Bibliography

Cover Page

The handle http://hdl.handle.net/1887/87513 holds various files of this Leiden University dissertation.

Author: Khachatryan, L. Title: Metagenomics : beyond the horizon of current implementations and methods Issue Date: 2020-04-28

Bibliography

[1] WB Whitman, DC Coleman, and ica et Biophysica Acta (BBA)-Bioenergetics, WJ Wiebe. Prokaryotes: the unseen 1707(2-3):231–253, 2005. majority. Proceedings of the National [8] PG Falkowski and LV Godfrey. Elec- Academy of Sciences, 95(12):6578–6583, trons, life and the evolution of earth’s 1998. oxygen cycle. Philosophical Transactions [2] AA Juwarkar, SK Yadav, PR Thawale, of the Royal Society of London B: Biological P Kumar, SK Singh, and T Chakrabarti. Sciences, 363(1504):2705–2716, 2008. Developmental strategies for sustain- [9] C Gougoulias, JM Clark, and LJ Shaw. able ecosystem on mine spoil dumps: a The role of soil microbes in the case of study. Environmental monitoring global carbon cycle: tracking the below- and assessment, 157(1-4):471–481, 2009. ground microbial processing of plant- [3] C Pedros-Alio. Dipping into the rare derived carbon for manipulating car- biosphere. Sciense, 5809:192, 2007. bon dynamics in agricultural systems. Journal of the Science of Food and Agricul- [4] C Pedros-Alio. The rare bacterial bio- ture, 94(12):2362–2371, 2014. sphere. Annual review of marine science, [10] MG Klotz, DA Bryant, and TE Hanson. 4:449–466, 2012. The microbial sulfur cycle. Frontiers in [5] GT Pecl, MB Araujo, JD Bell, J Blan- microbiology, 2:241, 2011. chard, TC Bonebrake, I-C Chen, [11] J Chen, Y Li, Y Tian, C Huang, D Li, TD Clark, RK Colwell, F Danielsen, Q Zhong, and X Ma. Interaction be- B Evengaard, et al. Biodiversity tween microbes and host intestinal redistribution under climate change: health: modulation by dietary nutri- Impacts on ecosystems and human ents and gut-brain-endocrine-immune well-being. Science, 355(6332):eaai9214, axis. Current Protein and Peptide Science, 2017. 16(7):592–603, 2015. [6] K Todar. Bacteria and archaea and the [12] SE Erdman and T Poutahidis. Microbes cycles of elements in the environment. and oxytocin: beneﬁts for host physi- Retrieved June, 7:2014, 2012. ology and behavior. In International re- [7] M Paumann, G Regelsberger, C Ob- view of neurobiology, volume 131, pages inger, and GA Peschek. The bioener- 91–126. Elsevier, 2016. getic role of dioxygen and the terminal [13] E Patterson, JF Cryan, GF Fitzgerald, oxidase(s) in cyanobacteria. Biochim- RP Ross, TG Dinan, and C Stanton. Gut

121 122 Bibliography

microbiota, the pharmabiotics they pro- [23] J Rifkin. The biotech century. Sonoma duce and host health. Proceedings of the County Earth First/Biotech Last, 1998. Nutrition Society, 73(4):477–489, 2014. [24] S Farmer. Probiotic, lactic acid- [14] LK Ursell, W van Treuren, JL Metcalf, producing bacteria and uses thereof, M Pirrung, A Gewirtz, and R Knight. October 8 2002. US Patent 6,461,607. Replenishing our defensive microbes. [25] JR Postgate. Economic importance of Bioessays, 35(9):810–817, 2013. sulphur bacteria. Phil. Trans. R. Soc. [15] TA Van der Meulen, HJM Harm- Lond. B, 298(1093):583–600, 1982. sen, H Bootsma, FKL Spijkervet, [26] M Fernandez, B Del Rio, DM Linares, FGM Kroese, and A Vissink. The MC Martin, and MA Alvarez. Real- microbiome–systemic diseases connec- time polymerase chain reaction for tion. Oral diseases, 22(8):719–734, 2016. quantitative detection of histamine- [16] GJM Christensen and H Bruggemann. producing bacteria: use in cheese pro- Bacterial skin commensals and their duction. Journal of dairy science, role as host guardians. Beneﬁcial mi- 89(10):3763–3769, 2006. crobes, 5(2):201–215, 2013. [27] A Mayra-Makinen and M Bigret. Indus- trial use and production of lactic acid [17] Y Belkaid and S Tamoutounour. The bacteria. Food sciense and Technology, inﬂuence of skin microorganisms on 139:175–198, 2004. cutaneous immunity. Nature Reviews Immunology, 16(6):353, 2016. [28] BS Dien, MA Cotta, and TW Jeffries. Bacteria engineered for fuel ethanol [18] PC Calder. Feeding the immune sys- production: current status. Applied mi- tem. Proceedings of the Nutrition Society, crobiology and biotechnology, 63(3):258– 72(3):299–309, 2013. 266, 2003. [19] DA Cowan, J-B Ramond, TP Makha- [29] SF Bender, C Wagg, and MGA van der lanyane, and P de Maayer. Metageno- Heijden. An underground revolution: mics of extreme environments. Current biodiversity and soil ecological engi- opinion in microbiology, 25:97–102, 2015. neering for agricultural sustainability. [20] P Blum. Archaea: Ancient Microbes, Ex- Trends in Ecology & Evolution, 31(6):440– treme Environments, and the Origin of Life, 452, 2016. volume 50. Gulf Professional Publish- [30] M-N Xing, X-Z Zhang, and H Huang. ing, 2001. Application of metagenomic tech- [21] L Tazi, DP Breakwell, AR Harker, and niques in mining enzymes from micro- KA Crandall. Life in extreme environ- bial communities for biofuel synthe- ments: microbial diversity in great salt sis. Biotechnology advances, 30(4):920– lake, utah. Extremophiles, 18(3):525–535, 929, 2012. 2014. [31] M Wainwright, J Lederberg, and [22] C Bang, T Dagan, P Deines, N Dubilier, J Lederberg. History of microbiology. WJ Duschl, S Fraune, U Hentschel, Encyclopedia of microbiology, 2:419–437, H Hirt, N Hulter, T Lachnit, et al. 1992. Metaorganisms in extreme environ- [32] Y Stanier, M Doudoroff, EA Adelberg, ments: do microbes play a role in or- et al. General microbiology. General ganismal adaptation? Zoology, 2018. microbiology., 1958. BIBLIOGRAPHY 123

[33] N Hall. Advanced sequencing tech- mination of 16s ribosomal rna sequen- nologies and their wider impact in mi- ces for phylogenetic analyses. Proceed- crobiology. Journal of Experimental Biol- ings of the National Academy of Sciences, ogy, 210(9):1518–1525, 2007. 82(20):6955–6959, 1985. [34] SE Hasnain. Impact of human genome [42] TM Schmidt, EF DeLong, and NR Pace. sequencing on microbiology. Indian Analysis of a marine picoplankton com- journal of medical microbiology, 19(3):114, munity by 16s rrna gene cloning and 2001. sequencing. Journal of bacteriology, [35] JT Staley and A Konopka. Measure- 173(14):4371–4378, 1991. ment of in situ activities of nonpho- [43] PJ Turnbaugh, RE Ley, M Hamady, tosynthetic microorganisms in aquatic CM Fraser-Liggett, R Knight, and and terrestrial habitats. Annual Reviews JI Gordon. The human microbiome in Microbiology, 39(1):321–346, 1985. project. Nature, 449(7164):804, 2007. [36] A Escobar-Zepeda, A Vera-Ponce de [44] HMP Integrative. The integrative hu- Leon, and A Sanchez-Flores. The road man microbiome project: dynamic anal- to metagenomics: from microbiology to ysis of microbiome-host omics proﬁles dna sequencing technologies and bioin- during periods of human health and formatics. Frontiers in genetics, 6:348, disease. Cell host & microbe, 16(3):276, 2015. 2014. [37] National Research Council et al. The [45] V Robles-Alonso and F Guarner. From new science of metagenomics: revealing the basic to applied research: lessons from secrets of our microbial planet. National the human microbiome projects. Jour- Academies Press, 2007. nal of clinical gastroenterology, 48:S3–S4, [38] C Simon and R Daniel. Achieve- 2014. ments and new knowledge unraveled by metagenomic approaches. Applied [46] SM Bakhtiar, JG LeBlanc, E Salvucci, microbiology and biotechnology, 85(2):265– A Ali, R Martin, P Langella, J-M Chatel, 276, 2009. A Miyoshi, LG Bermudez-Humaran, and V Azevedo. Implications of the [39] R Knight, A Vrbanac, B C Taylor, human microbiome in inﬂammatory A Aksenov, C Callewaert, J Debelius, bowel diseases. FEMS microbiology let- A Gonzalez, T Kosciolek, L-I McCall, ters, 342(1):10–17, 2013. D McDonald, et al. Best practices for analysing microbiomes. Nature Reviews [47] J Lloyd-Price, G Abu-Ali, and C Hut- Microbiology, page 1, 2018. tenhower. The healthy human microbiome. Genome medicine, 8(1):51, 2016. [40] S Junemann, N Kleinbolting, S Jaenicke, C Henke, J Hassa, J Nelkner, Y Stolze, [48] XC Morgan, N Segata, and C Hutten- S P Albaum, A Schluter, A Goesmann, hower. Biodiversity and functional et al. Bioinformatics for ngs-based genomics in the human microbiome. metagenomics and the application to Trends in genetics, 29(1):51–58, 2013. biogas research. Journal of biotechnology, [49] X C Morgan, T L Tickle, H Sokol, D Gev- 261:10–23, 2017. ers, K L Devaney, D V Ward, J A Reyes, [41] DJ Lane, B Pace, GJ Olsen, DA Stahl, S A Shah, N LeLeiko, S B Snapper, ML Sogin, and NR Pace. Rapid deter- et al. Dysfunction of the intestinal 124 Bibliography

microbiome in inflammatory bowel dis- [58] JL Metcalf, ZZ Xu, A Bouslimani, ease and treatment. Genome biology, P Dorrestein, DO Carter, and R Knight. 13(9):R79, 2012. Microbiome tools for forensic science. [50] D Gevers, S Kugathasan, L A Den- Trends in biotechnology, 35(9):814–823, son, Y Vazquez-Baeza, W Van Treuren, 2017. B Ren, E Schwager, D Knights, S J Song, [59] SE Schmedes, AE Woerner, NMM M Yassour, et al. The treatment-naive Novroski, FR Wendt, JL King, microbiome in new-onset crohn’s dis- KM Stephens, and B Budowle. ease. Cell host & microbe, 15(3):382–392, Targeted sequencing of clade-specific 2014. markers from skin microbiomes for [51] C Pedros-Alio. Genomics and marine forensic human identification. Forensic microbial ecology. International Microbi- Science International: Genetics, 32:50–61, ology, 9(3):191–197, 2006. 2018. [52] PG Falkowski, RT Barber, and [60] EN Hanssen, E Avershina, K Rudi, V Smetacek. Biogeochemical controls P Gill, and L Snipen. Body fluid predic- and feedbacks on ocean primary tion from microbial patterns for foren- production. Science, 281(5374):200–206, sic application. Forensic Science Interna- 1998. tional: Genetics, 30:10–17, 2017. [53] CA Suttle. Marine viruses—major play- [61] L Brinkac, TH Clarke, H Singh, C Greco, ers in the global ecosystem. Nature Re- A Gomez, MG Torralba, B Frank, and views Microbiology, 5(10):801, 2007. KE Nelson. Spatial and environmental variation of the human hair microbiota. [54] NA Bokulich, ZT Lewis, K Boundy- Scientific reports, 8(1):9017, 2018. Mills, and DA Mills. A new perspective on microbial landscapes within food [62] N Fierer, CL Lauber, N Zhou, D McDon- production. Current opinion in biotech- ald, EK Costello, and R Knight. Foren- nology, 37:182–189, 2016. sic identification using skin bacterial communities. Proceedings of the National [55] M Trindade, LJ van Zyl, J Navarro- Academy of Sciences, 107(14):6477–6481, Fernández, and A Abd Elrazak. Tar- 2010. geted metagenomics as a tool to tap into marine natural product diversity [63] S Lax, JT Hampton-Marcell, SM Gib- for the discovery and production of bons, GB Colares, D Smith, JA Eisen, drug candidates. Frontiers in microbi- and JA Gilbert. Forensic analysis of ology, 6:890, 2015. the microbiome of phones and shoes. Microbiome, 3(1):21, 2015. [56] MM Zhang, Y Qiao, EL Ang, and H Zhao. Using natural products for [64] RR Dunn, N Fierer, JB Henley, JW Leff, drug discovery: the impact of the ge- and HL Menninger. Home life: fac- nomics era. Expert opinion on drug dis- tors structuring the bacterial diversity covery, 12(5):475–487, 2017. found within and between homes. PloS one [57] SM Techtmann and TC Hazen. Meta- , 8(5):e64133, 2013. genomic applications in environmental [65] GE Flores, ST Bates, JG Caporaso, monitoring and bioremediation. Jour- CL Lauber, JW Leff, R Knight, and nal of industrial microbiology & biotech- N Fierer. Diversity, distribution nology, 43(10):1345–1354, 2016. and sources of bacteria in residential BIBLIOGRAPHY 125

kitchens. Environmental microbiology, Evaluation of pacbio sequencing for 15(2):588–596, 2013. full-length bacterial 16s rrna gene clas- [66] GE Flores, ST Bates, D Knights, sification. BMC microbiology, 16(1):274, CL Lauber, J Stombaugh, R Knight, 2016. and N Fierer. Microbial biogeography [74] GJ Olsen, R Overbeek, N Larsen, of public restroom surfaces. PloS one, TL Marsh, MJ McCaughey, 6(11):e28132, 2011. MA Maciukenas, W-M Kuan, TJ Macke, [67] S Lax, DP Smith, J Hampton-Marcell, Y Xing, and CR Woese. The ribosomal SM Owens, KM Handley, NM Scott, database project. Nucleic Acids Research, SM Gibbons, P Larsen, BD Shogan, 20(suppl):2199–2200, 1992. S Weiss, et al. Longitudinal analysis of [75] JR Cole, Q Wang, JA Fish, B Chai, microbial interaction between humans DM McGarrell, Y Sun, CT Brown, and the indoor environment. Science, A Porras-Alfaro, CR Kuske, and 345(6200):1048–1052, 2014. JM Tiedje. Ribosomal database project: [68] SE Schmedes, AE Woerner, and B Bu- data and tools for high throughput dowle. Forensic human identification rRNA analysis. Nucleic acids research, using skin microbiomes. Applied and 42(D1):D633–D642, 2013. environmental microbiology, pages AEM– [76] P Yilmaz, LW Parfrey, P Yarza, J Gerken, 01672, 2017. E Pruesse, C Quast, T Schweer, [69] F Schluenzen, A Tocilj, R Zarivach, J Peplies, W Ludwig, and FO Glock- J Harms, M Gluehmann, D Janell, ner. The SILVA and “all-species A Bashan, H Bartels, I Agmon, living tree project (ltp)” taxonomic F Franceschi, et al. Structure of frameworks. Nucleic acids research, functionally activated small ribosomal 42(D1):D643–D648, 2013. subunit at 3.3 å resolution. Cell, [77] D McDonald, MN Price, J Goodrich, 102(5):615–623, 2000. EP Nawrocki, TZ DeSantis, A Probst, [70] CR Woese, O Kandler, and ML Wheelis. GL Andersen, R Knight, and P Hugen- Towards a natural system of organisms: holtz. An improved Greengenes taxon- proposal for the domains archaea, bac- omy with explicit ranks for ecological teria, and eucarya. Proceedings of the Na- and evolutionary analyses of bacteria tional Academy of Sciences, 87(12):4576– and archaea. The ISME journal, 6(3):610, 4579, 1990. 2012. [71] CR Woese and GE Fox. Phyloge- [78] B Yang, Y Wang, and P-Y Qian. Sensitiv- netic structure of the prokaryotic do- ity and correlation of hypervariable re- main: the primary kingdoms. Proceed- gions in 16s rrna genes in phylogenetic ings of the National Academy of Sciences, analysis. BMC bioinformatics, 17(1):135, 74(11):5088–5090, 1977. 2016. [72] WG Weisburg, SM Barns, DA Pelletier, [79] CM Burke and AE Darling. A method and DJ Lane. 16s ribosomal dna ampli- for high precision sequencing of near fication for phylogenetic study. Journal full-length 16s rrna genes on an illu- of bacteriology, 173(2):697–703, 1991. mina miseq. PeerJ, 4:e2492, 2016. [73] J Wagner, P Coupland, H P Browne, [80] J Shin, S Lee, M-J Go, SY Lee, SC Kim, T D Lawley, S C Francis, and J Parkhill. C-H Lee, and B-K Cho. Analysis of 126 Bibliography

the mouse gut microbiome using full- community profiles through lineage- length 16s rrna amplicon sequencing. specific gene copy number correction. Scientific reports, 6:29681, 2016. Microbiome, 2(1):11, 2014. [81] S Ceuppens, D De Coninck, N Bot- [87] M Perisin, M Vetter, JA Gilbert, and tledoorn, F Van Nieuwerburgh, and J Bergelson. 16stimator: statistical es- M Uyttendaele. Microbial commu- timation of ribosomal gene copy num- nity profiling of fresh basil and pitfalls bers from draft genome assemblies. The in taxonomic assignment of enterobac- ISME journal, 10(4):1020, 2016. terial pathogenic species based upon [88] S Louca, M Doebeli, and L W Parfrey. 16S rRNA amplicon sequencing. In- Correcting for 16s rrna gene copy num- ternational journal of food microbiology, bers in microbiome surveys remains an 257:148–156, 2017. unsolved problem. Microbiome, 6(1):41, [82] FE Dewhirst, Z Shen, MS Scimeca, 2018. LN Stokes, T Boumenna, T Chen, [89] MGI Langille, J Zaneveld, JG Caporaso, BJ Paster, and JG Fox. Discordant 16S D McDonald, D Knights, JA Reyes, and 23S rRNA gene phylogenies for JC Clemente, DE Burkepile, RLV the genus helicobacter: implications for Thurber, R Knight, et al. Predic- phylogenetic inference and systemat- tive functional profiling of microbial ics. Journal of bacteriology, 187(17):6106– communities using 16s rrna marker 6118, 2005. gene sequences. Nature biotechnology, [83] S Hong, J Bunge, C Leslin, S Jeon, and 31(9):814, 2013. SS Epstein. Polymerase chain reaction [90] R Ranjan, A Rani, A Metwally, primers miss half of rRNA microbial HS McGee, and DL Perkins. Analysis diversity. The ISME Journal, 3(12):1365, of the microbiome: advantages of 2009. whole genome shotgun versus 16s [84] PHA Timmers, HCA Widjaja-Greefkes, amplicon sequencing. Biochemical and CM Plugge, and AJM Stams. Evalua- biophysical research communications, tion and optimization of PCR primers 469(4):967–977, 2016. for selective and quantitative detection [91] M Tessler, J S Neumann, E Afshinnekoo, of marine anme subclusters involved in M Pineda, R Hersch, L F M Velho, B T sulfate-dependent anaerobic methane Segovia, F A Lansac-Toha, M Lemke, oxidation. Applied microbiology and R DeSalle, et al. Large-scale differences biotechnology, 101(14):5847–5859, 2017. in microbial biodiversity discovery be- [85] RJ Case, Y Boucher, I Dahllof, C Holm- tween 16s amplicon and shotgun se- strom, WF Doolittle, and S Kjelleberg. quencing. Scientific reports, 7(1):6589, Use of 16s rrna and rpob genes as 2017. molecular markers for microbial ecol- [92] CB Driscoll, TG Otten, NM Brown, and ogy studies. Applied and environmental TW Dreher. Towards long-read meta- microbiology, 73(1):278–288, 2007. genomics: complete assembly of three [86] FE Angly, PG Dennis, A Skarshewski, novel genomes from bacteria depen- I Vanwonterghem, P Hugenholtz, and dent on a diazotrophic cyanobacterium GW Tyson. Copyrighter: a rapid tool in a freshwater lake co-culture. Stan- for improving the accuracy of microbial dards in genomic sciences, 12(1):9, 2017. BIBLIOGRAPHY 127

[93] BL Brown, M Watson, SS Minot, [102] Stephen F Altschul, W Gish, W Miller, MC Rivera, and RB Franklin. Minion EW Myers, and DJ Lipman. Basic local nanopore sequencing of environmen- alignment search tool. Journal of molec- tal metagenomes: a synthetic approach. ular biology, 215(3):403–410, 1990. GigaScience, 6(3):1–10, 2017. [103] B Buchfink, C Xie, and DH Huson. [94] Simon Andrews et al. Fastqc: a qual- Fast and sensitive protein alignment us- ity control tool for high throughput se- ing diamond. Nature methods, 12(1):59, quence data. 2010. 2014. [95] M Martin. Cutadapt removes adapter [104] M Hamada, Y Ono, K Asai, and sequences from high-throughput se- MC Frith. Training alignment pa- quencing reads. EMBnet. journal, rameters for arbitrary sequencers with 17(1):pp–10, 2011. last-train. Bioinformatics, 33(6):926–928, 2016. [96] AM Bolger, M Lohse, and B Usadel. Trimmomatic: a flexible trimmer for il- [105] H Li and R Durbin. Fast and accurate lumina sequence data. Bioinformatics, short read alignment with Burrows– 30(15):2114–2120, 2014. Wheeler transform. bioinformatics, 25(14):1754–1760, 2009. [97] S Lindgreen, KL Adair, and PP Gard- ner. An evaluation of the accuracy and [106] B Langmead and SL Salzberg. Fast speed of metagenome analysis tools. gapped-read alignment with Bowtie 2. Scientific reports, 6:19233, 2016. Nature methods, 9(4):357, 2012. [107] WJ Kent. BLAT - the blast-like align- [98] PHA Sneath, RR Sokal, et al. Numerical ment tool. Genome research, 12(4):656– taxonomy. The principles and practice of 664, 2002. numerical classification. 1973. [108] AV Aho, JE Hopcroft, and JD Ullman. [99] PD Schloss, SL Westcott, T Ryabin, On finding lowest common ancestors JR Hall, M Hartmann, EB Hollister, in trees. SIAM Journal on computing, RA Lesniewski, BB Oakley, DH Parks, 5(1):115–132, 1976. CJ Robinson, et al. Introducing mothur: open-source, platform-independent, [109] DH Huson, AF Auch, J Qi, and community-supported software for SC Schuster. Megan analysis of metage- describing and comparing microbial nomic data. Genome research, 17(3):000– communities. Applied and environmental 000, 2007. microbiology, 75(23):7537–7541, 2009. [110] DE Wood and SL Salzberg. Kraken: ul- [100] JG Caporaso, J Kuczynski, trafast metagenomic sequence classifi- J Stombaugh, K Bittinger, FD Bush- cation using exact alignments. Genome man, EK Costello, N Fierer, AG Pena, biology, 15(3):R46, 2014. JK Goodrich, JI Gordon, et al. QIIME [111] D Kim, L Song, FP Breitwieser, and allows analysis of high-throughput SL Salzberg. Centrifuge: rapid and community sequencing data. Nature sensitive classification of metagenomic methods, 7(5):335, 2010. sequences. Genome research, 2016. [101] RC Edgar. Search and clustering orders [112] M Burrows and DJ Wheeler. A block- of magnitude faster than blast. Bioinfor- sorting lossless data compression algo- matics, 26(19):2460–2461, 2010. rithm. 1994. 128 Bibliography

[113] P Ferragina and G Manzini. Indexing metagenomic shotgun sequences. Ge- compressed text. Journal of the ACM nome biology, 12(1):P11, 2011. (JACM), 52(4):552–581, 2005. [122] S Sunagawa, DR Mende, G Zeller, [114] AL Delcher, S Kasif, RD Fleischmann, F Izquierdo-Carrasco, SA Berger, J Peterson, O White, and SL Salzberg. JR Kultima, LP Coelho, M Arumugam, Alignment of whole genomes. Nucleic J Tap, HB Nielsen, et al. Metagenomic acids research, 27(11):2369–2376, 1999. species profiling using universal phylogenetic marker genes. Nature [115] R Ounit, S Wanamaker, TJ Close, and methods, 10(12):1196, 2013. S Lonardi. Clark: fast and accurate classification of metagenomic and genomic [123] D Koslicki, S Foucart, and G Rosen. sequences using discriminative k-mers. Quikr: a method for rapid recon- BMC genomics, 16(1):236, 2015. struction of bacterial communities via compressive sensing. Bioinformatics, [116] TAK Freitas, P-E Li, MB Scholz, and 29(17):2096–2102, 2013. PSG Chain. Accurate read-based metagenome characterization using a hier- [124] D Koslicki, S Foucart, and G Rosen. archical suite of unique signatures. Nu- Wgsquikr: fast whole-genome shotgun cleic acids research, 43(10):e69–e69, 2015. metagenomic classification. PloS one, 9(3):e91784, 2014. [117] N Segata, L Waldron, A Ballarini, [125] P Menzel, KL Ng, and A Krogh. Fast V Narasimhan, O Jousson, and C Hut- and sensitive taxonomic classification tenhower. Metagenomic microbial com- for metagenomics with kaiju. Nature munity profiling using unique clade- communications, 7:11257, 2016. specific marker genes. Nature methods, 9(8):811, 2012. [126] N-P Nguyen, S Mirarab, B Liu, M Pop, and T Warnow. Tipp: taxonomic iden- [118] F Meyer, D Paarmann, M D’Souza, tification and phylogenetic profiling. R Olson, EM Glass, M Kubal, T Paczian, Bioinformatics, 30(24):3548–3555, 2014. A Rodriguez, R Stevens, A Wilke, et al. The metagenomics RAST server - a [127] GGZ Silva, DA Cuevas, BE Dutilh, and public resource for the automatic phy- RA Edwards. Focus: an alignment- logenetic and functional analysis of free model to identify organisms in metagenomes. BMC bioinformatics, metagenomes using non-negative least PeerJ 9(1):386, 2008. squares. , 2:e425, 2014. [128] S Hunter, M Corbett, H Denise, [119] M Rho, H Tang, and Y Ye. FragGe- M Fraser, A Gonzalez-Beltran, neScan: predicting genes in short and C Hunter, P Jones, R Leinonen, error-prone reads. Nucleic acids research, C McAnulla, E Maguire, et al. Ebi 38(20):e191–e191, 2010. metagenomics—a new resource for [120] J Droge, I Gregor, and AC McHardy. the analysis and archiving of meta- Taxator-tk: precise taxonomic assign- genomic data. Nucleic acids research, ment of metagenomes by fast approxi- 42(D1):D600–D606, 2013. mation of evolutionary neighborhoods. [129] E Quevillon, V Silventoinen, S Pillai, Bioinformatics, 31(6):817–824, 2014. N Harte, N Mulder, R Apweiler, and [121] B Liu, T Gibbons, M Ghodsi, T Trean- R Lopez. Interproscan: protein do- gen, and M Pop. Accurate and fast mains identifier. Nucleic acids research, estimation of taxonomic profiles from 33(suppl_2):W116–W120, 2005. BIBLIOGRAPHY 129

[130] J-H Lee, H Yi, and J Chun. rrnaselector: [139] C Lozupone, M Hamady, and R Knight. a computer program for selecting ri- Unifrac–an online tool for comparing bosomal rna encoding sequences from microbial community diversity in a metagenomic and metatranscriptomic phylogenetic context. BMC bioinformat- shotgun libraries. The Journal of Micro- ics, 7(1):371, 2006. biology, 49(4):689, 2011. [140] A Kislyuk, S Bhatnagar, J Dushoff, [131] A Bateman, L Coin, R Durbin, RD Finn, and JS Weitz. Unsupervised statisti- V Hollich, S Griffiths-Jones, A Khanna, cal clustering of environmental shot- M Marshall, S Moxon, ELL Sonnham- gun sequences. BMC bioinformatics, mer, et al. The pfam protein fami- 10(1):316, 2009. lies database. Nucleic acids research, 32(suppl_1):D138–D141, 2004. [141] DD Roumpeka, RJ Wallace, F Es- calettes, I Fotheringham, and M Wat- [132] DH Haft, JD Selengut, and O White. son. A review of bioinformatics tools The tigrfams database of protein fami- for bio-prospecting from metagenomic lies. Nucleic acids research, 31(1):371–373, sequence data. Frontiers in genetics, 8:23, 2003. 2017. [133] TK Attwood and ME Beck. Prints–a [142] Y-W Wu and Y Ye. A novel abundance- protein motif fingerprint database. Pro- based algorithm for binning metageno- tein Engineering, Design and Selection, mic sequences using l-tuples. Journal 7(7):841–848, 1994. of Computational Biology, 18(3):523–534, [134] N Hulo, A Bairoch, V Bulliard, 2011. L Cerutti, E De Castro, PS Langendijk- Genevaux, M Pagni, and CJA Sigrist. [143] Y Wang, HCM Leung, S-M Yiu, and The prosite database. Nucleic acids FYL Chin. Metacluster 4.0: a novel bin- research, 34(suppl_1):D227–D230, 2006. ning algorithm for NGS reads and huge number of species. Journal of Computa- [135] DWA Buchan, SCG Rison, JE Bray, tional Biology, 19(2):241–249, 2012. D Lee, F Pearl, JM Thornton, and CA Orengo. Gene3d: structural assign- [144] T Van Lang, T Van Hoai, et al. A ments for the biologist and bioinfor- two-phase binning algorithm using maticist alike. Nucleic acids research, l-mer frequency on groups of non- 31(1):469–473, 2003. overlapping reads. Algorithms for Molec- [136] IF Spellerberg and PJ Fedor. A tribute ular Biology, 10(1):2, 2015. to claude shannon (1916–2001) and a [145] K Song, J Ren, G Reinert, M Deng, plea for more rigorous use of species MS Waterman, and F Sun. New de- richness, species diversity and the velopments of alignment-free sequence ‘shannon–wiener’index. Global ecology comparison: measures, statistics and and biogeography, 12(3):177–179, 2003. next-generation sequencing. Briefings [137] EH Simpson. Measurement of diversity. in bioinformatics, 15(3):343–353, 2013. nature, 1949. [146] S Girotto, C Pizzi, and M Comin. [138] JR Bray and JT Curtis. An ordination Metaprob: accurate metagenomic reads of the upland forest communities of binning based on probabilistic se- southern wisconsin. Ecological mono- quence signatures. Bioinformatics, graphs, 27(4):325–349, 1957. 32(17):i567–i575, 2016. 130 Bibliography

[147] X Ding, F Cheng, C Cao, and X Sun. [155] VB Dubinkina, DS Ischenko, VI Ulyant- Dectico: an alignment-free supervised sev, AV Tyakht, and DG Alexeev. As- metagenomic classification method sessment of k-mer spectrum applicabil- based on feature extraction and dy- ity for metagenomic dissimilarity anal- namic selection. BMC bioinformatics, ysis. BMC bioinformatics, 17(1):38, 2016. 16(1):323, 2015. [156] S Chatterji, I Yamazaki, Z Bai, and [148] H Cui and X Zhang. Alignment-free su- JA Eisen. Compostbin: A dna pervised classification of metagenomes composition-based algorithm for bin- by recursive svm. BMC genomics, ning environmental shotgun reads. In 14(1):641, 2013. Annual International Conference on Re- [149] W Liao, J Ren, K Wang, S Wang, F Zeng, search in Computational Molecular Biol- Y Wang, and F Sun. Alignment- ogy, pages 17–28. Springer, 2008. free transcriptomic and metatranscriptomic comparison using sequencing [157] M Comin and M Schimd. Fast com- signatures with variable length markov parison of genomic and meta-genomic chains. Scientific reports, 6:37243, 2016. reads with alignment-free measures based on quality values. BMC medical [150] CC Laczny, C Kiefer, V Galata, genomics, 9(1):36, 2016. T Fehlmann, C Backes, and A Keller. Busybee web: metagenomic data [158] G Benoit, P Peterlongo, M Mariadas- analysis by bootstrapped supervised sou, E Drezen, S Schbath, D Lavenier, binning and annotation. Nucleic acids and C Lemaitre. Multiple compara- research, 45(W1):W171–W179, 2017. tive metagenomics using multiset k- [151] Y Wang, H Hu, and X Li. Mbmc: An mer counting. PeerJ Computer Science, effective markov chain approach for 2:e94, 2016. binning metagenomic reads from envi- [159] SV Thankachan, SP Chockalingam, ronmental shotgun sequencing projects. Y Liu, A Apostolico, and S Aluru. Al- Omics: a journal of integrative biology, fred: a practical method for alignment- 20(8):470–479, 2016. free distance computation. Journal [152] RM Kotamarti, M Hahsler, D Raiford, of Computational Biology, 23(6):452–460, M McGee, and MaH Dunham. Analyz- 2016. ing taxonomic classification using ex- tensible markov models. Bioinformatics, [160] Y Wang, X Lei, S Wang, Z Wang, 26(18):2235–2241, 2010. N Song, F Zeng, and T Chen. Effect of [153] H-S Seok, W Hong, and J Kim. Es- k-tuple length on sample-comparison timating the composition of species with high-throughput sequencing data. in metagenomes by clustering of next- Biochemical and biophysical research com- generation read sequences. Methods, munications, 469(4):1021–1027, 2016. 69(3):213–219, 2014. [161] C Rinke, P Schwientek, A Sczyrba, [154] VI Ulyantsev, SV Kazakov, VB Du- NN Ivanova, IJ Anderson, J-F Cheng, binkina, AV Tyakht, and DG Alex- A Darling, S Malfatti, BK Swan, eev. Metafast: fast reference-free graph- EA Gies, et al. Insights into the phy- based comparison of shotgun metage- logeny and coding potential of micro- nomic data. Bioinformatics, 32(18):2760– bial dark matter. Nature, 499(7459):431, 2767, 2016. 2013. BIBLIOGRAPHY 131

[162] CE Mason and S Tighe. Focus on meta- [172] Atsushi Kouzuma, Shunichi Ishii, and genomics. Journal of Biomolecular Tech- Kazuya Watanabe. Metagenomic in- niques: JBT, 28(1):1, 2017. sights into the ecology and physiology [163] S Kumar, KK Krishnani, B Bhushan, of microbes in bioelectrochemical sys- and MP Brahmane. Metagenomics: ret- tems. Bioresource technology, 2018. rospect and prospects in high through- [173] FH Coutinho, GB Gregoracci, JM Wal- put age. Biotechnology research interna- ter, CC Thompson, and FL Thomp- tional, 2015, 2015. son. Metagenomics sheds light on the [164] DB Roszak and RR Colwell. Survival ecology of marine microbes and their strategies of bacteria in the natural viruses. Trends in Microbiology, 2018. environment. Microbiological reviews, [174] RJ Boissy, DJ Romberger, WA Roug- 51(3):365, 1987. head, L Weissenburger-Moser, [165] EJ Stewart. Growing unculturable bac- JA Poole, and TD LeVan. Shot- teria. Journal of bacteriology, pages JB– gun pyrosequencing metagenomic 00345, 2012. analyses of dusts from swine conﬁne- [166] KI Mohr. Diversity of myxobacteria-we ment and grain facilities. PloS one, only see the tip of the iceberg. Microor- 9(4):e95578, 2014. ganisms, 6(3), 2018. [175] B Carbonetto, N Rascovan, R Alvarez, [167] M Hamady, C Fraser-Liggett, R Knight, A Mentaberry, and MP Vazquez. Struc- et al. The human microbiome project: ture, composition and metagenomic Exploring the microbial part of our- proﬁle of soil microbiomes associated selves in a changing world. Nature, to agricultural land use and tillage sys- 449(7164):804–10, 2007. tems in argentine pampas. PloS one, [168] W-L Wang, S-Y Xu, Z-G Ren, L Tao, J-W 9(6):e99949, 2014. Jiang, and S-S Zheng. Application of [176] JQ Su, B Wei, CY Xu, M Qiao, and metagenomics in the human gut micro- YG Zhu. Functional metagenomic biome. World journal of gastroenterology: characterization of antibiotic resistance WJG, 21(3):803, 2015. genes in agricultural soils from China. [169] S Al Khodor, B Reichert, and IF Shatat. Environment international, 65:9–15, 2014. The microbiome and blood pressure: [177] SJ Finley, ME Benbow, and GT Javan. can microbes regulate our blood pres- Microbial communities associated with sure? Frontiers in pediatrics, 5:138, 2017. human decomposition and their poten- [170] R Kolde, EA Franzosa, G Rahnavard, tial use as postmortem clocks. Interna- AB Hall, H Vlamakis, C Stevens, tional journal of legal medicine, 129(3):623– MJ Daly, RJ Xavier, and C Huttenhower. 632, 2015. Host genetic variation and its microbiome interactions within the human [178] A Fornaciari. Environmental micro- microbiome project. Genome medicine, bial forensics and archaeology of past 10(1):6, 2018. pandemics. Microbiology spectrum, 5(1), 2017. [171] M Hattori and T D Taylor. The human intestinal microbiome: a new frontier of [179] Q Peng, X Wang, M Shang, J Huang, human biology. DNA research, 16(1):1– G Guan, Y Li, and B Shi. Isolation of 12, 2009. a novel alkaline-stable lipase from a 132 Bibliography

metagenomic library and its specific ap- [187] SW Kembel, M Wu, JA Eisen, and plication for milkfat flavor production. JL Green. Incorporating 16S gene Microbial cell factories, 13(1):1, 2014. copy number information improves [180] M Drancourt, C Bollet, A Carlioz, estimates of microbial diversity and R Martelin, J-P Gayral, and D Raoult. abundance. PLoS computational biology, 16S ribosomal DNA sequence analy- 8(10):e1002743, 2012. sis of a large collection of environmen- [188] EN Hanssen, KH Liland, P Gill, and tal and clinical unidentifiable bacterial L Snipen. Optimizing body fluid recog- isolates. Journal of clinical microbiology, nition from microbial taxonomic pro- 38(10):3623–3630, 2000. files. Forensic Science International: Ge- [181] G Muyzer, EC De Waal, and AG Uitter- netics, 37:13–20, 2018. linden. Profiling of complex microbial [189] GJ Olsen and CR Woese. Ribosomal populations by denaturing gradient gel rna: a key to phylogeny. The FASEB electrophoresis analysis of polymerase journal, 7(1):113–123, 1993. chain reaction-amplified genes coding [190] P Yilmaz, R Kottmann, E Pruesse, for 16S rRNA. Applied and environmental C Quast, and FO Glockner. Analysis microbiology, 59(3):695–700, 1993. of 23s rrna genes in metagenomes–a [182] M Balvociute and DH Huson. SILVA, case study from the global ocean sam- RDP, Greengenes, NCBI and OTT — pling expedition. Systematic and applied how do these taxonomies compare? microbiology, 34(6):462–469, 2011. BMC genomics, 18(2):114, 2017. [191] L Yang, Z Tan, D Wang, L Xue, M-X [183] JM Janda and SL Abbott. 16S rRNA Guan, T Huang, and R Li. Species gene sequencing for bacterial identi- identification through mitochondrial fication in the diagnostic laboratory: rrna genetic analysis. Scientific reports, pluses, perils, and pitfalls. Journal 4:4089, 2014. of clinical microbiology, 45(9):2761–2764, [192] AE Budding, M Hoogewerf, CMJE 2007. Vandenbroucke-Grauls, and PHM [184] J-H Ahn, B-Y Kim, J Song, and H-Y Savelkoul. Automated broad-range Weon. Effects of PCR cycle number molecular detection of bacteria in and DNA polymerase type on the 16S clinical samples. Journal of clinical rRNA gene pyrosequencing analysis of microbiology, 54(4):934–943, 2016. bacterial communities. Journal of Micro- [193] FCA Quaak, T van Duijn, J Hoogen- biology, 50(6):1071–1074, 2012. boom, AD Kloosterman, and I Kuiper. [185] JP Brooks, DJ Edwards, MD Harwich, Human-associated microbial popula- MC Rivera, JM Fettweis, MG Serrano, tions as evidence in forensic casework. RA Reris, NU Sheth, B Huang, P Girerd, Forensic Science International: Genetics, et al. The truth about metagenomics: 36:176–185, 2018. quantifying and counteracting bias in [194] AE Woerner, NMM Novroski, 16S rRNA studies. BMC microbiology, FR Wendt, A Ambers, R Wiley, 15(1):66, 2015. SE Schmedes, and B Budowle. Forensic [186] AJ Pinto and L Raskin. PCR biases dis- human identification with targeted tort bacterial and archaeal community microbiome markers using nearest structure in pyrosequencing datasets. neighbor classification. Forensic Science PloS one, 7(8):e43093, 2012. International: Genetics, 38:130–139, 2019. BIBLIOGRAPHY 133

[195] J Jovel, J Patterson, W Wang, N Hotte, [202] A Sczyrba, P Hofmann, P Belmann, S O’Keefe, T Mitchel, T Perry, D Kao, D Koslicki, S Janssen, J Droge, I Gre- AL Mason, KL Madsen, et al. Charac- gor, S Majda, J Fiedler, E Dahms, and terization of the gut microbiome using et al. Critical assessment of metage- 16S or shotgun metagenomics. Frontiers nome interpretation—a benchmark of in microbiology, 7:459, 2016. metagenomics software. Nature methods, 14(11):1063, 2017. [196] N Shah, H Tang, TG Doak, and Y Ye. Comparing bacterial communities in- [203] MA Peabody, T Van Rossum, R Lo, and ferred from 16S rRNA gene sequencing FSL Brinkman. Evaluation of shotgun and shotgun metagenomics. In Biocom- metagenomics sequence classification puting 2011, pages 165–176. World Sci- methods using in silico and in vitro sim- entific, 2011. ulated communities. BMC bioinformatics, 16(1):362, 2015. [197] B Steven, LV Gallegos-Graves, SR Starkenburg, PS Chain, and [204] K Mavromatis, N Ivanova, K Barry, CR Kuske. Targeted and shotgun meta- H Shapiro, E Goltsman, AC McHardy, genomic approaches provide different I Rigoutsos, A Salamov, F Korze- descriptions of dryland soil microbial niewski, M Land, and et al. Use of sim- communities in a manipulated field ulated data sets to evaluate the fidelity study. Environmental microbiology of metagenomic processing methods. reports, 4(2):248–256, 2012. Nature methods, 4(6):495, 2007. [205] ABR McIntyre, R Ounit, E Afshin- [198] A Almeida, AL Mitchell, A Tarkowska, nekoo, RJ Prill, E Henaff, N Alexander, and RD Finn. Benchmarking tax- SS Minot, D Danko, J Foox, S Ahsanud- onomic assignments based on 16s din, and et al. Comprehensive bench- rrna gene profiling of the micro- marking and ensemble approaches for biota from commonly sampled environ- metagenomic classifiers. Genome biol- ments. BMC Genomics, 17(1), 2016. ogy, 18(1):182, 2017. [199] T Sijen. Molecular approaches for foren- [206] AM Walsh, F Crispie, O O’Sullivan, sic cell type identification: on mrna, L Finnegan, MJ Claesson, and PD Cot- mirna, dna methylation and microbial ter. Species classifier choice is a markers. Forensic Science International: key consideration when analysing Genetics, 18:21–32, 2015. low-complexity food microbiome data. [200] TH Clarke, A Gomez, H Singh, KE Nel- Microbiome, 6(1):50, 2018. son, and LM Brinkac. Integrating the [207] VC Piro, M Matschkowski, and BY Re- microbiome as a resource in the foren- nard. Metameta: integrating metage- sics toolkit. Forensic Science Interna- nome analysis tools to improve taxo- tional: Genetics, 30:141–147, 2017. nomic profiling. Microbiome, 5(1):101, [201] R D’Amore, U Z Ijaz, M Schirmer, 2017. JG Kenny, R Gregory, AC Darby, [208] A Escobar-Zepeda, EE Godoy-Lozano, M Shakya, M Podar, C Quince, and L Raggi, L Segovia, E Merino, N Hall. A comprehensive benchmark- RM Gutierrez-Rios, K Juarez, AF Licea- ing study of protocols and sequencing Navarro, L Pardo-Lopez, and platforms for 16s rrna community pro- A Sanchez-Flores. Analysis of se- filing. BMC genomics, 17(1):55, 2016. quencing strategies and tools for 134 Bibliography

taxonomic annotation: Defining stan- V Dubourg, et al. Scikit-learn: Ma- dards for progressive metagenomics. chine learning in python. Journal of Scientific reports, 8(1):12034, 2018. machine learning research, 12(Oct):2825– [209] E Plummer, J Twin, D M Bulach, 2830, 2011. SM Garland, and SN Tabrizi. A compar- [215] T Magoc and SL Salzberg. FLASH: fast ison of three bioinformatics pipelines length adjustment of short reads to im- for the analysis of preterm gut micro- prove genome assemblies. Bioinformat- biota using 16S rRNA gene sequencing ics, 27(21):2957–2963, 2011. data. Journal of Proteomics & Bioinformat- [216] NA O’Leary, MW Wright, JR Bris- ics, 8(12):283, 2015. ter, S Ciufo, D Haddad, R McVeigh, [210] H Hasman, D Saputra, T Sicheritz- B Rajput, B Robbertse, B Smith-White, Ponten, O Lund, CA Svendsen, D Ako-Adjei, et al. Reference sequence N Frimodt-Moller, and FM Aarestrup. (RefSeq) database at NCBI: current sta- Rapid whole genome sequencing for tus, taxonomic expansion, and func- the detection and characterization of tional annotation. Nucleic acids research, microorganisms directly from clinical 44(D1):D733–D745, 2015. samples. Journal of clinical microbiology, pages JCM–02452, 2013. [217] FP Breitwieser and SL Salzberg. Pavian: Interactive analysis of metagenomics [211] A Klindworth, E Pruesse, T Schweer, data for microbiomics and pathogen J Peplies, C Quast, M Horn, and identification. BioRxiv, page 084715, FO Glockner. Evaluation of general 2016. 16S ribosomal RNA gene PCR primers for classical and next-generation [218] A Wilke, T Harrison, J Wilkening, sequencing-based diversity studies. D Field, EM Glass, N Kyrpides, Nucleic acids research, 41(1):e1–e1, 2013. K Mavrommatis, and F Meyer. The m5nr: a novel non-redundant database [212] A Bankevich, S Nurk, D Antipov, containing protein sequences and an- AA Gurevich, M Dvorkin, AS Ku- notations from multiple sources and likov, VM Lesin, SI Nikolenko, S Pham, associated tools. BMC bioinformatics, AD Prjibelski, et al. SPAdes: a new ge- 13(1):141, 2012. nome assembly algorithm and its applications to single-cell sequencing. Jour- [219] HB Mann and DR Whitney. On a test of nal of computational biology, 19(5):455– whether one of two random variables is 477, 2012. stochastically larger than the other. The annals of mathematical statistics, pages [213] SY Anvar, L Khachatryan, M Ver- 50–60, 1947. maat, M van Galen, I Pulyakhina, Y Ariyurek, K Kraaijeveld, JT den Dun- [220] Y Benjamini, Yand Hochberg. Control- nen, P de Knijff, P Ac’t Hoen, et al. ling the false discovery rate: a practical Determining the quality and complex- and powerful approach to multiple test- ity of next-generation sequencing data ing. Journal of the Royal statistical society: without a reference genome. Genome series B (Methodological), 57(1):289–300, biology, 15(12):555, 2014. 1995. [214] F Pedregosa, G Varoquaux, A Gram- [221] C Van Rijsbergen. Information retrieval: fort, V Michel, B Thirion, O Grisel, theory and practice. In Proceedings M Blondel, P Prettenhofer, R Weiss, of the Joint IBM/University of Newcastle BIBLIOGRAPHY 135

upon Tyne Seminar on Data Base Systems, [229] SL Edmonds-Wilson, NI Nurinova, pages 1–14, 1979. CA Zapka, N Fierer, and M Wilson. Re- [222] N Nagarajan, C Cook, MP Di Bonaven- view of human hand microbiome re- Journal of dermatological science tura, H Ge, A Richards, KA Bishop- search. , Lilly, R DeSalle, TD Read, and M Pop. 80(1):3–12, 2015. Finishing genomes with limited re- [230] HE Blum. The human microbiome. Ad- sources: lessons from an ensemble of vances in medical sciences, 62(2):414–420, microbial genomes. BMC genomics, 2017. 11(1):242, 2010. [231] E Holmes, JV Li, JR Marchesi, and [223] DJ Edwards and KE Holt. Begin- JK Nicholson. Gut microbiota compo- ner’s guide to comparative bacterial ge- sition and activity in relation to host nome analysis using next-generation metabolic phenotype and disease risk. sequence data. Microbial informatics and Cell metabolism, 16(5):559–564, 2012. experimentation, 3(1):2, 2013. [232] AP Bhatt, MR Redinbo, and SJ Bultman. The role of the microbiome in cancer [224] EA Grice and JA Segre. The skin micro- development and therapy. CA: a can- biome. Nature Reviews Microbiology, cer journal for clinicians, 67(4):326–344, 9(4):244, 2011. 2017. [225] S Bikel, A Valdez-Lara, F Cornejo- [233] I Cho and MJ Blaser. The human micro- Granados, K Rico, S Canizales- biome: at the interface of health and dis- Quinteros, X Soberon, L Del Pozo- ease. Nature Reviews Genetics, 13(4):260, Yauner, and A Ochoa-Leyva. Com- 2012. bining metagenomics, metatranscrip- [234] JL Sonnenburg and F Backhed. Diet– tomics and viromics to explore novel microbiota interactions as modera- microbial interactions: towards a tors of human metabolism. Nature, systems-level understanding of human 535(7610):56, 2016. microbiome. Computational and structural biotechnology journal, 13:390–401, [235] BH Mullish, JR Marchesi, MR Thursz, 2015. and HRT Williams. Microbiome manip- ulation with faecal microbiome trans- [226] MJ Gosalbes, JJ Abellan, A Dur- plantation as a therapeutic strategy in ban, AE Perez-Cobas, A Latorre, and clostridium difﬁcile infection. QJM: A Moya. Metagenomics of human An International Journal of Medicine, microbiome: beyond 16S rDNA. Clini- 108(5):355–359, 2014. cal Microbiology and Infection, 18:47–49, [236] RD Moloney, L Desbonnet, G Clarke, 2012. TG Dinan, and JF Cryan. The micro- [227] S Maccaferri, E Biagi, and P Brigidi. biome: stress, health and disease. Mam- Metagenomics: key to human gut mi- malian Genome, 25(1-2):49–74, 2014. Digestive diseases crobiota. , 29(6):525– [237] AV Contreras, B Cocom-Chan, 530, 2011. G Hernandez-Montes, T Portillo- [228] R Martin, S Miquel, P Langella, and Bobadilla, and O Resendis-Antonio. LG Bermudez-Humaran. The role of Host-microbiome interaction and can- metagenomics in understanding the cer: Potential application in precision human microbiome in health and dis- medicine. Frontiers in physiology, 7:606, ease. Virulence, 5(3):413–423, 2014. 2016. 136 Bibliography

[238] C He, Y Shan, and W Song. Targeting challenge of annotating 200 genomes gut microbiota as a possible therapy for with 4 million publications. EMBO re- diabetes. Nutrition Research, 35(5):361– ports, 6(5):397–399, 2005. 367, 2015. [247] KB Akondi and VV Lakshmi. Emerging [239] CJ Marx. Can you sequence ecology? trends in genomic approaches for mi- metagenomics of adaptive diversifica- crobial bioprospecting. Omics: a journal tion. PLoS biology, 11(2):e1001487, 2013. of integrative biology, 17(2):61–70, 2013. [240] S Hiraoka, C-C Yang, and W Iwasaki. [248] JC Hunter-Cevera. The value of micro- Metagenomics and bioinformatics in bial diversity. Current Opinion in Micro- microbial ecology: current status and biology, 1(3):278–285, 1998. beyond. Microbes and environments, [249] NR Pace. Mapping the tree of life: 31(3):204–212, 2016. progress and prospects. Microbiology [241] R Tiwari, L Nain, N E Labrou, and and molecular biology reviews, 73(4):565– P Shukla. Bioprospecting of functional 576, 2009. cellulases from metagenome for second generation biofuel production: a review. [250] J-D Grattepanche, LF Santoferrara, Critical reviews in microbiology, 44(2):244– GB McManus, and LA Katz. Diversity 257, 2018. of diversity: conceptual and methodological differences in biodiversity es- [242] MOA Sommer, GM Church, and G Dan- timates of eukaryotic microbes as com- tas. A functional metagenomic ap- pared to bacteria. Trends in microbiology, proach for expanding the synthetic bi- 22(8):432–437, 2014. ology toolbox for biomass conversion. Molecular systems biology, 6(1):360, 2010. [251] L Zinger, A Gobet, and T Pommier. Two decades of describing the unseen [243] V Kunin, A Copeland, A Lapidus, majority of aquatic microbial diver- K Mavromatis, and P Hugenholtz. A sity. Molecular Ecology, 21(8):1878–1896, bioinformatician’s guide to metageno- 2012. mics. Microbiology and molecular biology reviews, 72(4):557–578, 2008. [252] B Szalkai, I Scheer, K Nagy, BG Vertessy, and V Grolmusz. The metagenomic [244] SS Mande, MH Mohammed, and telescope. PloS one, 9(7):e101605, 2014. TS Ghosh. Classification of metagenomic sequences: methods and chal- [253] GL Rosen, R Polikar, DA Caseiro, lenges. Briefings in bioinformatics, SD Essinger, and BA Sokhansanj. Dis- 13(6):669–681, 2012. covering the unknown: improving detection of novel species and genera [245] Leandro N Lemos, Roberta R from short reads. BioMed Research Inter- Fulthorpe, Eric W Triplett, and national, 2011, 2011. Luiz FW Roesch. Rethinking microbial diversity analysis in the high [254] Y Ono, K Asai, and M Hamada. Pbsim: throughput sequencing era. Journal Pacbio reads simulator—toward accu- of microbiological methods, 86(1):42–51, rate genome assembly. Bioinformatics, 2011. 29(1):119–121, 2012. [246] P Janssen, L Goldovsky, V Kunin, [255] E Van Eijk, SY Anvar, HP Browne, N Darzentas, and CA Ouzounis. Ge- WY Leung, J Frank, AM Schmitz, nome coverage, literally speaking: The AP Roberts, and WK Smits. Complete BIBLIOGRAPHY 137

genome sequence of the Clostridium dif- human genetics: design and interpreta- ficile laboratory strain 630δ erm reveals tion. Nature Reviews Genetics, 14(7):460, differences from strain 630, including 2013. translocation of the mobile element ctn [263] A Nekrutenko and J Taylor. Next- BMC genomics 5. , 16(1):31, 2015. generation sequencing data interpre- [256] MF Haroon, S Hu, Y Shi, M Imelfort, tation: enhancing reproducibility and J Keller, P Hugenholtz, Z Yuan, and accessibility. Nature Reviews Genetics, GW Tyson. Anaerobic oxidation of 13(9):667, 2012. methane coupled to nitrate reduction [264] M Costello, TJ Pugh, TJ Fennell, C Stew- Nature in a novel archaeal lineage. , art, L Lichtenstein, JC Meldrim, JL Fos- 500(7464):567, 2013. tel, DC Friedrich, D Perrin, D Dionne, [257] MJ Chaisson and G Tesler. Mapping et al. Discovery and characterization of single molecule sequencing reads us- artifactual mutations in deep coverage ing basic local alignment with succes- targeted capture sequencing data due sive refinement (blasr): application and to oxidative DNA damage during sam- theory. BMC bioinformatics, 13(1):238, ple preparation. Nucleic acids research, 2012. 41(6):e67–e67, 2013. [258] C-S Chin, P Peluso, FJ Sedlazeck, [265] C Alkan, BP Coe, and EE Eichler. Ge- M Nattestad, GT Concepcion, A Clum, nome structural variation discovery C Dunn, R O’Malley, R Figueroa- and genotyping. Nature Reviews Genet- Balderas, A Morales-Cruz, et al. Phased ics, 12(5):363, 2011. diploid genome assembly with single- [266] JM Kidd, N Sampas, F Antonacci, Nature molecule real-time sequencing. T Graves, R Fulton, HS Hayden, methods , 13(12):1050, 2016. C Alkan, M Malig, M Ventura, G Gian- [259] L van der Maaten and G Hinton. Vi- nuzzi, et al. Characterization of missing sualizing data using t-sne. Journal of human genome sequences and copy- machine learning research, 9(Nov):2579– number polymorphic insertions. Na- 2605, 2008. ture methods, 7(5):365, 2010. [260] M Ester, H-P Kriegel, J Sander, X Xu, [267] H Li and N Homer. A survey of se- et al. A density-based algorithm for dis- quence alignment algorithms for next- covering clusters in large spatial data- generation sequencing. Briefings in bases with noise. In Kdd, volume 96, bioinformatics, 11(5):473–483, 2010. pages 226–231, 1996. [268] J Kuczynski, CL Lauber, WA Walters, [261] J Frank, S Lucker, RHAM Vossen, MSM LW Parfrey, JC Clemente, D Gevers, Jetten, RJ Hall, HJM Op den Camp, and and R Knight. Experimental and an- SY Anvar. Resolving the complete ge- alytical tools for studying the human nome of kuenenia stuttgartiensis from microbiome. Nature Reviews Genetics, a membrane bioreactor enrichment us- 13(1):47, 2012. ing single-molecule real-time sequenc- [269] S Subramanian and S Kumar. Neutral Scientific reports ing. , 8(1):4580, 2018. substitutions occur at a faster rate in ex- [262] DB Goldstein, A Allen, J Keebler, ons than in noncoding DNA in primate EH Margulies, S Petrou, S Petrovski, genomes. Genome research, 13(5):838– and S Sunyaev. Sequencing studies in 844, 2003. 138 Bibliography

[270] J Sved and A Bird. The expected k-mer and k-flank patterns provides ev- equilibrium of the CpG dinucleotide idence for CpG island sequence evolu- in vertebrate genomes under a mutation in mammalian genomes. Nucleic tion model. Proceedings of the National acids research, 41(9):4783–4791, 2013. Academy of Sciences, 87(12):4692–4696, [279] DR Kelley, MC Schatz, and SL Salzberg. 1990. Quake: quality-aware detection and [271] Ms Csuros, L Noe, and G Kucherov. Re- correction of sequencing errors. Genome considering the significance of genomic biology, 11(11):R116, 2010. word frequencies. Trends in Genetics, [280] R Chikhi and P Medvedev. Informed 23(11):543–546, 2007. and automated k-mer size selection [272] C Acquisti, G Poste, D Curtiss, and for genome assembly. Bioinformatics, S Kumar. Nullomers: really a matter of 30(1):31–37, 2013. natural selection? PloS one, 2(10):e1022, [281] A Brazma, I Jonassen, J Vilo, and 2007. E Ukkonen. Predicting gene regulatory [273] J Josse, AD Kaiser, and A Kornberg. En- elements in silico on a genomic scale. zymatic synthesis of deoxyribonucleic Genome research, 8(11):1202–1215, 1998. acid VIII. frequencies of nearest neigh- [282] GE Sims, S-R Jun, GA Wu, and S-H bor base sequences in deoxyribonucleic Kim. Alignment-free genome compari- acid. Journal of Biological Chemistry, son with feature frequency profiles (ffp) 236(3):864–875, 1961. and optimal resolutions. Proceedings of the National Academy of Sciences, pages [274] B Chor, D Horn, N Goldman, Y Levy, pnas–0813249106, 2009. and T Massingham. Genomic DNA k- mer spectra: models and modalities. Ge- [283] JT Simpson. Exploring genome charac- nome biology, 10(10):R108, 2009. teristics and sequence quality without a reference. Bioinformatics, 30(9):1228– [275] R Hariharan, R Simon, MR Pillai, and 1235, 2014. TD Taylor. Comparative analysis of DNA word abundances in four yeast [284] T Lappalainen, M Sammeth, MR Fried- genomes using a novel statistical back- lander, P AC’t Hoen, J Monlong, MA Ri- ground model. PloS one, 8(3):e58038, vas, M Gonzalez-Porta, N Kurbatova, 2013. T Griebel, PG Ferreira, et al. Transcrip- tome and genome sequencing uncovers [276] B Jiang, JS Liu, and ML Bulyk. Bayesian functional variation in humans. Nature, hierarchical model of protein-binding 501(7468):506, 2013. microarray k-mer data reduces noise [285] P AC’t Hoen, MR Friedlander, J Almlof, and identifies transcription factor sub- M Sammeth, I Pulyakhina, SY Anvar, classes and preferred k-mers. Bioinfor- JFJ Laros, HPJ Buermans, O Karlberg, matics, 29(11):1390–1398, 2013. M Brannvall, et al. Reproducibility of [277] Y Liu, J Schroder, and B Schmidt. high-throughput mrna and small rna Musket: a multistage k-mer spectrum- sequencing across laboratories. Nature based error corrector for Illumina se- biotechnology, 31(11):1015, 2013. quence data. Bioinformatics, 29(3):308– [286] WA Kosters and JFJ Laros. Metrics for 315, 2012. mining multisets. In Research and De- [278] H Chae, J Park, S-W Lee, KP Nephew, velopment in Intelligent systems XXIV, and S Kim. Comparative analysis using pages 293–303. Springer, 2008. BIBLIOGRAPHY 139

[287] PJ Rousseeuw. Silhouettes: a graphical [295] KJV Nordstrom, MC Albani, GVe aid to the interpretation and validation James, C Gutjahr, B Hartwig, F Turck, of cluster analysis. Journal of computa- U Paszkowski, G Coupland, and tional and applied mathematics, 20:53–65, K Schneeberger. Mutation identifica- 1987. tion by direct comparison of whole- [288] J Cohen. Weighted kappa: Nominal genome sequencing data from mu- scale agreement provision for scaled tant and wild-type individuals using disagreement or partial credit. Psycho- k-mers. Nature biotechnology, 31(4):325, logical bulletin, 70(4):213, 1968. 2013. [289] G Lunter and M Goodson. Stampy: a [296] SN Gardner and BG Hall. When whole- statistical algorithm for sensitive and genome alignments just won’t work: fast mapping of Illumina sequence kSNP v2 software for alignment-free reads. Genome research, 21(6):936–939, snp discovery and phylogenetics of 2011. hundreds of microbial genomes. PloS [290] AR Quinlan and IM Hall. BEDTools: one, 8(12):e81760, 2013. a flexible suite of utilities for compar- [297] G Marcais and C Kingsford. A fast, ing genomic features. Bioinformatics, lock-free approach for efficient paral- 26(6):841–842, 2010. lel counting of occurrences of k-mers. [291] HH Li, B Handsaker, A Wysoker, T Fen- Bioinformatics, 27(6):764–770, 2011. nell, J Ruan, N Homer, G Marth, [298] M Crusoe, G Edvenson, J Fish, A Howe, G Abecasis, and R Durbin. The se- E McDonald, J Nahum, K Nanlohy, quence alignment/map format and H Ortiz-Zuazaga, J Pell, J Simpson, SAMtools. Bioinformatics, 25(16):2078– et al. The khmer software package: en- 2079, 2009. abling efficient sequence analysis. URL [292] JG Caporaso, CL Lauber, EK Costello, http://dx. doi. org/10.6084/m9. figshare, D Berg-Lyons, A Gonzalez, 979190, 2014. J Stombaugh, D Knights, P Gajer, [299] DS DeLuca, JZ Levin, A Sivachenko, J Ravel, N Fierer, et al. Moving pictures T Fennell, M-D Nazaire, C Williams, of the human microbiome. Genome M Reich, W Winckler, and G Getz. biology, 12(5):R50, 2011. RNA-SeQC: RNA-seq metrics for qual- [293] KJ Stacey, GR Young, F Clark, DP Ses- ity control and process optimization. ter, TL Roberts, S Naik, MJ Sweet, and Bioinformatics, 28(11):1530–1532, 2012. DA Hume. The molecular basis for the lack of immunostimulatory activity of [300] N Segata, D Boernigen, TL Tickle, vertebrate DNA. The Journal of Immunol- XC Morgan, WS Garrett, and C Hutten- ogy, 170(7):3614–3620, 2003. hower. Computational metaomics for microbial community studies. Molecu- [294] P Kaufmann, A Pfefferkorn, M Teuber, lar systems biology, 9(1):666, 2013. and L Meile. Identification and quan- tification of bifidobacterium species iso- [301] KT Konstantinidis, A Ramette, and lated from food with genus-specific 16S JM Tiedje. The bacterial species defi- rRNA-targeted probes by colony hy- nition in the genomic era. Philosophical bridization and PCR. Applied and Envi- Transactions of the Royal Society of London ronmental Microbiology, 63(4):1268–1273, B: Biological Sciences, 361(1475):1929– 1997. 1940, 2006. 140 Bibliography

[302] M Schloter, M Lebuhn, T Heulin, and [311] MCJ Maiden, JA Bygraves, E Feil, A Hartmann. Ecology and evolution of G Morelli, J E Russell, R Urwin, bacterial microdiversity. FEMS microbi- Q Zhang, J Zhou, K Zurth, DA Cau- ology reviews, 24(5):647–660, 2000. gant, et al. Multilocus sequence typ- [303] DL Hartl and DE Dykhuizen. The pop- ing: a portable approach to the identifi- ulation genetics of Escherichia coli. An- cation of clones within populations of nual review of genetics, 18(1):31–68, 1984. pathogenic microorganisms. Proceed- ings of the National Academy of Sciences, [304] PA Cotter and VJ DiRita. Bacterial viru- 95(6):3140–3145, 1998. lence gene regulation: an evolutionary perspective. Annual Reviews in Microbi- [312] M Dreyer, L Aguilar-Bultet, S Rupp, ology, 54(1):519–565, 2000. C Guldimann, R Stephan, Al Schock, [305] RW Jackson, E Athanassopoulos, A Otter, Ge Schupbach, S Brisse, G Tsiamis, JW Mansfield, A Sesma, M Lecuit, et al. Listeria monocytogenes DL Arnold, MJ Gibbon, J Murillo, sequence type 1 is predominant in ru- JD Taylor, and A Vivian. Identification minant rhombencephalitis. Scientific re- of a pathogenicity island, which ports, 6:36419, 2016. contains genes for virulence and aviru- [313] MD Ismail, I Ali, S Hatt, EA Salz- lence, on a large native plasmid in the man, AW Cronenwett, CF Marrs, bean pathogen pseudomonas syringae AH Rickard, and B Foxman. Associ- pathovar phaseolicola. Proceedings ation of Escherichia coli ST131 lineage of the National Academy of Sciences, with risk of urinary tract infection re- 96(19):10875–10880, 1999. currence among young women. Journal [306] Antimicrobial Resistance WHO. Global of global antimicrobial resistance, 13:81– report on surveillance. Antimicrobial 84, 2018. Resistance, Global Report on Surveillance, [314] S Jena, S Panda, KC Nayak, and 2014. DV Singh. Identification of major [307] PM Bennett. Plasmid encoded antibi- sequence types among multidrug- otic resistance: acquisition and trans- resistant Staphylococcus epidermidis fer of antibiotic resistance genes in bac- strains isolated from infected eyes teria. British journal of pharmacology, and healthy conjunctiva. Frontiers in 153(S1):S347–S357, 2008. Microbiology, 8:1430, 2017. [308] T Foster. Staphylococcus. 1996. [315] C-R Usein, AS Ciontea, CM Militaru, [309] S Jarraud, C Mougel, J Thioulouse, M Condei, S Dinu, M Oprea, D Cristea, G Lina, H Meugnier, F Forey, X Nesme, V Michelacci, G Scavia, LC Zota, et al. J Etienne, and F Vandenesch. Relation- Molecular characterisation of human ships between Staphylococcus aureus ge- shiga toxin-producing Escherichia coli netic background, virulence factors, agr OMLST26 strains: results of an out- groups (alleles), and human disease. break investigation, romania, february Infection and immunity, 70(2):631–641, to august 2016. Eurosurveillance, 22(47), 2002. 2017. [310] R Urwin and MCJ Maiden. Multi- [316] MH Antwerpen, K Prior, A Mellmann, locus sequence typing: a tool for global S Höppner, WD Splettstoesser, and epidemiology. Trends in microbiology, D Harmsen. Rapid high resolution 11(10):479–487, 2003. genotyping of Francisella tularensis by BIBLIOGRAPHY 141

whole genome sequence comparison of [324] D Smajs, M Strouhal, and S Knauf. annotated genes (“MLST+”). PLoS One, Genetics of human and animal uncul- 10(4):e0123298, 2015. tivable treponemal pathogens. Infection, [317] VI Siarkou, F Vorimore, N Vicari, Genetics and Evolution, 61:92–107, 2018. S Magnino, A Rodolakis, Y Pannekoek, [325] KW Larssen, A Nor, and K Bergh. K Sachse, D Longbottom, and K Larou- Rapid discrimination of Staphylococcus cau. Diversification and distribution of epidermidis genotypes in a routine clin- ruminant Chlamydia abortus clones as- ical microbiological laboratory using sessed by MLST and mlva. PLoS One, single nucleotide polymorphisms in 10(5):e0126433, 2015. housekeeping genes. Journal of medical [318] B Heym, M Le Moal, L Armand- microbiology, 67(2):169–182, 2018. Lefevre, and M-H Nicolas-Chanoine. Multilocus sequence typing (MLST) [326] SA Nachappa, SM Neelambike, C Am- shows that the ‘Iberian’clone of ruthavalli, and NB Ramachandra. De- methicillin-resistant Staphylococcus au- tection of first-line drug resistance mu- reus has spread to france and acquired tations and drug–protein interaction reduced susceptibility to teicoplanin. dynamics from tuberculosis patients in Microbial Drug Resistance Journal of Antimicrobial Chemotherapy, south india. , 50(3):323–329, 2002. 24(4):377–385, 2018. [319] Y Yamaoka. Helicobacter pylori typing [327] SS Khoramrooz, SA Dolatabad, as a tool for tracking human migra- FM Dolatabad, M Marashifard, tion. Clinical Microbiology and Infection, M Mirzaii, H Dabiri, A Haddadi, 15(9):829–834, 2009. SM Rabani, HRG Shirazi, and [320] Z Qi, Y Cui, Q Zhang, and R Yang. D Darban-Sarokhalil. Detection Taxonomy of Yersinia pestis. In of tetracycline resistance genes, amino- Yersinia pestis: Retrospective and Perspec- glycoside modifying enzymes, and tive, pages 35–78. Springer, 2016. coagulase gene typing of clinical isolates of Staphylococcus aureus in the [321] W Wade. Unculturable bacteria—the southwest of iran. Iranian journal of uncharacterized organisms that cause basic medical sciences, 20(8):912, 2017. oral infections. Journal of the Royal Soci- ety of Medicine, 95(2):81–83, 2002. [328] J Sarvari, A Bazargani, MR Kandekar- [322] S Bhattacharya, N Vijayalakshmi, and Ghahraman, A Nazari-Alam, M Mo- SC Parija. Uncultivable bacteria: Im- tamedifar, et al. Molecular typing plications and recent trends towards of methicillin-resistant and methicillin- identification. Indian journal of medical susceptible Staphylococcus aureus iso- microbiology, 20(4):174, 2002. lates from shiraz teaching hospitals by PCR-rflp of coagulase gene. Iranian [323] M Pinto, V Borges, M Antelo, M Pin- journal of microbiology, 6(4):246, 2014. heiro, A Nunes, J Azevedo, MJ Borrego, J Mendonca, D Carpinteiro, L Vieira, [329] RA Viau, LM Kiedrowski, and et al. Genome-scale analysis BN Kreiswirth, M Adams, F Perez, of the non-cultivable treponema pal- D Marchaim, DM Guerrero, KS Kaye, lidum reveals extensive within-patient LK Logan, MV Villegas, et al. A com- genetic variation. Nature microbiology, parison of molecular typing methods 2(1):16190, 2017. applied to Enterobacter cloacae complex: 142 Bibliography

hsp60 sequencing, rep-PCR, and MLST. data. Bioinformatics, 27(21):2987–2993, Pathogens & immunity, 2(1):23, 2017. 2011. [330] KA Jolley and MCJ Maiden. BIGSdb: [338] P Danecek, A Auton, G Abecasis, scalable analysis of bacterial genome CA Albers, E Banks, MA DePristo, variation at the population level. BMC RE Handsaker, G Lunter, GT Marth, bioinformatics, 11(1):595, 2010. ST Sherry, et al. The variant call format and VCFtools. Bioinformatics, [331] M Inouye, H Dashnow, L-A Raven, 27(15):2156–2158, 2011. MB Schultz, BJ Pope, T Tomita, J Zo- bel, and KE Holt. SRST2: Rapid ge- [339] VI Levenshtein. Binary codes capa- nomic surveillance for public health ble of correcting deletions, insertions, and hospital microbiology labs. Genome and reversals. Soviet physics doklady, medicine, 6(11):90, 2014. 10(8):707–710, 1966. [332] R Tewolde, T Dallman, U Schaefer, [340] T Wirth, D Falush, R Lan, F Colles, CL Sheppard, P Ashton, B Pichon, P Mensa, LH Wieler, H Karch, M Ellington, C Swift, J Green, and PR Reeves, MCJ Maiden, H Ochman, A Underwood. MOST: a modiﬁed and et al. Sex and virulence in MLST typing tool based on short read escherichia coli: an evolutionary sequencing. PeerJ, 4:e2308, 2016. perspective. Molecular microbiology, 60(5):1136–1151, 2006. [333] MV Larsen, S Cosentino, S Rasmussen, C Friis, H Hasman, R Marvig, L Jelsbak, [341] A Koehler, H Karch, T Beikler, TF Flem- TS Pontén, DW Ussery, FM Aarestrup, mig, S Suerbaum, and H Schmidt. et al. Multilocus sequence typing of Multilocus sequence analysis of por- total genome sequenced bacteria. Jour- phyromonas gingivalis indicates fre- nal of clinical microbiology, pages JCM– quent recombination. Microbiology, 06094, 2012. 149(9):2407–2415, 2003. [342] R Leinonen, H Sugawara, M Shumway, [334] N-F Alikhan, Z Zhou, MJ Sergeant, and and International Nucleotide Se- M Achtman. A genomic overview of quence Database Collaboration. The the population structure of salmonella. sequence read archive. Nucleic acids PLoS genetics, 14(4):e1007261, 2018. research, 39(suppl_1):D19–D21, 2010. [335] A Gupta, IK Jordan, and L Rishishwar. [343] M Enersen, I Olsen, AJ van Winkel- stringMLST: a fast k-mer based tool for hoff, and DA Caugant. Multilocus se- multilocus sequence typing. Bioinfor- quence typing of porphyromonas gingi- matics, 33(1):119–121, 2016. valis strains from different geographic [336] AJ Page, N-F Alikhan, HA Carleton, origins. Journal of clinical microbiology, T Seemann, JA Keane, and LS Katz. 44(1):35–41, 2006. Comparison of classical multi-locus [344] F Alhashash, X Wang, K Paszkiewicz, sequence typing software for next- M Diggle, Z Zong, and A McNally. generation sequencing data. Microbial Increase in bacteraemia cases in the genomics, 3(8), 2017. east midlands region of the uk due to [337] H Li. A statistical framework for SNP mdr escherichia coli ST73: high levels calling, mutation discovery, association of genomic and plasmid diversity in mapping and population genetical pa- causative isolates. Journal of Antimicro- rameter estimation from sequencing bial Chemotherapy, 71(2):339–343, 2015. BIBLIOGRAPHY 143

[345] T Cohen, PD van Helden, D Wilson, Strengths and limitations of 16s rrna C Colijn, MM McLaughlin, I Abubakar, gene amplicon sequencing in revealing and RM Warren. Mixed-strain my- temporal microbial community dynam- cobacterium tuberculosis infections ics. PLoS One, 9(4):e93827, 2014. and the implications for tuberculosis treatment and control. Clinical microbiology reviews, 25(4):708–719, 2012. [346] M Dzunkova, A Moya, X Chen, C Kelly, and G D’Auria. Detection of mixed- strain infections by facs and ultra-low input genome sequencing. Gut microbes, pages 1–5, 2018. [347] KE Raven, T Gouliouris, J Parkhill, and SJ Peacock. Genome-based analysis of enterococcus faecium bacteremia associated with recurrent and mixed-strain infection. Journal of clinical microbiology, 56(3):e01520–17, 2018. [348] G Yu, D Fadrosh, JJ Goedert, J Ravel, and AM Goldstein. Nested pcr biases in interpreting microbial community structure in 16s rrna gene sequence datasets. PLoS One, 10(7):e0132253, 2015. [349] M Schirmer, UZ Ijaz, R D’Amore, N Hall, WT Sloan, and C Quince. In- sight into biases and sequencing errors for amplicon sequencing with the illumina miseq platform. Nucleic acids research, 43(6):e37–e37, 2015. [350] D-L Sun, X Jiang, QL Wu, and N-Y Zhou. Intragenomic heterogeneity in 16s rrna genes causes overestimation of prokaryotic diversity. Applied and environmental microbiology, pages AEM– 01282, 2013. [351] K Kennedy, MW Hall, MDJ Lynch, G Moreno-Hagelsieb, and JD Neufeld. Evaluating bias of illumina-based bacterial 16s rrna gene proﬁles. Applied and environmental microbiology, pages AEM– 01451, 2014. [352] R Poretsky, LM Rodriguez, C Luo, D Tsementzi, and KT Konstantinidis. 144 Bibliography