Chen YE, Fischbach MA, Belkaid Y. Skin microbiota-host interactions. Nature. 2018;553(7689):427–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, et al. Microbe-host interplay in atopic dermatitis and psoriasis. Nat Commun. 2019;10(1):4703.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007;449(7164):811–8.
Article
CAS
PubMed
Google Scholar
Harkins CP, Kong HH, Segre JAJJ. Manipulating the human microbiome to manage disease; 2019.
Google Scholar
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014;32(8):834–41.
Article
CAS
PubMed
Google Scholar
Ma B, France MT, Crabtree J, Holm JB, Humphrys MS, Brotman RM, Ravel J. A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. Nat Commun. 2020;11(1):940.
Article
CAS
PubMed
PubMed Central
Google Scholar
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16(7):410–22.
Article
CAS
PubMed
Google Scholar
Oh J, Byrd AL, Deming C, Conlan S, Program NCS, Kong HH, Segre JA. Biogeography and individuality shape function in the human skin metagenome. Nature. 2014;514(7520):59–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leung MH, Wilkins D, Lee PK. Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups. Sci Rep. 2015;5:11845.
Article
CAS
PubMed
PubMed Central
Google Scholar
Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14.
Article
CAS
Google Scholar
Oh J, Byrd AL, Park M, Program NCS, Kong HH, Segre JA. Temporal stability of the human skin microbiome. Cell. 2016;165(4):854–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, et al. Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare. Nat Microbiol. 2016;1(9):16106.
Article
CAS
PubMed
Google Scholar
Tett A, Pasolli E, Farina S, Truong DT, Asnicar F, Zolfo M, Beghini F, Armanini F, Jousson O, De Sanctis V, et al. Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis. NPJ Biofilms Microbiomes. 2017;3:14.
Article
PubMed
PubMed Central
Google Scholar
Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, et al. Understanding the microbial basis of body odor in pre-pubescent children and teenagers. Microbiome. 2018;6(1):213.
Article
PubMed
PubMed Central
Google Scholar
Salasar LEB, Leite JG, Louzada FJS. On the integrated maximum likelihood estimators for a closed population capture–recapture model with unequal capture probabilities. Statistics. 2015;49(6):1204–20.
Article
Google Scholar
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, et al. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
D'Costa VM, McGrann KM, Hughes DW, Wright GD. Sampling the antibiotic resistome. Science. 2006;311(5759):374–7.
Article
CAS
PubMed
Google Scholar
Bertrand D, Shaw J, Kalathiyappan M, Ng AHQ, Kumar MS, Li C, Dvornicic M, Soldo JP, Koh JY, Tong C, et al. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat Biotechnol. 2019;37(8):937–44.
Article
CAS
PubMed
Google Scholar
Sun J, Liao XP, D'Souza AW, Boolchandani M, Li SH, Cheng K, Luis Martinez J, Li L, Feng YJ, Fang LX, et al. Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms. Nat Commun. 2020;11(1):1427.
Article
CAS
PubMed
PubMed Central
Google Scholar
Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. Country-specific antibiotic use practices impact the human gut resistome. Genome Res. 2013;23(7):1163–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Navon-Venezia S, Ben-Ami R, Carmeli Y. Update on Pseudomonas aeruginosa and Acinetobacter baumannii infections in the healthcare setting. Curr Opin Infect Dis. 2005;18(4):306–13.
Article
PubMed
Google Scholar
Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh JJC. Host-specific evolutionary and transmission dynamics shape the functional diversification of Staphylococcus epidermidis in human skin. Cell. 2020;180(3):454–70 e418.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dalhoff A. Global fluoroquinolone resistance epidemiology and implictions for clinical use. Interdiscip Perspect Infect Dis. 2012;2012:976273.
Article
PubMed
PubMed Central
CAS
Google Scholar
Feldman S, Careccia RE, Barham KL, Hancox JGJAFP. Diagnosis and treatment of acne. Am Fam Physician. 2004;69(9):2123–30.
PubMed
Google Scholar
Geroulanos S, Marathias K, Kriaras J, Kadas B. Cephalosporins in surgical prophylaxis. J Chemother. 2001;13 Spec No 1(1):23–6.
Article
CAS
PubMed
Google Scholar
Oh J, Byrd AL, Deming C, Conlan S, Barnabas B, Blakesley R, Bouffard G, Brooks S, Coleman H, Dekhtyar MJN. Biogeography and individuality shape function in the human skin metagenome. Nature. 2014;514(7520):59–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kotrba P, Inui M, Yukawa H. Bacterial phosphotransferase system (PTS) in carbohydrate uptake and control of carbon metabolism. J Biosci Bioeng. 2001;92(6):502–17.
Article
CAS
PubMed
Google Scholar
Juni E. Simple genetic transformation assay for rapid diagnosis of Moraxella osloensis. Appl Microbiol. 1974;27(1):16–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Juni E, Bøvre K. Moraxella. In: Bergey's Manual of Systematics of Archaea and Bacteria; 2015. p. 1–17.
Google Scholar
Baumann P, Doudoroff M, Stanier RY. Study of the Moraxella group. I. Genus Moraxella and the Neisseria catarrhalis group. J Bacteriol. 1968;95(1):58–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moss CW, Wallace PL, Hollis DG, Weaver RE. Cultural and chemical characterization of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis. J Clin Microbiol. 1988;26(3):484–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shu M, Kuo S, Wang Y, Jiang Y, Liu YT, Gallo RL, Huang CM. Porphyrin metabolisms in human skin commensal Propionibacterium acnes bacteria: potential application to monitor human radiation risk. Curr Med Chem. 2013;20(4):562–8.
CAS
PubMed
PubMed Central
Google Scholar
Baron SA, Diene SM, Rolain J-M. Human microbiomes and antibiotic resistance. Hum Microbiome J. 2018;10:43–52.
Article
Google Scholar
Szemraj M, Kwaszewska A, Pawlak R, Szewczyk EM. Macrolide, lincosamide, and streptogramin B resistance in lipophilic Corynebacteria inhabiting healthy human skin. Microb Drug Resist. 2014;20(5):404–9.
Article
CAS
PubMed
Google Scholar
Collignon P, Voss A. China, what antibiotics and what volumes are used in food production animals? Antimicrob Resist Infect Control. 2015;4:16.
Article
PubMed
PubMed Central
Google Scholar
Hvistendahl M. Public health. China takes aim at rampant antibiotic resistance. Science. 2012;336(6083):795.
Article
CAS
PubMed
Google Scholar
Paterson DL, van Duin D. China's antibiotic resistance problems. Lancet Infect Dis. 2017;17(4):351–2.
Article
PubMed
Google Scholar
Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One. 2012;7(3):e33865.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fang C, Zhong H, Lin Y, Chen B, Han M, Ren H, Lu H, Luber JM, Xia M, Li W, et al. Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing. Gigascience. 2018;7(3):1–8.
Article
CAS
PubMed
Google Scholar
Lu N, Hu Y, Zhu L, Yang X, Yin Y, Lei F, Zhu Y, Du Q, Wang X, Meng Z, et al. DNA microarray analysis reveals that antibiotic resistance-gene diversity in human gut microbiota is age related. Sci Rep. 2014;4:4302.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sommer MOA, Dantas G, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science. 2009;325(5944):1128–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kareru PG, Keriko JM, Kenji GM, Thiong'o GT, Gachanja AN, Mukiira HN. Antimicrobial activities of skincare preparations from plant extracts. Afr J Tradit Complement Altern Med. 2010;7(3):214–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, et al. The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biol. 2019;17(1):47.
Article
PubMed
PubMed Central
Google Scholar
Kim HJ, Kim H, Kim JJ, Myeong NR, Kim T, Park T, Kim E, Choi JY, Lee J, An S, et al. Fragile skin microbiomes in megacities are assembled by a predominantly niche-based process. Sci Adv. 2018;4(3):e1701581.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ling Z, Liu X, Luo Y, Yuan L, Nelson KE, Wang Y, Xiang C, Li L. Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates. BMC Genomics. 2013;14:390.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu T, Liu X, Kong FQ, Duan YY, Yee AL, Kim M, Galzote C, Gilbert JA, Quan ZX. Age and mothers: potent influences of children’s skin microbiota. J Invest Dermatol. 2019;139(12):2497–505.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lim JY, Hwang I, Ganzorig M, Huang S-L, Cho G-S, Franz CM, Lee KJG. Complete genome sequences of three Moraxella osloensis strains isolated from human skin. Genome Announc. 2018;6(3):e01509-17.
PubMed
PubMed Central
Google Scholar
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6(3):610–8.
Article
CAS
PubMed
Google Scholar
Alekseyenko AV, Perez-Perez GI, De Souza A, Strober B, Gao Z, Bihan M, Li K, Methe BA, Blaser MJ. Community differentiation of the cutaneous microbiota in psoriasis. Microbiome. 2013;1(1):31.
Article
PubMed
PubMed Central
Google Scholar
Juge R, Rouaud-Tinguely P, Breugnot J, Servaes K, Grimaldi C, Roth MP, Coppin H, Closs B. Shift in skin microbiota of Western European women across aging. J Appl Microbiol. 2018;125(3):907–16.
Article
CAS
PubMed
Google Scholar
Zhai W, Huang Y, Zhang X, Fei W, Chang Y, Cheng S, Zhou Y, Gao J, Tang X, Zhang X, et al. Profile of the skin microbiota in a healthy Chinese population. J Dermatol. 2018;45(11):1289–300.
Article
PubMed
Google Scholar
Wilantho A, Deekaew P, Srisuttiyakorn C, Tongsima S, Somboonna N. Diversity of bacterial communities on the facial skin of different age-group Thai males. PeerJ. 2017;5:e4084.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shibagaki N, Suda W, Clavaud C, Bastien P, Takayasu L, Iioka E, Kurokawa R, Yamashita N, Hattori Y, Shindo C, et al. Aging-related changes in the diversity of women's skin microbiomes associated with oral bacteria. Sci Rep. 2017;7(1):10567.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nimrod AC, Benson WH. Environmental estrogenic effects of alkylphenol ethoxylates. Crit Rev Toxicol. 1996;26(3):335–64.
Article
CAS
PubMed
Google Scholar
Silva LA, Ferraz Carbonel AA, de Moraes ARB, Simoes RS, Sasso G, Goes L, Nunes W, Simoes MJ, Patriarca MT. Collagen concentration on the facial skin of postmenopausal women after topical treatment with estradiol and genistein: a randomized double-blind controlled trial. Gynecol Endocrinol. 2017;33(11):845–8.
Article
CAS
PubMed
Google Scholar
Coyle DH, Pezdirc K, Hutchesson MJ, Collins CE. Intake of specific types of fruit and vegetables is associated with higher levels of skin yellowness in young women: a cross-sectional study. Nutr Res. 2018;56:23–31.
Article
CAS
PubMed
Google Scholar
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Costea PI, Hildebrand F, Arumugam M, Backhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, et al. Enterotypes in the landscape of gut microbial community composition. Nat Microbiol. 2018;3(1):8–16.
Article
CAS
PubMed
Google Scholar
Grice EA, Kong HH, Renaud G, Young AC, Program NCS, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA. A diversity profile of the human skin microbiota. Genome Res. 2008;18(7):1043–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang J, Liang X, Xuan Y, Geng C, Li Y, Lu H, Qu S, Mei X, Chen H, Yu T, et al. A reference human genome dataset of the BGISEQ-500 sequencer. Gigascience. 2017;6(5):1–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, Li Y, Ye J, Yu C, Li Z, et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 2018;7(1):1–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25(15):1966–7.
Article
CAS
PubMed
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38(12):e132.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–9.
Article
CAS
PubMed
Google Scholar
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55–60.
Article
CAS
PubMed
Google Scholar
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. 2014;32(8):822–8.
Article
CAS
PubMed
Google Scholar
Chao A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics. 1987;43(4):783–91.
Article
CAS
PubMed
Google Scholar
Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma ANJNA. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2016:gkw1004.
Buchfink B, Xie C, Huson DHJN. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59–60.
Article
CAS
PubMed
Google Scholar
Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015;12(10):902–3.
Article
CAS
PubMed
Google Scholar
Dray S, Dufour A-B. The ade4 package: implementing the duality diagram for ecologists. J Stat Softw. 2007;22(4):1–20.
Article
Google Scholar
Strimmer K. fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics. 2008;24(12):1461–2.
Article
CAS
PubMed
Google Scholar
McArdle BH, Anderson MJ. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology. 2001;82(1):290–7.
Article
Google Scholar
Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14(6):927–30.
Article
Google Scholar
Shannon CE. A mathematical theory of communication. Bell Syst Tech J. 1948;27(3):379–423.
Article
Google Scholar
Fuglede B, Topsoe F. Jensen-Shannon divergence and Hilbert space embedding. IEEE. 2004:31.
Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K. Cluster: cluster analysis basics and extensions. R package version. 2012;1(2):56.
Google Scholar
Walesiak M, Dudek A, Dudek MA: clusterSim package.2011 http://www.R-project.org.
Google Scholar