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

Ecological Importance of Cross-Feeding of the Intermediate Metabolite 1,2-Propanediol between Bacterial Gut Symbionts

(2020) Christopher C. Cheng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

GToTree: a user-friendly workflow for phylogenomics

(2019) Michael D Lee   BIOINFORMATICS

The Preterm Gut Microbiota: An Inconspicuous Challenge in Nutritional Neonatal Care

(2019) Jannie G. E. Henderickx et al.   Frontiers in Cellular and Infection Microbiology

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

Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis

(2019) Mikiyasu Sakanaka et al.   Science Advances

Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation

(2019) Mikiyasu Sakanaka et al.   Nutrients

Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum

(2019) Korin Albert et al.   Microorganisms

Characterization and Quantification of Oligosaccharides in Human Milk and Infant Formula

(2018) Rose M. Nijman et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

An integrated bioprocess to recover bovine milk oligosaccharides from colostrum whey permeate

(2018) Juliana M.L.N. de Moura Bell et al.   JOURNAL OF FOOD ENGINEERING

Neonatal intestinal dysbiosis in necrotizing enterocolitis

(2018) Naomi-Liza Denning et al.   MOLECULAR MEDICINE

Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century

(2018) Bethany M. Henrick et al.   mSphere

Human milk oligosaccharides and infant gut bifidobacteria: Molecular strategies for their utilization

(2017) Pamela Thomson et al.   FOOD MICROBIOLOGY

Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets

(2017) Blair Lawley et al.   PeerJ

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

(2017) Steven A. Frese et al.   mSphere

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

Host-derived glycans serve as selected nutrients for the gut microbe: human milk oligosaccharides and bifidobacteria

(2016) Takane Katayama   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

(2016) Kathleen Sprouffske et al.   BMC BIOINFORMATICS

Fucosyllactose and L-fucose utilization of infant Bifidobacterium longum and Bifidobacterium kashiwanohense

(2016) Vera Bunesova et al.   BMC MICROBIOLOGY

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts

(2016) Philippe Remigi et al.   TRENDS IN MICROBIOLOGY

A key genetic factor for fucosyllactose utilization affects infant gut microbiota development

(2016) Takahiro Matsuki et al.   Nature Communications

hybridSPAdes: an algorithm for hybrid assembly of short and long reads

(2015) Dmitry Antipov et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

High level of fecal calprotectin at age 2 months as a marker of intestinal inflammation predicts atopic dermatitis and asthma by age 6

(2015) L. Orivuori et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Short communication: Quantification of carbohydrates in whey permeate products using high-performance anion-exchange chromatography with pulsed amperometric detection

(2015) Hyeyoung Lee et al.   JOURNAL OF DAIRY SCIENCE

Validating bifidobacterial species and subspecies identity in commercial probiotic products

(2015) Zachery T. Lewis et al.   PEDIATRIC RESEARCH

Early infancy microbial and metabolic alterations affect risk of childhood asthma

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

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Zachery T Lewis et al.   Microbiome

Breast Milk Oligosaccharides: Structure-Function Relationships in the Neonate

(2014) Jennifer T. Smilowitz et al.   Annual Review of Nutrition

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol

(2014) Christian Milani et al.   FEMS MICROBIOLOGY ECOLOGY

Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut

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

Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

(2013) C. Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

The Predominance of Type I Oligosaccharides Is a Feature Specific to Human Breast Milk

(2012) Tadasu Urashima et al.   Advances in Nutrition

A Molecular Basis for Bifidobacterial Enrichment in the Infant Gastrointestinal Tract

(2012) Daniel Garrido et al.   Advances in Nutrition

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Carbohydrate metabolism in Bifidobacteria

(2011) Karina Pokusaeva et al.   Genes and Nutrition

Physiology of Consumption of Human Milk Oligosaccharides by Infant Gut-associated Bifidobacteria

(2011) Sadaki Asakuma et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evolutionary Glycomics: Characterization of Milk Oligosaccharides in Primates

(2011) Nannan Tao et al.   JOURNAL OF PROTEOME RESEARCH

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Oligosaccharide Binding Proteins from Bifidobacterium longum subsp. infantis Reveal a Preference for Host Glycans

(2011) Daniel Garrido et al.   PLoS One

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

(2011) Steven A. Frese et al.   PLoS Genetics

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Genomic Evolution of Domesticated Microorganisms

(2010) Grace L. Douglas et al.   Annual Review of Food Science and Technology

A single regulatory gene is sufficient to alter bacterial host range

(2009) Mark J. Mandel et al.   NATURE

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

A versatile and scalable strategy for glycoprofiling bifidobacterial consumption of human milk oligosaccharides

(2008) Riccardo G. LoCascio et al.   Microbial Biotechnology