Anatomy promotes neutral coexistence of strains in the human skin microbiome

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

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

Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin

(2020) Wei Zhou et al.   CELL

Specificity and mutagenesis bias of the mycobacterial alternative mismatch repair analyzed by mutation accumulation studies

(2020) A. Castañeda-García et al.   Science Advances

Out of your skin

(2020) Charlie Schmidt   NATURE BIOTECHNOLOGY

The Skin Microbiota: Balancing Risk and Reward

(2020) Laurice Flowers et al.   Cell Host & Microbe

The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages

(2020) Marta Lourenço et al.   Cell Host & Microbe

Diversity within species: interpreting strains in microbiomes

(2020) Thea Van Rossum et al.   NATURE REVIEWS MICROBIOLOGY

A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles

(2020) Jan Claesen et al.   Science Translational Medicine

Reconsidering Named Honorifics in Medicine—the Troubling Legacy of Dermatologist Albert Kligman

(2020) Adewole S. Adamson et al.   JAMA Dermatology

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

(2019) Nandita R. Garud et al.   PLOS BIOLOGY

Adaptive Evolution within Gut Microbiomes of Healthy People

(2019) Shijie Zhao et al.   Cell Host & Microbe

Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology

(2019) Joshua Ladau et al.   TRENDS IN MICROBIOLOGY

High-resolution mapping reveals that microniches in the gastric glands control Helicobacter pylori colonization of the stomach

(2019) Connie Fung et al.   PLOS BIOLOGY

Skin microbiome modulation induced by probiotic solutions

(2019) Bernhard Paetzold et al.   Microbiome

Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies

(2019) Joseph McLaughlin et al.   Microorganisms

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes

(2018) Aura Ferreiro et al.   CELL

Isolation and Identification of the Follicular Microbiome: Implications for Acne Research

(2018) Jacob B. Hall et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Cutibacterium acnes (Propionibacterium acnes ) and acne vulgaris: a brief look at the latest updates

(2018) B. Dréno et al.   JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY

The human skin microbiome

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

Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is required for high fidelity DNA replication

(2018) Sonoko Ishino et al.   NUCLEIC ACIDS RESEARCH

Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris

(2018) Alan M. O’Neill et al.   Microbiome

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung

(2017) Hattie Chung et al.   Nature Communications

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

The microbiome beyond the horizon of ecological and evolutionary theory

(2017) Britt Koskella et al.   Nature Ecology & Evolution

Temporal Stability of the Human Skin Microbiome

(2016) Julia Oh et al.   CELL

Strain competition restricts colonization of an enteric pathogen and prevents colitis

(2016) Aaron L Hecht et al.   EMBO REPORTS

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis

(2016) Tami D Lieberman et al.   NATURE MEDICINE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

Phylogeny-aware identification and correction of taxonomically mislabeled sequences

(2016) Alexey M. Kozlov et al.   NUCLEIC ACIDS RESEARCH

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome stability of Propionibacterium acnes: a comprehensive study of indels and homopolymeric tracts

(2016) Christian F. P. Scholz et al.   Scientific Reports

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs

(2015) Peter Jorth et al.   Cell Host & Microbe

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Three dimensional distribution ofPropionibacterium acnesbiofilms in human skin

(2014) Anika C. Jahns et al.   EXPERIMENTAL DERMATOLOGY

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

A Novel High-Resolution Single Locus Sequence Typing Scheme for Mixed Populations of Propionibacterium acnes In Vivo

(2014) Christian F. P. Scholz et al.   PLoS One

Comparative genomics reveals distinct host-interacting traits of three major human-associated propionibacteria

(2013) Tim N Mak et al.   BMC GENOMICS

Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne

(2013) Sorel Fitz-Gibbon et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

Long-Term Dynamics of Adaptation in Asexual Populations

(2013) M. J. Wiser et al.   SCIENCE

Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome

(2013) S. Tomida et al.   mBio

Analysis of Complete Genomes ofPropionibacterium acnesReveals a Novel Plasmid and Increased Pseudogenes in an Acne Associated Strain

(2013) Gabriela Kasimatis et al.   Biomed Research International

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

CRISPR/cas Loci of Type II Propionibacterium acnes Confer Immunity against Acquisition of Mobile Elements Present in Type I P. acnes

(2012) Holger Brüggemann et al.   PLoS One

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

(2012) S. Wielgoss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

The skin microbiome

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

Comparative Genomics and Transcriptomics of Propionibacterium acnes

(2011) Elzbieta Brzuszkiewicz et al.   PLoS One

Mutators in cystic fibrosis chronic lung infection: Prevalence, mechanisms, and consequences for antimicrobial therapy

(2010) Antonio Oliver   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Bacterial Community Variation in Human Body Habitats Across Space and Time

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY