Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium

A portable CRISPR-Cas9N system for flexible genome engineering in Lactobacillus acidophilus, Lactobacillus gasseri and Lactobacillus paracasei.

(2021) Yong Jun Goh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CRISPR-mediated host genomic DNA damage is efficiently repaired through microhomology-mediated end joining in Zymomonas mobilis

(2021) Xiaojie Wang et al.   Journal of Genetics and Genomics

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing

(2021) Alan Tourancheau et al.   NATURE METHODS

Genome Editing in Bacteria: CRISPR-Cas and Beyond

(2021) Ruben D. Arroyo-Olarte et al.   Microorganisms

Bifidobacteria-mediated immune system imprinting early in life

(2021) Bethany M. Henrick et al.   CELL

The Tetracycline Resistance Gene, tet(W) in Bifidobacterium animalis subsp. lactis Follows Phylogeny and Differs From tet(W) in Other Species

(2021) Katrine Nøhr-Meldgaard et al.   Frontiers in Microbiology

A split protease-E. coli ClpXP system quantifies protein–protein interactions in Escherichia coli cells

(2021) Shengchen Wang et al.   Communications Biology

Bifidobacterium animalis subsp. lactis HN019 Effects on Gut Health: A Review

(2021) Jing Cheng et al.   Frontiers in Nutrition

Applications of CRISPR-Cas systems in Lactic Acid Bacteria

(2020) Avery Roberts et al.   FEMS MICROBIOLOGY REVIEWS

Epigenetics: A New Frontier in Probiotic Research

(2020) Wesley Morovic et al.   TRENDS IN MICROBIOLOGY

Conserved DNA Methyltransferases: A Window into Fundamental Mechanisms of Epigenetic Regulation in Bacteria

(2020) Pedro H. Oliveira et al.   TRENDS IN MICROBIOLOGY

Bifidobacterium longum Subspecies infantis (B. infantis) in Pediatric Nutrition: Current State of Knowledge

(2020) Maciej Chichlowski et al.   Nutrients

Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium

(2020) Meichen Pan et al.   Microorganisms

Insights into the reason of Human-Residential Bifidobacteria (HRB) being the natural inhabitants of the human gut and their potential health-promoting benefits

(2020) Chyn Boon Wong et al.   FEMS MICROBIOLOGY REVIEWS

A compact Cascade–Cas3 system for targeted genome engineering

(2020) Bálint Csörgő et al.   NATURE METHODS

Engineer probiotic bifidobacteria for food and biomedical applications - Current status and future prospective

(2020) Fanglei Zuo et al.   BIOTECHNOLOGY ADVANCES

Development of a RecE/T‐Assisted CRISPR–Cas9 Toolbox for Lactobacillus

(2019) He Huang et al.   Biotechnology Journal

Systematic evasion of the restriction-modification barrier in bacteria

(2019) Christopher D. Johnston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus

(2019) Claudio Hidalgo-Cantabrana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inducible Plasmid Self-Destruction (IPSD) Assisted Genome Engineering in Lactobacilli and Bifidobacteria

(2019) Fanglei Zuo et al.   ACS Synthetic Biology

Using an Endogenous CRISPR-Cas System for Genome Editing in the Human Pathogen Clostridium difficile

(2019) Anna Maikova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System

(2018) Ryan Marshall et al.   MOLECULAR CELL

Structure basis for RNA-guided DNA degradation by Cascade and Cas3

(2018) Yibei Xiao et al.   SCIENCE

A Transposon Mutagenesis System for Bifidobacterium longum subsp. longum Based on an IS3 Family Insertion Sequence, ISBlo11

(2018) Mikiyasu Sakanaka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve

(2017) Francesca Bottacini et al.   NUCLEIC ACIDS RESEARCH

Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum

(2017) Claudio Hidalgo-Cantabrana et al.   Frontiers in Microbiology

A decade of discovery: CRISPR functions and applications

(2017) Rodolphe Barrangou et al.   Nature Microbiology

Target DNA recognition and cleavage by a reconstituted Type I-G CRISPR-Cas immune effector complex

(2016) Sonali Majumdar et al.   EXTREMOPHILES

Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach

(2016) Francesca Turroni et al.   ISME Journal

Applications of CRISPR technologies in research and beyond

(2016) Rodolphe Barrangou et al.   NATURE BIOTECHNOLOGY

Probing the impact of chromatin conformation on genome editing tools

(2016) Xiaoyu Chen et al.   NUCLEIC ACIDS RESEARCH

The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells

(2016) René M. Daer et al.   ACS Synthetic Biology

Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences

(2016) Katelyn Brandt et al.   Frontiers in Microbiology

A Single Mutation in the Gene Responsible for the Mucoid Phenotype of Bifidobacterium animalis subsp. lactis Confers Surface and Functional Characteristics

(2015) Claudio Hidalgo-Cantabrana et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CRISPR-based screening of genomic island excision events in bacteria

(2015) Kurt Selle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

Unravelling the structural and mechanistic basis of CRISPR–Cas systems

(2014) John van der Oost et al.   NATURE REVIEWS MICROBIOLOGY

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

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

Lacto-N-biosidase Encoded by a Novel Gene ofBifidobacterium longumSubspecieslongumShows Unique Substrate Specificity and Requires a Designated Chaperone for Its Active Expression

(2013) Haruko Sakurama et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Strong bias in the bacterial CRISPR elements that confer immunity to phage

(2013) David Paez-Espino et al.   Nature Communications

Accessing the Inaccessible: Molecular Tools for Bifidobacteria

(2012) Zhongke Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3

(2012) Edze R. Westra et al.   MOLECULAR CELL

In Vivo Protein Interactions and Complex Formation in the Pectobacterium atrosepticum Subtype I-F CRISPR/Cas System

(2012) Corinna Richter et al.   PLoS One

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system

(2011) Tomas Sinkunas et al.   EMBO JOURNAL

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

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

Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression

(2010) Douglas F Browning et al.   CURRENT OPINION IN MICROBIOLOGY

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

Human milk glycobiome and its impact on the infant gastrointestinal microbiota

(2010) A. M. Zivkovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Comparison of the Complete Genome Sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04

(2009) R. Barrangou et al.   JOURNAL OF BACTERIOLOGY

Characterization of ApuB, an Extracellular Type II Amylopullulanase from Bifidobacterium breve UCC2003

(2008) M. O'Connell Motherway et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transport of Glucose by Bifidobacterium animalis subsp. lactis Occurs via Facilitated Diffusion

(2008) E. P. Briczinski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

(2008) J. Carte et al.   GENES & DEVELOPMENT

Analysis of tetracycline resistance tet(W) genes and their flanking sequences in intestinal Bifidobacterium species

(2008) M. S. Ammor et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE

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

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