The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis

Digestion of Human Milk Oligosaccharides by Bifidobacterium breve in the Premature Infant

(2017) Mark A. Underwood et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Identification of small molecules using accurate mass MS/MS search

(2017) Tobias Kind et al.   MASS SPECTROMETRY REVIEWS

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites

(2017) Dylan Dodd et al.   NATURE

Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth

(2017) Alex Grier et al.   Microbiome

Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants

(2017) Steven A. Frese et al.   mSphere

Oligosaccharides Released from Milk Glycoproteins Are Selective Growth Substrates for Infant-Associated Bifidobacteria

(2016) Sercan Karav et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Necrotizing Enterocolitis-Associated Gut Microbiota Is Present in the Meconium: Results of a Prospective Study

(2016) Fardou H. Heida et al.   CLINICAL INFECTIOUS DISEASES

How stable is the human gut microbiota? And why this question matters

(2016) Harald Brüssow   ENVIRONMENTAL MICROBIOLOGY

Use of Shotgun Metagenome Sequencing To Detect Fecal Colonization with Multidrug-Resistant Bacteria in Children

(2016) Heidi Andersen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Association Between Antibiotic Use and Neonatal Mortality and Morbidities in Very Low-Birth-Weight Infants Without Culture-Proven Sepsis or Necrotizing Enterocolitis

(2016) Joseph Y. Ting et al.   JAMA Pediatrics

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

(2016) Christopher J. Stewart et al.   Microbiome

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

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

Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics

(2015) Tomas Cajka et al.   ANALYTICAL CHEMISTRY

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

Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function

(2015) Caleb J. Kelly et al.   Cell Host & Microbe

Clostridium butyricumStrains and Dysbiosis Linked to Necrotizing Enterocolitis in Preterm Neonates

(2015) Nadim Cassir et al.   CLINICAL INFECTIOUS DISEASES

Metabolomic Analysis of Human Fecal Microbiota: A Comparison of Feces-Derived Communities and Defined Mixed Communities

(2015) Sandi Yen et al.   JOURNAL OF PROTEOME RESEARCH

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

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

Risks of Antibiotic Exposures Early in Life on the Developing Microbiome

(2015) Anjelique Schulfer et al.   PLoS Pathogens

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

(2014) Laura M. Cox et al.   CELL

Prenatal and post-natal exposure to antibiotics and risk of asthma in childhood

(2014) J. Metsälä et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Dysbiosis Anticipating Necrotizing Enterocolitis in Very Premature Infants

(2014) K. Sim et al.   CLINICAL INFECTIOUS DISEASES

Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity

(2014) N T Mueller et al.   INTERNATIONAL JOURNAL OF OBESITY

Patterned progression of bacterial populations in the premature infant gut

(2014) P. S. La Rosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

Maternal intrapartum antibiotics and decreased vertical transmission ofLactobacillusto neonates during birth

(2013) Leea Keski-Nisula et al.   ACTA PAEDIATRICA

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

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

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

Prevalence and Predictors of Antibiotic Administration during Pregnancy and Birth

(2013) Jakob Stokholm et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

(2013) Ardythe L Morrow et al.   Microbiome

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Antibiotics and the resistant microbiome

(2011) Morten OA Sommer et al.   CURRENT OPINION IN MICROBIOLOGY

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

The Mechanism of Excessive Intestinal Inflammation in Necrotizing Enterocolitis: An Immature Innate Immune Response

(2011) Nanda Nanthakumar et al.   PLoS One

Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

(2010) Carles Ubeda et al.   JOURNAL OF CLINICAL INVESTIGATION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry

(2009) Tobias Kind et al.   ANALYTICAL CHEMISTRY

Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota

(2009) Shigemitsu Tanaka et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Mortality of necrotizing enterocolitis expressed by birth weight categories

(2009) Shimae Cross Fitzgibbons et al.   JOURNAL OF PEDIATRIC SURGERY

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

(2009) W. R. Wikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY