Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Revising the Structural Diversity of Ribosomal Proteins Across the Three Domains of Life

(2018) Sergey Melnikov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Design, Synthesis, and Evaluation of Novel Immunomodulatory Small Molecules Targeting the CD40–CD154 Costimulatory Protein-Protein Interaction

(2018) Damir Bojadzic et al.   MOLECULES

Comparative analysis of probiotic bacteria based on a new definition of core genome

(2018) Maria Satti et al.   Journal of Bioinformatics and Computational Biology

Streptococcus pyogenesEndopeptidase O Contributes to Evasion from Complement-mediated Bacteriolysis via Binding to Human Complement Factor C1q

(2017) Mariko Honda-Ogawa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DnaJ (hsp40) of Streptococcus pneumoniae is involved in bacterial virulence and elicits a strong natural immune reaction via PI3K/JNK

(2017) Jin Cui et al.   MOLECULAR IMMUNOLOGY

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

Regulation of Telomere Homeostasis during Epstein-Barr virus Infection and Immortalization

(2017) Siamak Kamranvar et al.   Viruses-Basel

Bifidobacterium bifidum Extracellular Sialidase Enhances Adhesion to the Mucosal Surface and Supports Carbohydrate Assimilation

(2017) Keita Nishiyama et al.   mBio

Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

(2017) Guojun Wu et al.   mBio

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota

(2017) Aitor Blanco-Míguez et al.   Database-The Journal of Biological Databases and Curation

Capsular polysaccharide inhibits adhesion of Bifidobacterium longum 105-A to enterocyte-like Caco-2 cells and phagocytosis by macrophages

(2017) Amin Tahoun et al.   Gut Pathogens

Bifidobacteria and Their Molecular Communication with the Immune System

(2017) Lorena Ruiz et al.   Frontiers in Microbiology

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin

(2017) Javier Querol-García et al.   Frontiers in Microbiology

Analysis of newly detected tetracycline resistance genes and their flanking sequences in human intestinal bifidobacteria

(2017) Na Wang et al.   Scientific Reports

Microbial interactions: ecology in a molecular perspective

(2016) Raíssa Mesquita Braga et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Efficacy of oral Bifidobacterium bifidum ATCC 29521 on microflora and antioxidant in mice

(2016) Bao-gui Wang et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

(2016) María X. Maldonado-Gómez et al.   Cell Host & Microbe

Heat shock proteins (HSPs) in the homeostasis of regulatory T cells (Tregs)

(2016) Tomasz Koliński et al.   Central European Journal of Immunology

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

Complete genome sequence of Bifidobacterium animalis subsp. lactis KLDS 2.0603, a probiotic strain with digestive tract resistance and adhesion to the intestinal epithelial cells

(2016) Dequan Zhu et al.   JOURNAL OF BIOTECHNOLOGY

Bifidobacterium infantis NLS Super Strain Reduces the Expression of α-Defensin-5, a Marker of Innate Immunity, in the Mucosa of Active Celiac Disease Patients

(2016) Maria I. Pinto-Sánchez et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Bifidobacteria—Insight into clinical outcomes and mechanisms of its probiotic action

(2016) Amrita Sarkar et al.   MICROBIOLOGICAL RESEARCH

Antimicrobial Activity of Lactoferrin-Related Peptides and Applications in Human and Veterinary Medicine

(2016) Natascia Bruni et al.   MOLECULES

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity

(2016) Mylène M Maury et al.   NATURE GENETICS

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Genome Analysis and Characterisation of the Exopolysaccharide Produced by Bifidobacterium longum subsp. longum 35624™

(2016) Friedrich Altmann et al.   PLoS One

The Wnt pathway: a key network in cell signalling dysregulated by viruses

(2016) Wendy J. van Zuylen et al.   REVIEWS IN MEDICAL VIROLOGY

Systematic Targeting of Protein–Protein Interactions

(2016) Ashley E. Modell et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

A multistrain probiotic formulation attenuates skin symptoms of atopic dermatitis in a mouse model through the generation of CD4+Foxp3+ T cells

(2016) Joo-Hyun Shin et al.   Food & Nutrition Research

Gut Bifidobacteria Populations in Human Health and Aging

(2016) Silvia Arboleya et al.   Frontiers in Microbiology

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics

(2016) Xian Zhang et al.   Frontiers in Microbiology

Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut

(2016) Audrey Rivière et al.   Frontiers in Microbiology

Comparative Genomics of Herpesviridae Family to Look for Potential Signatures of Human Infecting Strains

(2016) Vikas Sharma et al.   International Journal of Genomics

Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis

(2016) Sabrina Duranti et al.   Scientific Reports

BPGA- an ultra-fast pan-genome analysis pipeline

(2016) Narendrakumar M. Chaudhari et al.   Scientific Reports

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

(2015) A. O’Callaghan et al.   BMC GENOMICS

Inside the Pan-genome - Methods and Software Overview

(2015) Luis Carlos Guimaraes et al.   CURRENT GENOMICS

SecA: a potential antimicrobial target

(2015) Arpana S Chaudhary et al.   Future Medicinal Chemistry

Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines

(2015) David Kamanda Ngugi et al.   ISME Journal

Complete genome sequence of the probiotic bacterium Bifidobacterium breve KCTC 12201BP isolated from a healthy infant

(2015) Min-Jung Kwak et al.   JOURNAL OF BIOTECHNOLOGY

Complete genome sequence of Bifidobacterium longum KCTC 12200BP, a probiotic strain promoting the intestinal health

(2015) Soon-Kyeong Kwon et al.   JOURNAL OF BIOTECHNOLOGY

Complete genome sequence of Bifidobacterium adolesentis BBMN23, a probiotic strain from healthy centenarian

(2015) Songling Liu et al.   JOURNAL OF BIOTECHNOLOGY

Complete genome sequence of Bifidobacterium animalis subsp. lactis A6, a probiotic strain with high acid resistance ability

(2015) Erna Sun et al.   JOURNAL OF BIOTECHNOLOGY

Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes

(2015) Natalia V. Zakharevich et al.   MICROBIAL ECOLOGY

EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems

(2015) Valerie Eichinger et al.   NUCLEIC ACIDS RESEARCH

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Endogenous heat shock protein GroEL of A. actinomycetemcomitans preferentially targets primary human CD8+ T cells

(2015) Melis KANT et al.   TURKISH JOURNAL OF BIOLOGY

Exploring Amino Acid Auxotrophy in Bifidobacterium bifidum PRL2010

(2015) Chiara Ferrario et al.   Frontiers in 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

Bacterial Chaperones CsgE and CsgC Differentially Modulate Human α-Synuclein Amyloid Formation via Transient Contacts

(2015) Erik Chorell et al.   PLoS One

Genomic Characterization and Transcriptional Studies of the Starch-Utilizing Strain Bifidobacterium adolescentis 22L

(2014) Sabrina Duranti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium

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

Investigation of the Evolutionary Development of the Genus Bifidobacterium by Comparative Genomics

(2014) Gabriele Andrea Lugli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomics of the Bifidobacterium breve taxon

(2014) Francesca Bottacini et al.   BMC GENOMICS

Streptococcus pneumoniaePhosphoglycerate Kinase Is a Novel Complement Inhibitor Affecting the Membrane Attack Complex Formation

(2014) Anna M. Blom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Complete genome sequence of Bifidobacterium animalis RH, a probiotic bacterium producing exopolysaccharides

(2014) Lei Liu et al.   JOURNAL OF BIOTECHNOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Bifidobacteria Exhibit LuxS-Dependent Autoinducer 2 Activity and Biofilm Formation

(2014) Zhongke Sun et al.   PLoS One

Functional genomics of Lactobacillus casei establishment in the gut

(2014) H. Licandro-Seraut et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroencapsulatedBifidobacterium longumsubsp.infantisATCC 15697 Favorably Modulates Gut Microbiota and Reduces Circulating Endotoxins in F344 Rats

(2014) Laetitia Rodes et al.   Biomed Research International

Bifidobacterium bifidum as an example of a specialized human gut commensal

(2014) Francesca Turroni et al.   Frontiers in Microbiology

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

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

Selective transport by SecA2: An expanding family of customized motor proteins

(2013) Barbara A. Bensing et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes

(2013) Mohamed Barakat et al.   BMC GENOMICS

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

(2013) Gijs den Besten et al.   JOURNAL OF LIPID RESEARCH

Mechanisms of Cholesterol-Lowering Effects of Lactobacilli and Bifidobacteria Strains as Potential Probiotics with TheirbshGene Analysis

(2013) Özer Öner et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

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

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

How bacteria survive an acid trip

(2013) K. S. Hingorani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

(2012) S. Kumar et al.   BIOINFORMATICS

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

(2012) Jon Bohlin et al.   BMC GENOMICS

Patterns and architecture of genomic islands in marine bacteria

(2012) Beatriz Fernández-Gómez et al.   BMC GENOMICS

Proteomics reveals evidence of cross-talk between protein modifications in bacteria: focus on acetylation and phosphorylation

(2012) Boumediene Soufi et al.   CURRENT OPINION IN MICROBIOLOGY

Complete Genome Sequences of Probiotic Strains Bifidobacterium animalis subsp. lactis B420 and Bi-07

(2012) B. Stahl et al.   JOURNAL OF BACTERIOLOGY

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

BIPS: BIANA Interolog Prediction Server. A tool for protein–protein interaction inference

(2012) Javier Garcia-Garcia et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The Lon Protease Is Essential for Full Virulence in Pseudomonas aeruginosa

(2012) Elena B. M. Breidenstein et al.   PLoS One

Lateral gene transfer as a support for the tree of life

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

cAMP During HIV Infection: Friend or Foe?

(2011) Maria E. Moreno-Fernandez et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Interactions Between the Host Innate Immune System and Microbes in Inflammatory Bowel Disease

(2011) Clara Abraham et al.   GASTROENTEROLOGY

Carbohydrate metabolism in Bifidobacteria

(2011) Karina Pokusaeva et al.   Genes and Nutrition

Genome Sequence of the Probiotic Strain Bifidobacterium animalis subsp. lactis CNCM I-2494

(2011) C. Chervaux et al.   JOURNAL OF BACTERIOLOGY

Extraribosomal functions of bacterial ribosomal proteins

(2011) L. V. Aseev et al.   MOLECULAR BIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

(2011) Alessandro M Varani et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparative genomics of the genus Bifidobacterium

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

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

(2009) Kevin R. Brown et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes

(2009) Aditi Kanhere et al.   BMC EVOLUTIONARY BIOLOGY

Characterization of a Glutamate Transporter Operon, glnQHMP, in Streptococcus mutans and Its Role in Acid Tolerance

(2009) K. Krastel et al.   JOURNAL OF BACTERIOLOGY

ATP-binding cassette transporters in Escherichia coli

(2008) Anastassiia Moussatova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Evaluation of genomic island predictors using a comparative genomics approach

(2008) Morgan GI Langille et al.   BMC BIOINFORMATICS

The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

(2008) Wagied Davids et al.   BMC EVOLUTIONARY BIOLOGY

Protein Translocation Across the Bacterial Cytoplasmic Membrane

(2007) Arnold J.M. Driessen et al.   Annual Review of Biochemistry