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Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems.

Defois C, Ratel J, Garrait G, Denis S, Le Goff O, Talvas J, Mosoni P, Engel E, Peyret P.

Sci Rep. 2018 Jul 20;8(1):11006. doi: 10.1038/s41598-018-29376-9.


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

Cariou M, Ribière C, Morlière S, Gauthier JP, Simon JC, Peyret P, Charlat S.

BMC Res Notes. 2018 Jul 11;11(1):461. doi: 10.1186/s13104-018-3559-3.


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

Batut B, Gravouil K, Defois C, Hiltemann S, Brugère JF, Peyretaillade E, Peyret P.

Gigascience. 2018 Jun 1;7(6). doi: 10.1093/gigascience/giy057.


Chloromethane formation and degradation in the fern phyllosphere.

Jaeger N, Besaury L, Röhling AN, Koch F, Delort AM, Gasc C, Greule M, Kolb S, Nadalig T, Peyret P, Vuilleumier S, Amato P, Bringel F, Keppler F.

Sci Total Environ. 2018 Sep 1;634:1278-1287. doi: 10.1016/j.scitotenv.2018.03.316. Epub 2018 Apr 18.


Hybridization capture reveals microbial diversity missed using current profiling methods.

Gasc C, Peyret P.

Microbiome. 2018 Mar 27;6(1):61. doi: 10.1186/s40168-018-0442-3.


FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota.

Comtet-Marre S, Chaucheyras-Durand F, Bouzid O, Mosoni P, Bayat AR, Peyret P, Forano E.

Front Microbiol. 2018 Feb 13;9:215. doi: 10.3389/fmicb.2018.00215. eCollection 2018.


PtxtPME1 and homogalacturonans influence xylem hydraulic properties in poplar.

Allario T, Tixier A, Awad H, Lemaire C, Brunel N, Badel E, Barigah TS, Julien JL, Peyret P, Mellerowicz EJ, Cochard H, Herbette S.

Physiol Plant. 2018 Aug;163(4):502-515. doi: 10.1111/ppl.12702. Epub 2018 Apr 23.


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

Defois C, Ratel J, Denis S, Batut B, Beugnot R, Peyretaillade E, Engel E, Peyret P.

Front Microbiol. 2017 Aug 15;8:1562. doi: 10.3389/fmicb.2017.01562. eCollection 2017.


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

Gasc C, Constantin A, Jaziri F, Peyret P.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/baw172.


Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes.

Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E.

DNA Res. 2017 Jun 1;24(3):251-260. doi: 10.1093/dnares/dsx002.


Revealing large metagenomic regions through long DNA fragment hybridization capture.

Gasc C, Peyret P.

Microbiome. 2017 Mar 14;5(1):33. doi: 10.1186/s40168-017-0251-0.


Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet.

Comtet-Marre S, Parisot N, Lepercq P, Chaucheyras-Durand F, Mosoni P, Peyretaillade E, Bayat AR, Shingfield KJ, Peyret P, Forano E.

Front Microbiol. 2017 Jan 31;8:67. doi: 10.3389/fmicb.2017.00067. eCollection 2017.


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

Ranchou-Peyruse M, Gasc C, Guignard M, Aüllo T, Dequidt D, Peyret P, Ranchou-Peyruse A.

Microb Biotechnol. 2017 Mar;10(2):469-479. doi: 10.1111/1751-7915.12426. Epub 2016 Oct 21.


Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model.

Ribière C, Peyret P, Parisot N, Darcha C, Déchelotte PJ, Barnich N, Peyretaillade E, Boucher D.

Sci Rep. 2016 Aug 9;6:31027. doi: 10.1038/srep31027.


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

Gasc C, Peyretaillade E, Peyret P.

Nucleic Acids Res. 2016 Jun 2;44(10):4504-18. doi: 10.1093/nar/gkw309. Epub 2016 Apr 21. Review.


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

Gasc C, Richard JY, Peyret P.

Genome Announc. 2016 Apr 14;4(2). pii: e00275-16. doi: 10.1128/genomeA.00275-16.


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

Gasc C, Richard JY, Peyret P.

Genome Announc. 2016 Apr 14;4(2). pii: e00274-16. doi: 10.1128/genomeA.00274-16.


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

Gasc C, Richard JY, Peyret P.

Genome Announc. 2016 Apr 14;4(2). pii: e00273-16. doi: 10.1128/genomeA.00273-16.


Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning.

Ribière C, Beugnot R, Parisot N, Gasc C, Defois C, Denonfoux J, Boucher D, Peyretaillade E, Peyret P.

Methods Mol Biol. 2016;1399:167-82. doi: 10.1007/978-1-4939-3369-3_10.


Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes.

Biderre-Petit C, Dugat-Bony E, Mege M, Parisot N, Adrian L, Moné A, Denonfoux J, Peyretaillade E, Debroas D, Boucher D, Peyret P.

PLoS One. 2016 Jan 6;11(1):e0145558. doi: 10.1371/journal.pone.0145558. eCollection 2016.


Probe Design Strategies for Oligonucleotide Microarrays.

Parisot N, Peyretaillade E, Dugat-Bony E, Denonfoux J, Mahul A, Peyret P.

Methods Mol Biol. 2016;1368:67-82. doi: 10.1007/978-1-4939-3136-1_6.


The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes.

Belkorchia A, Gasc C, Polonais V, Parisot N, Gallois N, Ribière C, Lerat E, Gaspin C, Pombert JF, Peyret P, Peyretaillade E.

PLoS One. 2015 Sep 30;10(9):e0139075. doi: 10.1371/journal.pone.0139075. eCollection 2015.


Capturing prokaryotic dark matter genomes.

Gasc C, Ribière C, Parisot N, Beugnot R, Defois C, Petit-Biderre C, Boucher D, Peyretaillade E, Peyret P.

Res Microbiol. 2015 Dec;166(10):814-30. doi: 10.1016/j.resmic.2015.06.001. Epub 2015 Jun 20. Review.


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

Borrel G, Gaci N, Peyret P, O'Toole PW, Gribaldo S, Brugère JF.

Archaea. 2015 Feb 2;2015:941836. doi: 10.1155/2015/941836. eCollection 2015.


Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils.

Cébron A, Beguiristain T, Bongoua-Devisme J, Denonfoux J, Faure P, Lorgeoux C, Ouvrard S, Parisot N, Peyret P, Leyval C.

Environ Sci Pollut Res Int. 2015 Sep;22(18):13724-38. doi: 10.1007/s11356-015-4117-3. Epub 2015 Jan 25.


Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples.

Bragalini C, Ribière C, Parisot N, Vallon L, Prudent E, Peyretaillade E, Girlanda M, Peyret P, Marmeisse R, Luis P.

DNA Res. 2014 Dec;21(6):685-94. doi: 10.1093/dnares/dsu030. Epub 2014 Oct 3.


Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems.

Peyretaillade E, Boucher D, Parisot N, Gasc C, Butler R, Pombert JF, Lerat E, Peyret P.

Heredity (Edinb). 2015 May;114(5):441-9. doi: 10.1038/hdy.2014.78. Epub 2014 Sep 3. Review.


Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans.

Parisot N, Pelin A, Gasc C, Polonais V, Belkorchia A, Panek J, El Alaoui H, Biron DG, Brasset E, Vaury C, Peyret P, Corradi N, Peyretaillade É, Lerat E.

Genome Biol Evol. 2014 Aug 28;6(9):2289-300. doi: 10.1093/gbe/evu178.


Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine.

Borrel G, Parisot N, Harris HM, Peyretaillade E, Gaci N, Tottey W, Bardot O, Raymann K, Gribaldo S, Peyret P, O'Toole PW, Brugère JF.

BMC Genomics. 2014 Aug 13;15:679. doi: 10.1186/1471-2164-15-679.


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

Girault G, Parisot N, Peyretaillade E, Peyret P, Derzelle S.

Genome Announc. 2014 Jul 31;2(4). pii: e00736-14. doi: 10.1128/genomeA.00736-14.


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

Panek J, El Alaoui H, Mone A, Urbach S, Demettre E, Texier C, Brun C, Zanzoni A, Peyretaillade E, Parisot N, Lerat E, Peyret P, Delbac F, Biron DG.

PLoS One. 2014 Jun 26;9(6):e100791. doi: 10.1371/journal.pone.0100791. eCollection 2014.


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

Jaziri F, Parisot N, Abid A, Denonfoux J, Ribière C, Gasc C, Boucher D, Brugère JF, Mahul A, Hill DR, Peyretaillade E, Peyret P.

Database (Oxford). 2014 Apr 26;2014(0):bau036. doi: 10.1093/database/bau036. Print 2014.


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

Borrel G, Gaci N, Peyret P, O'Toole PW, Gribaldo S, Brugère JF.

Archaea. 2014 Jan 27;2014:374146. doi: 10.1155/2014/374146. eCollection 2014. Erratum in: Archaea. 2015;2015:941836.


Large scale explorative oligonucleotide probe selection for thousands of genetic groups on a computing grid: application to phylogenetic probe design using a curated small subunit ribosomal RNA gene database.

Jaziri F, Peyretaillade E, Missaoui M, Parisot N, Cipière S, Denonfoux J, Mahul A, Peyret P, Hill DR.

ScientificWorldJournal. 2014 Jan 6;2014:350487. doi: 10.1155/2014/350487. eCollection 2014.


Three-stage continuous culture system with a self-generated anaerobia to study the regionalized metabolism of the human gut microbiota.

Feria-Gervasio D, Tottey W, Gaci N, Alric M, Cardot JM, Peyret P, Martin JF, Pujos E, Sébédio JL, Brugère JF.

J Microbiol Methods. 2014 Jan;96:111-8. doi: 10.1016/j.mimet.2013.11.015. Epub 2013 Dec 11.


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

Plewniak F, Koechler S, Navet B, Dugat-Bony E, Bouchez O, Peyret P, Séby F, Battaglia-Brunet F, Bertin PN.

Mol Ecol. 2013 Oct;22(19):4870-83. doi: 10.1111/mec.12432. Epub 2013 Sep 3.


Phylogenomic data support a seventh order of Methylotrophic methanogens and provide insights into the evolution of Methanogenesis.

Borrel G, O'Toole PW, Harris HM, Peyret P, Brugère JF, Gribaldo S.

Genome Biol Evol. 2013;5(10):1769-80. doi: 10.1093/gbe/evt128.


Genome Sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces.

Borrel G, Harris HM, Parisot N, Gaci N, Tottey W, Mihajlovski A, Deane J, Gribaldo S, Bardot O, Peyretaillade E, Peyret P, O'Toole PW, Brugère JF.

Genome Announc. 2013 Jul 11;1(4). pii: e00453-13. doi: 10.1128/genomeA.00453-13.


Wood ash amendment to biogas reactors as an alternative to landfilling? A preliminary study on changes in process chemistry and biology.

Podmirseg SM, Seewald MS, Knapp BA, Bouzid O, Biderre-Petit C, Peyret P, Insam H.

Waste Manag Res. 2013 Aug;31(8):829-42. doi: 10.1177/0734242X13497077. Epub 2013 Jul 5.


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

Polonais V, Belkorchia A, Roussel M, Peyretaillade E, Peyret P, Diogon M, Delbac F.

FEMS Microbiol Lett. 2013 Sep;346(1):36-44. doi: 10.1111/1574-6968.12198. Epub 2013 Jul 17.


The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level.

Tottey W, Denonfoux J, Jaziri F, Parisot N, Missaoui M, Hill D, Borrel G, Peyretaillade E, Alric M, Harris HM, Jeffery IB, Claesson MJ, O'Toole PW, Peyret P, Brugère JF.

PLoS One. 2013 May 17;8(5):e62544. doi: 10.1371/journal.pone.0062544. Print 2013.


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

Denonfoux J, Parisot N, Dugat-Bony E, Biderre-Petit C, Boucher D, Morgavi DP, Le Paslier D, Peyretaillade E, Peyret P.

DNA Res. 2013 Apr;20(2):185-96. doi: 10.1093/dnares/dst001. Epub 2013 Jan 30.


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

Dufourt J, Pouchin P, Peyret P, Brasset E, Vaury C.

Mob DNA. 2013 Jan 1;4(1):1. doi: 10.1186/1759-8753-4-1.


Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens.

Borrel G, Harris HM, Tottey W, Mihajlovski A, Parisot N, Peyretaillade E, Peyret P, Gribaldo S, O'Toole PW, Brugère JF.

J Bacteriol. 2012 Dec;194(24):6944-5. doi: 10.1128/JB.01867-12.


Annotation of microsporidian genomes using transcriptional signals.

Peyretaillade E, Parisot N, Polonais V, Terrat S, Denonfoux J, Dugat-Bony E, Wawrzyniak I, Biderre-Petit C, Mahul A, Rimour S, Gonçalves O, Bornes S, Delbac F, Chebance B, Duprat S, Samson G, Katinka M, Weissenbach J, Wincker P, Peyret P.

Nat Commun. 2012;3:1137. doi: 10.1038/ncomms2156.


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

Parisot N, Denonfoux J, Dugat-Bony E, Peyret P, Peyretaillade E.

Bioinformatics. 2012 Dec 1;28(23):3161-2. doi: 10.1093/bioinformatics/bts597. Epub 2012 Oct 9.


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

Dugat-Bony E, Biderre-Petit C, Jaziri F, David MM, Denonfoux J, Lyon DY, Richard JY, Curvers C, Boucher D, Vogel TM, Peyretaillade E, Peyret P.

Microb Biotechnol. 2012 Sep;5(5):642-53. doi: 10.1111/j.1751-7915.2012.00339.x. Epub 2012 Mar 21.


Fed-batch anaerobic valorization of slaughterhouse by-products with mesophilic microbial consortia without methane production.

Pessiot J, Nouaille R, Jobard M, Singhania RR, Bournilhas A, Christophe G, Fontanille P, Peyret P, Fonty G, Larroche C.

Appl Biochem Biotechnol. 2012 Jul;167(6):1728-43. doi: 10.1007/s12010-011-9516-4. Epub 2012 Jan 6.


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

Dugat-Bony E, Peyretaillade E, Parisot N, Biderre-Petit C, Jaziri F, Hill D, Rimour S, Peyret P.

Environ Microbiol. 2012 Feb;14(2):356-71. doi: 10.1111/j.1462-2920.2011.02559.x. Epub 2011 Sep 5. Review.


Production and consumption of methane in freshwater lake ecosystems.

Borrel G, Jézéquel D, Biderre-Petit C, Morel-Desrosiers N, Morel JP, Peyret P, Fonty G, Lehours AC.

Res Microbiol. 2011 Nov;162(9):832-47. doi: 10.1016/j.resmic.2011.06.004. Epub 2011 Jun 13.


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