Dusko Ehrlich

2022

Rifaximin reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial

Patel, V. C., Lee, S., McPhail, M. J. W., Zamalloa, A., Witherden, E., Stoy, S., Vijay, G. M., Huang, X., Gencer, S., Coen, M., Tranah, T., Wendon, J., Bruce, K., Ehrlich, D., Edwards, L. A., Shoaie, S. & Shawcross, D. L., Feb 2022, In: Journal of Hepatology. 76, 2, p. 332-342 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

101 Citations (Scopus)

2020

Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial

Cox, S. R., Lindsay, J., Fromentin, S., Stagg, A. J., McCarthy, N. E., Galleron, N., Ibrahim, S., Roume, H., Levenez, F., Pons, N., Maziers, N., Lomer, M., Ehrlich, S., Irving, P. M. & Whelan, K., 1 Jan 2020, In: Gastroenterology. 158, 1, p. P176-188.E7

Research output: Contribution to journal › Article › peer-review

Open Access

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238 Citations (Scopus)

638 Downloads (Pure)

2017

Using systems biology approaches to elucidate cause and effect in host-microbiome interactions

Witherden, E. A., Moyes, D., Bruce, K., Ehrlich, S. & Shoaie, S., Jun 2017, In: Current Opinion in Systems Biology. p. 141-146

Research output: Contribution to journal › Review article › peer-review

Open Access

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10 Citations (Scopus)

420 Downloads (Pure)

2016

Dissemination of the mcr-1 colistin resistance gene

Ruppé, E., Chatelier, E. L., Pons, N., Andremont, A. & Ehrlich, S. D., Mar 2016, In: Lancet Infectious Diseases. 16, 3, p. 290-291 2 p.

Research output: Contribution to journal › Article › peer-review

147 Citations (Scopus)

ERRATUM: Subcortical brain volume abnormalities in 2028 individuals with schizophrenia and 2540 healthy controls via the ENIGMA consortium

van Erp, T. G. M., Hibar, D. P., Rasmussen, J. M., Glahn, D. C., Pearlson, G. D., Andreassen, O. A., Agartz, I., Westlye, L. T., Haukvik, U. K., Dale, A. M., Melle, I., Hartberg, C. B., Gruber, O., Kraemer, B., Zilles, D., Donohoe, G., Kelly, S., McDonald, C., Morris, D. W., Cannon, D. M., & 38 othersCorvin, A., Machielsen, M. W. J., Koenders, L., de Haan, L., Veltman, D. J., Satterthwaite, T. D., Wolf, D. H., Gur, R. C., Gur, R. E., Potkin, S. G., Mathalon, D. H., Mueller, B. A., Preda, A., Macciardi, F., Ehrlich, S., Walton, E., Hass, J., Calhoun, V. D., Bockholt, H. J., Sponheim, S. R., Shoemaker, J. M., van Haren, N. E. M., Pol, H. E. H., Ophoff, R. A., Kahn, R. S., Roiz-Santiañez, R., Crespo-Facorro, B., Wang, L., Alpert, K. I., Jönsson, E. G., Dimitrova, R., Bois, C., Whalley, H. C., McIntosh, A. M., Lawrie, S. M., Hashimoto, R., Thompson, P. M. & Turner, J. A., Apr 2016, In: Molecular Psychiatry. 21, 4, p. 585

Research output: Contribution to journal › Article › peer-review

141 Citations (Scopus)

Human gut microbes impact host serum metabolome and insulin sensitivity

Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A. H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., Le Chatelier, E., Levenez, F., Doré, J., Mattila, I., Plichta, D. R., Pöhö, P., Hellgren, L. I., Arumugam, M., Sunagawa, S., Vieira-silva, S., & 14 othersJørgensen, T., Holm, J. B., Trošt, K., Consortium, M., Kristiansen, K., Brix, S., Raes, J., Wang, J., Hansen, T., Bork, P., Brunak, S., Oresic, M., Ehrlich, S. D. & Pedersen, O., 21 Jul 2016, In: Nature. 535, 7612, p. 376-381

Research output: Contribution to journal › Article › peer-review

1462 Citations (Scopus)

Tongue Coating and the Salivary Microbial Communities Vary in Children with Halitosis

Ren, W., Xun, Z., Wang, Z., Zhang, Q., Liu, X., Zheng, H., Zhang, Q., Zhang, Y., Zhang, L., Wu, C., Zheng, S., Qin, N., Ehrlich, D., Li, Y., He, X., Xu, T., Chen, T. & Chen, F., 15 Apr 2016, (E-pub ahead of print) In: Scientific Reports. 6, 24481.

Research output: Contribution to journal › Article › peer-review

Open Access

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55 Citations (Scopus)

222 Downloads (Pure)

2015

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., Krogh Pedersen, H., Arumugam, M., Kristiansen, K., Yvonne Voigt, A., Vestergaard, H., Hercog, R., Igor Costea, P., Roat Kultima, J., Li, J., Jørgensen, T., Levenez, F., & 9 othersDore, J., Bjørn Nielsen, H., Brunak, S., Raes, J., Hansen, T., Wang, J., Ehrlich, D., Bork, P. & Pedersen, O., 10 Dec 2015, In: NATURE. 528, 7581, p. 262-266 5 p.

Research output: Contribution to journal › Letter › peer-review

Open Access

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1543 Citations (Scopus)

619 Downloads (Pure)

Systematic review: bile acids and intestinal inflammation-luminal aggressors or regulators of mucosal defence?

Pavlidis, P., Powell, N., Vincent, R. P., Ehrlich, D., Bjarnason, I. & Hayee, B., Oct 2015, In: Alimentary Pharmacology & Therapeutics. 42, 7, p. 802-17 16 p.

Research output: Contribution to journal › Article › peer-review

109 Citations (Scopus)

2014

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, J. M., Kennedy, S. P., Leonard, P., Yuan, C., Ding, W., Chen, Y., & 7 othersHu, X., Zheng, B., Qian, G., Xu, W., Ehrlich, S. D., Zheng, S. & Li, L., 4 Sept 2014, In: NATURE. 513, 7516, p. 59-+ 19 p.

Research output: Contribution to journal › Article › peer-review

1581 Citations (Scopus)

A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning

Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R. & Ehrlich, D., 2014, (Accepted/In press) In: Nature Biotechnology.

Research output: Contribution to journal › Article › peer-review

An integrated catalog of reference genes in the human gut microbiome

Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., Nielsen, T., Juncker, A. S., Manichanh, C., Chen, B., Zhang, W., Levenez, F., Wang, J., Xu, X., Xiao, L., Liang, S., Zhang, D., & 67 othersZhang, Z., Chen, W., Zhao, H., Al-aama, J. Y., Edris, S., Yang, H., Wang, J., Hansen, T., Nielsen, H. B., Brunak, S., Kristiansen, K., Guarner, F., Pedersen, O., Dor??, J., Ehrlich, S. D., Pons, N., Le Chatelier, E., Batto, J., Kennedy, S., Haimet, F., Winogradski, Y., Pelletier, E., Lepaslier, D., Artiguenave, F., Bruls, T., Weissenbach, J., Turner, K., Parkhill, J., Antolin, M., Casellas, F., Borruel, N., Varela, E., Torrejon, A., Denariaz, G., Derrien, M., Van Hylckama Vlieg, J. E. T., Viega, P., Oozeer, R., Knoll, J., Rescigno, M., Brechot, C., M'rini, C., M??rieux, A., Yamada, T., Tims, S., Zoetendal, E. G., Kleerebezem, M., De Vos, W. M., Cultrone, A., Leclerc, M., Juste, C., Guedon, E., Delorme, C., Layec, S., Khaci, G., Van De Guchte, M., Vandemeulebrouck, G., Jamet, A., Dervyn, R., Sanchez, N., Blotti??re, H., Maguin, E., Renault, P., Tap, J., Mende, D. R., Bork, P. & Wang, J., 2014, In: Nature Biotechnology. 32, 8, p. 834-841 8 p.

Research output: Contribution to journal › Article › peer-review

1461 Citations (Scopus)

Anti-inflammatory properties of Streptococcus salivarius, a commensal bacterium of the oral cavity and digestive tract

Kaci, G., Goudercourt, D., Dennin, V., Pot, B., Doré, J., Ehrlich, S. D., Renault, P., Blottière, H. M., Daniel, C. & Delorme, C., Feb 2014, In: Applied and Environmental Microbiology. 80, 3, p. 928-934 7 p.

Research output: Contribution to journal › Article › peer-review

136 Citations (Scopus)

Bacterial protein signals are associated with Crohn's disease

Juste, C., Kreil, D. P., Beauvallet, C., Guillot, A., Vaca, S., Carapito, C., Mondot, S., Sykacek, P., Sokol, H., Blon, F., Lepercq, P., Levenez, F., Valot, B., Carré, W., Loux, V., Pons, N., David, O., Schaeffer, B., Lepage, P., Martin, P., & 7 othersMonnet, V., Seksik, P., Beaugerie, L., Ehrlich, S. D., Gibrat, J-F., Van Dorsselaer, A. & Doré, J., 2014, (E-pub ahead of print) In: Gut. 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

78 Citations (Scopus)

Changes of the human gut microbiome induced by a fermented milk product

Veiga, P., Pons, N., Agrawal, A., Oozeer, R., Guyonnet, D., Brazeilles, R., Faurie, J-M., van Hylckama Vlieg, J. E. T., Houghton, L. A., Whorwell, P. J., Ehrlich, S. D. & Kennedy, S. P., 11 Sept 2014, In: Scientific Reports. 4, 9 p., 6328.

Research output: Contribution to journal › Article › peer-review

Open Access

203 Citations (Scopus)

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

Kyrpides, N. C., Hugenholtz, P., Eisen, J. A., Woyke, T., Göker, M., Parker, C. T., Amann, R., Beck, B. J., Chain, P. S. G., Chun, J., Colwell, R. R., Danchin, A., Dawyndt, P., Dedeurwaerdere, T., DeLong, E. F., Detter, J. C., De Vos, P., Donohue, T. J., Dong, X-Z., Ehrlich, D., & 44 othersFraser, C., Gibbs, R., Gilbert, J., Gilna, P., Glöckner, F. O., Jansson, J. K., Keasling, J. D., Knight, R., Labeda, D., Lapidus, A., Lee, J-S., Li, W-J., Ma, J., Markowitz, V., Moore, E. R. B., Morrison, M., Meyer, F., Nelson, K. E., Ohkuma, M., Ouzounis, C. A., Pace, N., Parkhill, J., Qin, N., Rossello-Mora, R., Sikorski, J., Smith, D., Sogin, M., Stevens, R., Stingl, U., Suzuki, K-I., Taylor, D., Tiedje, J. M., Tindall, B., Wagner, M., Weinstock, G., Weissenbach, J., White, O., Wang, J., Zhang, L., Zhou, Y-G., Field, D., Whitman, W. B., Garrity, G. M. & Klenk, H-P., Aug 2014, In: PL o S Biology. 12, 8, e1001920.

Research output: Contribution to journal › Article › peer-review

Open Access

162 Citations (Scopus)

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

Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., Le Chatelier, E., Pelletier, E., Bonde, I., Nielsen, T., Manichanh, C., Arumugam, M., Batto, J-M., Quintanilha Dos Santos, M. B., Blom, N., Borruel, N., Burgdorf, K. S., & 31 othersBoumezbeur, F., Casellas, F., Doré, J., Dworzynski, P., Guarner, F., Hansen, T., Hildebrand, F., Kaas, R. S., Kennedy, S., Kristiansen, K., Kultima, J. R., 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, D. W., Yamada, T., Renault, P., Sicheritz-Ponten, T., Bork, P., Ehrlich, S. D. & MetaHIT consortium, Aug 2014, In: Nature Biotechnology. 32, 8, p. 822-8 7 p.

Research output: Contribution to journal › Article › peer-review

771 Citations (Scopus)

2013

A metagenomic insight into our gut's microbiome

Lepage, P., Leclerc, M. C., Joossens, M., Mondot, S., Blottière, H. M., Raes, J., Ehrlich, D. & Doré, J., Jan 2013, In: Gut. 62, 1, p. 146-158 13 p.

Research output: Contribution to journal › Article › peer-review

275 Citations (Scopus)

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

Tanaka, K., Henry, C. S., Zinner, J. F., Jolivet, E., Cohoon, M. P., Xia, F., Bidnenko, V., Ehrlich, S. D., Stevens, R. L. & Noirot, P., 7 Jan 2013, In: Nucleic Acids Research. 41, 1, p. 687-699 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

73 Citations (Scopus)

Dietary intervention impact on gut microbial gene richness

Cotillard, A., Kennedy, S. P., Kong, L. C., Prifti, E., Pons, N., Le Chatelier, E., Almeida, M., Quinquis, B., Levenez, F., Galleron, N., Gougis, S., Rizkalla, S., Batto, J-M., Renault, P., Doré, J., Zucker, J-D., Clément, K., Ehrlich, S. D. & ANR MicroObes consortium, 29 Aug 2013, In: NATURE. 500, 7464, p. 585-588 4 p.

Research output: Contribution to journal › Article › peer-review

1431 Citations (Scopus)

Human intestinal metagenomics: state of the art and future

Blottière, H. M., de Vos, W. M., Ehrlich, S. D. & Doré, J., Jun 2013, In: Current Opinion in Microbiology. 16, 3, p. 232-239 8 p.

Research output: Contribution to journal › Article › peer-review

55 Citations (Scopus)

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., de Vos, W. M., Wang, J., Li, J., Doré, J., Ehrlich, S. D., Stamatakis, A., & 1 othersBork, P., Dec 2013, In: NATURE METHODS. 10, 12, p. 1196-1199 4 p.

Research output: Contribution to journal › Article › peer-review

361 Citations (Scopus)

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, J-M., Kennedy, S., Leonard, P., Li, J., Burgdorf, K., Grarup, N., Jørgensen, T., Brandslund, I., Nielsen, H. B., Juncker, A. S., Bertalan, M., Levenez, F., & 22 othersPons, N., Rasmussen, S., Sunagawa, S., Tap, J., Tims, S., Zoetendal, E. G., Brunak, S., Clément, K., Doré, J., Kleerebezem, M., Kristiansen, K., Renault, P., Sicheritz-Ponten, T., de Vos, W. M., Zucker, J-D., Raes, J., Hansen, T., Bork, P., Wang, J., Ehrlich, S. D., Pedersen, O. & MetaHIT consortium, 29 Aug 2013, In: NATURE. 500, 7464, p. 541-546 6 p.

Research output: Contribution to journal › Article › peer-review

3356 Citations (Scopus)

2012

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., & 36 othersDai, 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, J-M., Zhang, Z., Chen, H., Yang, R., Zheng, W., Li, S., Yang, H., Wang, J., Ehrlich, S. D., Nielsen, R., Pedersen, O., Kristiansen, K. & Wang, J., 4 Oct 2012, In: NATURE. 490, 7418, p. 55-60 6 p.

Research output: Contribution to journal › Article › peer-review

4912 Citations (Scopus)

2011

Complete genome sequence of the clinical Streptococcus salivarius strain CCHSS3

Delorme, C., Guédon, E., Pons, N., Cruaud, C., Couloux, A., Loux, V., Chiapello, H., Poyart, C., Gautier, C., Sanchez, N., Almeida, M., Kennedy, S. P., Ehrlich, S. D., Gibrat, J-F., Wincker, P. & Renault, P., Sept 2011, In: Journal of Bacteriology. 193, 18, p. 5041-5042 2 p.

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Complete genome sequence of the commensal Streptococcus salivarius strain JIM8777

Guédon, E., Delorme, C., Pons, N., Cruaud, C., Loux, V., Couloux, A., Gautier, C., Sanchez, N., Layec, S., Galleron, N., Almeida, M., van de Guchte, M., Kennedy, S. P., Ehrlich, S. D., Gibrat, J-F., Wincker, P. & Renault, P., Sept 2011, In: Journal of Bacteriology. 193, 18, p. 5024-5025 2 p.

Research output: Contribution to journal › Article › peer-review

16 Citations (Scopus)

Enterotypes of the human gut microbiome

Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J-M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., & 31 othersLeclerc, M., Levenez, F., Manichanh, C., Nielsen, H. B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E. G., Wang, J., Guarner, F., Pedersen, O., de Vos, W. M., Brunak, S., Doré, J., Antolín, M., Artiguenave, F., Blottiere, H. M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Ehrlich, S. D. & MetaHIT consortium, 12 May 2011, In: NATURE. 473, 7346, p. 174-80 7 p.

Research output: Contribution to journal › Article › peer-review

5378 Citations (Scopus)

Inhibition of the NF-kappaB pathway in human intestinal epithelial cells by commensal Streptococcus salivarius

Kaci, G., Lakhdari, O., Doré, J., Ehrlich, S. D., Renault, P., Blottière, H. M. & Delorme, C., Jul 2011, In: Applied and Environmental Microbiology. 77, 13, p. 4681-4 4 p.

Research output: Contribution to journal › Article › peer-review

77 Citations (Scopus)

2010

A human gut microbial gene catalogue established by metagenomic sequencing

Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D. R., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H., Xie, Y., & 31 othersTap, J., Lepage, P., Bertalan, M., Batto, J-M., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H. B., 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., Ehrlich, S. D. & MetaHIT consortium, 4 Mar 2010, In: NATURE. 464, 7285, p. 59-65 7 p.

Research output: Contribution to journal › Article › peer-review

8609 Citations (Scopus)

Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut

Lakhdari, O., Cultrone, A., Tap, J., Gloux, K., Bernard, F., Ehrlich, S. D., Lefèvre, F., Doré, J. & Blottière, H. M., Sept 2010, In: PLoS ONE. 5, 9

Research output: Contribution to journal › Article › peer-review

Open Access

81 Citations (Scopus)

2008

Rerouting of pyruvate metabolism during acid adaptation in Lactobacillus bulgaricus

Fernandez, A., Ogawa, J., Penaud, S., Boudebbouze, S., Ehrlich, D., van de Guchte, M. & Maguin, E., Aug 2008, In: Proteomics. 8, 15, p. 3154-63 10 p.

Research output: Contribution to journal › Article › peer-review

82 Citations (Scopus)

Dusko Ehrlich

Research output

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