1. Marchesi JR, Ravel J. 2015. The vocabulary of microbiome research: a proposal. Microbiome 3:31.
2. Human Microbiome Project, Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.
3. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. 2008. Evolution of mammals and their gut microbes. Science 320:1647-1651.
4. Chase J, Fouquier J, Zare M, Sonderegger DL, Knight R, Kelley ST, Siegel J, Caporaso JG. 2016. Geography and Location Are the Primary Drivers of Office Microbiome Composition. mSystems 1:e00022-16.
5. Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sorensen SJ, Hansen LH, Jakobsen M. 2010. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5:e9085.
6. Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD, Program NCS, Murray PR, Turner ML, Segre JA. 2012. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 22:850-859.
7. Urushiyama D, Suda W, Ohnishi E, Araki R, Kiyoshima C, Kurakazu M, Sanui A, Yotsumoto F, Murata M, Nabeshima K, Yasunaga S, Saito S, Nomiyama M, Hattori M, Miyamoto S, Hata K. 2017. Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome. Sci Rep 7:12171.
8. Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143- 169.
9. Byrd AL, Belkaid Y, Segre JA. 2018. The human skin microbiome. Nat Rev Microbiol 16:143-155.
10. Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. 2018. Best practices for analysing microbiomes. Nat Rev Microbiol 16:410-422.
11. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. 2010. Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A 107:6477-6481.
12. Oh J, Byrd AL, Deming C, Conlan S, Program NCS, Kong HH, Segre Ja. 2014. Biogeography and individuality shape function in the human skin metagenome. Nature 514:59-64.
13. Oh J, Byrd AL, Park M, Program NCS, Kong HH, Segre JA. 2016. Temporal Stability of the Human Skin Microbiome. Cell 165:854-866.
14. Fierer N, Hamady M, Lauber CL, Knight R. 2008. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 105:17994-17999.
15. Schmedes SE, Woerner AE, Budowle B. 2017. Forensic human identification using skin microbiomes. Appl Environ Microbiol 83:e01672-17.
16. Lax S, Hampton-Marcell JT, Gibbons SM, Colares GB, Smith D, Eisen JA, 81 Gilbert JA. 2015. Forensic analysis of the microbiome of phones and shoes. Microbiome 3:21.
17. Grice EA, Kong HH, Renaud G, Young AC, Program NCS, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA. 2008. A diversity profile of the human skin microbiota. Genome Res 18:1043-50.
18. Daly DJ, Murphy C, McDermott SD. 2012. The transfer of touch DNA from hands to glass, fabric and wood. Forensic Sci Int Genet 6:41-46.
19. National Police Agenecy, Japan. 2021. Keisatsu hakusho (White Paper on Police 2021).112.
20. Costello EEK, Lauber CCL, Hamady M, Fierer N, Gordon JI, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694-1697.
21. Quaak FCA, van Duijn T, Hoogenboom J, Kloosterman AD, Kuiper I. 2018. Human-associated microbial populations as evidence in forensic casework. Forensic Sci Int Genet 36:176-185.
22. Benschop CCG, Quaak FCA, Boon ME, Sijen T, Kuiper I. 2012. Vaginal microbial flora analysis by next generation sequencing and microarrays; can microbes indicate vaginal origin in a forensic context? Int J Legal Med 126:303- 310.
23. Nishi E, Tashiro Y, Sakai K. 2015. Discrimination among individuals using terminal restriction fragment length polymorphism profiling of bacteria derived from forensic evidence. Int J Legal Med 129:425-433.
24. Wilkins D, Leung MHY, Lee PKH. 2017. Microbiota fingerprints lose individually identifying features over time. Microbiome 5:1.
25. Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJM, Huttenhower C. 2015. Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A 112:E2930-E2938.
26. Ghebremedhin B, Layer F, König W, König B. 2008. Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences. J Clin Microbiol 46:1019- 1025.
27. Yang J, Tsukimi T, Yoshikawa M, Suzuki K, Takeda T, Tomita M, Fukuda S. 2019. Cutibacterium acnes ( Propionibacterium acnes ) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification. mSystems 4:e00594-19.
28. Bhaya D, Davison M, Barrangou R. 2011. CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation. Annu Rev Genet 45:273-297.
29. Barrangou R, Marraffini LA. 2014. CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol Cell 54:234-244.
30. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero Da, Horvath P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712.
31. Abeles SR, Robles-Sikisaka R, Ly M, Lum AG, Salzman J, Boehm TK, Pride DT. 2014. Human oral viruses are personal, persistent and gender-consistent. ISME J 8:1753-1767.
32. Naidu M, Robles-Sikisaka R, Abeles SR, Boehm TK, Pride DT. 2014. Characterization of bacteriophage communities and CRISPR profiles from dental 83 plaque. BMC Microbiol 14:175.
33. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35:907-914.
34. Hoe N, Nakashima K, Grigsby D, Pan X, Dou SJ, Naidich S, Garcia M, Kahn E, Bergmire-Sweat D, Musser JM. 1999. Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains. Emerg Infect Dis 5:254-263.
35. Schouls LM, Reulen S, Duim B, Wagenaar JA, Willems RJ, Dingle KE, Colles FM, Van Embden JD. 2003. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J Clin Microbiol 41:15-26.
36. Pourcel C, Salvignol G, Vergnaud G. 2005. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151:653-663.
37. Mokrousov I, Narvskaya O, Limeschenko E, Vyazovaya A. 2005. Efficient discrimination within a Corynebacterium diphtheriae epidemic clonal group by a novel macroarray-based method. J Clin Microbiol 43:1662-1668.
38. Horvath P, Romero DA, Coute-Monvoisin AC, Richards M, Deveau H, Moineau S, Boyaval P, Fremaux C, Barrangou R. 2008. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190:1401-1412.
39. Fabre L, Zhang J, Guigon G, Le Hello S, Guibert V, Accou-Demartin M, de Romans S, Lim C, Roux C, Passet V, Diancourt L, Guibourdenche M, Issenhuth- 84 Jeanjean S, Achtman M, Brisse S, Sola C, Weill FX. 2012. CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PLoS One 7:e36995.
40. Lier C, Baticle E, Horvath P, Haguenoer E, Valentin AS, Glaser P, Mereghetti L, Lanotte P. 2015. Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages. Front Genet 6:214.
41. Beauruelle C, Pastuszka A, Horvath P, Perrotin F, Mereghetti L, Lanotte P. 2017. CRISPR: A useful genetic feature to follow vaginal carriage of group B Streptococcus. Front Microbiol 8:1981.
42. Hu T, Cui Y, Qu X. 2020. Characterization and comparison of CRISPR Loci in Streptococcus thermophilus. Arch Microbiol 202:695-710.
43. Shariat N, Dudley EG. 2014. CRISPRs: molecular signatures used for pathogen subtyping. Appl Environ Microbiol 80:430-439.
44. Sun CL, Thomas BC, Barrangou R, Banfield JF. 2016. Metagenomic reconstructions of bacterial CRISPR loci constrain population histories. ISME J 10:858-870.
45. Rho M, Wu Y-W, Tang H, Doak TG, Ye Y. 2012. Diverse CRISPRs Evolving in Human Microbiomes. PLoS Genetics 8:e1002441.
46. Gogleva AA, Gelfand MS, Artamonova II. 2014. Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs. BMC Genomics 15:202.
47. Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC. 2016. Uncovering Earth’s 85 virome. Nature 536:425-430.
48. Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA. 2011. Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res 21:126-136.
49. Robles-Sikisaka R, Ly M, Boehm T, Naidu M, Salzman J, Pride DT. 2013. Association between living environment and human oral viral ecology. ISME J 7:1710-1724.
50. Robles-Sikisaka R, Naidu M, Ly M, Salzman J, Abeles SR, Boehm TK, Pride DT. 2014. Conservation of streptococcal CRISPRs on human skin and saliva. BMC Microbiol 14:146.
51. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120.
52. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. 2015. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674-1676.
53. Edgar RC. 2007. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8:18.
54. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodriguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, 86 Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852-857.
55. Rognes T, Flouri T, Nichols B, Quince C, Mahé F. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584.
56. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
57. Godde JS, Bickerton A. 2006. The repetitive DNA elements called CRISPRs and their associated genes: Evidence of horizontal transfer among prokaryotes. J Mol Evol 62:718-729.
58. Hunter JD. 2007. Matplotlib: A 2D Graphics Environment. Comput Sci Eng 9:90- 95.
59. Pourcel C, Touchon M, Villeriot N, Vernadet JP, Couvin D, Toffano-Nioche C, Vergnaud G. 2020. CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. Nucleic Acids Res 48:D535-D544.
60. Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Neron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C. 2018. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 46:W246-W251.
61. Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, 87 Shah SA, Siksnys V, Terns MP, Venclovas C, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. 2020. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 18:67-83.
62. Nethery MA, Barrangou R. 2019. CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline. RNA Biol 16:577-584.
63. Hao M, Cui Y, Qu X. 2018. Analysis of CRISPR-Cas System in Streptococcus thermophilus and Its Application. Front Microbiol 9:257.
64. Liu J, Yan R, Zhong Q, Ngo S, Bangayan NJ, Nguyen L, Lui T, Liu M, Erfe MC, Craft N, Tomida S, Li H. 2015. The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. ISME J 9:2078-2093.
65. Fitz-Gibbon S, Tomida S, Chiu B-H, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, Modlin RL, Miller JF, Sodergren E, Craft N, Weinstock GM, Li H. 2013. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol 133:2152-2160.
66. Brüggemann H, Lomholt HB, Tettelin H, Kilian M. 2012. CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes. PLoS One 7:e34171.
67. Acuna-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F. 2018. Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics 19:54.
68. Pride DT, Salzman J, Relman DA. 2012. Comparisons of clustered regularly 88 interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ Microbiol 14:2564-2576.
69. Lum AG, Ly M, Santiago-Rodriguez TM, Naidu M, Boehm TK, Pride DT. 2015. Global transcription of CRISPR loci in the human oral cavity. BMC Genomics 16:401.
70. Castelino M, Eyre S, Moat J, Fox G, Martin P, Ho P, Upton M, Barton A. 2017. Optimisation of methods for bacterial skin microbiome investigation: Primer selection and comparison of the 454 versus MiSeq platform. BMC Microbiol 17:23.
71. Zheng W, Tsompana M, Ruscitto A, Sharma A, Genco R, Sun Y, Buck MJ. 2015. An accurate and efficient experimental approach for characterization of the complex oral microbiota. Microbiome 3:48.
72. Kong HH, Andersson B, Clavel T, Common JE, Jackson SA, Olson ND, Segre JA, Traidl-Hoffmann C. 2017. Performing Skin Microbiome Research: A Method to the Madness. J Invest Dermatol 137:561-568.
73. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13:581-583.
74. Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R. 2017. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5:27.
75. Kruskal WH, Wallis WA. 1952. Use of Ranks in One-Criterion Variance Analysis. J Am Statist Assoc 47:583-621.
76. Oksanen J, Blanchet F, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin P, O′Hara R, Simpson G, Solymos P, Stevens M, Szoecs E, Wagner H. 2019. Vegan: Community Ecology Package, version 2.5-4, https://CRAN.Rproject.org/package=vegan.
77. Guyon I, Weston J, Barnhill S, Vapnik V. 2002. Gene Selection for Cancer Classification using Support Vector Machines. Machine Learning 46:389–422.
78. Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay É. 2011. Scikit-learn: Machine learning in Python. Journal of machine learning research 12:2825-2830.
79. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590-596.
80. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. 2014. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87.
81. Callahan BJ, McMurdie PJ, Holmes SP. 2017. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J 11:2639-2643.
82. Gotelli NJ, Chao A. 2013. Measuring and Estimating Species Richness, Species Diversity, and Biotic Similarity from Sampling Data, p 195-211. In Levin S (ed), Encyclopedia of Biodiversity doi:10.1016/B978-0-12-384719-5.00424-X. Academic Press.
83. Cottier F, Srinivasan KG, Yurieva M, Liao W, Poidinger M, Zolezzi F, Pavelka N. 90 2018. Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities. NPJ Biofilms Microbiomes 4:2.
84. McGinn J, Marraffini LA. 2019. Molecular mechanisms of CRISPR–Cas spacer acquisition. Nat Rev Microbiol 17:7-12.
85. Rascovan N, Duraisamy R, Desnues C. 2016. Metagenomics and the Human Virome in Asymptomatic Individuals. Annu Rev Microbiol 70:125-141.
86. Knights D, Costello EK, Knight R. 2011. Supervised classification of human microbiota. FEMS Microbiol Rev 35:343-359.
87. Statnikov A, Henaff M, Narendra V, Konganti K, Li Z, Yang L, Pei Z, Blaser MJ, Aliferis CF, Alekseyenko AV. 2013. A comprehensive evaluation of multicategory classification methods for microbiomic data. Microbiome 1:11.
88. Watanabe H, Nakamura I, Mizutani S, Kurokawa Y, Mori H, Kurokawa K, Yamada T. 2018. Minor taxa in human skin microbiome contribute to the personal identification. PLoS One 13:e0199947.
89. Paez-Espino D, Sharon I, Morovic W, Stahl B, Thomas BC, Barrangou R, Banfield JF. 2015. CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus. mBio 6:e00262-15.
90. Kutmutia SK, Drautz-Moses DI, Uchida A, Purbojati RW, Wong A, Kushwaha KK, Putra A, Premkrishnan BNV, Heinle CE, Vettath VK, Junqueira ACM, Schuster SC. 2019. Complete Genome Sequence of Micrococcus luteus Strain SGAir0127, Isolated from Indoor Air Samples from Singapore. Microbiol Resour Announc 8:e00646-19. 91. Tomida S, Nguyen L, Chiu BH, Liu J, Sodergren E, Weinstock GM, Li H. 2013.
91 Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome. mBio 4:e00003-13.
92. Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. 1998. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140-3145.
93. Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D. 2006. Proposal for standardization of optimized Mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 44:4498-4510.
94. Zolfo M, Tett A, Jousson O, Donati C, Segata N. 2017. MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. Nucleic Acids Res 45:e7.
95. Shevchenko SG, Radey M, Tchesnokova V, Kisiela D, Sokurenko EV. 2019. Escherichia coli Clonobiome: Assessing the Strain Diversity in Feces and Urine by Deep Amplicon Sequencing. Appl Environ Microbiol 85:e01866-19.
96. Meadow JF, Altrichter AE, Green JL. 2014. Mobile phones carry the personal microbiome of their owners. PeerJ 2:e447.
97. Hidalgo-Cantabrana C, Sanozky-Dawes R, Barrangou R. 2018. Insights into the human virome using CRISPR spacers from microbiomes. Viruses 10:479.
98. Nadkarni MA, Martin FE, Jacques NA, Hunter N. 2002. Determination of 92 bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148:257-266.
99. Li R. 2015. Autosomal Short Tandem Repeat Profiling, p 369-406, Forensic Biology, 2 ed. CRC Press.
100. Schmedes SE, Woerner AE, Novroski NMM, Wendt FR, King JL, Stephens KM, Budowle B. 2018. Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification. Forensic Sci Int Genet 32:50-61.
101. Nishi E, Watanabe K, Tashiro Y, Sakai K. 2017. Terminal restriction fragment length polymorphism profiling of bacterial flora derived from single human hair shafts can discriminate individuals. Leg Med 25:75-82.
102. Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ. 2012. Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome. PLoS One 7:e33865.
103. Hornung BVH, Zwittink RD, Kuijper EJ. 2019. Issues and current standards of controls in microbiome research. FEMS Microbiol Ecol 95:fiz045.
104. Bjerre RD, Hugerth LW, Boulund F, Seifert M, Johansen JD, Engstrand L. 2019. Effects of sampling strategy and DNA extraction on human skin microbiome investigations. Sci Rep 9:17287.
105. Davis CP, King JL, Budowle B, Eisenberg AJ, Turnbough MA. 2012. Extraction platform evaluations: a comparison of AutoMate Express, EZ1(R) Advanced XL, and Maxwell(R) 16 Bench-top DNA extraction systems. Leg Med 14:36-39.
106. Fujii K, Inokuchi S, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K. 2013. A comparison of DNA extraction using AutoMate Express and EZ1 advanced XL from liquid blood, bloodstains, and semen stains. J Forensic Sci 58:981-988.
107. Akutsu T, Kitayama T, Watanabe K, Sakurada K. 2015. Comparison of automated and manual purification of total RNA for mRNA-based identification of body fluids. Forensic Sci Int Genet 14:11-17.
108. Gu Z, Eils R, Schlesner M. 2016. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32:2847-2849.
109. Fiedorova K, Radvansky M, Nemcova E, Grombirikova H, Bosak J, Cernochova M, Lexa M, Smajs D, Freiberger T. 2019. The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery. Front Microbiol 10:821.
110. Lim MY, Song EJ, Kim SH, Lee J, Nam YD. 2018. Comparison of DNA extraction methods for human gut microbial community profiling. Syst Appl Microbiol 41:151-157.
111. Erb-Downward JR, Falkowski NR, D'Souza JC, McCloskey LM, McDonald RA, Brown CA, Shedden K, Dickson RP, Freeman CM, Stringer KA, Foxman B, Huffnagle GB, Curtis JL, Adar SD. 2020. Critical Relevance of Stochastic Effects on Low-Bacterial-Biomass 16S rRNA Gene Analysis. mBio 11:e00258-20.
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