Cindy Boer

The Gut Microbiome of Childen and Adults | 225 5.1 20. Yatsunenko T, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–227. doi: 10.1038/nature11053.- DOI- PMC- PubMed 21. Kozyrskyj AL, Ernst P, Becker AB. Increased risk of childhood asthma from antibiotic use in early life. Chest. 2007;131:1753–1759. doi: 10.1378/chest.06-3008.- DOI- PubMed 22. Risnes KR, Belanger K, Murk W, Bracken MB. Antibiotic exposure by 6 months and asthma and allergy at 6 years: findings in a cohort of 1,401 US children. Am. J. Epidemiol. 2011;173:310–318. doi: 10.1093/aje/kwq400.- DOI- PMC- PubMed 23. Hviid A, Svanström H, Frisch M. Antibiotic use and inflammatory bowel diseases in childhood. Gut. 2011;60:49–54. doi: 10.1136/gut.2010.219683.- DOI- PubMed 24. Kooijman MN, et al. The Generation R Study: design and cohort update 2017. Eur. J. Epidemiol. 2016;31:1243–1264. doi: 10.1007/s10654-016-0224-9.- DOI- PMC- PubMed 25. Ikram MA, et al. The Rotterdam Study: 2018 update on objectives, design and main results. Eur. J. Epidemiol. 2017;32:807–850. doi: 10.1007/s10654-017-0321-4.- DOI- PMC- PubMed 26. Fadrosh DW, et al. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome. 2014;2:6. doi: 10.1186/2049-2618-2-6.- DOI- PMC - PubMed 27. Caporaso JG, et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 2010;7:335–336. doi: 10.1038/nmeth.f.303.- DOI- PMC- PubMed 28. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods. 2013;10:996–998. doi: 10.1038/nmeth.2604.- DOI- PubMed 29. Schmieder R, Lim YW, Rohwer F, Edwards R. TagCleaner: Identification and removal of tag se- quences from genomic and metagenomic datasets. BMC bioinformatics. 2010;11:341–341. doi: 10.1186/1471-2105-11-341.- DOI- PMC- PubMed 30. Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina Paired-End reAd merg- eR. Bioinformatics. 2014;30:614–620. doi: 10.1093/bioinformatics/btt593.- DOI- PMC- PubMed 31. Quast C, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596. doi: 10.1093/nar/gks1219.- DOI- PMC - PubMed 32. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007;73:5261–5267. doi: 10.1128/AEM.00062-07.- DOI- PMC- PubMed 33. Benson AK, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc. Natl. Acad. Sci. USA. 2010;107:18933– 18938. doi: 10.1073/pnas.1007028107.- DOI- PMC- PubMed 34. Bokulich NA, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon se- quencing. Nat. Methods. 2013;10:57–59. doi: 10.1038/nmeth.2276.- DOI- PMC- PubMed 35. R Foundation for Statistical Computing, Vienna, Austria. A language and environment for statistical computing, https://www.R-project.org (2010). 36. Oksanen, J. et al. Vegan: community ecology package, http://CRAN.R-project.org/package= vegan (2013). 37. McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS One. 2013;8:e61217–e61217. doi: 10.1371/journal.pone.0061217. - DOI- PMC- PubMed 38. Morgan XC, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13:R79–R79. doi: 10.1186/gb-2012-13-9-r79.- DOI- PMC- PubMed 39. Stokholm J, et al. Maturation of the gut microbiome and risk of asthma in childhood. Nat. Com- mun. 2018;9:141. doi: 10.1038/s41467-017-02573-2.- DOI- PMC- PubMed 40. Fu J, et al. The gut microbiome contributes to a substantial proportion of the variation in blood lipids. Circ. Res. 2015;117:817–824. doi: 10.1161/CIRCRESAHA.115.306807.- DOI- PMC- PubMed