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 micro- biome. 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.