Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

(2018) Moran Yassour et al.   Cell Host & Microbe

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

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Maturation of the gut microbiome and risk of asthma in childhood

(2018) Jakob Stokholm et al.   Nature Communications

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

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Stereotypic Immune System Development in Newborn Children

(2018) Axel Olin et al.   CELL

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Differences in the fecal microbiota of neonates born at home or in the hospital

(2018) Joan L. Combellick et al.   Scientific Reports

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study

(2018) Tommi Vatanen et al.   NATURE

Temporal development of the gut microbiome in early childhood from the TEDDY study

(2018) Christopher J. Stewart et al.   NATURE

Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes

(2018) Aimee M. Baumann-Dudenhoeffer et al.   NATURE MEDICINE

Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential

(2018) Linda Wampach et al.   Nature Communications

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Population Structure of Multidrug-Resistant Klebsiella oxytoca within Hospitals across the United Kingdom and Ireland Identifies Sharing of Virulence and Resistance Genes with K. pneumoniae

(2017) Danesh Moradigaravand et al.   Genome Biology and Evolution

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

(2017) Derrick M Chu et al.   NATURE MEDICINE

Bacterial colonization and succession in a newly opened hospital

(2017) Simon Lax et al.   Science Translational Medicine

A pilot study to understand feasibility and acceptability of stool and cord blood sample collection for a large-scale longitudinal birth cohort

(2017) S. R. Bailey et al.   BMC Pregnancy and Childbirth

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

(2016) Tommi Vatanen et al.   CELL

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

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

Cesarean section changes neonatal gut colonization

(2016) Jakob Stokholm et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

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

(2016) Hilary P. Browne et al.   NATURE

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

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

Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation

(2016) Kei E Fujimura et al.   NATURE MEDICINE

The microbiome in early life: implications for health outcomes

(2016) Sabrina Tamburini et al.   NATURE MEDICINE

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

Antibiotics, birth mode, and diet shape microbiome maturation during early life

(2016) Nicholas A. Bokulich et al.   Science Translational Medicine

The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland

(2016) Danesh Moradigaravand et al.   Nature Microbiology

Genome-based characterization of hospital-adapted Enterococcus faecalis lineages

(2016) Kathy E. Raven et al.   Nature Microbiology

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

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

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

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

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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Early infancy microbial and metabolic alterations affect risk of childhood asthma

(2015) Marie-Claire Arrieta et al.   Science Translational Medicine

Preterm gut microbiota and metabolome following discharge from intensive care

(2015) Christopher J. Stewart et al.   Scientific Reports

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

(2015) Hakdong Shin et al.   Microbiome

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Kraken: ultrafast metagenomic sequence classification using exact alignments

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ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

(2013) Marti J. Anderson et al.   ECOLOGICAL MONOGRAPHS

Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section

(2013) Hedvig E Jakobsson et al.   GUT

Infection and immunity from a lifecourse perspective: Life Study Enhancement

(2013) Nigel Field et al.   LANCET

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

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

(2013) Paul J. McMurdie et al.   PLoS One

Mom Knows Best: The Universality of Maternal Microbial Transmission

(2013) Lisa J. Funkhouser et al.   PLOS BIOLOGY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig 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

Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America

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