Metagenomics methods for the study of plant-associated microbial communities: A review.
Identifieur interne : 000251 ( PubMed/Corpus ); précédent : 000250; suivant : 000252Metagenomics methods for the study of plant-associated microbial communities: A review.
Auteurs : Ayomide Emmanuel Fadiji ; Olubukola Oluranti BabalolaSource :
- Journal of microbiological methods [ 1872-8359 ] ; 2020.
Abstract
Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.
DOI: 10.1016/j.mimet.2020.105860
PubMed: 32027927
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Electronic address: olubukola.babalola@nwu.ac.za.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32027927</idno><idno type="pmid">32027927</idno><idno type="doi">10.1016/j.mimet.2020.105860</idno><idno type="wicri:Area/PubMed/Corpus">000251</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000251</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Metagenomics methods for the study of plant-associated microbial communities: A review.</title><author><name sortKey="Fadiji, Ayomide Emmanuel" sort="Fadiji, Ayomide Emmanuel" uniqKey="Fadiji A" first="Ayomide Emmanuel" last="Fadiji">Ayomide Emmanuel Fadiji</name><affiliation><nlm:affiliation>Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.</nlm:affiliation></affiliation></author><author><name sortKey="Babalola, Olubukola Oluranti" sort="Babalola, Olubukola Oluranti" uniqKey="Babalola O" first="Olubukola Oluranti" last="Babalola">Olubukola Oluranti Babalola</name><affiliation><nlm:affiliation>Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa. Electronic address: olubukola.babalola@nwu.ac.za.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of microbiological methods</title><idno type="eISSN">1872-8359</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32027927</PMID><DateRevised><Year>2020</Year><Month>02</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1872-8359</ISSN><JournalIssue CitedMedium="Internet"><Volume>170</Volume><PubDate><Year>2020</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Journal of microbiological methods</Title><ISOAbbreviation>J. Microbiol. Methods</ISOAbbreviation></Journal><ArticleTitle>Metagenomics methods for the study of plant-associated microbial communities: A review.</ArticleTitle><Pagination><MedlinePgn>105860</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0167-7012(19)31118-2</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.mimet.2020.105860</ELocationID><Abstract><AbstractText>Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.</AbstractText><CopyrightInformation>Copyright © 2020. Published by Elsevier B.V.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fadiji</LastName><ForeName>Ayomide Emmanuel</ForeName><Initials>AE</Initials><AffiliationInfo><Affiliation>Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Babalola</LastName><ForeName>Olubukola Oluranti</ForeName><Initials>OO</Initials><AffiliationInfo><Affiliation>Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa. Electronic address: olubukola.babalola@nwu.ac.za.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D016454">Review</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Microbiol Methods</MedlineTA><NlmUniqueID>8306883</NlmUniqueID><ISSNLinking>0167-7012</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bioinformatics</Keyword><Keyword MajorTopicYN="N">Endophytes</Keyword><Keyword MajorTopicYN="N">Illumina Hiseq</Keyword><Keyword MajorTopicYN="N">Microbiomes</Keyword><Keyword MajorTopicYN="N">Shotgun metagenomics</Keyword><Keyword MajorTopicYN="N">Zea mays</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest There is no conflict of interest whatsoever from the author.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>12</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>01</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32027927</ArticleId><ArticleId IdType="pii">S0167-7012(19)31118-2</ArticleId><ArticleId IdType="doi">10.1016/j.mimet.2020.105860</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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