Analysis and Interpretation of metagenomics data: an approach

Council NR. The New Science of Metagenomics: Revealing the secrets of our Microbial planet. ISBN 978-0-309-10676-4, Washington, DC: The National Academies Press; 2007, 12-31. Available from: https://nap.nationalacademies.org/catalog/11902/the-new-science-of-metagenomics-revealing-the-secrets-of-our.

Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5:R245-9 https://www.sciencedirect.com/science/article/pii/S1074552198901089.

Article  CAS  PubMed  Google Scholar 

Laudadio I, Fulci V, Stronati L, Carissimi C. Next-generation metagenomics methodological challenges and opportunities. Omi A J Integr Biol. 2019;23:327–33. https://doi.org/10.1089/omi.2019.0073 Mary Ann Liebert Inc, publishers.

Article  CAS  Google Scholar 

Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, et al. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol. 2021;4:604. https://doi.org/10.1038/s42003-021-02112-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Molefe RR, Amoo AE, Babalola OO. Metagenomic insights into the bacterial community structure and functional potentials in the rhizosphere soil of maize plants. J Plant Interact  2021;16:258–69. https://doi.org/10.1080/17429145.2021.1936228 Taylor Francis.

Article  CAS  Google Scholar 

Franzén O, Hu J, Bao X, Itzkowitz SH, Peter I, Bashir A. Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering. Microbiome. 2015;3:43. https://doi.org/10.1186/s40168-015-0105-6.

Article  PubMed  PubMed Central  Google Scholar 

Edgar RC. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. PeerJ. 2018;6:e4652.

Article  PubMed  PubMed Central  Google Scholar 

Piombo E, Abdelfattah A, Droby S, Wisniewski M, Spadaro D, Schena L. Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens. Microorganisms. 2021;9:188 https://www.mdpi.com/2076-2607/9/1/188.

Article  PubMed  PubMed Central  Google Scholar 

Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, et al. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered. 2020;11:356–74. https://doi.org/10.1080/21655979.2020.1736238 Taylor & Francis.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bush A, Compson ZG, Monk WA, Porter TM, Steeves R, Emilson E, et al. Studying ecosystems with DNA metabarcoding: lessons from biomonitoring of aquatic macroinvertebrates. Front Ecol Evol. 2019;7:434. https://doi.org/10.3389/fevo.2019.00434https://www.frontiersin.org/articles/.

Article  Google Scholar 

Sharon I, Bercovici S, Pinter RY, Shlomi T. Pathway-based functional analysis of metagenomes. J Comput Biol. 2011;18:495–505. https://doi.org/10.1089/cmb.2010.0260 Mary Ann Liebert Inc, publishers.

Article  CAS  PubMed  Google Scholar 

Bercovici S, Sharon I, Pinter RY, Shlomi T. Pathway-based functional analysis of Metagenomes BT - research in computational molecular biology. In: Berger B, editor. Berlin. Heidelberg: Springer, Berlin Heidelberg; 2010. p. 50–64.

Google Scholar 

Brown SM, Chen H, Hao Y, Laungani BP, Ali TA, Dong C, et al. MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. Gigascience. 2019;8:giz020. https://doi.org/10.1093/gigascience/giz020.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, et al. Automated and accurate estimation of gene family abundance from shotgun metagenomes PLOS Comput Biol Public Libr Sci. 2015;11:e1004573. https://doi.org/10.1371/journal.pcbi.1004573.

Article  CAS  Google Scholar 

Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human Distal Gut Microbiome  Sci. 2006;312:1355–9. https://doi.org/10.1126/science.1124234 Am Association Advancement Sci.

Article  CAS  Google Scholar 

Lam KN, Cheng J, Engel K, Neufeld JD, Charles TC. Current and future resources for functional metagenomics. Front Microbiol. 2015;6:1196. https://doi.org/10.3389/fmicb.2015.01196, https://www.frontiersin.org/articles/.

Article  PubMed  PubMed Central  Google Scholar 

Coughlan LM, Cotter PD, Hill C, Alvarez-Ordóñez A. Biotechnological applications of functional metagenomics in the food and pharmaceutical industries. Front Microbiol. 2015;6:1–22.

Article  Google Scholar 

Soni R, Goel R. Triphasic approach to assessment of bacterial population in different soil systems. Ekologija. 2010;6(3-4):99-104.

Vavourakis CD, Andrei A-S, Mehrshad M, Ghai R, Sorokin DY, Muyzer G. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome. 2018;6:168. https://doi.org/10.1186/s40168-018-0548-7.

Article  PubMed  PubMed Central  Google Scholar 

Hinsu A, Dumadiya A, Joshi A, Kotadiya R, Andharia K, Koringa P, et al. To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere. PeerJ. 2021;9:e12035.

Mogotsi MT, Mwangi PN, Bester PA, Mphahlele MJ, Seheri ML, O’Neill HG, et al. Metagenomic analysis of the enteric RNA virome of infants from the Oukasie clinic, North West Province, South Africa, reveals diverse Eukaryotic viruses. Viruses . 2020.

Saleem F, Azim MK, Mustafa A, Kori JA, Hussain MS. Metagenomic profiling of fresh water lakes at different altitudes in Pakistan. Ecol Inform. 2019;51:73–81 https://www.sciencedirect.com/science/article/pii/S1574954118302061.

Article  Google Scholar 

Felczykowska A, Krajewska A, Zielińska S, Łos JM. Sampling, metadata and DNA extraction - important steps in metagenomic studies. Acta Biochim Pol. 2015;62:151–60.

Article  CAS  PubMed  Google Scholar 

Bag S, Saha B, Mehta O, Anbumani D, Kumar N, Dayal M, et al. An improved method for high quality metagenomics DNA extraction from human and environmental samples. Sci Rep. 2016;6:26775. https://doi.org/10.1038/srep.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xu Y, Vaidya B, Patel AB, Ford SM, McCarley RL, Soper SA. Solid-phase reversible immobilization in microfluidic chips for the purification of dye-labeled DNA sequencing fragments. Anal Chem  2003;75:2975–84. https://doi.org/10.1021/ac030031n Ame Chem Soc.

Article  CAS  PubMed  Google Scholar 

Hess JF, Kohl TA, Kotrová M, Rönsch K, Paprotka T, Mohr V, et al. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv. 2020;41:107537 https://www.sciencedirect.com/science/article/pii/S0734975020300343.

Article  CAS  PubMed  Google Scholar 

Boers SA, Jansen R, Hays JP. Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory. Eur J Clin Microbiol Infect Dis. 2019;38:1059–70. https://doi.org/10.1007/s10096-019-03520-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chakravorty S, Helb D, Burday M, Connell N, Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods. 2007;69:330–9 https://www.sciencedirect.com/science/article/pii/S0167701207000565.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Federhen S. The NCBI Taxonomy database. Nucleic Acids Res. 2012;40:D136–43. https://doi.org/10.1093/nar/gkr1178.

Article  CAS  PubMed  Google Scholar 

Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188–96. https://doi.org/10.1093/nar/gkm864.

Article  CAS  PubMed  PubMed Central  Google Scholar 

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a Chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069–72 (LP).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, et al. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 2005;33:D294–6. https://doi.org/10.1093/nar/gki038.

Article  CAS  PubMed  Google Scholar 

She X, Yu L, Lan G, Tang Y, He Z. Identification and genetic characterization of ralstonia solanacearum species complex isolates from cucurbita maxima in China. Front Plant Sci. 2017;8:1794.

Article  PubMed  PubMed Central  Google Scholar 

Sharma R, Kumar A, Singh N, Sharma K. 16S rRNA gene profiling of rhizospheric microbial community of Eichhornia crassipes. Mol Biol Rep. 2021;48:4055–64. https://doi.org/10.1007/s11033-021-06413-x.

Article  CAS  PubMed  Google Scholar 

Muwawa EM, Obieze CC, Makonde HM, Jefwa JM, Kahindi JHP, Khasa DP. 16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay Kenya. PLoS One. 2021;16:1–22. https://doi.org/10.1371/journal.pone.0248485.

Article  CAS  Google Scholar 

Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS, et al. PIPITS an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol Evol John Wiley Sons Ltd; 2015;6:973–80. https://doi.org/10.1111/2041-210X.12399.

Article  Google Scholar 

Maike R, Maltez TA, Sato GS, Farage ML, Patrik I, Victoria K-C, et al. Microbiomes of field-grown maize and soybean in Southeastern and Central Brazil inferred by high-throughput 16S and internal transcribed spacer amplicon sequencing. Microbiol Resour Announc. 2021;10:e00528-21. https://doi.org/10.1128/MRA.00528-21 Ame Soc Microbiol.

Article  Google Scholar 

BenIsrael M, Habtewold JZ, Khosla K, Wanner P, Aravena R, Parker BL, et al. Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing. Int J Phytoremediation  2021;23:846–56. https://doi.org/10.1080/15226514.2020.1860901 Taylor & Francis.

Article  CAS  PubMed  Google Scholar 

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. Environmental genome shotgun sequencing of the Sargasso Sea.

留言 (0)

沒有登入
gif