Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

Surface Microbes in the Neonatal Intensive Care Unit: Changes with Routine Cleaning and over Time

(2013) N. A. Bokulich et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)

(2013) Krissi M. Hewitt et al.   PLoS One

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

(2013) Christopher S. Miller et al.   PLoS One

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

(2013) Swee Hoe Ong et al.   PLoS One

Studying the microbiology of the indoor environment

(2013) Scott T Kelley et al.   GENOME BIOLOGY

Efficacy of Biocides Used in the Modern Food Industry To Control Salmonella enterica, and Links between Biocide Tolerance and Resistance to Clinically Relevant Antimicrobial Compounds

(2012) Orla Condell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pyrosequencing-Derived Bacterial, Archaeal, and Fungal Diversity of Spacecraft Hardware Destined for Mars

(2012) Myron T. La Duc et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Adaptive and Mutational Resistance: Role of Porins and Efflux Pumps in Drug Resistance

(2012) L. Fernandez et al.   CLINICAL MICROBIOLOGY REVIEWS

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Emergence of resistance to antibacterial agents: the role of quaternary ammonium compounds—a critical review

(2012) Sylvie Buffet-Bataillon et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Architectural design influences the diversity and structure of the built environment microbiome

(2012) Steven W Kembel et al.   ISME Journal

The rise of the Enterococcus: beyond vancomycin resistance

(2012) Cesar A. Arias et al.   NATURE REVIEWS MICROBIOLOGY

Exploring Bacterial Diversity in Hospital Environments by GS-FLX Titanium Pyrosequencing

(2012) Margarita Poza et al.   PLoS One

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Effect of higher minimum inhibitory concentrations of quaternary ammonium compounds in clinical E. coli isolates on antibiotic susceptibilities and clinical outcomes

(2011) S. Buffet-Bataillon et al.   JOURNAL OF HOSPITAL INFECTION

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Biofilm Formation by and Multicellular Behavior of Escherichia coli O55:H7, an Atypical Enteropathogenic Strain

(2010) M. Weiss-Muszkat et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Last of the multidrug transporters

(2010) Hendrik W. van Veen   NATURE

Neonatal Outcomes of Extremely Preterm Infants From the NICHD Neonatal Research Network

(2010) B. J. Stoll et al.   PEDIATRICS

Redefining the Role of Intestinal Microbes in the Pathogenesis of Necrotizing Enterocolitis

(2010) M. J. Morowitz et al.   PEDIATRICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

(2010) M. J. Morowitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Forensic identification using skin bacterial communities

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

Mechanism of chromosomal transfer of Enterococcus faecalis pathogenicity island, capsule, antimicrobial resistance, and other traits

(2010) J. M. Manson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Outbreak of Acinetobacter baumannii in a Neonatal Intensive Care Unit: Antimicrobial Susceptibility and Genotyping Analysis

(2009) Arabella Touati et al.   ANNALS OF EPIDEMIOLOGY

Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit

(2009) S. D. Perkins et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis

(2009) Yunwei Wang et al.   ISME Journal

Convergent temporal dynamics of the human infant gut microbiota

(2009) Pål Trosvik et al.   ISME Journal

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Outbreak of Serratia marcescens in a neonatal intensive care unit: contaminated unmedicated liquid soap and risk factors

(2009) S. Buffet-Bataillon et al.   JOURNAL OF HOSPITAL INFECTION

Intestinal Microbial Ecology in Premature Infants Assessed with Non–Culture-Based Techniques

(2009) Maka Mshvildadze et al.   JOURNAL OF PEDIATRICS

Diversity and seasonal dynamics of bacterial community in indoor environment

(2008) Helena Rintala et al.   BMC MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Washing toys in a neonatal intensive care unit decreases bacterial load of potential pathogens

(2008) R. Naesens et al.   JOURNAL OF HOSPITAL INFECTION

The Airborne Metagenome in an Indoor Urban Environment

(2008) Susannah G. Tringe et al.   PLoS One

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY