714. 10.1128/AEM.067 59–6711
McLean SJ et al (2013) Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Res. https://doi.org/10.1101/gr.150433.112
Medvedev P, Georgiou K, Myers G et al (2007) Computability of models for sequence assembly. Gene 4645:289–301. https://link.springer.com/content/pdf/10.1007/978-3-540-74126-8.pdf#page=300
Mitchell A, Bucchini F, Cochrane G et al (2015) EBI metagenomics in 2016 – an expanding and evolving resource for the analysis and archiving of metagenomic data. In: Nucleic acids research. https://doi.org/10.1093/nar/gkv1195
Moldes AB, Paradelo R, Rubinos D, Devesa-Rey R, Cruz JM, Barral MT (2011) Ex situ treatment of hydrocarbon-contaminated soil using biosurfactants from Lactobacillus pentosus. J Agric Food Chem 59:9443–9447. https://doi.org/10.1021/jf201807r
Mokili JL, Dutilh BE, Lim YW, Schneider BS, Taylor T, Haynes MR, Metzgar D, Myers CA, Blair PJ, Nosrat B, Wolfe ND, Rohwer F, Burk RD (2013) Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness. PLoS One 8(3):e58404
Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV et al (2012) Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13:R79. https://doi.org/10.1186/gb-2012-13-9-r79
Myers EW (1995) Toward simplifying and accurately formulating fragment assembly. J Comput Biol 2:275–290. https://doi.org/10.1089/cmb.1995.2.275
National Academy of Sciences (2005) Mineral tolerance of animals. 2nd Revised Edition
Nielsen TH, Sorensen D, Tobiasen C, Andersen JB, Christophersen C, Givskov M, Sorensen J (2002) Antibiotic and biosurfactant properties of cyclic Lipopeptides produced by fluorescent pseudomonas spp. from the sugar beet Rhizosphere. Appl Environ Microbiol 68(7):3416–3423
Nihorimbere V, Marc Ongena M, Smargiassi M, Thonart P (2011) Beneficial effect of the rhizosphere microbial community for plant growth and health. Biotechnol Agron Soc Environ 15:327–337. http://orbi.ulg.ac.be/bitstream/2268/113786/1/2011%20Nihorimbere%20Base.pdf
Noguchi H, Taniguchi T, Itoh T (2008) MetaGeneAnnotator: detecting species specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA research : an international journal for rapid publication of reports on genes and genomes 15(6):387–396. https://doi.org/10.1093/dnares/dsn027
Ogram A, Sayler GS, Barbay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7:57–66. https://doi.org/10.1016/0167-7012(87)90025-X
Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv Microb Ecol 9:1–55. https://doi.org/10.1007/978-1-4757-0611-6
Pacwa-Płociniczak M, Płaza GA, Piotrowska-Seget Z, Cameotra SS (2010) Environmental applications of biosurfactants: recent advances. Int J Mol Sci 12(1):633–654. https://doi.org/10.3390/ijms12010633
Parada AE, Needham DM, Fuhrman JA (2016) Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol 18(5):1403–1414
Partovinia A, Naeimpoor F, Hejazi P (2010) Carbon content reduction in a model reluctant clayey soil: slurry phase n-hexadecane bioremediation. J Hazard Mater 181(1–3):133–139. https://doi.org/10.1016/j.jhazmat.2010.04.106
Patel RK, Jain M (2012) NGS QC Toolkit: a Toolkit for quality control of next generation sequencing data. PLoS One 7:e30619. https://doi.org/10.1371/journal.pone.0030619
Patel RN, Banerjee A, Ko RY, Howell JM, Li WS, Comezoglu FT, Partyka RA, Szarka FT (1994) Enzymic preparation of (3R-cis)-3-(acetyloxy)-4-phenyl-2-azetidinone: a taxol side-chain synthon. Biotechnol Appl Biochem 20(1):23–33. https://doi.org/10.1111/j.1470-8744.1994.tb00304.x
Payne RB, May HD, Sowers KR (2011) Enhanced reductive Dechlorination of polychlorinated biphenyl impacted sediment by bioaugmentation with a Dehalorespiring bacterium. Environ Sci Technol 45(20):8772–8779
Pevzner PA, Tang H, Tesler G (2004) De novo repeat classification and fragment assembly. Genome Res 14:1786–1796. https://doi.org/10.1101/gr.2395204
Pop M (2009) Genome assembly reborn: recent computational challenges. Brief Bioinform 10:354–366. https://doi.org/10.1093/bib/bbp026
Pop M, Salzberg SL (2008) Bioinformatics challenges of new sequencing technology. Trends Genet 24:142–149. https://doi.org/10.1016/j.tig.2007.12.006
Prosser JI (2015) Dispersing misconceptions and identifying opportunities for the use of “omics” in soil microbial ecology. Nat Rev Microbiol 13:439–446
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. https://doi.org/10.1093/nar/gks1219
Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ (2011) Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci 108(Supplement_1):4680–4687
Redmond MC, Valentine DL (2012) Natural gas and temperature structured a microbial community response to the Deepwater horizon oil spill. Proc Natl Acad Sci 109(50):20292–20297
Reich JG, Drabsch H, Dimuler A (1984) On the statistical assessment of similarities in DNA sequences. Nucleic Acids Res 12(13):5529–5543. https://doi.org/10.1093/nar/12.13.5529
Rho M, Tang H, Ye Y (2010) FragGeneScan: predicting genes in short and error prone reads. Nucleic Acids Res 38(20):e191. https://doi.org/10.1093/nar/gkq747
Richter DC, Schuster SC, Oslay HDH (2007) Optimal syntenic layout of unfinished assemblies. Bioinformatics 23(13):1573–1579. https://doi.org/10.1093/bioinformatics/btm153
Salanitro JP, Johnson PC, Spinnler GE, Maner PM, Wisniewski HL, Bruce C (2000) Field-scale demonstration of enhanced MTBE bioremediation through aquifer bioaugmentation and oxygenation. Environ Sci Technol 34(19):4152–4162
Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14(3):303–310. https://doi.org/10.1016/S0958-1669(03)00067-3
Schloss PD (2008) Evaluating different approaches that test whether microbial communities have the same structure. ISME J 2(3):265–275
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. https://doi.org/10.1128/AEM.01541-09
Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864. https://doi.org/10.1093/bioinformatics/btr026
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9(8):811–814. https://doi.org/10.1038/nmeth.2066
Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5(3):e75. https://doi.org/10.1371/journal.pbio.0050075
Seth-Smith HMB, Harris SR, Skilton RJ, Radebe FM, Golparian D, Shipitsyna E, Duy PT, Scott P, Cutcliffe LT, O’Neill C, Parmar S, Pitt R, Baker S, Ison CA, Marsh P, Jalal H, Lewis DA, Unemo M, Clarke IN, Parkhill J, Thomson NR (2013) Whole-genome sequences of chlamydia trachomatis directly from clinical samples without culture. Genome Res 23(5):855–866
Sha R, Jiang L, Meng Q, Zhang G, Song Z (2011) Producing cell-free culture broth of rhamnolipids as a cost-effective fungicide against plant pathogens. J Basic Microbiol 52(4):458–466. https://doi.org/10.1002/jobm.201100295
Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, Muchero W, Bonito G, Vilgalys R, Tuskan G, Podar M, Schadt CW, Shah V (2013) A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature populus deltoides trees. PLoS One 8(10):e76382
Sharma S, Khan FG, Qazi GN (2010) Molecular cloning and characterization of amylase from soil metagenomic library derived from Northwestern Himalayas. Appl Microbiol Biotechnol 86(6):1821–1828. https://doi.org/10.1007/s00253-009-2404-y
Sharma PK (2012) Optimization of process parameters for fruit juice clarification using silica immobilized xylanase from Pseudomonas sp. Pure Appl Biol 1(2):52–55
Sharpton TJ (2014) An introduction to the analysis of shotgun metagenomic data. Front Plant Sci 5:209
Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O’Dwyer JP, Green JL et al (2011) PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol 7:e1001061. https://doi.org/10.1371/journal.pcbi.1001061
Sierra-García IN, Alvarez JC, de Vasconcellos SP, de Souza AP, Neto EV d S, de Oliveira VM, Mormile MR (2014) New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. PLoS One 9(2):e90087
Silva CC, Hayden H, Sawbridge T, Mele P, Paula SOD, Silva LCF, Vidigal PMP, Vicentini R, Sousa MP, Torres APR, Santiago VMJ, Oliveira VM (2013) Identification of genes and pathways related to phenol degradation in metagenomic libraries from petroleum refinery wastewater. PLoS One 8(4):1–11. https://doi.org/10.1371/journal.pone.0061811
Singh A, Van Hamme JD, Ward OP (2007) Surfactants in microbiology and biotechnology: Part 2 Application aspects. Biotechnol Adv 25(2):99–121. https://doi.org/10.1016/j.biotechadv.2006.10.004
Sirohi SK, Singh N, Dagar SS, Puniya AK (2012) Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 95:1135–1154
Soni R, Nazir A, Chaddha BS, Saini HS (2008) Novel sources of fungal cellulases for efficient deinking of composite paper waste. Bio Resources 3(1):234–246. http://152.1.0.246/index.php/BioRes/article/view/BioRes_03_1_0234_Soni_CS_FungalCellulases/179
Soo RM, Wood SA, Grzymski JJ, McDonald IR, Cary SC (2009) Microbial biodiversity of thermophilic communities in hot mineral soils of Tramway Ridge, Mount Erebus. Antarctica Environ Microbiol 11:715–728. https://doi.org/10.1111/j.1462-2920.2009.01859.x
Straube WL, Nestler CC, Hansen LD, Ringleberg D, Pritchard PH, Jones-Meehan J (2003) Remediation of polyaromatic hydrocarbons (PAHs) through landfarming with biostimulation and bioaugmentation. Acta Biotechnol 23(2–3):179–196. https://doi.org/10.1002/abio.200390025
Sun X, Wu L, Luo Y (2006) Application of organic agents in remediation of heavy metals- contaminated soil. Ying Yong Sheng Tai Xue Bao 17(6):1123–1128. PMID:16964954
The NIH HMP Working Group, Peterson J, Garges S, Giovanni M, Mc Innes P, Wang L et al (2009) The NIH human microbiome project. Genome Res 19(12):2317–2323. https://doi.org/10.1101/gr.096651.109
Thomas CM, Nielsen KM (2005) Mechanisms of and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3(9):711–721. https://doi.org/10.1038/nrmicro1234
Thomas T, Gilbert J, Meyer F (2012) Metagenomics - a guide from sampling to data analysis. Microb Inf Exp 2(1):3
Uchiyama T, Miyazaki K (2009) Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 20(6):616–622
Van Hijum SAFT, Zomer AL, Kuipers OP, Kok J (2005) Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res 33(SUPPL. 2):560–566. https://doi.org/10.1093/nar/gki356
Van EJD, Mantynen V, Wolters AC (1997) Soil DNA extraction and assessment of the fate of Mycobacterium cholorophenolicum strain PC-1 in different soils by 16S ribosomal gene sequence based most probable number PCR and immunofluorescence. Biol Fertil Soils 24:188–195. https://doi.org/10.1007/s003740050230
Vatsa P, Sanchez L, Clement C, Baillieul F, Dorey S (2010) Rhamnolipid biosurfactants as new players in animal and plant defense against microbes. Int J Mol Sci 11(12):5095–5108. https://doi.org/10.3390/ijms11125095
Velho RV, Medina LF, Segalin J, Brandelli A (2011) Production of lipopeptides among Bacillus strains showing growth inhibition of phytopathogenic fungi. Folia Microbiol 56(4):297–303. https://doi.org/10.1007/s12223-011-0056-7
Victor M, et al. (2005) Biological Data Management and Technology Center. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Microbial Genomics and Metagenomics Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA: https://doi.org/10.1093/nar/gkm869
Virgin HW, Todd JA (2011) Metagenomics and personalized medicine. Cell 147(1):44–56
Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840. https://doi.org/10.1038/nrmicro2910
Wan X-F, Barnett JL, Cunningham F, Chen S, Yang G, Nash S, Long L-P, Ford L, Blackmon S, Zhang Y, Hanson L, He Q (2013) Detection of African swine fever virus-like sequences in ponds in the Mississippi Delta through metagenomic sequencing. Virus Genes 46(3):441–446
Wang L, Wang S, Li W (2012) RSeQC: quality control of RNA-seq experiments. Bioinformatics 28(16):2184–2185. https://doi.org/10.1093/bioinformatics/bts356
Wattanaphon HT, Kerdsin A, Thammacharoen C, Sangvanich P, Vangnai AS (2008) A biosurfactant from BSP3 and its enhancement of pesticide solubilization. J Appl Microbiol 105(2):416–423
Wilke A, Bischof J et al (2016) The MG-RAST metagenomics database and portal. Nucleic Acids Res 44(D1):D590–D594. https://doi.org/10.1093/nar/gkv1322
Wilson DB (2009) Cellulases and biofuels. Curr Opin Biotechnol 20(3):295–299. https://doi.org/10.1016/j.copbio.2009.05.007
Wilson MC, Piel J (2013) Metagenomic approaches for exploiting uncultivated bacteria as are source for novel biosynthetic enzymology. Chem Biol 20(5):636–647. https://doi.org/10.1016/j.chembiol.2013.04.011
Wooley JC, Godzik A, Friedberg I (2010) A primer on metagenomics. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1000667
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF (2012) Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337(6102):1661–1665
Wu S, Zhu W, Fu L, Niu B, Li W (2011) WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12(1):444. https://doi.org/10.1186/1471-2164-12-444
Xu B, Liu L, Huang X, Ma H, Zhang Y, Du Y, Wang P, Tang X, Wang H, Kang K, Zhang S, Zhao G, Wu W, Yang Y, Chen H, Mu F, Chen W, Palacios G (2011) Metagenomic analysis of fever, thrombocytopenia and leukopenia syndrome (FTLS) in Henan province, China: discovery of a new bunya virus. PLoS Pathog 7(11):e1002369
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M et al (2012) Human gut microbiome viewed across age and geography. Nature 486:222–227. https://doi.org/10.1038/nature11053
Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL, Rico-Hesse R (2012) Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 6(2):e1485
Zerbino DR, Velvet BE (2008) Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. https://doi.org/10.1101/gr.074492.107
Zhou Q, Su X, Ning K (2014) Assessment of quality control approaches for metagenomic data analysis. Sci Rep 4:6957. https://doi.org/10.1038/srep06957
Zhu W, Lomsadze A, Borodovsky M (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38(12):e132. https://doi.org/10.1093/nar/gkq275
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Yadav, B.S., Yadav, A.K., Singh, S., Singh, N.K., Mani, A. (2019). Methods in Metagenomics and Environmental Biotechnology. In: Gothandam, K., Ranjan, S., Dasgupta, N., Lichtfouse, E. (eds) Nanoscience and Biotechnology for Environmental Applications. Environmental Chemistry for a Sustainable World, vol 22. Springer, Cham. https://doi.org/10.1007/978-3-319-97922-9_4
Download citation
DOI: https://doi.org/10.1007/978-3-319-97922-9_4
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-97921-2
Online ISBN: 978-3-319-97922-9
eBook Packages: Earth and Environmental ScienceEarth and Environmental Science (R0)