Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics (Q34261103)

1 August 2017

title

Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics (English)

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1 August 2017

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11

Douwe van Sinderen

1 reference

1 August 2017

Christian Milani

2

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Marta Mangifesta

Marta Mangifesta

8

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Francesca Turroni

Francesca Turroni

3

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Gabriele Andrea Lugli

Gabriele Andrea Lugli

1

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Sabrina Duranti

Sabrina Duranti

4

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Marco Ventura

Marco Ventura

12

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author name string

Chiara Ferrario

5

1 reference

1 August 2017

Alice Viappiani

6

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1 August 2017

Leonardo Mancabelli

7

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1 August 2017

Bernard Taminiau

9

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1 August 2017

Véronique Delcenserie

10

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1 August 2017

language of work or name

English

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publication date

8 August 2014

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Applied and Environmental Microbiology

1 August 2017

published in

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1 August 2017

volume

80

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1 August 2017

issue

20

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1 August 2017

page(s)

6383-6394

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Genomic encyclopedia of type strains of the genus Bifidobacterium

1 August 2017

cites work

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

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6 July 2018

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6 July 2018

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Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces

6 July 2018

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

6 July 2018

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Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract

6 July 2018

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QIIME allows analysis of high-throughput community sequencing data

6 July 2018

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Bifidobacterium stercoris sp. nov., isolated from human faeces

6 July 2018

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The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity

6 July 2018

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Shifting the genomic gold standard for the prokaryotic species definition

6 July 2018

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Bifidobacterium bombi sp. nov., from the bumblebee digestive tract

6 July 2018

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Bifidobacterium mongoliense sp. nov., from airag, a traditional fermented mare's milk product from Mongolia

6 July 2018

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Lactobacillus phylogenomics--towards a reclassification of the genus

6 July 2018

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Human gut microbiota and bifidobacteria: from composition to functionality

6 July 2018

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Bifidobacterium tsurumiense sp. nov., from hamster dental plaque

6 July 2018

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Clustal W and Clustal X version 2.0

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum

6 July 2018

1 reference

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Phylogenomic analysis of natural selection pressure in Streptococcus genomes

6 July 2018

1 reference

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KaKs_Calculator: calculating Ka and Ks through model selection and model averaging

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Description of a new species, Bifidobacterium crudilactis sp. nov., isolated from raw milk and raw milk cheeses

6 July 2018

1 reference

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Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates

6 July 2018

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6 July 2018

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Genomic insights that advance the species definition for prokaryotes

6 July 2018

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6 July 2018

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Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at the subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis subsp. nov. and [...]

6 July 2018

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Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum

6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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The Ka/Ks ratio: diagnosing the form of sequence evolution

6 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

6 July 2018

https://pubmed.ncbi.nlm.nih.gov/25107967

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Bifidobacterium scardovii sp. nov., from human sources

6 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

6 July 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

An efficient algorithm for large-scale detection of protein families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Genome trees constructed using five different approaches suggest new major bacterial clades

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Universal trees based on large combined protein sequence data sets.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

The species concept for 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=4178631

From complete genomes to measures of substitution rate variability within and between proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Bifidobacterium thermacidophilum sp. nov., isolated from an anaerobic digester

6 July 2018

1 reference

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Whole genome-based phylogenetic analysis of free-living microorganisms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

The genomic tree as revealed from whole proteome comparisons

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Genome phylogeny based on gene content

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Bifid bacteria in bovine rumen. New species of the genus Bifidobacterium: B. globosum n.sp. and B. ruminale n.sp

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Comparative studies on bifidobacteria isolated from the alimentary tract of man and animals (including descriptions of bifidobacterium thermophilum nov. spec. and bifidobacterium pseudolongum nov. spec)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Bifidobacterium suis n. sp.: a new species of the genus Bifidobacterium isolated from pig feces

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

New species of bifid bacteria from Apis mellifica L. and Apis indica F. A contribution to the taxonomy and biochemistry of the genus Bifidobacterium

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Bifidobacterium pullorum sp. nov.: a new species isolated from chicken feces and a related group of bifidobacteria isolated from rabbit feces

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial 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=4178631

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=4178631

Bifidobacterium gallicum sp. nov. isolated from human feces

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

A genomic distance based on MUM indicates discontinuity between most bacterial species and genera.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Analysis of bifidobacterial evolution using a multilocus approach

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Phylogenetic trees based on gene content

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

COMPARATIVE STUDIES ON THE BIFIDUS FLORA IN THE FECES OF INFANTS AND ADULTS. WITH A CONTRIBUTION TO CLASSIFICATION AND NOMENCLATURE OF BIFIDUS STRAINS

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4178631

Electrophoretic types of transaldolase, transketolase, and other enzymes in bifidobacteria

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25107967

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1128/AEM.02004-14

1 reference

1 August 2017

1 reference

1 August 2017

1 reference