Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants

(2016) Tali Raveh-Sadka et al.   ISME Journal

Rapid evolution of microbe-mediated protection against pathogens in a worm host

(2016) Kayla C King et al.   ISME Journal

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

(2016) Maria G Dominguez-Bello et al.   NATURE MEDICINE

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

(2016) Doyle V. Ward et al.   Cell Reports

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

(2016) Molly K. Gibson et al.   Nature Microbiology

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories

(2015) Christine L Sun et al.   ISME Journal

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Identifying strains that contribute to complex diseases through the study of microbial inheritance

(2015) Jeremiah J. Faith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

(2015) M. J. Rosen et al.   SCIENCE

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Early infancy microbial and metabolic alterations affect risk of childhood asthma

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The infant microbiome development: mom matters

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Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

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The first microbial environment of infants born by C-section: the operating room microbes

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Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Strain/species identification in metagenomes using genome-specific markers

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

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Infernal 1.1: 100-fold faster RNA homology searches

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Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels

(2013) Julia Cahenzli et al.   Cell Host & Microbe

Multifactorial diversity sustains microbial community stability

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Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Data, information, knowledge and principle: back to metabolism in KEGG

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Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants

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The neonatal gastrointestinal microbiota: the foundation of future health?

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

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Bacterial colonization and gut development in preterm neonates

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

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Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

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Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

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The Application of Ecological Theory Toward an Understanding of the Human Microbiome

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Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

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CRISPR Distribution within the Escherichia coli Species Is Not Suggestive of Immunity-Associated Diversifying Selection

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Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

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Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

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Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time

(2010) D. T. Pride et al.   GENOME RESEARCH

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

The population genetics of commensal Escherichia coli

(2010) Olivier Tenaillon et al.   NATURE REVIEWS MICROBIOLOGY

The Small, Slow and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella

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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

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

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Multidrug-Resistant Enterococci Lack CRISPR-cas

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Reordering contigs of draft genomes using the Mauve Aligner

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VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

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Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial diversity and the genetic nature of microbial species

(2008) Mark Achtman et al.   NATURE REVIEWS MICROBIOLOGY