Adaptation of Propionibacterium freudenreichii to long-term survival under gradual nutritional shortage

[1]  Y. Le Loir,et al.  The long‐term survival of Propionibacterium freudenreichii in a context of nutrient shortage , 2016, Journal of applied microbiology.

[2]  G. Jan,et al.  Emmental Cheese Environment Enhances Propionibacterium freudenreichii Stress Tolerance , 2015, PloS one.

[3]  Marie-Agnès Dillies,et al.  SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data , 2015, bioRxiv.

[4]  H. Falentin,et al.  New insights about phenotypic heterogeneity within Propionibacterium freudenreichii argue against its division into subspecies , 2015, Dairy science & technology.

[5]  Y. Le Loir,et al.  Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii , 2015, BMC Genomics.

[6]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[7]  Robert D. Finn,et al.  Rfam 12.0: updates to the RNA families database , 2014, Nucleic Acids Res..

[8]  Paul Theodor Pyl,et al.  HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[9]  V. Péton,et al.  Surface proteins of Propionibacterium freudenreichii are involved in its anti-inflammatory properties. , 2015, Journal of proteomics.

[10]  M. Dimopoulou,et al.  Exopolysaccharide (EPS) Synthesis by Oenococcus oeni: From Genes to Phenotypes , 2014, PloS one.

[11]  Aurélie Le Cam,et al.  A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment , 2013, BMC Genomics.

[12]  D. Gautheret,et al.  Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline. , 2013, Methods.

[13]  M. Grillo-Puertas,et al.  Polyphosphate Degradation in Stationary Phase Triggers Biofilm Formation via LuxS Quorum Sensing System in Escherichia coli , 2012, PloS one.

[14]  H. Falentin,et al.  Accumulation of Intracellular Glycogen and Trehalose by Propionibacterium freudenreichii under Conditions Mimicking Cheese Ripening in the Cold , 2012, Applied and Environmental Microbiology.

[15]  H. Falentin,et al.  A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold , 2012, PloS one.

[16]  M. Kahala,et al.  Determination of aspartase activity in dairy Propionibacterium strains. , 2011, FEMS microbiology letters.

[17]  H. Falentin,et al.  Multilocus sequence typing of Propionibacterium freudenreichii. , 2011, International journal of food microbiology.

[18]  J. Gibrat,et al.  The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications , 2010, PloS one.

[19]  H. Falentin,et al.  Correlation of the Capsular Phenotype in Propionibacterium freudenreichii with the Level of Expression of gtf, a Unique Polysaccharide Synthase-Encoding Gene , 2010, Applied and Environmental Microbiology.

[20]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[21]  W. Bishai,et al.  Phosphate depletion: a novel trigger for Mycobacterium tuberculosis persistence. , 2009, The Journal of infectious diseases.

[22]  M. Vos.  Why do bacteria engage in homologous recombination? , 2009, Trends in microbiology.

[23]  Peter J. Woolf,et al.  GAGE: generally applicable gene set enrichment for pathway analysis , 2009, BMC Bioinformatics.

[24]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[25]  Bernard Martin,et al.  Induction of competence regulons as a general response to stress in gram-positive bacteria. , 2006, Annual review of microbiology.

[26]  M. Madec,et al.  Rapid and cost-effective method for micro organism enumeration based on miniaturization of the conventional plate-counting technique , 2006 .

[27]  S. Miura,et al.  Propionibacterium freudenreichii component 1.4-dihydroxy-2-naphthoic acid (DHNA) attenuates dextran sodium sulphate induced colitis by modulation of bacterial flora and lymphocyte homing , 2005, Gut.

[28]  M. Trost,et al.  Enzymes Involved in Anaerobic Respiration Appear To Play a Role in Actinobacillus pleuropneumoniae Virulence , 2005, Infection and Immunity.

[29]  G. Jan,et al.  Mass spectrometry proteomic analysis of stress adaptation reveals both common and distinct response pathways in Propionibacterium freudenreichii , 2004, Archives of Microbiology.

[30]  H. Sahm,et al.  The Phosphate Starvation Stimulon of Corynebacterium glutamicum Determined by DNA Microarray Analyses , 2003, Journal of bacteriology.

[31]  G. Jan,et al.  Susceptibility and Adaptive Response to Bile Salts in Propionibacterium freudenreichii: Physiological and Proteomic Analysis , 2003, Applied and Environmental Microbiology.

[32]  N. Yoda,et al.  Isolation and Identification of a New Bifidogenic Growth Stimulator Produced by Propionibacterium freudenreichii ET-3 , 2002, Bioscience, biotechnology, and biochemistry.

[33]  G. Jan,et al.  Changes in Protein Synthesis and Morphology during Acid Adaptation of Propionibacterium freudenreichii , 2001, Applied and Environmental Microbiology.

[34]  C. Hill,et al.  A glutamate decarboxylase system protects Listeria monocytogenes in gastric fluid , 2001, Molecular microbiology.

[35]  M. Leisola,et al.  Effect of glycine betaine on osmoadaptation of Propionibacterium acidipropionici cultivated in elevated osmolarities , 2000, Applied Microbiology and Biotechnology.

[36]  G. Jan,et al.  Acid stress susceptibility and acid adaptation of Propionibacterium freudenreichii subsp. shermanii , 2000 .

[37]  B. Schink,et al.  Humic Acid Reduction by Propionibacterium freudenreichii and Other Fermenting Bacteria , 1998, Applied and Environmental Microbiology.

[38]  V. Crow.  Metabolism of Aspartate by Propionibacterium freudenreichii subsp. shermanii: Effect on Lactate Fermentation , 1986, Applied and environmental microbiology.

[39]  E. Vedamuthu,et al.  An evaluation of the taxonomy of Propionibacterium. , 1968, Canadian journal of microbiology.

[40]  Panel on Biological Hazards ( BIOHAZ ) ; Scientific Opinion on Scientific Opinion on risk based control of biogenic amine formation in fermented foods , 2018 .

[41]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[42]  G. Jan,et al.  In vitro tolerance to digestive stresses of propionibacteria: influence of food matrices , 2005 .

[43]  P. Piveteau.  Metabolism of lactate and sugars by dairy propionibacteria: A review , 1999 .

[44]  P. Fox,et al.  Cheese: physical, biochemical, and nutritional aspects. , 1996, Advances in food and nutrition research.