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Items: 15

1.

Prediction of the intestinal resistome by a three-dimensional structure-based method.

Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD.

Nat Microbiol. 2019 Jan;4(1):112-123. doi: 10.1038/s41564-018-0292-6. Epub 2018 Nov 26.

PMID:
30478291
2.

Quality control of microbiota metagenomics by k-mer analysis.

Plaza Onate F, Batto JM, Juste C, Fadlallah J, Fougeroux C, Gouas D, Pons N, Kennedy S, Levenez F, Dore J, Ehrlich SD, Gorochov G, Larsen M.

BMC Genomics. 2015 Mar 14;16:183. doi: 10.1186/s12864-015-1406-7.

3.

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

Almeida M, Hébert A, Abraham AL, Rasmussen S, Monnet C, Pons N, Delbès C, Loux V, Batto JM, Leonard P, Kennedy S, Ehrlich SD, Pop M, Montel MC, Irlinger F, Renault P.

BMC Genomics. 2014 Dec 13;15:1101. doi: 10.1186/1471-2164-15-1101.

4.

Alterations of the human gut microbiome in liver cirrhosis.

Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, Guo J, Le Chatelier E, Yao J, Wu L, Zhou J, Ni S, Liu L, Pons N, Batto JM, Kennedy SP, Leonard P, Yuan C, Ding W, Chen Y, Hu X, Zheng B, Qian G, Xu W, Ehrlich SD, Zheng S, Li L.

Nature. 2014 Sep 4;513(7516):59-64. doi: 10.1038/nature13568. Epub 2014 Jul 23.

PMID:
25079328
5.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium.

Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6.

PMID:
24997787
6.

Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action.

El Kafsi H, Binesse J, Loux V, Buratti J, Boudebbouze S, Dervyn R, Kennedy S, Galleron N, Quinquis B, Batto JM, Moumen B, Maguin E, van de Guchte M.

BMC Genomics. 2014 May 28;15:407. doi: 10.1186/1471-2164-15-407.

7.

Dietary intervention impact on gut microbial gene richness.

Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, Almeida M, Quinquis B, Levenez F, Galleron N, Gougis S, Rizkalla S, Batto JM, Renault P; ANR MicroObes consortium, Doré J, Zucker JD, Clément K, Ehrlich SD.

Nature. 2013 Aug 29;500(7464):585-8. doi: 10.1038/nature12480. Erratum in: Nature. 2013 Oct 24;502(7472)580.

PMID:
23985875
8.

Richness of human gut microbiome correlates with metabolic markers.

Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O.

Nature. 2013 Aug 29;500(7464):541-6. doi: 10.1038/nature12506.

PMID:
23985870
9.

A metagenome-wide association study of gut microbiota in type 2 diabetes.

Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M, LeChatelier E, Renault P, Pons N, Batto JM, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J, Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J.

Nature. 2012 Oct 4;490(7418):55-60. doi: 10.1038/nature11450. Epub 2012 Sep 26.

PMID:
23023125
10.

Genomic characterization of the Taylorella genus.

Hébert L, Moumen B, Pons N, Duquesne F, Breuil MF, Goux D, Batto JM, Laugier C, Renault P, Petry S.

PLoS One. 2012;7(1):e29953. doi: 10.1371/journal.pone.0029953. Epub 2012 Jan 3.

11.

Enterotypes of the human gut microbiome.

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P.

Nature. 2011 May 12;473(7346):174-80. doi: 10.1038/nature09944. Epub 2011 Apr 20. Erratum in: Nature. 2011 Jun 30;474(7353):666. Nature. 2014 Feb 27;506(7489):516.

12.

Genome sequence of Taylorella equigenitalis MCE9, the causative agent of contagious equine metritis.

Hébert L, Moumen B, Duquesne F, Breuil MF, Laugier C, Batto JM, Renault P, Petry S.

J Bacteriol. 2011 Apr;193(7):1785. doi: 10.1128/JB.01547-10. Epub 2011 Jan 28.

13.

A human gut microbial gene catalogue established by metagenomic sequencing.

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J.

Nature. 2010 Mar 4;464(7285):59-65. doi: 10.1038/nature08821.

14.

Development of software facilities to characterize regulatory binding motifs and application to streptococcaceae.

Pons N, Batto JM, Ehrlich SD, Renault P.

J Mol Microbiol Biotechnol. 2008;14(1-3):67-73.

PMID:
17957112
15.

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

van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K, Nicolas P, Robert C, Oztas S, Mangenot S, Couloux A, Loux V, Dervyn R, Bossy R, Bolotin A, Batto JM, Walunas T, Gibrat JF, Bessières P, Weissenbach J, Ehrlich SD, Maguin E.

Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9274-9. Epub 2006 Jun 5.

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