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Last update: May 2021

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Publications from the FInE team

All publications since 2008


Al Assal K, Prifti E, Belda E, Sala P, Clément K, Dao MC, Doré J, Levenez F, Taddei CR, Fonseca DC, Rocha IM, Balmant BD, Thomas AM, Santo MA, Dias-Neto E, Setubal JC, Zucker JD, Belarmino G, Torrinhas RS, Waitzberg DL. Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes Remission. Nutrients. 2020 Jan 21;12(2). pii: E278. doi: 10.3390/nu12020278.

Kayser BD, Prifti E, Lhomme M, Belda E, Dao MC, Aron-Wisnewsky J; MICRO-Obes Consortium, Kontush A, Zucker JD, Rizkalla SW, Dugail I, Clément K. Elevated serum ceramides are linked with obesity-associated gut dysbiosis and impaired glucose metabolism. Metabolomics. 2019 Oct 11;15(11):140. doi: 10.1007/s11306-019-1596-0. [Epub ahead of print].

Martin-Gallausiaux C, Marinelli L, Blottière HM, Larraufie P, Lapaque N. SCFA: mechanisms and functional importance in the gut. Proc Nutr Soc. 2020 Apr 2:1-13. doi: 10.1017/S0029665120006916.

Partula V, Deschasaux M, Druesne-Pecollo N, Latino-Martel P, Desmetz E, Chazelas E, Kesse-Guyot E, Julia C, Fezeu LK, Galan P, Hercberg S, Mondot S, Lantz O, Quintana-Murci L, Albert ML, Duffy D; Milieu Intérieur Consortium, Srour B, Touvier M. Associations between consumption of dietary fibers and the risk of cardiovascular diseases, cancers, type 2 diabetes, and mortality in the prospective NutriNet-Santé cohort. Am J Clin Nutr. 2020 May 5. pii: nqaa063. doi: 10.1093/ajcn/nqaa063. [Epub ahead of print].

Sterlin D, Fadlallah J, Adams O, Fieschi C, Parizot C, Dorgham K, Rajkumar A, Autaa G, El-Kafsi H, Charuel JL, Juste C, Jönsson F, Candela T, Wardemann H, Aubry A, Capito C, Brisson H, Tresallet C, Cummings RD, Larsen M, Yssel H, von Gunten S, Gorochov G. Human IgA binds a diverse array of commensal bacteria. J Exp Med. 2020 Mar 2;217(3). pii: e20181635. doi: 10.1084/jem.20181635..


Archambaud C, Derré-Bobillot A, Lapaque N, Rigottier-Gois L, Serror P. Intestinal translocation of enterococci requires a threshold level of enterococcal overgrowth in the lumen. Sci Rep. 2019 Jun 20;9(1):8926. doi: 10.1038/s41598-019-45441-3.

Burz SD, Abraham AL, Fonseca F, David O, Chapron A, Béguet-Crespel F, Cénard S, Le Roux K, Patrascu O, Levenez F, Schwintner C, Blottière HM, Béra-Maillet C, Lepage P, Doré J, Juste C. A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation. Sci Rep. 2019 Jun 20;9(1):8897. doi: 10.1038/s41598-019-45173-4.

Mohamed AB, Rémond D, Chambon C, Sayd T, Hebraud M, Capel F, Cohade B, Hafnaoui N, Béchet D, Coudy-Gandilhon C, Migné C, David J, Dardevet D, Doré J, Polakof S, Savary-Auzeloux I. A mix of dietary fermentable fibers improves lipids handling by the liver of overfed minipigs. J Nutr. Biochem 2019 65: 72-82.

Dao MC, Sokolovska N, Brazeilles R, Affeldt S, Pelloux, Prifti E, Chilloux J, Verger EO, Kayser B, Aron-Wisnewsky J, Ichou F, Pujos-Guillot E, Hoyles L, Juste C, Doré J, Dumas ME Rizkalla SW, Holmes BA, Zucker JD, Clément K; MICRO-Obes Consortium. A data integration multi-omics approach to study calorie restriction-induced changes in insulin sensitivity. Frontiers in Physiology, 2019,9:1958 doi: 10.3389/fphys.2018.01958.

Dao MC, Belda E, Prifti E, Everard A, Kayser BD, Bouillot JL, Chevallier JM, Pons N, Le Chatelier E, Ehrlich D, Doré J, Aron-Wisnewsky J, Zucker JD, Cani PD, Clément K. Akkermansia muciniphila abundance is lower in severe obesity but its increased level after bariatric surgery is not associated with metabolic health improvement. Am J Physiol Endocrinol Metab. 2019 Jul 2. doi: 10.1152/ajpendo.00140.2019. [Epub ahead of print].

Hanachi M, Manichanh C, Schoenenberger A, Pascal V, Levenez F, Cournède N, Doré J, Melchior JC.Altered host-gut microbes symbiosis in severely malnourished anorexia nervosa (AN) patients undergoing enteral nutrition: An explicative factor of functional intestinal disorders? Clin Nutr. 2019 Oct;38(5):2304-2310. doi: 10.1016/j.clnu.2018.10.004.

Iannone LF, Preda A, Blottière HM, Clarke G, Albani D, Belcastro V, Carotenuto M, Cattaneo A, Citraro R, Ferraris C, Ronchi F, Luongo G, Santocchi E, Guiducci L, Baldelli P, Iannetti P, Pedersen S, Petretto A, Provasi S, Selmer K, Spalice A, Tagliabue A, Verrotti A, Segata N, Zimmermann J, Minetti C, Mainardi P, Giordano C, Sisodiya S, Zara F, Russo E, Striano P. Microbiota-gut brain axis involvement in neuropsychiatric disorders. Expert Rev Neurother. 2019 Jul 1. doi: 10.1080/14737175.2019.1638763.

Kayser BD, Prifti E, Lhomme M, Belda E, Dao MC, Aron-Wisnewsky J; MICRO-Obes Consortium, Kontush A, Zucker JD, Rizkalla SW, Dugail I, Clément K. Elevated serum ceramides are linked with obesity-associated gudysbiosis and impaired glucose metabolism. Metabolomics. 2019 Oct 11;15(11):140. doi: 10.1007/s11306-019-1596-0.

Keravec M, Mounier J, Guilloux CA, Fangous MS, Mondot S, Vallet S, Gouriou S, Le Berre R, Rault G, Férec C, Barbier G, Lepage P, Héry-Arnaud G. Porphyromonas, a potential predictive biomarker of Pseudomonas aeruginosa pulmonary infection in cystic fibrosis. BMJ Open Respir Res. 2019 Mar 12;6(1):e000374. doi: 10.1136/bmjresp-2018-000374. eCollection 2019.

Marinelli L, Martin-Gallausiaux C, Bourhis JM, Béguet-Crespel F, Blottière HM, Lapaque N. Identification of the novel role of butyrate as AhR ligand in human intestinal epithelial cells. Sci Rep. 2019 Jan 24;9(1):643. doi: 10.1038/s41598-018-37019-2.

Magadan S, Krasnov A, Hadi-Saljoqi S, Afanasyev S, Mondot S, Lallias D, Castro R, Salinas I, Sunyer O, Hansen J, Koop BF, Lefranc MP, Boudinot P.Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires. Front Immunol. 2019 Nov 12;10:2541. doi: 10.3389/fimmu.2019.02541..

Mondot S, Lantz O, Lefranc MP, Boudinot P. The T cell receptor (TRA) locus in the rabbit (Oryctolagus cuniculus): Genomic features and consequences for invariant T cells. Eur J Immunol. 2019 Jul 29. doi: 10.1002/eji.201948228.

Partula V, Mondot S, Torres MJ, Kesse-Guyot E, Deschasaux M, Assmann K, Latino-Martel P, Buscail C, Julia C, Galan P, Hercberg S, Rouilly V, Thomas S, Quintana-Murci L, Albert ML, Duffy D, Lantz O, Touvier M; Milieu Intérieur Consortium. Associations between usual diet and gut microbiota composition: results from the Milieu Intérieur cross-sectional study. Am J Clin Nutr. 2019 May 1;109(5):1472-1483. doi: 10.1093/ajcn/nqz029.

Pigneur B, Lepage P, Mondot S, Schmitz J, Goulet O, Doré J, Ruemmele FM. Mucosal healing and bacterial composition in response to enteral nutrition versus steroid based induction therapy - a randomized prospective clinical trial in children with Crohn's disease. J Crohns Colitis. 2019 13(7)846-855. doi: 10.1093/ecco-jcc/jjy207.

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. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nat Microbiol. 2019 4:112-123. doi: 10.1038/s41564-018-0292-6. [Epub 2018 26 Nov].

Scepanovic P, Hodel F, Mondot S, Partula V, Byrd A, Hammer C, Alanio C, Bergstedt J, Patin E, Touvier M, Lantz O, Albert ML, Duffy D, Quintana-Murci L, Fellay J; Milieu Intérieur Consortium. A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals. Microbiome. 2019 Sep 13;7(1):130. doi: 10.1186/s40168-019-0747-x.

Zhang X, Grosfeld A, Williams E, Vasiliauskas D, Barretto S, Smith L, Mariadassou M, Philippe C, Devime F, Melchior C, Gourcerol G, Dourmap N, Lapaque N, Larraufie P, Blottière HM, Herberden C, Gerard P, Rehfeld JF, Ferraris RP, Fritton JC, Ellero-Simatos S, Douard V. Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism. FASEB J. 2019 Jun;33(6):7126-7142. doi: 10.1096/fj.201801526RR. Epub 2019 Apr 2.


Aron-Wisnewsky J, Prifti E, Belda E, Ichou F, Kayser BD, Dao MC, Verger EO, Hedjazi L, Bouillot JL, Chevallier JM, Pons N, Le Chatelier E, Levenez F, Ehrlich SD, Doré J, Zucker JD, Clément K. Major microbiota dysbiosis in severe obesity: fate after bariatric surgery. Gut. 2018 Jun 13. pii: gutjnl-2018-316103. doi: 10.1136/gutjnl-2018-316103

Bennet SMP, Sundin J, Magnusson MK, Strid H, Tap J, Derrien M, Le Nevé B, Doré J, Törnblom H, Simrén M, Öhman L. Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation  Neurogastroenterol Motil. 2018 Sep 17:e13468. doi: 10.1111/nmo.13468.

Couvigny B, Kulakauskas S, Pons N, Quinquis B, Abraham AL, Meylheuc T, Delorme C, Renault P, Briandet R, Lapaque N, Guédon E. Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius. Front Microbiol. 2018 Feb 20;9:273. doi: 10.3389/fmicb.2018.00273.

Darnaud M, Santos AD, Gonzalez P, Augui S, Lacoste C, Desterke C, De Hertogh G, Valentino E, Braun E, Zheng J, Boisgard R, Neut C, Dubuquoy L, Chiappini F, Samuel D, Lepage P, Guerrieri F, Doré J, Bréchot C, Moniaux N, Faivre J. Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis. Gastroenterology. 2018 Mar;154(4):1009-1023.e14. doi: 10.1053/j.gastro.2017.11.003.

Dubuisson JF, Juste C, Fonseca F, Lepage P, Bera-Maillet C, Béguet-Crespel F, Le Roux K, Burz F, Levenez F, Leroux A, Boucinha L, Deprez A, Schwinter C, Dussurgey S, Andrieu T, Affagard H, Blottière H, Bourlioux P, Doré J. Nouveaux dispositifs médicaux et nouveau procédé de fabrication pour un transfert de microbiote fécal par voie rectale, sans risque, standardisé et prêt à l’emploi. J  Pharma Clin 37 : 73-83, 2018.

Fadlallah J, El Kafsi H, Sterlin D, Juste C, Parizot C, Dorgham K, Autaa G, Gouas D, Almeida M, Lepage P, Pons N, Le Chatelier E, Levenez F, Kennedy S, Galleron N, Pais de Barros JP, Malphettes M, Galicier L, Boutboul D, Mathian A, Miyara M, Oksenhendler E, Amoura A, Doré J, Fieschi C, Ehrlich SD, Larsen M, Gorochov G. Microbial ecology perturbation in human IgA deficiency. Science Translational Medicine  02 May 2018: Vol. 10, Issue 439, eaan1217DOI: 10.1126/scitranslmed.aan1217

Fadlallah J, Sterlin D, Fieschi C, Parizot C, Dorgham K, El Kafsi H, Autaa G, Ghillani-Dalbin P, Juste C, Lepage P, Malphettes M, Galicier L, Boutboul D, Clément K, André S, Marquet F, Tresallet C, Mathian A, Miyara M, Oksenhendler E, Amoura Z, Yssel H, Larsen M, Gorochov G. Synergistic convergence of microbiota-specific systemic IgG and secretory IgA. J Allergy Clin Immunol. 2018 Dec 7. pii: S0091-6749(18)31570-7. doi: 10.1016/j.jaci.2018.09.036. [Epub ahead of print].

Girard PM, Peynot N, Lelièvre JM. Differential correlations between changes to glutathione redox state, protein ubiquitination, and stress-inducible HSPA chaperone expression after different types of oxidative stress. Cell Stress Chaperones. 2018 May 12. doi: 10.1007/s12192-018-0909-y.

Hanachi M, Manichanh C, Schoenenberger A, Pascal V, Levenez F, Cournède N, Doré J, Melchior JC. Altered host-gut microbes symbiosis in severely malnourished anorexia nervosa (AN) patients undergoing enteral nutrition: An explicative factor of functional intestinal disorders? Clin Nutr. 2018 Oct 9. pii: S0261-5614(18)32474-9. doi: 10.1016/j.clnu.2018.10.004. [Epub ahead of print].

Larraufie P, Martin-Gallausiaux C, Lapaque N, Dore J, Gribble FM, Reimann F, Blottiere HM. SCFAs strongly stimulate PYY production in human enteroendocrine cells. Sci Rep. 2018 Jan 8;8(1):74. doi: 10.1038/s41598-017-18259-0.

Malard F, Gasc C, Plantamura E, Doré J. High gastrointestinal microbial diversity and clinical outcome in graft-versus-host disease patients. Bone Marrow Transplant. 2018 Jun 14. doi: 10.1038/s41409-018-0254-x.

Martin-Gallausiaux C, Béguet-Crespel F, Marinelli L, Jamet A, Ledue F, Blottière HM, Lapaque N. Butyrate produced by gut commensal bacteria activates TGF-beta1 expression through the transcription factor SP1 in human intestinal epithelial cells. Sci Rep. 2018 Jun 27;8(1):9742. doi: 10.1038/s41598-018-28048-y.

Martin-Gallausiaux C, Larraufie P, Jarry A, Béguet-Crespel F, Marinelli L, Ledue F, Reimann F, Blottière HM, Lapaque N. Butyrate Produced by Commensal Bacteria Down-Regulates Indolamine 2,3-Dioxygenase 1 (IDO-1) Expression via a Dual Mechanism in Human Intestinal Epithelial Cells. Front Immunol. 2018 Dec 11;9:2838. doi: 10.3389/fimmu.2018.02838. eCollection 2018..

Roume H, Blottière HM. Le microbiote, médiateur des relationq alimentation/physiologie tout au long de la vie. Innovations Agronomiques, 65 : 113-124, 2018.

Sundin J, Stridsberg M, Tap J, Derrien M, Le Nevé B, Doré J, Törnblom H, Simrén M, Öhman L. Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects. Sci Rep. 2018 Nov 14;8(1):16821. doi: 10.1038/s41598-018-35241-6.

van de Guchte M, Blottière HM, Doré J. Humans as holobionts: implications for prevention and therapy. Microbiome. 2018 May 1;6(1):81. doi: 10.1186/s40168-018-0466-8.


Arufe S, Chiron H, Doré J, Savary-Auzeloux I, Saulnier L, Della Valle G. Processing & rheological properties of wheat flour dough and bread containing high levels of soluble dietary fibres blends. Food research International 97 (2017) 123-132.

Blottière HM. Chapter 11. The gut microbiota and obesity (2017) In :Romieu I, Dossus L, Willett WC (Eds) IARC Working Group Reports Volume 10: Energy balance and obesity. 

Calder PC, Bosco N, Bourdet-Sicard R, Capuron L, Delzenne N, Doré J, Franceschi C, Lehtinen MJ, Recker T, Salvioli S, Visioli F. Health relevance of the modification of low grade inflammation in ageing (inflammageing) and the role of nutrition. Ageing Res Rev. 2017 Sep 9. pii: S1568-1637(17)30003-X. doi: 10.1016/j.arr.2017.09.001.

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol. 2017 Oct 2. doi: 10.1038/nbt.3960. [Epub ahead of print]

Couvigny B, Lapaque N, Rigottier-Gois L, Guillot A, Chat S, Meylheuc T, Kulakauskas S, Rohde M, Mistou MY, Renault P, Doré J, Briandet R, Serror P, Guédon E. Three glycosylated serine-rich repeat proteins play a pivotal role in adhesion and colonization of the pioneer commensal bacterium, Streptococcus salivarius. Environ Microbiol. 2017 Jul 11. doi: 10.1111/1462-2920.13853. [Epub ahead of print]

Darnaud M, Santos AD, Gonzalez P, Augui S, Lacoste C, Desterke C, De Hertogh G, Valentino E, Braun E, Zheng J, Boisgard R, Neut C, Dubuquoy L, Chiappini F, Samuel D, Lepage P, Guerrieri F, Doré J, Bréchot C, Moniaux N, Faivre J. Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis. Gastroenterology. 2017 Nov 11. pii: S0016-5085(17)36349-7. doi: 10.1053/j.gastro.2017.11.003.

Doré J, Multon MC, Béhier JM; les participants à la table ronde 2 des Ateliers de Giens XXXII, Affagard H, Andremont A, Barthélémy P, Batista R, Bonneville M, Bonny C, Boyaval G, Chamaillard M, Chevalier MP, Cordaillat-Simmons M, Cournarie F, Diaz I, Guillaume E, Guyard C, Jouvin-Marche E, Martin FP, Petiteau D. Microbiote intestinal : qu’en attendre au plan physiologique et thérapeutique ? Therapie. 2017 Feb;72(1):1-19. doi: 10.1016/j.therap.2017.01.001.

Doré J, Multon MC, Béhier JM; participants of Giens XXXII, Round Table No. 2. The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect? Therapie. 2017 Feb;72(1):21-38. doi: 10.1016/j.therap.2016.12.007.

El Kafsi H, Loux V , Mariadassou M , Blin C, Chiapello H, Abraham AL, Maguin E, van de Guchte M. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Sci Rep. 2017 Mar 10;7:44331. doi: 10.1038/srep44331.

Jamet A, Dervyn R, Lapaque N, Bugli F, Perez-Cortez NG, Blottière HM , Twizere JC, Sanguinetti M, Posteraro B, Serror P, Maguin E. The Enterococcus faecalis virulence factor ElrA interacts with the human Four-and-a-Half LIM Domains Protein 2. Scientific RepoRts | 7: 4581 | DOI:10.1038/s41598-017-04875-3

Nepelska M, de Wouters T, Jacouton E, Béguet-Crespel F, Lapaque N, Doré J, Arulampalam V, Blottière HM. Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells. Sci Rep. 2017 Mar 7;7:43199. doi: 10.1038/srep43199.

O Cuiv P, de Wouters T, Giri R, Mondot S, Smith WJ, Blottière HM, Morrison M. The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner. Anaerobe 47 (2017) 209-217

Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottière HM, DoréJ, Béra-Maillet C. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic Scientific Reports 7, Article number: 40248 (2017) doi:10.1038/srep40248

Romieu I, Dossus L, Barquera S, Blottière HM, Franks PW, Gunter M, Hwalla N, Hursting SD, Leitzmann M, Margetts B, Nishida C, Potischman N, Seidell J, Stepien M, Wang Y, Westerterp K, Winichagoon P, Wiseman M, Willett WC;IARC working group on Energy Balance and Obesity. Energy balance and obesity: what are the main drivers? Cancer Causes Control 2017 Feb 17. doi: 10.1007/s10552-017-0869-z.

Tauzin, A., Laville, E., Cecchini, D., Blottiere, H., Leclerc, M., Dore, J., Veronese, G. (2017). Human gut metagenomics: success and limits of the activity-based approaches. In: Charles TC, Liles MR, Sessitsch (Eds)" Functional Metagenomics: Tools and Applications" . Editions Springer. November 6, 2017.

Van de Guchte M. Horizontal Gene Transfer and Ecosystem Function Dynamics. Trends Microbiol. 2017 Sep;25(9):699-700. doi: 10.1016/j.tim.2017.07.002. Epub 2017 Jul 24.

Versalovic J, Dore J, Guarner F, Luna RA, Ringel Y. Microbiome-Based Diagnostics: Ready for Applications in Laboratory Medicine?
Clin Chem. 2017 Sep 7. pii: clinchem.2016.264473. doi: 10.1373/clinchem.2016.264473.


Dao MC, Everard A, Aron-Wisnewsky J, Sokolovska N, Prifti E, Verger EO, Kayser BD, Levenez F, Chilloux J, Hoyles L; MICRO-Obes Consortium, Dumas ME, Rizkalla SW, Doré J, Cani PD, Clément K (2016) Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut, 65(3):426-36.

Dobrijevic D, Abraham AL, Jamet A, Maguin E, van de Guchte M. Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment. PLoS One. 2016 Jul 14;11(7):e0159030. doi: 10.1371/journal.pone.0159030.

Duca FA, Sakar Y, Lepage P, Devime F, Langelier B, Doré J, Covasa M. Statement of Retraction. Replication of Obesity and Associated Signaling Pathways Through Transfer of Microbiota From Obese-Prone Rats. Diabetes 2014;63:1624-1636. DOI: 10.2337/db13-1526. Diabetes. 2016 May;65(5):1447. doi: 10.2337/db16-rt05.

Hoffmann TW, Pham HP, Bridonneau C, Aubry C, Lamas B, Martin-Gallausiaux C, Moroldo M, Rainteau D, Lapaque N, Six A, Richard ML, Fargier E, Le Guern ME, Langella P, Sokol H. (2016). Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice. ISME J. 2016 Feb;10(2):460-77. doi: 10.1038/ismej.2015.127. Epub 2015 Jul 28.

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Ramayo-Caldas Y, Mach N, Lepage P, Levenez F, Denis C, Lemonnier G, Leplat JJ, Billon Y, Berri M, Doré J, Rogel-Gaillard C, Estellé J. Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits. ISME J. 2016 May 13. doi: 10.1038/ismej.2016.77. [Epub ahead of print]

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Zhang C, Derrien M, Levenez F, Brazeilles R, Ballal SA, Kim J, Degivry MC, Quéré G, Garault P, van Hylckama Vlieg JE, Garrett WS, Doré J, Veiga P. (2016) Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME J. 2016 Mar 8. doi: 10.1038/ismej.2016.13. [Epub ahead of print]


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Doré J, Clément K. (2014) Reply to C Matuchansky. Am J Clin NutrReply 99(3):650-1.

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Kaci G, Goudercourt D, Dennin V, Pot B, Doré J, Ehrlich SD, Renault P, Blottière HM, Daniel C, Delorme C. (2014) Anti-inflammatory properties of Streptococcus salivarius, a commensal bacterium of the oral cavity and digestive tract. Appl Environ Microbiol, 80 :928-934.

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Aron-Wisnewsky J, Doré J, Clement K. (2012) The importance of the gut microbiota after bariatric surgery. Nat Rev Gastroenterol Hepatol. 9:590-8.

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Amar J, Serino M, Lange C, Chabo C, Iacovoni J, Mondot S, Lepage P, Klopp C, Mariette J, Bouchez O, Perez L, Courtney M, Marre M, Klopp P, Lantieri O, Doré J, Charles M, Balkau B, Burcelin R; D.E.S.I.R. Study Group. (2011) Involvement of tissue bacteria in the onset of diabetes in humans: evidence for a concept. Diabetologia, 54:3055-61.

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. (2011) Enterotypes of the human gut microbiome. Nature, 473:174–180.

Dumetz F, Jouvion G, Khun H, Glomski IJ, Corre JP, Rougeaux C, Tang WJ, Mock M, Huerre M, Goossens PL. (2011) Noninvasive imaging technologies reveal edema toxin as a key virulence factor in anthrax. Am J Pathol, 178(6):2523-35.

Fallani M, Amarri S, Uusijarvi A, Adam R, Khanna S, Aguilera M, Gil A, Vieites JM, Norin E, Young D, Scott JA, Doré J, Edwards CA; INFABIO team. (2011) Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres. Microbiology 2011 157:1385-92.

Gloux, K., Berteau, O., El Oumami, H., Béguet, F., Leclerc, M., and Dore, J. (2011) A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci USA, 108 Suppl 1:4539-46.

Guardia S, Konsak B, Combes S, Levenez F, Cauquil L, Guillot JF, Moreau-Vauzelle C, Lessire M, Juin H, Gabriel I. (2011) Effects of stocking density on the growth performance and digestive microbiota of broiler chickens. 2011 Poultry Science 90: 1878–1889.

Kaci G, Lakhdari O, Doré J, Ehrlich SD, Renault P, Blottière HM*, Delorme C*. (2011) Inhibition of the NF-κB pathway in human intestinal epithelial cells by commensal Streptococcus salivarius. Appl Environ Microbiol 2011 77:4681-4684. (*equal contribution)

Lakhdari O, Tap J, Béguet-Crespel F, Le Roux K, de Wouters T, Cultrone A, Nepelska M, Lefèvre F, Doré J, Blottière HM. (2011) Identification of NF-κB modulation capabilities within human intestinal commensal bacteria. J Biomed Biotech 2011, Article ID 282356.

Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A, Begun A, Ott S, Kupcinskas L, Doré J, Raedler A, Schreiber S. (2011) Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011 141:227-236.

Mondot S, Kang S, Furet JP, Aguirre de Carcer D, McSweeney C, Morrison M, Marteau P, Doré J, Leclerc M. (2011) Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis  17:185-92.

Muñoz-Tamayo R, Laroche B, Walter E, Doré J, Duncan SH, Flint HJ, Leclerc M. (2011) Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. FEMS Microbiol Ecol, 76:615-624.

Rooijers K, Kolmeder C, Juste C, Doré J, de Been M, Boeren S, Galan P, Beauvallet C, de Vos WM, Schaap PJ. (2011) An iterative workflow for mining the human intestinal metaproteome. BMC Genomics. 2011 Jan 5;12:6. doi: 10.1186/1471-2164-12-6.

Thompson-Chagoyan OC, Fallani M, Maldonado J, Vieites JM, Khanna S, Edwards C, Doré J, Gil A. (2011) Faecal Microbiota and short-chain fatty acid levels in faeces from infants with cow's milk protein allergy. Int Arch Allergy Immunol 2011 156:325-332.

Rousseau C, Levenez F, Fouqueray C, Doré J, Collignon A, Lepage P. (2011) Clostridium difficile colonization in early infancy is accompanied by changes in intestinal microbiota composition. J Clin Microbiol, 49:858-65.

van Duynhoven J, Vaughan EE, Jacobs DM, Kemperman RA, van Velzen EJJ, Gross G, Roger LC, Possemiers S, Smilde AK, Doré J, Westerhuis JA, Van de Wiele T. (2011) Metabolic fate of polyphenols in the human superorganism. Proc Natl Acad Sci U S A 108 Suppl 1:4531-8.


Benard C, Cultrone A, Michel C, Rosales C, Segain JP, Lahaye M, Galmiche JP, Cherbut C, Blottière HM. (2010) Degraded Carrageenan Causing Colitis in Rats Induces TNF Secretion and ICAM-1 Upregulation in Monocytes through NF-kB Activation. PLoS ONE, 5:e8666.

Corthier G, Doré J. (2010) A new era in gut research concerning interactions between microbiota and human health. Gastroenterol Clin Biol, 34 Suppl 1:S1-6.

Donnet-Hughes A, Perez PF, Doré J, Leclerc M, Levenez F, Benyacoub J, Serrant P, Segura-Roggero I, Schiffrin EJ. (2010) Potential role of the intestinal microbiota of the mother in neonatal immune education. Proc Nutr Soc, 69:407-15.

Doré J, Corthier G. The human intestinal microbiota (2010) Gastroenterol Clin Biol, 34 Suppl 1:S7-15.

Ehrlich SD; MetaHIT consortium. Metagenomics of the intestinal microbiota: potential applications. Gastroenterol Clin Biol 2010 34 Suppl 1:S23-8. French..

Furet JP, Kong LC, Tap J, Poitou C, Basdevant A, Bouillot JL, Mariat D, Corthier G, Doré J, Henegar C, Rizkalla S, Clément K. (2010) Differential adaptation of human gut microbiota to bariatric surgery–induced weight loss. Links with metabolic and low-grade inflammation markers. Diabetes, 59:3049-3057.

Fallani M, Young D, Scott J, Norin E, Amarri S, Adam R, Aguilera M, Khanna S, Gil A, Edwards CA, Doré J; the INFABIO Team. (2010) Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. J Pediatr Gastroenterol Nutr, 51:77-84.

Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, Lefèvre F, Doré J, Blottière HM, (2010) Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-kB modulation in the human gut. PLoS One, 5(9). pii: e13092. Erratum in: PLoS One 2010;5(10).

Madi A, Lakhdari O, Blottière HM, Guyard M, Le Roux K, Svinareff P, Doré J, Orange N, Feuilloley MGJ, Connil N. (2010) The clinical Pseudomonas fluorescens MFN1032 strain exerts cytotoxic effect on epithelial intestinal cells and induces Interleukin-8 via the AP-1 signaling pathway. BMC Microbiol, 10:215.

Mihajlovski A, Doré J, Levenez F, Alric M, Brugère JF. (2010) Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity. Environ Microbiol Rep, 2:272-80.

Mirande C, Kadlecikova E, Matulova M, Capek P, Bernalier-Donadille A, Forano E, Béra-Maillet C. (2010) Dietary fibre degradation and fermentation by two xylanolytic bacteria Bacteroides xylanisolvens XB1AT and Roseburia intestinalis XB6B4 from the human intestine. J Appl Microbiol, 109:451–460.

Mirande C, Mosoni P, Béra-Maillet C, Bernalier-Donadille A, Forano E. (2010) Characterization of Xyn10A, a highly active xylanase from the human gut bacterium Bacteroides xylanisolvens XB1A. Appl Microbiol Biotechnol, 87:2097–2105.

Mondot, S., Kang, S., Furet, J.P., Aguirre de Carcer, D., McSweeney, C., Morrison, M., Marteau, P., Dore, J., and Leclerc, M. (2010) Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis, 17:185-192.

Muñoz-Tamayo R, Laroche B, Walter E, Doré J, Leclerc M. (2010) Mathematical modelling of carbohydrate degradation by human colonic microbiota. J Theor Biol 266:189-201. Epub 2010 Jun 16.

Qin, J., Ruiqiang, L., Raes, J., Arumugam M., Solvsten, K., Burgdorf, Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D., 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, 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., Zhang, X., Li, S., Yang, H., Wang, J., Brunak, S., Doré, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., MetaHIT Consortium, Bork, P., Ehrlich, S. D. and Wang, J. (2010) A human gut microbial gene catalog established by deep metagenomic sequencing. Nature 464, 59-65.

Rehman A, Lepage P, Nolte A, HellmigS, Schreiber S, Ott SJ. (2010) Transcriptional activity of dominant gut mucosal microbiota in chronic inflammatory bowel diseases. J Med Microbiol 59:1114-22.

Sun L, Yu Z, Ye X, Zou S, Li H, Yu D, Wu H, Chen Y, Dore J, Clément K, Hu FB, Lin X. (2010) A marker of endotoxemia is associated with obesity and related metabolic disorders in apparently healthy Chinese. Diabetes Care. 33:1925-32.

Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G. (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 2010 20:1605-12.


Furet JP, Firmesse O, Gourmelon M, Bridonneau C, Tap J, Mondot S, Doré S, Corthier G. Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol 2009, 68, 351362.

Gao X, Pujos-Guillot E, Martin JF, Galan P, Juste C, Jia W, Sebedio JL. (2009). Metabolite analysis of human fecal water by gas chromatography/mass spectrometry with ethyl chloroformate derivatization. Anal Biochem 393:163-175.

Mariat D, Firmesse O, Levenez F, Guimarăes V, Sokol H, Doré J, Corthier G, Furet JP. (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9:123.

Sokol H, Seksik P, Furet JP, Firmesse O, Nion-larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Doré J. (2009) Low counts of Faecalibacterium prausnitzii in Colitis Microbiota. Inflamm Bowel Dis15, 1183-1189.

Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-TamayoR, Le Paslier D, Nalin R, Doré J, Leclerc M. (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol11, 25742584.


Barc MC, Charrin-Sarnel C, Rochet V, Bourlioux F, Sandré C, Boureau H, Doré J, Collignon A. (2008) Molecular analysis of the digestive microbiota in a gnotobiotic mouse model during antibiotic treatment: Influence of Saccharomyces boulardii. Anaerobe, 14:229-33.

Firmesse O, Alvaro E, Mogenet A, Bresson JL, Lemée R, Le Ruyet P, Bonhomme C, Lambert D, Andrieux C, Doré J, Corthier G, Furet JP, Rigottier-Gois L. (2008) Fate and effects of Camembert cheese micro-organisms in the human colonic microbiota of healthy volunteers after regular Camembert consumption. Int J Food Microbiol, 125:176-81.

Guigoz Y, Doré J, Schiffrin EJ. (2008) The inflammatory status of old age can be nurtured from the intestinal environment. Curr Opin Clin Nutr Metab Care, 11:13-20.

Lepage P, Colombet J, Marteau P, Sime-Ngando T, Doré J, Leclerc M. (2008) Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut 57:424-5.

Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J. (2008) A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res, 36:5180-8.

Manichanh C, Varela E, Martinez C, Antolin M, Llopis M, Doré J, Giralt J, Guarner F, Malagelada JR. (2008) The gut microbiota predispose to the pathophysiology of acute postradiotherapy diarrhea. Am J Gastroenterol, 103:1754-61.

Rochet V, Rigottier-Gois L, Ledaire A, Andrieux C, Sutren M, Rabot S, Mogenet A, Bresson JL, Cools S, Picard C, Goupil-Feuillerat N, Doré J. (2008) Survival of bifidobacterium animalis DN-173010 in the faecal microbiota after administration in lyophilised form or in fermented product - A randomised study in healthy adults.J Mol Microbiol Biotech, 14:128-36.

Rochet V, Rigottier-Gois L, Levenez F, Cadiou J, Marteau P, Bresson JL, Goupil-Feillerat N, Doré J. (2008) Modulation of Lactobacillus casei in ileal and fecal samples from healthy volunteers after consumption of a fermented milk containing Lactobacillus casei DN-114 001Rif. Can J Microbiol, 54:660-7.

Spehlmann ME, Begun AZ, Burghardt J, Lepage P, Raedler A, Schreiber S. (2008) Epidemiology of inflammatory bowel disease in a German twin cohort: Results of a nationwide study. Inflamm Bowel Dis, 14:968-976.

Sokol H, Pigneur B,Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux J-J, Blugeon S, Bridonneau C, Furet J-P, Corthier G, Grangette C, Vasquez N, Pochart Ph, Trugnan G, Thomas G, Blottière HM, Doré J, Marteau P, Seksik P & Langella P. (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn's diease patients. Proc Nat Acad Sci USA, 105:16731-16736.

Spehlmann ME, Begun AZ, Burghardt J, Lepage P, Andreas Raedler, Stefan Schreiber. (2008) Epidemiology of Inflammatory Bowel Disease in a German Twin Cohort: Results of a Nationwide Study. Inflamm Bowel Dis, 14:968-976.