Publications by authors named "Pierre Peyret"

65Publications

Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis.

BMC Res Notes 2018 Jul 11;11(1):461. Epub 2018 Jul 11.

Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université de Lyon, Université Lyon 1, 43 Boulevard du 11 novembre 1918, 69622, Villeurbanne, France.

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July 2018

ASaiM: a Galaxy-based framework to analyze microbiota data.

Gigascience 2018 06;7(6)

Université Clermont Auvergne, EA 4678 CIDAM, 63000 Clermont-Ferrand, France (previous address).

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June 2018

Chloromethane formation and degradation in the fern phyllosphere.

Sci Total Environ 2018 Sep 18;634:1278-1287. Epub 2018 Apr 18.

Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany; Heidelberg Center for the Environment HCE, Heidelberg University, Heidelberg, Germany. Electronic address:

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September 2018

Hybridization capture reveals microbial diversity missed using current profiling methods.

Microbiome 2018 03 27;6(1):61. Epub 2018 Mar 27.

Université Clermont Auvergne, INRA, UMR 454 MEDIS, 28, place Henri Dunant, F-63000, Clermont-Ferrand, France.

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March 2018

Environmental Pollutant Benzo[]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota.

Front Microbiol 2017 15;8:1562. Epub 2017 Aug 15.

MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France.

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August 2017

OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture.

Database (Oxford) 2017 01;2017(1)

Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France.

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January 2017

Revealing large metagenomic regions through long DNA fragment hybridization capture.

Microbiome 2017 03 14;5(1):33. Epub 2017 Mar 14.

Université Clermont Auvergne, INRA, MEDIS, 63000, Clermont-Ferrand, France.

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March 2017

The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer.

Microb Biotechnol 2017 03 21;10(2):469-479. Epub 2016 Oct 21.

Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie, IPREM-CNRS 5254, F-64013, Pau, France.

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March 2017

Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.

Nucleic Acids Res 2016 Jun 21;44(10):4504-18. Epub 2016 Apr 21.

EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France

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June 2016

Genome Sequence of Pseudomonas sp. HUK17, Isolated from Hexachlorocyclohexane-Contaminated Soil.

Genome Announc 2016 Apr 14;4(2). Epub 2016 Apr 14.

EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, France

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April 2016

Genome Sequence of Staphylococcus aureus Strain HUK16, Isolated from Hexachlorocyclohexane-Contaminated Soil.

Genome Announc 2016 Apr 14;4(2). Epub 2016 Apr 14.

EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, France

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April 2016

Genome Sequence of Bacillus subtilis Strain HUK15, Isolated from Hexachlorocyclohexane-Contaminated Soil.

Genome Announc 2016 Apr 14;4(2). Epub 2016 Apr 14.

EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, France

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April 2016

Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning.

Methods Mol Biol 2016 ;1399:167-82

EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France.

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October 2016

Probe Design Strategies for Oligonucleotide Microarrays.

Methods Mol Biol 2016 ;1368:67-82

Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France.

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September 2016

Capturing prokaryotic dark matter genomes.

Res Microbiol 2015 Dec 20;166(10):814-30. Epub 2015 Jun 20.

Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France. Electronic address:

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December 2015

Draft Genomes of Three Strains Representative of the Bacillus anthracis Diversity Found in France.

Genome Announc 2014 Jul 31;2(4). Epub 2014 Jul 31.

University Paris-Est, ANSES, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France

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July 2014

Hijacking of host cellular functions by an intracellular parasite, the microsporidian Anncaliia algerae.

PLoS One 2014 26;9(6):e100791. Epub 2014 Jun 26.

Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France; CNRS, UMR 6023, LMGE, Aubière, France.

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February 2015

PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification.

Database (Oxford) 2014 26;2014(0):bau036. Epub 2014 Apr 26.

Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France, UMR CNRS 6158, ISIMA/LIMOS, Clermont Université, Université Blaise Pascal, F-63173 Aubière, France, CNRS, UMR 6023, LMGE, F-63171 Aubière, France and Clermont Université, CRRI, F-63177 Aubière, France.

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October 2014

Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette.

Archaea 2014 27;2014:374146. Epub 2014 Jan 27.

1EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Place Henri Dunant, 63001 Clermont-Ferrand, France.

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November 2014

Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments.

Mol Ecol 2013 Oct 3;22(19):4870-83. Epub 2013 Sep 3.

Département Microorganismes, Génomes, Environnement, Génétique Moléculaire, Génomique et Microbiologie, UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France.

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October 2013

Identification of two new polar tube proteins related to polar tube protein 2 in the microsporidian Antonospora locustae.

FEMS Microbiol Lett 2013 Sep 17;346(1):36-44. Epub 2013 Jul 17.

Clermont Université, Université d'Auvergne, Laboratoire Microorganismes: Génome et Environnement, Clermont-ferrand, France.

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September 2013

Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration.

DNA Res 2013 Apr 30;20(2):185-96. Epub 2013 Jan 30.

Centre de Recherche en Nutrition Humaine Auvergne, Clermont Université, Université d'Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, BP 10448, Clermont-Ferrand 63000, France.

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April 2013

NucBase, an easy to use read mapper for small RNAs.

Mob DNA 2013 Jan 1;4(1). Epub 2013 Jan 1.

Clermont Université, Université d'Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France.

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January 2013

Annotation of microsporidian genomes using transcriptional signals.

Nat Commun 2012 ;3:1137

Clermont Université, Université d'Auvergne, Centre de Recherche en Nutrition Humaine Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, BP 10448, F63000 Clermont-Ferrand, France.

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March 2013

KASpOD--a web service for highly specific and explorative oligonucleotide design.

Bioinformatics 2012 Dec 9;28(23):3161-2. Epub 2012 Oct 9.

Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, France.

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December 2012

In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes.

Microb Biotechnol 2012 Sep 21;5(5):642-53. Epub 2012 Mar 21.

Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F63000, Clermont-Ferrand, France.

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September 2012

Detecting unknown sequences with DNA microarrays: explorative probe design strategies.

Environ Microbiol 2012 Feb 5;14(2):356-71. Epub 2011 Sep 5.

Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France.

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February 2012

Production and consumption of methane in freshwater lake ecosystems.

Res Microbiol 2011 Nov 13;162(9):832-47. Epub 2011 Jun 13.

Clermont Université, Universite Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, UMR CNRS 6023, 63000 Clermont-Ferrand, France.

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November 2011

Bacterial community composition of biological degreasing systems and health risk assessment for workers.

Microb Ecol 2011 Nov 23;62(4):868-81. Epub 2011 Jun 23.

Clermont Université, Université d'Auvergne, Laboratoire: Microorganismes Génome et Environnement (LMGE), BP 10448, F-63000 Clermont-Ferrand, France.

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November 2011

Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake.

FEMS Microbiol Ecol 2011 Sep 20;77(3):533-45. Epub 2011 Jun 20.

Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, France.

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September 2011

Extreme reduction and compaction of microsporidian genomes.

Res Microbiol 2011 Jul-Aug;162(6):598-606. Epub 2011 Mar 21.

Clermont Université, Université d'Auvergne, Laboratoire Microorganismes Génome et Environnement, BP 10448, F-63000 Clermont-Ferrand, France.

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December 2011

HiSpOD: probe design for functional DNA microarrays.

Bioinformatics 2011 Mar 6;27(5):641-8. Epub 2011 Jan 6.

Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, Clermont-Ferrand, France.

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March 2011

Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers.

Microb Ecol 2011 Feb 25;61(2):313-27. Epub 2010 Nov 25.

Laboratoire Microorganismes, Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, F63000 Clermont-Ferrand, France.

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February 2011

Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil.

FEMS Microbiol Ecol 2010 Dec 2;74(3):669-81. Epub 2010 Nov 2.

Clermont Université, Université d'Auvergne, Laboratoire: Microorganismes Génome et Environnement, Clermont-Ferrand, France.

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December 2010

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development.

BMC Bioinformatics 2010 Sep 23;11:478. Epub 2010 Sep 23.

Clermont Université, Université d'Auvergne, Laboratoire: Microorganismes Génome et Environnement, BP 10448, F-63000 Clermont-Ferrand, France.

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September 2010

Tools for stools: the challenge of assessing human intestinal microbiota using molecular diagnostics.

Expert Rev Mol Diagn 2009 May;9(4):353-65

ERT-18 CIDAM, Université d'Auvergne, CRNH Auvergne, Place Henri Dunant, Clermont-Ferrand, France.

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May 2009

A comparison of algorithms for a complete backtranslation of oligopeptides.

Int J Comput Biol Drug Des 2008 ;1(1):26-38

ISIMA/LIMOS UMR CNRS 6158, Blaise Pascal University, BP 10125, 63173 Aubière Cedex, France.

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February 2010

In vitro propagation of the microsporidian pathogen Brachiola algerae and studies of its chromosome and ribosomal DNA organization in the context of the complete genome sequencing project.

Parasitol Int 2008 Mar 20;57(1):62-71. Epub 2007 Sep 20.

Laboratoire de Biologie des Protistes, UMR CNRS 6023, Université Blaise Pascal, 24 avenue des Landais, Campus des Cézeaux, 63177 Aubière Cedex, France.

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March 2008

PhylArray: phylogenetic probe design algorithm for microarray.

Bioinformatics 2007 Oct 12;23(19):2550-7. Epub 2007 Aug 12.

Génomique Intégrée des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des Cézeaux, France.

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October 2007

EnP1 and EnP2, two proteins associated with the Encephalitozoon cuniculi endospore, the chitin-rich inner layer of the microsporidian spore wall.

Int J Parasitol 2006 Mar 22;36(3):309-18. Epub 2005 Nov 22.

Equipe Parasitologie Moléculaire et Cellulaire, LBP, UMR CNRS 6023, Université Blaise Pascal, 24 Avenue des Landais, 63177 Aubière Cedex, France.

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March 2006

GoArrays: highly dynamic and efficient microarray probe design.

Bioinformatics 2005 Apr 5;21(7):1094-103. Epub 2004 Nov 5.

LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II BP 10125, 63177 Aubiere Cedex, France.

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April 2005

The microsporidian polar tube: evidence for a third polar tube protein (PTP3) in Encephalitozoon cuniculi.

Mol Biochem Parasitol 2002 Jun;122(1):69-80

Equipe Parasitologie Moléculaire et Cellulaire, Laboratoire Biologie des Protistes, UMR CNRS 6023, Université Blaise Pascal, Aubiere, France.

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June 2002