Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems

Subspeciation of Bifidobacterium longum by multilocus approaches and amplified fragment length polymorphism: Description of B. longum subsp. suillum subsp. nov., isolated from the faeces of piglets

(2015) Emiko Yanokura et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Comparative Genomic Analysis of 45 Type Strains of the Genus Bifidobacterium: A Snapshot of Its Genetic Diversity and Evolution

(2015) Zhihong Sun et al.   PLoS One

Discovery of a Conjugative Megaplasmid in Bifidobacterium breve

(2014) Francesca Bottacini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolism of Sialic Acid by Bifidobacterium breve UCC2003

(2014) Muireann Egan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium

(2014) Christian Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomics of the Bifidobacterium breve taxon

(2014) Francesca Bottacini et al.   BMC GENOMICS

Identification of Restriction-Modification Systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT Sequencing and Associated Methylome Analysis

(2014) Mary O′Connell Motherway et al.   PLoS One

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

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

Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation

(2013) Tyson A Clark et al.   BMC BIOLOGY

Bifidobacteria and humans: our special friends, from ecological to genomics perspectives

(2013) Marco Ventura et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Conjugative type IV secretion systems in Gram-positive bacteria

(2013) Nikolaus Goessweiner-Mohr et al.   PLASMID

Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle

(2013) J. B. Kozdon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of sortase-dependent pili of Bifidobacterium bifidum PRL2010 in modulating bacterium-host interactions

(2013) F. Turroni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tough nuts to crack

(2013) Vincenzo F. Brancaccio et al.   Bioengineered

Development of a Double-Crossover Markerless Gene Deletion System in Bifidobacterium longum: Functional Analysis of the α-Galactosidase Gene for Raffinose Assimilation

(2012) Yosuke Hirayama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exploration of the Genomic Diversity and Core Genome of the Bifidobacterium adolescentis Phylogenetic Group by Means of a Polyphasic Approach

(2012) Sabrina Duranti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A targeted gene knockout method using a newly constructed temperature-sensitive plasmid mediated homologous recombination in Bifidobacterium longum

(2012) Kouta Sakaguchi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Developing an efficient and reproducible conjugation-based gene transfer system for bifidobacteria

(2012) W. Dominguez et al.   MICROBIOLOGY-SGM

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

The methylomes of six bacteria

(2012) Iain A. Murray et al.   NUCLEIC ACIDS RESEARCH

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut

(2012) Francesca Bottacini et al.   PLoS One

Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection

(2012) S. Fanning et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host–microbe interactions that facilitate gut colonization by commensal bifidobacteria

(2012) Marco Ventura et al.   TRENDS IN MICROBIOLOGY

PGAP: pan-genomes analysis pipeline

(2011) Yongbing Zhao et al.   BIOINFORMATICS

Carbohydrate metabolism in Bifidobacteria

(2011) Karina Pokusaeva et al.   Genes and Nutrition

Progress in genomics, metabolism and biotechnology of bifidobacteria

(2011) Michelle Cronin et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor

(2011) M. O'Connell Motherway et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete Genome Sequence of Bifidobacterium longum JDM301

(2010) Y.-X. Wei et al.   JOURNAL OF BACTERIOLOGY

Improvement of transformation efficiency through in vitro methylation and SacII site mutation of plasmid vector in Bifidobacterium longum MG1

(2010) Geun Eog Ji   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Comparative genomics of the genus Bifidobacterium

(2010) F. Bottacini et al.   MICROBIOLOGY-SGM

Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging

(2010) F. Turroni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides

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

Comparative Analyses of Prophage-Like Elements Present in Bifidobacterial Genomes

(2009) M. Ventura et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity

(2009) Marco Ventura et al.   PLoS Genetics

Proposal to reclassify the three biotypes of Bifidobacterium longum as three subspecies: Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. nov.

(2008) P. Mattarelli et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Improvement of bacterial transformation efficiency using plasmid artificial modification

(2008) Kazumasa Yasui et al.   NUCLEIC ACIDS RESEARCH

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

Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis inBifidobacterium breveUCC2003

(2008) Mary O'Connell Motherway et al.   Microbial Biotechnology