The Skin Microbiome: Current Techniques, Challenges, and Future Directions

Using strain-resolved analysis to identify contamination in metagenomics data

(2023) Yue Clare Lou et al.   Microbiome

Anatomy promotes neutral coexistence of strains in the human skin microbiome

(2022) Arolyn Conwill et al.   Cell Host & Microbe

Aged related human skin microbiome and mycobiome in Korean women

(2022) Hye-Jin Kim et al.   Scientific Reports

MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons

(2022) Miquel Rozas et al.   Frontiers in Cellular and Infection Microbiology

Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome

(2022) Hao Jin et al.   Gut Microbes

A metatranscriptomic approach to explore longitudinal tissue specimens from non‐healing diabetes related foot ulcers

(2022) Michael Radzieta et al.   APMIS

Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing

(2022) Anika Wahl et al.   Scientific Reports

A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities

(2022) Justin P Shaffer et al.   BIOTECHNIQUES

A 3D-printed transepidermal microprojection array for human skin microbiome sampling

(2022) Kun Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites

(2022) Qingzhen Wei et al.   Frontiers in Microbiology

The immunomodulatory potential of phage therapy to treat acne: a review on bacterial lysis and immunomodulation

(2022) Juan Farfán et al.   PeerJ

Application of Microbiome in Forensics

(2022) Jun Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Strains to go: interactions of the skin microbiome beyond its species

(2022) Ryan Caldwell et al.   CURRENT OPINION IN MICROBIOLOGY

Comparing different sample collection and storage methods for field‐based skin microbiome research

(2021) Melissa B. Manus et al.   AMERICAN JOURNAL OF HUMAN BIOLOGY

Cutibacterium acnes as an Opportunistic Pathogen: An Update of Its Virulence-Associated Factors

(2021) Constance Mayslich et al.   Microorganisms

Identifying biases and their potential solutions in human microbiome studies

(2021) Jacob T. Nearing et al.   Microbiome

Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota

(2021) Djalma S. Lima-Junior et al.   CELL

Diagnostic Value of 16S Ribosomal RNA Gene Polymerase Chain Reaction/Sanger Sequencing in Clinical Practice

(2021) Madiha Fida et al.   CLINICAL INFECTIOUS DISEASES

Dissecting and tuning primer editing by proofreading polymerases

(2021) Daryl M Gohl et al.   NUCLEIC ACIDS RESEARCH

Measuring and mitigating PCR bias in microbiota datasets

(2021) Justin D. Silverman et al.   PLoS Computational Biology

Forensic Analysis of Human Microbiome in Skin and Body Fluids Based on Geographic Location

(2021) Hye-Won Cho et al.   Frontiers in Cellular and Infection Microbiology

Challenges in exploring and manipulating the human skin microbiome

(2021) Manon Boxberger et al.   Microbiome

Ultra-accurate microbial amplicon sequencing with synthetic long reads

(2021) Benjamin J. Callahan et al.   Microbiome

Bacteriotherapy with human skin commensals in atopic dermatitis

(2021) Raquel Castillo‐González et al.   ALLERGY

Aging-Associated Changes in the Adult Human Skin Microbiome and the Host Factors that Affect Skin Microbiome Composition

(2021) Brian Howard et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Multi ‘omic data integration: A review of concepts, considerations, and approaches

(2021) Tasha M. Santiago-Rodriguez et al.   SEMINARS IN PERINATOLOGY

The Skin Microbiome of Patients With Atopic Dermatitis Normalizes Gradually During Treatment

(2021) Veda D. Khadka et al.   Frontiers in Cellular and Infection Microbiology

Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples

(2021) Sarah Ahannach et al.   iScience

Development of the Microbiota and Associations With Birth Mode, Diet, and Atopic Disorders in a Longitudinal Analysis of Stool Samples, Collected From Infancy Through Early Childhood

(2020) Gianluca Galazzo et al.   GASTROENTEROLOGY

Impact of sampling and DNA extraction methods on skin microbiota assessment

(2020) Yanisse Boulesnane et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Porphyrin Production and Regulation in Cutaneous Propionibacteria

(2020) Emma Barnard et al.   mSphere

The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection

(2020) Harris Onywera et al.   BMC MICROBIOLOGY

Current challenges and future opportunities of phage therapy

(2020) Diana P Pires et al.   FEMS MICROBIOLOGY REVIEWS

Retroviruses of the Human Virobiota: The Recycling of Viral Genes and the Resulting Advantages for Human Hosts During Evolution

(2020) Anna Luganini et al.   Frontiers in Microbiology

Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT medium

(2020) Rebecca R. Young et al.   MicrobiologyOpen

Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics

(2020) Jordan J. McGhee et al.   PeerJ

Metatranscriptomic assessment of burn wound infection clearance

(2020) Teija Ojala et al.   CLINICAL MICROBIOLOGY AND INFECTION

Staphylococcus epidermidis protease EcpA can be a deleterious component of the skin microbiome in atopic dermatitis

(2020) Laura Cau et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

The Penile Microbiota in Uncircumcised and Circumcised Men: Relationships With HIV and Human Papillomavirus Infections and Cervicovaginal Microbiota

(2020) Harris Onywera et al.   Frontiers in Medicine

Metagenomic Studies in Inflammatory Skin Diseases

(2020) Urszula Godlewska et al.   CURRENT MICROBIOLOGY

The skin microbiome and its relationship with the human body explained

(2020) Michael Eisenstein   NATURE

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass

(2019) Vincent Caruso et al.   mSystems

Elevated Local Senescence in Diabetic Wound Healing Is Linked to Pathological Repair via CXCR2

(2019) Holly N. Wilkinson et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Investigation of the skin microbiome: swabs vs. biopsies

(2019) S. Prast‐Nielsen et al.   BRITISH JOURNAL OF DERMATOLOGY

The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data

(2019) Marc A. Sze et al.   mSphere

Correction: Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

(2019) Jose Manuel Martí   PLoS Computational Biology

Optimisation and Benchmarking of Targeted Amplicon Sequencing for Mycobiome Analysis of Respiratory Specimens

(2019) Ali et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Effects of sampling strategy and DNA extraction on human skin microbiome investigations

(2019) Rie Dybboe Bjerre et al.   Scientific Reports

Investigation of direct and indirect transfer of microbiomes between individuals

(2019) Ana Neckovic et al.   Forensic Science International-Genetics

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair

(2018) Jonathan L. Linehan et al.   CELL

Longitudinal Study of the Psoriasis-Associated Skin Microbiome during Therapy with Ustekinumab in a Randomized Phase 3b Clinical Trial

(2018) Michael A. Loesche et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

The human skin microbiome

(2018) Allyson L. Byrd et al.   NATURE REVIEWS MICROBIOLOGY

Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates

(2018) Francesco Multinu et al.   mSphere

Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption

(2018) Jessica L. Metcalf   Forensic Science International-Genetics

A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping

(2018) Kazuhiro Ogai et al.   Frontiers in Microbiology

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Performing Skin Microbiome Research: A Method to the Madness

(2017) Heidi H. Kong et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

The skin microbiome: impact of modern environments on skin ecology, barrier integrity, and systemic immune programming

(2017) Susan L. Prescott et al.   World Allergy Organization Journal

Skin Microbiome Surveys Are Strongly Influenced by Experimental Design

(2016) Jacquelyn S. Meisel et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Microbial Ecology of the Human Skin

(2016) Anthony M. Cundell   MICROBIAL ECOLOGY

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

The maternal microbiota drives early postnatal innate immune development

(2016) M. Gomez de Aguero et al.   SCIENCE

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

(2016) Yu-Chih Tsai et al.   mBio

Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare

(2016) Kern Rei Chng et al.   Nature Microbiology

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon

(2016) Riccardo Rosselli et al.   Scientific Reports

The balance of metagenomic elements shapes the skin microbiome in acne and health

(2016) Emma Barnard et al.   Scientific Reports

Seasonal variation of postmortem microbial communities

(2015) David O. Carter et al.   Forensic Science Medicine and Pathology

Microbial community assembly and metabolic function during mammalian corpse decomposition

(2015) J. L. Metcalf et al.   SCIENCE

Vitamin B 12 modulates the transcriptome of the skin microbiota in acne pathogenesis

(2015) Dezhi Kang et al.   Science Translational Medicine

The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome

(2015) Geoffrey D. Hannigan et al.   mBio

Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces

(2014) Sean M. Gibbons et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

The skin microbiome: potential for novel diagnostic and therapeutic approaches to cutaneous disease

(2014) Elizabeth Grice   SEMINARS IN CUTANEOUS MEDICINE AND SURGERY

The skin microbiome: Current perspectives and future challenges

(2013) Yiyin Erin Chen et al.   JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY

Topographic diversity of fungal and bacterial communities in human skin

(2013) Keisha Findley et al.   NATURE

Functions of the skin microbiota in health and disease

(2013) James A. Sanford et al.   SEMINARS IN IMMUNOLOGY

Male Circumcision Significantly Reduces Prevalence and Load of Genital Anaerobic Bacteria

(2013) C. M. Liu et al.   mBio

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

Multilocus Sequence Typing and Phylogenetic Analysis of Propionibacterium acnes

(2012) M. Kilian et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

The skin microbiome

(2011) Elizabeth A. Grice et al.   NATURE REVIEWS MICROBIOLOGY

Male Circumcision Decreases Acquisition and Increases Clearance of High‐Risk Human Papillomavirus in HIV‐Negative Men: A Randomized Trial in Rakai, Uganda

(2010) Ronald H. Gray et al.   JOURNAL OF INFECTIOUS DISEASES

The Effects of Circumcision on the Penis Microbiome

(2010) Lance B. Price et al.   PLoS One

Forensic identification using skin bacterial communities

(2010) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Aging influences wound healing in patients with chronic lower extremity wounds treated in a specialized wound care center

(2009) Corinna Wicke et al.   WOUND REPAIR AND REGENERATION

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

(2008) P.C.Y. Woo et al.   CLINICAL MICROBIOLOGY AND INFECTION

A diversity profile of the human skin microbiota

(2008) E. A. Grice et al.   GENOME RESEARCH

The influence of sex, handedness, and washing on the diversity of hand surface bacteria

(2008) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA