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

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

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children

(2016) Katri Korpela et al.   Nature Communications

Impact of maternal intrapartum antibiotics, method of birth and breastfeeding on gut microbiota during the first year of life: a prospective cohort study

(2015) MB Azad et al.   BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY

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

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

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

Regulatory T cells generated early in life play a distinct role in maintaining self-tolerance

(2015) S. Yang et al.   SCIENCE

Early infancy microbial and metabolic alterations affect risk of childhood asthma

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

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

(2015) Yael R. Nobel et al.   Nature Communications

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

Sphingolipids from a Symbiotic Microbe Regulate Homeostasis of Host Intestinal Natural Killer T Cells

(2014) Dingding An et al.   CELL

A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria

(2014) Conor J. Meehan et al.   Genome Biology and Evolution

Infant antibiotic exposure and the development of childhood overweight and central adiposity

(2014) M B Azad et al.   INTERNATIONAL JOURNAL OF OBESITY

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

(2014) Michelle G Rooks et al.   ISME Journal

Persistent gut microbiota immaturity in malnourished Bangladeshi children

(2014) Sathish Subramanian et al.   NATURE

The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition

(2014) Pamela V. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months

(2013) M. B. Azad et al.   CANADIAN MEDICAL ASSOCIATION JOURNAL

Low gut microbiota diversity in early infancy precedes asthma at school age

(2013) T. R. Abrahamsson et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Mother’s and Offspring’s Use of Antibiotics and Infant Allergy to Cow’s Milk

(2013) Johanna Metsälä et al.   EPIDEMIOLOGY

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

(2013) Hedvig E Jakobsson et al.   GUT

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

U.S. Outpatient Antibiotic Prescribing, 2010

(2013) Lauri A. Hicks et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

Effect of breastfeeding compared with formula feeding on infant body composition: a systematic review and meta-analysis

(2012) Chris Gale et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

(2012) Fiona Fouhy et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Delivery by caesarean section and risk of obesity in preschool age children: a prospective cohort study

(2012) Susanna Y Huh et al.   ARCHIVES OF DISEASE IN CHILDHOOD

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Butyrate Produced by Commensal Bacteria Potentiates Phorbol Esters Induced AP-1 Response in Human Intestinal Epithelial Cells

(2012) Malgorzata Nepelska et al.   PLoS One

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

(2012) T. Olszak et al.   SCIENCE

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

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

(2011) Daniel McDonald et al.   ISME Journal

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Antibiotic use and inflammatory bowel diseases in childhood

(2010) A. Hviid et al.   GUT

Quantitation of Major Human Cutaneous Bacterial and Fungal Populations

(2010) Z. Gao et al.   JOURNAL OF CLINICAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Human milk glycobiome and its impact on the infant gastrointestinal microbiota

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

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen 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

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

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

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Caesarean delivery and risk of atopy and allergic disesase: meta-analyses

(2008) P. Bager et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Caesarean section is associated with an increased risk of childhood-onset type 1 diabetes mellitus: a meta-analysis of observational studies

(2008) C. R. Cardwell et al.   DIABETOLOGIA

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

A meta-analysis of the association between Caesarean section and childhood asthma

(2007) S. Thavagnanam et al.   CLINICAL AND EXPERIMENTAL ALLERGY