Abstract
Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other “omics” disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.
Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30(9):418–426
PubMed: metagenomics – search results – PubMed (2022). https://pubmed.ncbi.nlm.nih.gov/?term=metagenomics&filter=datesearch.y_10. Accessed 24 June 2022
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380
Moore-Connors JM, Dunn KA, Bielawski JP, Van Limbergen J (2016) Novel strategies for applied metagenomics. Inflamm Bowel Dis 22(3):709–718. https://doi.org/10.1097/mib.0000000000000717
C. Huttenhower DG (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214. https://doi.org/10.1038/nature11234
Derksen F, Bensing J, Lagro-Janssen A (2013) Effectiveness of empathy in general practice: a systematic review. Br J Gen Pract 63(606):e76–e84
Suárez N, Weckx S, Minahk C, Hebert EM, Saavedra L (2020) Metagenomics-based approach for studying and selecting bioprotective strains from the bacterial community of artisanal cheeses. Int J Food Microbiol 335:108894. https://doi.org/10.1016/j.ijfoodmicro.2020.108894
Innovation at Illumina: the road to the $600 human genome (2021). https://www.nature.com/articles/d42473-021-00030-9. Accessed 20 July 2021
Yang X, Que G (2020) Advance in study on 16S rRNA gene sequencing technology in oral microbial diversity. J Cent South Univ 45(7):849–855. https://doi.org/10.11817/j.issn.1672-7347.2020.190236
Bukin YS, Galachyants YP, Morozov I, Bukin S, Zakharenko A, Zemskaya T (2019) The effect of 16S rRNA region choice on bacterial community metabarcoding results. Sci Data 6(1):1–14
Laudadio I, Fulci V, Stronati L, Carissimi C (2019) Next-generation metagenomics: methodological challenges and opportunities. OMICS 23(7):327–333
Tsou AM, Olesen SW, Alm EJ, Snapper SB (2020) 16S rRNA sequencing analysis: the devil is in the details. Gut Microbes 11(5):1139–1142. https://doi.org/10.1080/19490976.2020.1747336
Duan R, Zhu S, Wang B, Duan L (2019) Alterations of gut microbiota in patients with irritable bowel syndrome based on 16S rRNA-targeted sequencing: a systematic review. Clin Transl Gastroenterol 10(2):e00012
Peng W, Huang J, Yang J, Zhang Z, Yu R, Fayyaz S et al (2020) Integrated 16S rRNA sequencing, metagenomics, and metabolomics to characterize gut microbial composition, function, and fecal metabolic phenotype in non-obese type 2 diabetic Goto-Kakizaki rats. Front Microbiol 10:3141
DeBruyn JM, Nixon LT, Fawaz MN, Johnson AM, Radosevich M (2011) Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl Environ Microbiol 77(17):6295–6300
Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML (2015) Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J 9(4):968–979
Jiao X, Zheng X, Ma L, Kutty G, Gogineni E, Sun Q et al (2013) A benchmark study on error assessment and quality control of CCS reads derived from the PacBio RS. J Data Mining Genomics Proteomics 4(3):16008
Weinstock GM (2012) Genomic approaches to studying the human microbiota. Nature 489(7415):250–256
Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33(suppl_1):D501–D5D4
Erawijantari PP, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T et al (2020) Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles. Gut 69(8):1404–1415
Yu S, Xiong Y, Fu Y, Chen G, Zhu H, Mo X et al (2021) Shotgun metagenomics reveals significant gut microbiome features in different grades of acute pancreatitis. Microb Pathog 154:104849
Qian Y, Yang X, Xu S, Huang P, Li B, Du J et al (2020) Gut metagenomics-derived genes as potential biomarkers of Parkinson’s disease. Brain 143(8):2474–2489
Gacesa R, Kurilshikov A, Vich Vila A, Sinha T, Klaassen M, Bolte L et al (2022) Environmental factors shaping the gut microbiome in a Dutch population. Nature 604(7907):732–739
Akinola SA, Ayangbenro AS, Babalola OO (2021) The immense functional attributes of maize rhizosphere microbiome: a shotgun sequencing approach. Agriculture 11(2):118
Saxena G, Mitra S, Marzinelli EM, Xie C, Wei TJ, Steinberg PD et al (2018) Metagenomics reveals the influence of land use and rain on the benthic microbial communities in a tropical urban waterway. Msystems 3(3):e00136–e00117
Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 6(2):121–131
Durazzi F, Sala C, Castellani G, Manfreda G, Remondini D, De Cesare A (2021) Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota. Sci Rep 11(1):1–10
Wang Y, Tian RM, Gao ZM, Bougouffa S, Qian P-Y (2014) Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis. PLoS One 9(3):e90053
Blifernez-Klassen O, Klassen V, Doebbe A, Kersting K, Grimm P, Wobbe L et al (2012) Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii. Nat Commun 3(1):1–9
Wegener Parfrey L, Walters WA, Knight R (2011) Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front Microbiol 2:153
Audebert C, Even G, Cian A, Loywick A, Merlin S, Viscogliosi E et al (2016) Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota. Sci Rep 6(1):1–11
Eukaryotic 18S rRNA sequencing – CD genomics (2021). https://www.cd-genomics.com/microbioseq/eukaryotic-18s-rrna-sequencing.html. Accessed 20 July 2021
Jain M, Olsen HE, Paten B, Akeson M (2016) The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17(1):1–11
Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13(5):278–289
Badotti F, Fonseca PLC, Tomé LMR, Nunes DT, Góes-Neto A (2018) ITS and secondary biomarkers in fungi: review on the evolution of their use based on scientific publications. Rev Bras Bot 41(2):471–479
Kirk PM, Cannon PF, David J, Stalpers JA (2001) Ainsworth and Bisby’s dictionary of the fungi, vol 9. CABI Publishing
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci 109(16):6241–6246
Wagner K, Springer B, Pires V, Keller PM (2018) Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture. Sci Rep 8(1):1–7
Gotelli NJ, Colwell RK (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol Lett 4(4):379–391
Kim B-R, Shin J, Guevarra RB, Lee JH, Kim DW, Seol K-H et al (2017) Deciphering diversity indices for a better understanding of microbial communities. J Microbiol Biotechnol 27(12):2089–2093
Bunge J, Fitzpatrick M (1993) Estimating the number of species: a review. J Am Stat Assoc 88(421):364–373
Denslow JS (1995) Disturbance and diversity in tropical rain forests: the density effect. Ecol Appl 5(4):962–968
Anderson RS, Ashe JS (2000) Leaf litter inhabiting beetles as surrogates for establishing priorities for conservation of selected tropical montane cloud forests in Honduras, Central America (Coleoptera; Staphylinidae, Curculionidae). Biodivers Conserv 9(5):617–653
Stork N (1991) The composition of the arthropod fauna of Bornean lowland rain forest trees. J Trop Ecol 7(2):161–180
Hong M, Tao S, Zhang L, Diao L-T, Huang X, Huang S et al (2020) RNA sequencing: new technologies and applications in cancer research. J Hematol Oncol 13(1):1–16
Sikkema-Raddatz B, Johansson LF, de Boer EN, Almomani R, Boven LG, van den Berg MP et al (2013) Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics. Hum Mutat 34(7):1035–1042
Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D et al (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18(6):630–634
Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 34(suppl_1):D731–D7D5
Tucker T, Marra M, Friedman JM (2009) Massively parallel sequencing: the next big thing in genetic medicine. Am J Hum Genet 85(2):142–154
Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA et al (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318(5848):283–287
Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 7(2):e30087
Segerman B (2020) The most frequently used sequencing technologies and assembly methods in different time segments of the bacterial surveillance and RefSeq genome databases. Front Cell Infect Microbiol 10:527102
Porreca GJ, Shendure J, Church GM (2006) Polony DNA sequencing. Curr Protoc Mol Biol 76(1):7.8.1–7.8.22
Mitra RD, Church GM (1999) In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 27(24):e34–ee9
Kim JB, Porreca GJ, Song L, Greenway SC, Gorham JM, Church GM et al (2007) Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 316(5830):1481–1484
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309(5741):1728–1732
Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36(19):e122-e
Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K et al (2017) Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc 12(6):1261–1276
Zhang J, Su L, Wang Y, Deng S (2020) Improved high-throughput sequencing of the human oral microbiome: from Illumina to PacBio. Can J Infect Dis Med Microbiol 2020:6678872
Sanz-Martin I, Doolittle-Hall J, Teles RP, Patel M, Belibasakis GN, Hämmerle CH et al (2017) Exploring the microbiome of healthy and diseased peri-implant sites using Illumina sequencing. J Clin Periodontol 44(12):1274–1284
Paijmans JL, Baleka S, Henneberger K, Taron UH, Trinks A, Westbury MV et al (2017) Sequencing single-stranded libraries on the Illumina NextSeq 500 platform. arXiv preprint arXiv:171111004
Goswami C, Sheldon M, Bixby C, Keddache M, Bogdanowicz A, Wang Y et al (2022) Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program. BMC Infect Dis 22(1):1–12
Babalola OO, Fadiji AE, Ayangbenro AS (2020) Shotgun metagenomic data of root endophytic microbiome of maize (Zea mays L.). Data Brief 31:105893
Senabouth A, Andersen S, Shi Q, Shi L, Jiang F, Zhang W et al (2020) Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing. NAR Genom Bioinform 2(2):lqaa034
Pandey V, Nutter RC, Prediger E (2008) Applied biosystems solid™ system: ligation-based sequencing. In: Janitz M (ed) Next generation genome sequencing: towards personalized medicine. WileyVCH Verlag GmbH & Co. KGaA, Weinheim, pp 29–42
Park PJ (2009) ChIP–seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63
Liu L, Li Y, Li S, Hu N, He Y, Pong R et al (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364
Merriman B, D Team IT, Rothberg JM (2012) Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 33(23):3397–3417
Daum LT, Rodriguez JD, Worthy SA, Ismail NA, Omar SV, Dreyer AW et al (2012) Next-generation ion torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains. J Clin Microbiol 50(12):3831–3837
Brown SP, Callaham MA Jr, Oliver AK, Jumpponen A (2013) Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem. FEMS Microbiol Ecol 86(3):557–566
Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, Sengupta DJ et al (2014) Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl Environ Microbiol 80(24):7583–7591
Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B et al (2012) Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 91(1):80–88
Huang J, Liang X, Xuan Y, Geng C, Li Y, Lu H et al (2017) A reference human genome dataset of the BGISEQ-500 sequencer. Gigascience 6(5):gix024
Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG et al (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327(5961):78–81
Fang C, Zhong H, Lin Y, Chen B, Han M, Ren H et al (2018) Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing. Gigascience 7(3):gix133
Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding M-HS et al (2017) Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience 6(8):gix049
Porreca GJ (2010) Genome sequencing on nanoballs. Nat Biotechnol 28(1):43–44
Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J et al (2010) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465(7297):473–477
Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT et al (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328(5978):636–639
Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H (2020) The architecture of SARS-CoV-2 transcriptome. Cell 181(4):914–21.e10. https://doi.org/10.1016/j.cell.2020.04.011
Thompson JF, Steinmann KE (2010) Single molecule sequencing with a HeliScope genetic analysis system. Curr Protoc Mol Biol Chapter 7:Unit7.10. https://doi.org/10.1002/0471142727.mb0710s92
Steinmann KE, Hart CE, Thompson JF, Milos PM (2011) Helicos single-molecule sequencing of bacterial genomes. Methods Mol Biol 733:3–24. https://doi.org/10.1007/978-1-61779-089-8_1
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I et al (2008) Single-molecule DNA sequencing of a viral genome. Science 320(5872):106–109
van den Oever JME, Balkassmi S, Verweij EJ, van Iterson M, van Scheltema PNA, Oepkes D et al (2012) Single molecule sequencing of free DNA from maternal plasma for noninvasive trisomy 21 detection. Clin Chem 58(4):699–706. https://doi.org/10.1373/clinchem.2011.174698
Heather JM, Chain B (2016) The sequence of sequencers: the history of sequencing DNA. Genomics 107(1):1–8
Lee H, Gurtowski J, Yoo S, Nattestad M, Marcus S, Goodwin S et al (2016) Third-generation sequencing and the future of genomics. BioRxiv:048603
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(5):2159–2168
Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA et al (2013) Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci 110(50):E4821–E4E30
Wilbe M, Gudmundsson S, Johansson J, Ameur A, Stattin EL, Annerén G et al (2017) A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders. Prenat Diagn 37(11):1146–1154
Cavelier L, Ameur A, Häggqvist S, Höijer I, Cahill N, Olsson-Strömberg U et al (2015) Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing. BMC Cancer 15(1):1–12
Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C et al (2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 50(2):285–296. https://doi.org/10.1038/s41588-018-0040-0
Payne A, Holmes N, Rakyan V, Loose M (2019) BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics 35(13):2193–2198. https://doi.org/10.1093/bioinformatics/bty841
Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T et al (2010) The potential and challenges of nanopore sequencing. Nanosci Technol:261–268
Kono N, Arakawa K (2019) Nanopore sequencing: review of potential applications in functional genomics. Develop Growth Differ 61(5):316–326
Mitsuhashi S, Kryukov K, Nakagawa S, Takeuchi JS, Shiraishi Y, Asano K et al (2017) A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer. Sci Rep 7(1):1–9
Valliammai MG, Gopal NO, Anandham R (2021) Elucidation of microbial diversity and lignocellulolytic enzymes for the degradation of lignocellulosic biomass in the forest soils of Eastern and Western Ghats of Tamil Nadu, India. Biofuels Bioprod Biorefin 15(1):47–60
Stancu MC, Van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, De Ligt J et al (2017) Mapping and phasing of structural variation in patient genomes using nanopore sequencing. Nat Commun 8(1):1–13
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA et al (2018) Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol 36(4):338–345
Roche: DNA library prep for DNA nanoball technology sequencing platforms (2021). https://sequencing.roche.com/en/blog/dna-library-prep-for-dna-nanoball-technology-sequencing-platform.html. Accessed 10 Nov 2021
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Benz, S., Mitra, S. (2023). From Genomics to Metagenomics in the Era of Recent Sequencing Technologies. In: Mitra, S. (eds) Metagenomic Data Analysis. Methods in Molecular Biology, vol 2649. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3072-3_1
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3072-3_1
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3071-6
Online ISBN: 978-1-0716-3072-3
eBook Packages: Springer Protocols