Literature DB >> 26902128

Research Techniques Made Simple: Bacterial 16S Ribosomal RNA Gene Sequencing in Cutaneous Research.

Jay-Hyun Jo1, Elizabeth A Kennedy1, Heidi H Kong2.   

Abstract

Skin serves as a protective barrier and also harbors numerous microorganisms collectively comprising the skin microbiome. As a result of recent advances in sequencing (next-generation sequencing), our understanding of microbial communities on skin has advanced substantially. In particular, the 16S ribosomal RNA gene sequencing technique has played an important role in efforts to identify the global communities of bacteria in healthy individuals and patients with various disorders in multiple topographical regions over the skin surface. Here, we describe basic principles, study design, and a workflow of 16S ribosomal RNA gene sequencing methodology, primarily for investigators who are not familiar with this approach. This article will also discuss some applications and challenges of 16S ribosomal RNA sequencing as well as directions for future development.
Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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Year:  2016        PMID: 26902128      PMCID: PMC5482524          DOI: 10.1016/j.jid.2016.01.005

Source DB:  PubMed          Journal:  J Invest Dermatol        ISSN: 0022-202X            Impact factor:   8.551


  22 in total

Review 1.  Microbial ecology of human skin in health and disease.

Authors:  D N Fredricks
Journal:  J Investig Dermatol Symp Proc       Date:  2001-12

2.  Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

Authors:  T Z DeSantis; P Hugenholtz; N Larsen; M Rojas; E L Brodie; K Keller; T Huber; D Dalevi; P Hu; G L Andersen
Journal:  Appl Environ Microbiol       Date:  2006-07       Impact factor: 4.792

3.  A diversity profile of the human skin microbiota.

Authors:  Elizabeth A Grice; Heidi H Kong; Gabriel Renaud; Alice C Young; Gerard G Bouffard; Robert W Blakesley; Tyra G Wolfsberg; Maria L Turner; Julia A Segre
Journal:  Genome Res       Date:  2008-05-23       Impact factor: 9.043

Review 4.  Skin microbiome: genomics-based insights into the diversity and role of skin microbes.

Authors:  Heidi H Kong
Journal:  Trends Mol Med       Date:  2011-03-04       Impact factor: 11.951

5.  Skin microflora.

Authors:  J J Leyden; K J McGinley; K M Nordstrom; G F Webster
Journal:  J Invest Dermatol       Date:  1987-03       Impact factor: 8.551

6.  A comparison of five methods for extraction of bacterial DNA from human faecal samples.

Authors:  Alexandra L McOrist; Michelle Jackson; Anthony R Bird
Journal:  J Microbiol Methods       Date:  2002-07       Impact factor: 2.363

Review 7.  Dialogue between skin microbiota and immunity.

Authors:  Yasmine Belkaid; Julia A Segre
Journal:  Science       Date:  2014-11-21       Impact factor: 47.728

8.  Topographical and temporal diversity of the human skin microbiome.

Authors:  Elizabeth A Grice; Heidi H Kong; Sean Conlan; Clayton B Deming; Joie Davis; Alice C Young; Gerard G Bouffard; Robert W Blakesley; Patrick R Murray; Eric D Green; Maria L Turner; Julia A Segre
Journal:  Science       Date:  2009-05-29       Impact factor: 47.728

9.  Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.

Authors:  Heidi H Kong; Julia Oh; Clay Deming; Sean Conlan; Elizabeth A Grice; Melony A Beatson; Effie Nomicos; Eric C Polley; Hirsh D Komarow; Patrick R Murray; Maria L Turner; Julia A Segre
Journal:  Genome Res       Date:  2012-02-06       Impact factor: 9.043

10.  Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.

Authors:  Susannah J Salter; Michael J Cox; Elena M Turek; Szymon T Calus; William O Cookson; Miriam F Moffatt; Paul Turner; Julian Parkhill; Nicholas J Loman; Alan W Walker
Journal:  BMC Biol       Date:  2014-11-12       Impact factor: 7.431

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  21 in total

1.  Details Matter: Designing Skin Microbiome Studies.

Authors:  Heidi H Kong
Journal:  J Invest Dermatol       Date:  2016-05       Impact factor: 8.551

Review 2.  Performing Skin Microbiome Research: A Method to the Madness.

Authors:  Heidi H Kong; Björn Andersson; Thomas Clavel; John E Common; Scott A Jackson; Nathan D Olson; Julia A Segre; Claudia Traidl-Hoffmann
Journal:  J Invest Dermatol       Date:  2017-01-04       Impact factor: 8.551

Review 3.  Estrogen Action and Gut Microbiome Metabolism in Dermal Health.

Authors:  Edwin D Lephart; Frederick Naftolin
Journal:  Dermatol Ther (Heidelb)       Date:  2022-06-25

4.  Benchmarking of 16S rRNA gene databases using known strain sequences.

Authors:  Kunal Dixit; Dimple Davray; Diptaraj Chaudhari; Pratik Kadam; Rudresh Kshirsagar; Yogesh Shouche; Dhiraj Dhotre; Sunil D Saroj
Journal:  Bioinformation       Date:  2021-03-31

5.  Longitudinal profiling of the burn patient cutaneous and gastrointestinal microbiota: a pilot study.

Authors:  Kelly M Lima; Ryan R Davis; Stephenie Y Liu; David G Greenhalgh; Nam K Tran
Journal:  Sci Rep       Date:  2021-05-21       Impact factor: 4.379

6.  A systematic literature review of the human skin microbiome as biomarker for dermatological drug development.

Authors:  T Niemeyer-van der Kolk; H E C van der Wall; C Balmforth; M B A Van Doorn; R Rissmann
Journal:  Br J Clin Pharmacol       Date:  2018-07-19       Impact factor: 4.335

Review 7.  Revealing the secret life of skin - with the microbiome you never walk alone.

Authors:  R Sfriso; M Egert; M Gempeler; R Voegeli; R Campiche
Journal:  Int J Cosmet Sci       Date:  2019-12-25       Impact factor: 2.970

8.  Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization.

Authors:  Hsin-Wen Chang; Di Yan; Rasnik Singh; Jared Liu; Xueyan Lu; Derya Ucmak; Kristina Lee; Ladan Afifi; Douglas Fadrosh; John Leech; Kimberly S Vasquez; Margaret M Lowe; Michael D Rosenblum; Tiffany C Scharschmidt; Susan V Lynch; Wilson Liao
Journal:  Microbiome       Date:  2018-09-05       Impact factor: 14.650

Review 9.  Respiratory microbiome and epithelial interactions shape immunity in the lungs.

Authors:  Rachele Invernizzi; Clare M Lloyd; Philip L Molyneaux
Journal:  Immunology       Date:  2020-04-14       Impact factor: 7.397

Review 10.  Microbiome changes: an indicator of Parkinson's disease?

Authors:  Caroline Haikal; Qian-Qian Chen; Jia-Yi Li
Journal:  Transl Neurodegener       Date:  2019-12-24       Impact factor: 8.014

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