Bifidobacteria-mediated immune system imprinting early in life

Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States

(2021) Giorgio Casaburi et al.   Scientific Reports

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation

(2021) Marielle Nguyen et al.   Frontiers in Pediatrics

Infant gut microbiome is enriched with Bifidobacterium longum ssp. infantis in Old Order Mennonites with traditional farming lifestyle

(2021) Antti E. Seppo et al.   ALLERGY

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Indole-3-lactic acid, a metabolite of tryptophan, secreted by Bifidobacterium longum subspecies infantis is anti-inflammatory in the immature intestine

(2020) Di Meng et al.   PEDIATRIC RESEARCH

A genome-wide transcriptomic analysis of protein-coding genes in human blood cells

(2020) Mathias Uhlen et al.   SCIENCE

Microbiota-Induced Type I Interferons Instruct a Poised Basal State of Dendritic Cells

(2020) Laura Schaupp et al.   CELL

Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines

(2020) Eddie Cano-Gamez et al.   Nature Communications

A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level

(2020) Florian Mair et al.   Cell Reports

Galectin-1 Facilitates Macrophage Reprogramming and Resolution of Inflammation Through IFN-β

(2020) Hiba Yaseen et al.   Frontiers in Pharmacology

The Immune Modulating Properties of Mucosal-Associated Invariant T Cells

(2020) Melina Ioannidis et al.   Frontiers in Immunology

Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics

(2020) Rebbeca M. Duar et al.   Nutrients

Indole-3-lactic acid associated with Bifidobacterium-dominated microbiota significantly decreases inflammation in intestinal epithelial cells

(2020) Amy M. Ehrlich et al.   BMC MICROBIOLOGY

Role of the microbiome in human development

(2019) Maria Gloria Dominguez-Bello et al.   GUT

The repertoire of maternal anti-viral antibodies in human newborns

(2019) Christian Pou et al.   NATURE MEDICINE

A Weaning Reaction to Microbiota Is Required for Resistance to Immunopathologies in the Adult

(2019) Ziad Al Nabhani et al.   IMMUNITY

Nonclassical Monocytes in Health and Disease

(2019) Prakash Babu Narasimhan et al.   Annual Review of Immunology

The ancestral and industrialized gut microbiota and implications for human health

(2019) Erica D. Sonnenburg et al.   NATURE REVIEWS MICROBIOLOGY

A Call for Blood—In Human Immunology

(2019) Petter Brodin et al.   IMMUNITY

Colonization by B. infantis EVC001 modulates enteric inflammation in exclusively breastfed infants

(2019) Bethany M. Henrick et al.   PEDIATRIC RESEARCH

Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria

(2019) Giorgio Casaburi et al.   Antimicrobial Resistance and Infection Control

Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum

(2019) Korin Albert et al.   Microorganisms

Rebooting Human Immunology

(2018) Mark M. Davis et al.   Annual Review of Immunology

OUP accepted manuscript

(2018)   BIOINFORMATICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Galectins in Intestinal Inflammation: Galectin-1 Expression Delineates Response to Treatment in Celiac Disease Patients

(2018) Victoria Sundblad et al.   Frontiers in Immunology

Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC

(2018) Lee Call et al.   Microbiome

Stereotypic Immune System Development in Newborn Children

(2018) Axel Olin et al.   CELL

Infant Colic Represents Gut Inflammation and Dysbiosis

(2018) J. Marc Rhoads et al.   JOURNAL OF PEDIATRICS

GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets

(2018) Matthew D Czajkowski et al.   BIOINFORMATICS

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting

(2017) Marie-Claire Arrieta et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective

(2017) Isabelle Laforest-Lapointe et al.   Frontiers in Immunology

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

(2017) Steven A. Frese et al.   mSphere

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

(2016) Tommi Vatanen et al.   CELL

Human CD39hi regulatory T cells present stronger stability and function under inflammatory conditions

(2016) Jian Gu et al.   Cellular & Molecular Immunology

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

The Immunobiology of Interleukin-27

(2015) Hiroki Yoshida et al.   Annual Review of Immunology

Early-life compartmentalization of human T cell differentiation and regulatory function in mucosal and lymphoid tissues

(2015) Joseph J C Thome et al.   NATURE MEDICINE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Early infancy microbial and metabolic alterations affect risk of childhood asthma

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

Proteobacteria: microbial signature of dysbiosis in gut microbiota

(2015) Na-Ri Shin et al.   TRENDS IN BIOTECHNOLOGY

Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants

(2015) Zachery T Lewis et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis

(2014) Aurélien Trompette et al.   NATURE MEDICINE

Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut

(2014) Mark A. Underwood et al.   PEDIATRIC RESEARCH

Stool Microbiota and Vaccine Responses of Infants

(2014) M. N. Huda et al.   PEDIATRICS

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

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

Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children

(2013) Ekaterina Avershina et al.   FEMS MICROBIOLOGY ECOLOGY

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

(2013) Shuzhao Li et al.   NATURE IMMUNOLOGY

454 Pyrosequencing Analysis on Faecal Samples from a Randomized DBPC Trial of Colicky Infants Treated with Lactobacillus reuteri DSM 17938

(2013) Stefan Roos et al.   PLoS One

Dietary gluten triggers concomitant activation of CD4+ and CD8+    T cells and    T cells in celiac disease

(2013) A. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) P. M. Smith et al.   SCIENCE

Commensal Bacteria Calibrate the Activation Threshold of Innate Antiviral Immunity

(2012) Michael C. Abt et al.   IMMUNITY

Distinct Gut Microbiota in Southeastern African and Northern European Infants

(2012) Łukasz Grześkowiak et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

New Insights in Gut Microbiota Establishment in Healthy Breast Fed Neonates

(2012) Ted Jost et al.   PLoS One

CD62LnegCD38+ Expression on Circulating CD4+ T Cells Identifies Mucosally Differentiated Cells in Protein Fed Mice and in Human Celiac Disease Patients and Controls

(2011) M Fleur du Pré et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Bifidobacterial utilization of human milk oligosaccharides

(2011) David A. Sela   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Homogeneous antibody-based proximity extension assays provide sensitive and specific detection of low-abundant proteins in human blood

(2011) Martin Lundberg et al.   NUCLEIC ACIDS RESEARCH

Broad Conservation of Milk Utilization Genes in Bifidobacterium longum subsp. infantis as Revealed by Comparative Genomic Hybridization

(2010) R. G. LoCascio et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CD161 is a marker of all human IL-17-producing T-cell subsets and is induced by RORC

(2010) Laura Maggi et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Antibiotic use and inflammatory bowel diseases in childhood

(2010) A. Hviid et al.   GUT

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides

(2010) David A. Sela et al.   TRENDS IN MICROBIOLOGY

Faecal short chain fatty acid pattern and allergy in early childhood

(2009) Anna Sandin et al.   ACTA PAEDIATRICA

Role of β7 Integrins in Intestinal Lymphocyte Homing and Retention

(2009) G. Gorfu et al.   CURRENT MOLECULAR MEDICINE

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Is interleukin-1 a good or bad ‘guy’ in tumor immunobiology and immunotherapy?

(2008) Ron N. Apte et al.   IMMUNOLOGICAL REVIEWS

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

(2008) D. A. Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA