(Q34433445)

2 August 2017

title

Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation (English)

1 reference

2 August 2017

main subject

Lacticaseibacillus casei

1 reference

7

1 reference

2 August 2017

Rodolphe Barrangou

10

0 references

Wesley Morovic

object named as

Wesley Morovic

6

0 references

Jeff R Broadbent

object named as

Jeff R Broadbent

1

0 references

author name string

Eric C Neeno-Eckwall

2

1 reference

2 August 2017

Buffy Stahl

3

1 reference

2 August 2017

Kanokwan Tandee

4

1 reference

2 August 2017

Hui Cai

5

1 reference

2 August 2017

Jessie Heidenreich

8

1 reference

2 August 2017

Nicole T Perna

9

1 reference

2 August 2017

James L Steele

11

1 reference

2 August 2017

language of work or name

English

0 references

publication date

5 October 2012

1 reference

2 August 2017

1 reference

2 August 2017

volume

13

1 reference

2 August 2017

page(s)

533

1 reference

The infinitely many genes model for the distributed genome of bacteria.

2 August 2017

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1 reference

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6 July 2018

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Functional analysis of Lactobacillus rhamnosus GG pili in relation to adhesion and immunomodulatory interactions with intestinal epithelial cells

6 July 2018

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Evolution and classification of the CRISPR-Cas systems

6 July 2018

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Complete genome sequence of the probiotic bacterium Lactobacillus casei LC2W.

6 July 2018

1 reference

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Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model

6 July 2018

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Complete genome sequence of the probiotic strain Lactobacillus casei BD-II.

6 July 2018

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CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

6 July 2018

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Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates.

6 July 2018

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Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time.

6 July 2018

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

6 July 2018

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Complete genome sequence of Lactobacillus casei Zhang, a new probiotic strain isolated from traditional homemade koumiss in Inner Mongolia, China

6 July 2018

1 reference

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The distributed genome hypothesis as a rubric for understanding evolution in situ during chronic bacterial biofilm infectious processes

6 July 2018

1 reference

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progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

6 July 2018

1 reference

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The estimation of the bactericidal power of the blood

6 July 2018

1 reference

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Complete genome sequence of the probiotic Lactobacillus casei strain BL23.

6 July 2018

1 reference

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Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

CRISPR/Cas, the immune system of bacteria and archaea

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches

6 July 2018

1 reference

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RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Microbial comparative pan-genomics using binomial mixture models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Population genomics and the bacterial species concept

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae.

6 July 2018

1 reference

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Small CRISPR RNAs guide antiviral defense in prokaryotes

6 July 2018

1 reference

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The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates

6 July 2018

1 reference

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Virus population dynamics and acquired virus resistance in natural microbial communities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Phage response to CRISPR-encoded resistance in Streptococcus thermophilus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Optical mapping as a routine tool for bacterial genome sequence finishing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Functional analysis of the fructooligosaccharide utilization operon in Lactobacillus paracasei 1195.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Comparative genomics of the lactic acid bacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Identification of a putative operon involved in fructooligosaccharide utilization by Lactobacillus paracasei

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Lactate racemization as a rescue pathway for supplying D-lactate to the cell wall biosynthesis machinery in Lactobacillus plantarum

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

WebLogo: A Sequence Logo Generator

6 July 2018

1 reference

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Gradual evolution in bacteria: evidence from Bacillus systematics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Extensive gene gain associated with adaptive evolution of poxviruses

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

ASAP, a systematic annotation package for community analysis of genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Mechanisms of evolution in Rickettsia conorii and R. prowazekii

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Second-order selection in bacterial evolution: selection acting on mutation and recombination rates in the course of adaptation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Massive gene decay in the leprosy bacillus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Lateral gene transfer and the nature of bacterial innovation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Gene transfer, speciation, and the evolution of bacterial genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Molecular archaeology of the Escherichia coli genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Pathogenic adaptation of Escherichia coli by natural variation of the FimH adhesin.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Positive Darwinian selection after gene duplication in primate ribonuclease genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Lactic acid bacteria of foods and their current taxonomy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Determining divergence times of the major kingdoms of living organisms with a protein clock

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Basic local alignment search tool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Malolactic fermentation: electrogenic malate uptake and malate/lactate antiport generate metabolic energy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies.

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

Insertion sequence-driven evolution of Escherichia coli in chemostats.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

Significant differences between Lactobacillus casei subsp. casei ATCC 393T and a commonly used plasmid-cured derivative revealed by a polyphasic study.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

Comparative analysis of CRISPR loci in lactic acid bacteria genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

Viral biogeography revealed by signatures in Sulfolobus islandicus genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

The type strain of Lactobacillus casei is ATCC 393, ATCC 334 cannot serve as the type because it represents a different taxon, the name Lactobacillus paracasei and its subspecies names are not rejected and the revival of the name 'Lactobacillus zeae

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496567

Costs and Benefits of High Mutation Rates: Adaptive Evolution of Bacteria in the Mouse Gut

27 October 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-533

Gene gain and gene loss in streptococcus: is it driven by habitat?

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23035691

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23035691

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Role of malolactic fermentation in lactic acid bacteria

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23035691

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-13-533

1 reference

2 August 2017

1 reference

2 August 2017

1 reference