Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

The human skin microbiome

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

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Reply to Meisel et al.

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Temporal Stability in Chronic Wound Microbiota Is Associated With Poor Healing

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Origins and challenges of viral dark matter

(2017) Siddharth R. Krishnamurthy et al.   VIRUS RESEARCH

Filamentous Bacteriophage Produced by Pseudomonas aeruginosa Alters the Inflammatory Response and Promotes Noninvasive Infection In Vivo

(2016) Patrick R. Secor et al.   INFECTION AND IMMUNITY

Details Matter: Designing Skin Microbiome Studies

(2016) Heidi H. Kong   JOURNAL OF INVESTIGATIVE DERMATOLOGY

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

(2016) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

Clinical characteristics and outcomes of pediatric patients with CMV DNA detection in bronchoalveolar lavage fluid

(2016) Elizabeth B. Burgener et al.   PEDIATRIC PULMONOLOGY

Healthy human gut phageome

(2016) Pilar Manrique et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

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

(2016) Kern Rei Chng et al.   Nature Microbiology

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

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

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Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

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Trimmomatic: a flexible trimmer for Illumina sequence data

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

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A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

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Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Going viral: next-generation sequencing applied to phage populations in the human gut

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

(2012) Vincent Foulongne et al.   PLoS One

The skin microbiome

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota

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A diversity profile of the human skin microbiota

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