Abstract
The emergence of High-throughput sequencing and its implication in the analysis of microbial population has introduced a new area of scientific research-metagenomics. Metagenomic analysis has brought a revolution in various fields of biological research, notably drug discovery. The term refers to the collective examination of genome analysis of unculturable microbial communities residing in a specific type of environmental condition or niche. A comprehensive investigation of the microbial diversity of unexploited areas with the aid of molecular biology and High-throughput sequencing technologies has opened the floodgates to explore and profile varieties of novel bioactive metabolites and potential antibiotics that promise to be of immense gravity for the pharmaceutical sector. High-throughput sequencing has accelerated the process of metabolite identification from metagenomic samples. Several bioactive metabolites have been obtained from metagenomic samples with immense therapeutic potential. Some examples include malacidin, fluoroquinolone, minimide and erdacin. In this chapter, major benchmark studies executed on the pharmacologically significant bioactive metabolites, extracted from metagenomic samples, have been discussed elaborately. An extensive review has also been conducted on several specialised bioinformatics-based pipelines frequently employed for the purpose. The present approach also aims at highlighting the major unexplored areas of drug discovery from metagenomic samples and associated metabolites—a hidden treasure for the pharmaceutical sector.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aguiar-Pulido V, Huang W, Suarez-Ulloa V et al (2016) Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis. Evol Bioinforma 12:5–16
Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46:2159–2168
Ari Ş, Arikan M (2016) Next-generation sequencing: advantages, disadvantages, and future. In: Hakeem KR, Tombuloğlu H, Tombuloğlu G (eds) Plant omics: trends and applications. Springer, Berlin, pp 109–135
Arnold JW, Roach J, Azcarate-Peril MA (2016) Emerging technologies for gut microbiome research. Trends Microbiol 24:887–901
Buermans HPJ, den Dunnen JT (2014) Next generation sequencing technology: advances and applications. Biochim Biophys Acta Mol basis Dis 1842:1932–1941
Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351. https://doi.org/10.1038/nrg.2016.49
Haas MJ (2009) Polyketide pas de deux. Sci Exch 2:898–898. https://doi.org/10.1038/scibx.2009.898
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
Harrington CT, Lin EI, Olson MT, Eshleman JR (2013) Fundamentals of pyrosequencing. Arch Pathol Lab Med 137:1296–1303. https://doi.org/10.5858/arpa.2012-0463-RA
Henson J, Tischler G, Ning Z (2012) Next-generation sequencing and large genome assemblies. Pharmacogenomics 13:901–915
Hug JJ, Bader CD, Remškar M et al (2018) Concepts and methods to access novel antibiotics from actinomycetes. Antibiotics 7:44
Imhoff J (2016) New dimensions in microbial ecology—functional genes in studies to unravel the biodiversity and role of functional microbial groups in the environment. Microorganisms 4:19. https://doi.org/10.3390/microorganisms4020019
Lahens NF, Ricciotti E, Smirnova O et al (2017) A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. BMC Genomics 18:602. https://doi.org/10.1186/s12864-017-4011-0
Levy SE, Myers RM (2016) Advancements in next-generation sequencing. Annu Rev Genomics Hum Genet 17:95–115. https://doi.org/10.1146/annurev-genom-083115-022413
Liu L, Li Y, Li S et al (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:1–11. https://doi.org/10.1155/2012/251364
Mehrotra M, Duose DY, Singh RR et al (2017) Versatile ion S5XL sequencer for targeted next generation sequencing of solid tumors in a clinical laboratory. PLoS One 12:e0181968. https://doi.org/10.1371/journal.pone.0181968
Neelakanta G, Sultana H (2013) The use of metagenomic approaches to analyze changes in microbial communities. Microbiol Insights 6:MBI.S10819. https://doi.org/10.4137/mbi.s10819
Österlund T, Jonsson V, Kristiansson E (2017) HirBin: high-resolution identification of differentially abundant functions in metagenomes. BMC Genomics 18:1–11. https://doi.org/10.1186/s12864-017-3686-6
Osunmakinde CO, Selvarajan R, Sibanda T et al (2018) Overview of trends in the application of metagenomic techniques in the analysis of human enteric viral diversity in Africa’s environmental regimes. Viruses 10:429
Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52:413–435
Petrosino JF, Highlander S, Luna RA et al (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55:856–866
Quail MA, Kozarewa I, Smith F et al (2008) A large genome center’s improvements to the Illumina sequencing system. Nat Methods 5:1005–1010. https://doi.org/10.1038/nmeth.1270
Reuter JA, Spacek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58:586–597
Schirmer M, D’Amore R, Ijaz UZ et al (2016) Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinf 17:125. https://doi.org/10.1186/s12859-016-0976-y
Seshadri R, Leahy SC, Attwood GT et al (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol 36:359–367. https://doi.org/10.1038/nbt.4110
Stein JL, Marsh TL, Wu KY et al (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178:591–599. https://doi.org/10.1128/jb.178.3.591-599.1996
Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160
Stewart RD, Auffret MD, Warr A et al (2018) Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nat Commun 9:870. https://doi.org/10.1038/s41467-018-03317-6
Wanunu M (2012) Nanopores: a journey towards DNA sequencing. Phys Life Rev 9:125–158
Zhou J, He Z, Yang Y et al (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio 6:e02288-14. https://doi.org/10.1128/mBio.02288-14
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Singh, B., Roy, A. (2020). Metagenomics and Drug-Discovery. In: Chopra, R.S., Chopra, C., Sharma, N.R. (eds) Metagenomics: Techniques, Applications, Challenges and Opportunities. Springer, Singapore. https://doi.org/10.1007/978-981-15-6529-8_8
Download citation
DOI: https://doi.org/10.1007/978-981-15-6529-8_8
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-15-6528-1
Online ISBN: 978-981-15-6529-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)