Discordant transmission of bacteria and viruses from mothers to babies at birth

Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins

(2019) J. Leonardo Moreno-Gallego et al.   Cell Host & Microbe

Human placenta has no microbiome but can contain potential pathogens

(2019) Marcus C. de Goffau et al.   NATURE

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

(2018) Pamela Ferretti et al.   Cell Host & Microbe

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

(2018) Angela McCann et al.   PeerJ

Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community

(2018) Efrem S. Lim et al.   Microbiome

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

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

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

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

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

(2017) Guoyan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis

(2017) Guoyan Zhao et al.   VIROLOGY

A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome

(2017) Maria Elisa Perez-Muñoz et al.   Microbiome

Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission

(2017) Sabrina Duranti et al.   Microbiome

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

(2017) Francesco Asnicar et al.   mSystems

The Influence of Different Maternal Microbial Communities on the Development of Infant Gut and Oral Microbiota

(2017) Tiina Drell et al.   Scientific Reports

Transition from infant- to adult-like gut microbiota

(2016) E. Avershina et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice

(2016) Joseph D. Planer et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The Bacterial Microbiome and Virome Milestones of Infant Development

(2016) Efrem S. Lim et al.   TRENDS IN MICROBIOLOGY

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

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

Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid

(2016) Maria Carmen Collado et al.   Scientific Reports

Exploring Vertical Transmission of Bifidobacteria from Mother to Child

(2015) Christian Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Gut Colonization of Healthy Children and Their Mothers With Pathogenic Ciprofloxacin-ResistantEscherichia coli

(2015) Emily A. Gurnee et al.   JOURNAL OF INFECTIOUS DISEASES

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Gut resistome development in healthy twin pairs in the first year of life

(2015) Aimee M. Moore et al.   Microbiome

Fecal Carriage of Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococcus in Healthy Children

(2013) Emily A. Gurnee et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

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

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

Novel Developmental Analyses Identify Longitudinal Patterns of Early Gut Microbiota that Affect Infant Growth

(2013) Richard A. White et al.   PLoS Computational Biology

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

(2012) Y. Peng et al.   BIOINFORMATICS

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

(2012) T. Olszak et al.   SCIENCE

Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance

(2012) Robert A. Britton et al.   TRENDS IN MICROBIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Natural and Experimental Infection of Caenorhabditis Nematodes by Novel Viruses Related to Nodaviruses

(2011) Marie-Anne Félix et al.   PLOS BIOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases

(2010) Daniel N. Frank et al.   INFLAMMATORY BOWEL DISEASES

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS