After several internships in microbiology at Institut Pasteur (Patrick Grimont, Philippe Glaser, Sylvain Brisse), Julien Tap went to Joel Doré's Lab to do a PhD headed by Marion Leclerc (Jan 2007 to Dec 2009). His main project was to study dietary fiber impact on human gut microbiota using notably metagenomic and metatranscriptomic approach. Since his PhD, his research interest focused on interactions between nutrition, gut microbiota and human health. This allowed him to work with different AP-HP clinicians like Pr Karine Clément and Pr Iradj Sobhani. As post-doc successively done at EMBL in Peer Bork’s group and at INRA Metagenopolis unit (Joel Doré, Dusko Ehrlich), he used several approaches like numerical ecology and machine learning technics to untangle big omics data with clinical and dietary data. Julien is currently microbiome scientist at Danone Nutricia Research center settled in Paris-Saclay campus where he is working on microbiome science topics around nutrition and human health.

Research experience


Education


Publications

for up-to-date bibliography check:

1: Alvarez AS, Tap J, Chambaud I, Cools-Portier S, Quinquis L, Bourlioux P, Marteau P, Guillemard E, Schrezenmeir J, Derrien M. Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial. Sci Rep. 2020 Sep 29;10(1):15974. doi: 10.1038/s41598-020-72161-w. PMID: 32994487; PMCID: PMC7524715.

2: Le Nevé B, de la Torre AM, Tap J, Derrien M, Cotillard A, Barba E, Mego M, Nieto Ruiz A, Hernandez-Palet L, Dornic Q, Faurie JM, Butler J, Merino X, Lobo B, Batet FP, Accarino A, Pozuelo M, Manichanh C, Azpiroz F. A Fermented Milk Product with B. Lactis CNCM I-2494 and Lactic Acid Bacteria Improves Gastrointestinal Comfort in Response to a Challenge Diet Rich in Fermentable Residues in Healthy Subjects. Nutrients. 2020 Jan 25;12(2):320. doi: 10.3390/nu12020320. PMID: 31991794; PMCID: PMC7071254.

3: Le Nevé B, Derrien M, Tap J, Brazeilles R, Cools Portier S, Guyonnet D, Ohman L, Störsrud S, Törnblom H, Simrén M. Fasting breath H2 and gut microbiota metabolic potential are associated with the response to a fermented milk product in irritable bowel syndrome. PLoS One. 2019 Apr 4;14(4):e0214273. doi: 10.1371/journal.pone.0214273. PMID: 30946757; PMCID: PMC6448848.

4: Labus JS, Osadchiy V, Hsiao EY, Tap J, Derrien M, Gupta A, Tillisch K, Le Nevé B, Grinsvall C, Ljungberg M, Öhman L, Törnblom H, Simren M, Mayer EA. Evidence for an association of gut microbial Clostridia with brain functional connectivity and gastrointestinal sensorimotor function in patients with irritable bowel syndrome, based on tripartite network analysis. Microbiome. 2019 Mar 21;7(1):45. doi: 10.1186/s40168-019-0656-z. PMID: 30898151; PMCID: PMC6429755.

5: Tap J, Cools-Portier S, Pavan S, Druesne A, Öhman L, Törnblom H, Simren M, Derrien M. Effects of the long-term storage of human fecal microbiota samples collected in RNAlater. Sci Rep. 2019 Jan 24;9(1):601. doi: 10.1038/s41598-018-36953-5. PMID: 30679604; PMCID: PMC6345939.

6: 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 Jan;4(1):112-123. doi: 10.1038/s41564-018-0292-6. Epub 2018 Nov 26. PMID: 30478291.

7: 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. PMID: 30429499; PMCID: PMC6235916.

8: 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 Dec;30(12):e13468. doi: 10.1111/nmo.13468. Epub 2018 Sep 17. PMID: 30230134.

9: Breban M, Tap J, Leboime A, Said-Nahal R, Langella P, Chiocchia G, Furet JP, Sokol H. Faecal microbiota study reveals specific dysbiosis in spondyloarthritis. Ann Rheum Dis. 2017 Sep;76(9):1614-1622. doi: 10.1136/annrheumdis-2016-211064. Epub 2017 Jun 12. PMID: 28606969.

10: Veiga P, Tap J, Derrien M. Microbiote intestinal, la clé pour une meilleure alimentation ? [Gut microbiota, the key for a better diet?]. Med Sci (Paris). 2016 Nov;32(11):999-1002. French. doi: 10.1051/medsci/20163211016. Epub 2016 Dec

  1. PMID: 28008841.

11: Tap J, Derrien M, Törnblom H, Brazeilles R, Cools-Portier S, Doré J, Störsrud S, Le Nevé B, Öhman L, Simrén M. Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome. Gastroenterology. 2017 Jan;152(1):111-123.e8. doi: 10.1053/j.gastro.2016.09.049. Epub 2016 Oct 7. PMID: 27725146.

12: Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K; MetaHIT Consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. 2016 Jul 21;535(7612):376-81. doi: 10.1038/nature18646. Epub 2016 Jul 13. PMID: 27409811.

13: Le Nevé B, Brazeilles R, Derrien M, Tap J, Guyonnet D, Ohman L, Törnblom H, Simrén M. Reply. Clin Gastroenterol Hepatol. 2016 Aug;14(8):1222-3. doi: 10.1016/j.cgh.2016.03.031. Epub 2016 Mar 31. PMID: 27041478.

14: Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J; MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. 2015 Dec 10;528(7581):262-266. doi: 10.1038/nature15766. Epub 2015 Dec 2. Erratum in: Nature. 2017 May 3;545(7652):116. PMID: 26633628; PMCID: PMC4681099.

15: Le Nevé B, Brazeilles R, Derrien M, Tap J, Guyonnet D, Ohman L, Törnblom H, Simrén M. Lactulose Challenge Determines Visceral Sensitivity and Severity of Symptoms in Patients With Irritable Bowel Syndrome. Clin Gastroenterol Hepatol. 2016 Feb;14(2):226-33.e1-3. doi: 10.1016/j.cgh.2015.09.039. Epub 2015 Oct 20. PMID: 26492847.

16: Tap J, Furet JP, Bensaada M, Philippe C, Roth H, Rabot S, Lakhdari O, Lombard V, Henrissat B, Corthier G, Fontaine E, Doré J, Leclerc M. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol. 2015 Dec;17(12):4954-64. doi: 10.1111/1462-2920.13006. Epub 2015 Sep 3. PMID: 26235304.

17: Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol. 2014 Nov 28;10(11):766. doi: 10.15252/msb.20145645. PMID: 25432777; PMCID: PMC4299606.

18: 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. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6. PMID: 24997787.

19: Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD; MetaHIT Consortium, Bork P, Wang J; MetaHIT Consortium. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014 Aug;32(8):834-41. doi: 10.1038/nbt.2942. Epub 2014 Jul 6. PMID: 24997786.

20: Sunagawa S, Schloissnig S, Arumugam M, Forslund K, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Typas A, Weinstock GM, Bork P. Individuality and temporal stability of the human gut microbiome. Cent Asian J Glob Health. 2014 Mar 27;2(Suppl):120. doi: 10.5195/cajgh.2013.120. PMID: 29805877; PMCID: PMC5960903.

21: Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20. PMID: 24141494.

22: 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. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013 Aug 29;500(7464):541-6. doi: 10.1038/nature12506. PMID: 23985870.

23: Kong LC, Tap J, Aron-Wisnewsky J, Pelloux V, Basdevant A, Bouillot JL, Zucker JD, Doré J, Clément K. Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes. Am J Clin Nutr. 2013 Jul;98(1):16-24. doi: 10.3945/ajcn.113.058743. Epub 2013 May 29. PMID: 23719559.

24: Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Médigue C, Parkhill J, Cruveiller S, Brosch R. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet. 2013 Feb;45(2):172-9. doi: 10.1038/ng.2517. Epub 2013 Jan 6. PMID: 23291586; PMCID: PMC3856870.

25: Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. Genomic variation landscape of the human gut microbiome. Nature. 2013 Jan 3;493(7430):45-50. doi: 10.1038/nature11711. Epub 2012 Dec 5. PMID: 23222524; PMCID: PMC3536929.

26: Lakhdari O, Tap J, Béguet-Crespel F, Le Roux K, de Wouters T, Cultrone A, Nepelska M, Lefèvre F, Doré J, Blottière HM. Identification of NF-κB modulation capabilities within human intestinal commensal bacteria. J Biomed Biotechnol. 2011;2011:282356. doi: 10.1155/2011/282356. Epub 2011 Jun 14. PMID: 21765633; PMCID: PMC3134244.

27: 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. Enterotypes of the human gut microbiome. 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. Erratum in: Nature. 2014 Feb 27;506(7489):516. PMID: 21508958; PMCID: PMC3728647.

28: Sobhani I, Tap J, Roudot-Thoraval F, Roperch JP, Letulle S, Langella P, Corthier G, Tran Van Nhieu J, Furet JP. Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS One. 2011 Jan 27;6(1):e16393. doi: 10.1371/journal.pone.0016393. PMID: 21297998; PMCID: PMC3029306.

29: Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, Lefèvre F, Doré J, Blottière HM. Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut. PLoS One. 2010 Sep 30;5(9):e13092. doi: 10.1371/journal.pone.0013092. Erratum in: PLoS One. 2010;5(10). doi: 10.1371/annotation/4ea12169-7c97-497c-a45f-52203543065f. Erratum in: PLoS One. 2010;5(10). doi: 10.1371/annotation/9f1b7f00-bcc0-4442-9775-491ebdafc7bc. PMID: 20927194; PMCID: PMC2948039.

30: Furet JP, Kong LC, Tap J, Poitou C, Basdevant A, Bouillot JL, Mariat D, Corthier G, Doré J, Henegar C, Rizkalla S, Clément K. Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers. Diabetes. 2010 Dec;59(12):3049-57. doi: 10.2337/db10-0253. Epub 2010 Sep 28. PMID: 20876719; PMCID: PMC2992765.

31: 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. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res. 2010 Nov;20(11):1605-12. doi: 10.1101/gr.108332.110. Epub 2010 Sep 14. PMID: 20841432; PMCID: PMC2963823.

32: 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. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010 Mar 4;464(7285):59-65. doi: 10.1038/nature08821. PMID: 20203603; PMCID: PMC3779803.

33: Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz- Tamayo R, Paslier DL, Nalin R, Dore J, Leclerc M. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol. 2009 Oct;11(10):2574-84. doi: 10.1111/j.1462-2920.2009.01982.x. Epub 2009 Jul 6. PMID: 19601958.

34: Furet JP, Firmesse O, Gourmelon M, Bridonneau C, Tap J, Mondot S, Doré J, Corthier G. Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol. 2009 Jun;68(3):351-62. doi: 10.1111/j.1574-6941.2009.00671.x. Epub 2009 Mar 19. PMID: 19302550.