The metagenomics worldwide research

Ames SK, Hysom DA, Gardner SN et al (2013) Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics 29:2253–2260. doi: 10.1093/bioinformatics/btt389

Bentley DR, Balasubramanian S, Swerdlow HP et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59. doi: 10.1038/nature07517

Branton D, Deamer DW, Marziali A et al (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26:1146–1153. doi: 10.1038/nbt.1495

Cañas-Guerrero I, Mazarrón FR, Pou-Merina A et al (2013) Bibliometric analysis of research activity in the “Agronomy” category from the Web of Science, 1997–2011. Eur J Agron 50:19–28. doi: 10.1016/j.eja.2013.05.002

Choi J, Yi S, Lee KC (2011) Analysis of keyword networks in MIS research and implications for predicting knowledge evolution. Inf Manag 48:371–381. doi: 10.1016/j.im.2011.09.004

Chowdhury A, Mannan SBIN, Mazumdar RM (2012) Pyrosequencing–principles and applications. Int J Life Sci Pharma Res 2:65–76

Eisenstein M (2012) Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30:295–296. doi: 10.1038/nbt0412-295

Fantini E, Gianese G, Giuliano G, Fiore A (2015) Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing. Methods Mol Biol 1231:77–90. doi: 10.1007/978-1-4939-1720-4_5

Garrido-Cardenas JA, Garcia-Maroto F, Alvarez-Bermejo JA, Manzano-Agugliaro F (2017) DNA sequencing sensors: an overview. Sensors (Basel) 17(3):1–15. doi: 10.3390/s17030588

Gosalbes MJ, Durbán A, Pignatelli M et al (2011) Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One. doi: 10.1371/journal.pone.0017447

Grigoriev IV, Nordberg H, Shabalov I et al (2011) P@JGI-DOE@The Genome Portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res 40:1–7. doi: 10.1093/nar/gkr947

Handelsman J, Rondon MR, Brady SF et al (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249. doi: 10.1016/S1074-5521(98)90108-9

Hiraoka S, Yang C, Iwasaki W (2016) Metagenomics and bioinformatics in microbial ecology: current status and beyond. Microbes Environ 31:204–212. doi: 10.1264/jsme2.ME16024

Hyman ED (1988) A new method of sequencing DNA. Anal Biochem 174:423–436. doi: 10.1016/0003-2697(88)90041-3

Jerison ER, Desai MM (2015) Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments. Curr Opin Genet Dev 35:33–39. doi: 10.1016/j.gde.2015.08.008

Laabei M, Massey R (2016) Using functional genomics to decipher the complexity of microbial pathogenicity. Curr Genet 62:523–525. doi: 10.1007/s00294-016-0576-4

Lee H, Gurtowski J, Yoo S et al (2016a) Third-generation sequencing and the future of genomics. bioRxiv 48603. doi: 10.1101/048603

Lee HH, Park J, Kim J et al (2016b) Understanding the direction of evolution in Burkholderia glumae through comparative genomics. Curr Genet 62:115–123. doi: 10.1007/s00294-015-0523-9

Leggett RM, Heavens D, Caccamo M et al (2015) NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. Bioinformatics 32:142–144. doi: 10.1093/bioinformatics/btv540

Levene MJ, Korlach J, Turner SW et al (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682–686. doi: 10.1126/science.1079700

Li RW (2011) Metagenomics and its applications in agriculture, biomedicine, and environmental studies. Nova Science Publisher’s

Lundin S, Stranneheim H, Pettersson E et al (2010) Increased throughput by parallelization of library preparation for massive sequencing. PLoS ONE. doi: 10.1371/journal.pone.0010029

Mande SS, Mohammed MH, Ghosh TS (2012) Classification of metagenomic sequences: methods and challenges. Brief Bioinform 13:669–681. doi: 10.1093/bib/bbs054

Merriman B, Torrent I, Rothberg JM (2012) Progress in Ion Torrent semiconductor chip based sequencing. Electrophoresis 33:3397–3417

Miller RR, Montoya V, Gardy JL et al (2013) Metagenomics for pathogen detection in public health. Genome Med 5:81. doi: 10.1186/gm485

Milosavljevic A (2011) Emerging patterns of epigenomic variation. Trends Genet 27:242–250

Mitra S, Förster-Fromme K, Damms-Machado A et al (2013) Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics 14(Suppl 5):S16. doi: 10.1186/1471-2164-14-S5-S16

Montoya FG, Baños R, Meroño JE, Manzano-Agugliaro F (2016) The research of water use in Spain. J Clean Prod 112:4719–4732. doi: 10.1016/j.jclepro.2015.06.042

Morgan XC, Segata N, Huttenhower C (2013) Biodiversity and functional genomics in the human microbiome. Trends Genet 29:51–58

Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73:565–576. doi: 10.1128/MMBR.00033-09

Pace N, Stahl D, Lane D, Olsen G (1985) Analyzing natural microbial populations by rRNA sequences. ASM Am Soc Microbiol News 51:4–12

Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalog established by metagenomic sequencing. Nature 464:59–65. doi: 10.1038/nature08821.A

Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394. doi: 10.1146/annurev.micro.57.030502.090759

Rondon MR, August PR, Bettermann AD et al (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547. doi: 10.1128/AEM.66.6.2541-2547.2000

Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352. doi: 10.1038/nature10242

Rumble SM, Lacroute P, Dalca AV et al (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol. doi: 10.1371/journal.pcbi.1000386

Sanger F, Air GM, Barrell BG et al (1977) Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687–695

Scholz MB, Lo CC, Chain PSG (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23:9–15

Sharon I, Morowitz MJ, Thomas BC et al (2013) Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res 23:111–120. doi: 10.1101/gr.142315.112

Singh V, Perdigones A, García JL et al (2014) Analysis of worldwide research in the field of cybernetics during 1997–2011. Biol Cybern 108:757–776. doi: 10.1007/s00422-014-0617-3

Tun HM, Brar MS, Khin N et al (2012) Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing. J Microbiol Methods 88:369–376. doi: 10.1016/j.mimet.2012.01.001

Valouev A, Ichikawa J, Tonthat T et al (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18:1051–1063. doi: 10.1101/gr.076463.108

Wang WL, Xu SY, Ren ZG et al (2015) Application of metagenomics in the human gut microbiome. World J Gastroenterol 21:803–814

Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci 95:6578–6583. doi: 10.1073/pnas.95.12.6578

Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579. doi: 10.1073/pnas.87.12.4576

Wu J, Gao W, Johnson RH et al (2013) Integrated metagenomic and metatranscriptomic analyses of microbial communities in the meso- and bathypelagic realm of north Pacific ocean. Mar Drugs 11:3777–3801. doi: 10.3390/md11103777