Metagenomics: Techniques, Applications, Challenges and Opportunities PDF
Preview Metagenomics: Techniques, Applications, Challenges and Opportunities
Reena Singh Chopra Chirag Chopra Neeta Raj Sharma Editors Metagenomics: Techniques, Applications, Challenges and Opportunities Metagenomics: Techniques, Applications, Challenges and Opportunities (cid:129) (cid:129) Reena Singh Chopra Chirag Chopra Neeta Raj Sharma Editors Metagenomics: Techniques, Applications, Challenges and Opportunities Editors ReenaSinghChopra ChiragChopra SchoolofBioengineeringandBiosciences SchoolofBioengineeringandBiosciences LovelyProfessionalUniversity LovelyProfessionalUniversity Jalandhar,Punjab,India Jalandhar,Punjab,India NeetaRajSharma SchoolofBioengineeringandBiosciences LovelyProfessionalUniversity Jalandhar,Punjab,India ISBN978-981-15-6528-1 ISBN978-981-15-6529-8 (eBook) https://doi.org/10.1007/978-981-15-6529-8 #SpringerNatureSingaporePteLtd.2020 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. The publisher, the authors, and the editorsare safeto assume that the adviceand informationin this bookarebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor theeditorsgiveawarranty,expressedorimplied,withrespecttothematerialcontainedhereinorforany errorsoromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictional claimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSingaporePteLtd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Contents PartI IntroductiontoMetagenomics 1 TheNewScienceofMetagenomics:RevealingtheSecrets ofMicrobialPhysiology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 SaurabhSingh,HarpreetSingh,BiswaranjanRout, RajaBabuManiTripathi,ChiragChopra,andReenaSinghChopra 2 TheComingTogetherofSciences:MetagenomicsforMicrobial Biochemistry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 JyotsanaSharma,SarmeelaSharma,InduSharma,ChiragChopra, andVarunSharma PartII ApplicationsofMetagenomics 3 MetagenomicDNASequencing:TechnologicalAdvances andApplications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 DaljeetSinghDhanjal,ChiragChopra,andReenaSinghChopra 4 EnvironmentalMicrobialForensics:HowHiddenistheTruth?. . . 55 PetaPavanKumar,KiranYadav,VarunVevek,HarshitKhandal, andRajniKumari 5 MetagenomicsAnalyses:AQualitativeAssessmentTool forApplicationsinForensicSciences. . . . . . . . . .. . . . . . . . . . . .. . 69 DevikaDileep,AadyaRamesh,AarshaaSojan,DaljeetSingh Dhanjal,HarinderKaur,andAmandeepKaur 6 RealizingBioremediationThroughMetagenomics:ATechnical Review. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 DeepanshSharma,DeeptiSingh,MehakManzoor,KunalMeena, VikrantSharma,KajalButaney,andReshanGaleMarbaniang 7 MetagenomicsandEnzymes:TheNoveltyPerspective. . . . . . . . . . 109 DaljeetSinghDhanjal,ReenaSinghChopra,andChiragChopra vv vi Contents 8 MetagenomicsandDrug-Discovery. . . . . . . . . . . . . . . . . . . . . . . . . 133 BhupenderSinghandAyanRoy 9 EpidemiologicalPerspectivesofHumanHealthThrough MetagenomicResearch. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 HemenderSingh,InduSharma,andVarunSharma 10 MetagenomicApplicationsofWastewaterTreatment. . . . . . . . . . . 157 MamtaSharmaandNeetaRajSharma 11 MetagenomicsinAgriculture:State-of-the-Art. . . . . . . . . . . . . . . . 167 AchalaBakshi,MazaharMoin,andM.S.Madhav 12 TheSkinMetagenomes:InsightsintoInvolvementofMicrobes inDiseases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189 JyotsanaSharma,VarunSharma,andInduSharma 13 ComputationalMetagenomics:State-of-the-Art,Facts andArtifacts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199 HarpreetSingh,PurnimaSharma,RupinderPreetKaur, DikshaThakur,andPardeepKaur About the Editors ReenaSinghChopra isanAssistantProfessorattheSchoolofBioengineeringand Biosciences, Lovely Professional University. She holds a Ph.D. from Shri Mata Vaishno Devi University, India. She has received IARDO and RACE-Bangkok AwardsforBestTeacher(UniversityLevel).Herresearchfocusesonmetagenomics, microbial diversity, directed evolution, and mutagenesis for improving catalytic activity of microbial enzymes. She is currently exploring metagenomics for novel hydrolases and the production of bioactive molecules from myxobacteria. She has publishedtenpapers andbookchaptersandisontheeditorialboardsofsixjournals. SheisamemberoftheIndianScienceCongressAssociationandafoundingmember ofTheSocietyofBiologists,JammuandKashmir,India. Chirag Chopra is an Assistant Professor at the School of Bioengineering and Biosciences, Lovely Professional University. He holds a Bachelor of Technology in Industrial Biotechnology from Shri Mata Vaishno Devi University and an M.S.(Research)fromtheIndianInstituteofTechnologyMadras.Hehaspublished tenpapersinjournalsincludingOncogene,ScienceBulletin,andf1000Researchand abookchapter.Heisontheeditorialboardoffivejournals.HehasreceivedIARDO andRACE-BangkokYoungScientistAwards.Hisresearchfocusesontargetingkey oncogenic signaling proteins and T-cell checkpoint in cancer through plant-based naturalcompounds.Heiscurrentlyworkingonmicrobialremediationofpetroleum hydrocarbons. He is a member of the Indian Science Congress Association and a foundingmemberofTheSocietyofBiologists. Neeta Raj Sharma is the Additional Dean of the School of Bioengineering and Biosciences at Lovely Professional University, Phagwara, Punjab. Her research focuses on the fields of microbial biochemistry and biotechnology, wealth from wasteandactivemoleculesfrommedicinalplants.Shehasreceivedresearchgrants fromtheEuropeanCommission,IC-IMPACTS-DBT,andPunjabStateCouncilfor ScienceandTechnology.SheisafellowmemberoftheAssociationofBiotechnol- ogy and Pharmacy, Indian Science Congress Association, Association of vviiii viii AbouttheEditors MicrobiologistsofIndia,andIndo-USCollaborationofEngineeringEducationand alifememberoftheAssociationforthePromotionofDNAFingerprintingandOther DNATechnologies,IndianSocietyofAgriculturalBiochemists.Shehaspublished over55papersinleadingjournalsandtwobooksandholds20patents. Part I Introduction to Metagenomics 1 The New Science of Metagenomics: Revealing the Secrets of Microbial Physiology Saurabh Singh, Harpreet Singh, Biswaranjan Rout, Raja Babu Mani Tripathi, Chirag Chopra, and Reena Singh Chopra Abstract The role of microorganisms is well-established in regulating the nature’s activities and the applications in different industries. Whole-cells as well as microbial products such as enzyme, secondary metabolites and peptides are used in bioremediation, fermentation, pharmaceutics, food, textile industries, among others. The great plate anomaly advocates that around 99% of the microorganismsintheenvironmentareunculturable.Thecorollarytothisstate- mentisthattheapplicationsmentionedaboveariseoutoftheculturablefraction only,soitisonlyunimaginablewhattheother99%holdsforus.Metagenomics provides the necessary tools for exploring the diversity of the unculturable microbes andfor bioprospectingthenovelgenes fordifferent applications.This ispossibleduetotheadventofmodernmoleculartechniquesandDNAsequenc- inganddataanalytics.Thechapterhighlightsthesalientaspectsofthemolecular methods used in metagenomic analyses and an overview of the applications of metagenomicstoacquaintthereadersaboutthenewscienceofmetagenomics. Keywords High-throughputsequencing·Metagenomics·Microbialcommunities· Molecularmarkers S.Singh·R.B.M.Tripathi·C.Chopra·R.S.Chopra(*) SchoolofBioengineeringandBiosciences,LovelyProfessionalUniversity,Phagwara,Punjab, India e-mail:[email protected];[email protected] H.Singh DepartmentofBioinformatics,HansRajMahilaMahaVidyalaya,Jalandhar,Punjab,India B.Rout CentreforBiotechnology,Siksha‘O’AnusandhanUniversity,Bhubaneswar,Odisha,India #SpringerNatureSingaporePteLtd.2020 3 R.S.Chopraetal.(eds.),Metagenomics:Techniques,Applications,Challenges andOpportunities,https://doi.org/10.1007/978-981-15-6529-8_1
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