Julien Tap | About

Julien is currently research scientist at INRAE center settled in Paris-Saclay campus where he is working on microbiome science topics around nutrition and human health. 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 both at EMBL in Peer Bork’s group and at INRA Metagenopolis unit (Joel Doré, Dusko Ehrlich), he used approaches like numerical ecology and machine learning technics to untangle big omics data with clinical and dietary data in health and disease. At Danone Research, he contributed to generate novel scientific evidence on fermented products on human gut microbiome more precisely using functional analysis and he studied large-scale data to move to more personalized approaches taken gut microbiome into account.

Research experience

Since October 2022 INRAE Micalis Institute - Jouy-en-Josas - France
2015 - 2022 Danone Nutricia Research - Palaiseau - France
2013 - 2014 INRA : Metagenopolis – (D. Ehrlich, J. Doré) - Jouy-en-Josas - France
2010 - 2012 EMBL : Bork group Computational Biology – (P. Bork) Deciphering function and evolution of biological systems - Heidelberg - Germany
2007 - 2009 Phylogenetic and Functional Biodiversity of the Human Gut Microbiota - Ecology and Physiology of the Digestive Tract (UEPSD) - INRA - Jouy-en-Josas – (M.Leclerc, J. Doré)
Thesis project : Diet impact on structural and functional dynamics of the human intestinal microbiota
March/September 2006 Bacterial population genetics labs - Biodiversity of Emerging Pathogenic Bacteria - Pasteur Institute – (S. Brisse, P. Grimont) Paris XV
Master’s degree project: genetic structure of M. prototuberculosis and origin of M. tuberculosis
March/August 2005 Unit of Genomics of Microbial Pathogens Pasteur Genopole® Île-de-France - Pasteur Institute - (P. Glaser, C. Buchrieser, F. Kuntz) Paris XV
Master’s degree project : Development of a biodiversity DNA chips for molecular typing of Listeria
April/July 2004 National Reference Center for E. coli - Biodiversity of Emerging Pathogenic Bacteria - Pasteur Institute - (F. Grimont, P. Grimont) Paris XV
Bachelor’s degree project : molecular characterization of E. coli O111 and the diversity of isolated strains in France

Education

2007-2009 University of Pierre & Marie Curie Paris VI Ph.D. in Physiology and Pathophysiology
2005-2006 Pierre & Marie Curie Paris VI Master’s degree in Molecular Biology and Cellular - Genetics specialty
2001-2005 Paris Val de Marne University Paris XII
- “Maitrise”. Biotechnology and bio-industry .
- Bachelor’s degree. Biological engineering - Biochemical and Food specialty

Publications

for up-to-date bibliography check:

Year	Title & Details	Citations
2024	Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome N Carlino, A Blanco-Míguez, M Punčochář, C Mengoni, F Pinto, A Tatti, ... Cell 187 (20), 5775-5795. e15	2
2024	Next-gen fermented food: Harnessing gut microbiome diversity and functions J Tap, V Hervé, S Landaud, D Werner, MH Desmonts, S Chaillou Metabolomics & Fermented Foods	0
2024	A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain L Khatib, SJ Song, AH Dilmore, JG Sanders, C Brennan, AR Hernández, ... bioRxiv 2024.10. 01.616090	0
2023	Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors J Tap, F Lejzerowicz, A Cotillard, M Pichaud, D McDonald, SJ Song, ... Nature communications 14 (1), 3310	14
2023	Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy R Ladeira, J Tap, M Derrien Microbiome Research Reports 2 (2)	6
2023	Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans CI Rodriguez, A Keshavarzian, BR Hamaker, F Liu, GR Lunken, ... Scientific Data 10 (1), 346	2
2023	Branches and ecological states of the gut microbiome: Mapping for future personalized nutritional and therapeutic interventions J Tap Journées Polepharma de Microbiomique	0
2023	Food and gut microbiome modelizations to sustain health J Tap NutrEvent	0
2022	Drinking water source and intake are associated with distinct gut microbiota signatures in US and UK populations T Vanhaecke, O Bretin, M Poirel, J Tap The Journal of nutrition 152 (1), 171-182	45
2022	A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project A Cotillard, A Cartier-Meheust, NS Litwin, S Chaumont, M Saccareau, ... The American journal of clinical nutrition 115 (2), 432-443	43
2022	Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet I Oyarzun, B Le Nevé, F Yañez, Z Xie, M Pichaud, G Serrano-Gómez, ... Computational and Structural Biotechnology Journal 20, 1632-1641	1
2022	Representing Diet in a Tree-Based Format for Interactive and Exploratory Assessment of Dietary Intake Data N Litwin, K Cantrell, A Cotillard, M Derrien, A Johnson, R Knight, ... Current Developments in Nutrition 6, 774	0
2022	EXPLORATION DES LIENS ENTRE ALIMENTATION, MICROBIOTE INTESTINAL ET INCONFORT DIGESTIF J Tap	0
2021	Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome J Tap, S Störsrud, B Le Nevé, A Cotillard, N Pons, J Doré, L Öhman, ... Microbiome 9, 1-13	36
2021	The Human Gut Microbiota in all its States: From Disturbance to Resilience J Tap, E Ruppé, M Derrien Reference Module in Food Science	6
2021	A novel stepwise integrative analysis pipeline reveals distinct microbiota-host interactions and link to symptoms in irritable bowel syndrome A Polster, L Öhman, J Tap, M Derrien, B Le Nevé, J Sundin, H Törnblom, ... Scientific Reports 11 (1), 5521	4
2021	A Fermented Milk Product Containing B. lactis CNCM I-2494 Improves the Tolerance of a Plant-Based Diet in Patients with Disorders of Gut–Brain Interactions BL Nevé, A Martinez-De la Torre, J Tap, AN Ruiz, M Derrien, A Cotillard, ... Nutrients 13 (12), 4542	2
2021	Unsupervised diet partitions better explain variations of the gut microbiome compared to individual dietary markers in US adults of the American Gut Project cohort A Cotillard, S Chaumont, M Saccareau, NS Litwin, DG Lopez, J Tap, ... Current Developments in Nutrition 5, 397	1
2021	Diet and gut microbiome interactions in irritable bowel syndrome J Tap, S Störsrud, B Le Nevé, A Cotillard, N Pons, J Doré, L Öhman, ...	0
2021	Syndrome de l'intestin irritable: Quelles sont les interactions entre la diète et le microbiome intestinal? J Tap < bound method Organization. get_name_with_acronym of< Organization: INRAE …	0
2020	Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial AS Alvarez, J Tap, I Chambaud, S Cools-Portier, L Quinquis, P Bourlioux, ... Scientific Reports 10 (1), 15974	18
2020	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 … B Le Nevé, A Martinez-De la Torre, J Tap, M Derrien, A Cotillard, E Barba, ... Nutrients 12 (2), 320	10
2020	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 … J Tap, M Derrien, A Cotillard, E Barba, M Mego, AN Ruiz, ...	0
2020	Gut microbiome, diet and symptom interactions in irritable bowel syndrome J Tap, S Störsrud, BL Nevé, A Cotillard, N Pons, J Doré, L Öhman, ... bioRxiv 2020.02. 25.964528	0
2019	Prediction of the intestinal resistome by a three-dimensional structure-based method E Ruppé, A Ghozlane, J Tap, N Pons, AS Alvarez, N Maziers, T Cuesta, ... Nature microbiology 4 (1), 112-123	169
2019	Evidence for an association of gut microbial Clostridia with brain functional connectivity and gastrointestinal sensorimotor function in patients with irritable bowel syndrome … JS Labus, V Osadchiy, EY Hsiao, J Tap, M Derrien, A Gupta, K Tillisch, ... Microbiome 7, 1-15	110
2019	Effects of the long-term storage of human fecal microbiota samples collected in RNAlater J Tap, S Cools-Portier, S Pavan, A Druesne, L Öhman, H Törnblom, ... Scientific reports 9 (1), 601	51
2019	Fasting breath H2 and gut microbiota metabolic potential are associated with the response to a fermented milk product in irritable bowel syndrome B Le Nevé, M Derrien, J Tap, R Brazeilles, S Cools Portier, D Guyonnet, ... PLoS One 14 (4), e0214273	18
2019	Effects of a Flatulogenic Diet Combined with a Fermented Milk Product on Markers of Flatulence and Intestinal Microbiome Composition in Healthy Subjects AM de la Torre, B Le Nevé, J Tap, A Cotillard, M Pozuelo, FPB del Río, ... Gastroenterology 156 (6), S221-S221	0
2019	Gut microbiome hysteresis is associated with durable mucosal alterations J Tap, S Burz, A Cotillard, J Cadiou, HM Blottiere, J Dore, P Veiga, ...	0
2019	Alternative stable states of a holobiont: the intestinal microbiota-host relationship. M Van De Guchte, S Burz, J Tap, J Cadiou, J Wu, A Cotillard, C Mayeur, ...	0
2018	Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation SMP Bennet, J Sundin, MK Magnusson, H Strid, J Tap, M Derrien, ... Neurogastroenterology & Motility 30 (12), e13468	20
2018	Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects J Sundin, M Stridsberg, J Tap, M Derrien, B Le Nevé, J Doré, H Törnblom, ... Scientific Reports 8 (1), 16821	15
2018	Mo1942-Association Between Dietary Habits and the Gut Metagenome in Irritable Bowel Syndrome J Tap, M Derrien, B Le Nevé, L Ohman, H Törnblom, S Störsrud, M Simren Gastroenterology 154 (6), S-859	0
2018	Mikrobielle Biomarker zur Krebsfrüherkennung AY Voigt, G Zeller, P Bork TumorDiagnostik & Therapie 39 (01), 55-62	0
2017	Identification of an intestinal microbiota signature associated with severity of irritable bowel syndrome J Tap, M Derrien, H Törnblom, R Brazeilles, S Cools-Portier, J Doré, ... Gastroenterology 152 (1), 111-123. e8	643
2017	Faecal microbiota study reveals specific dysbiosis in spondyloarthritis M Breban, J Tap, A Leboime, R Said-Nahal, P Langella, G Chiocchia, ... Annals of the rheumatic diseases 76 (9), 1614-1622	362
2017	Clostridia from the gut microbiome are associated with brain functional connectivity and evoked symptoms in IBS JS Labus, E Hsiao, J Tap, M Derrien, A Gupta, B Le Nevé, R Brazeilles, ... Gastroenterology 152 (5), S40	9
2017	Prediction of the intestinal resistome by a novel 3D-based method E Ruppé, A Ghozlane, J Tap, N Pons, AS Alvarez, N Maziers, T Cuesta, ... bioRxiv 196014	4
2017	Granins are linked to bacterial richness, innate immunity, markers for intestinal permeability and symptom severity IBS patients J Sundin, J Tap, M Derrien, B Le Neve, M Stridsberg, H Tornblom, ... Neurogastroenterology And Motility 29, 21-21	0
2017	Mikrobielle Signatur für Patienten mit Reizdarmsyndrom M Hofmann-Aßmus Zeitschrift für Gastroenterologie 55 (04), 342-342	0
2016	Lactulose challenge determines visceral sensitivity and severity of symptoms in patients with irritable bowel syndrome B Le Nevé, R Brazeilles, M Derrien, J Tap, D Guyonnet, L Ohman, ... Clinical Gastroenterology and Hepatology 14 (2), 226-233. e3	45
2016	Microbiote intestinal, la clé pour une meilleure alimentation? P Veiga, J Tap, M Derrien médecine/sciences 32 (11), 999-1002	3
2016	Early Phenotypical Changes induced By Transfert of Human Fecal Microbiota from Colorectal Cancer Patients to Germ-Free Mice J Tap, A Amiot, V Jarrousse, S Guilmeau, J Tran VanNhieu, P Langella, ... International Journal of Cancer and Oncology 4 (1), 1-11	1
2016	Tripartite network analysis links symptoms to the gut microbiome brain axis in irritable bowel syndrome JS Labus, K Tillisch, J Tap, M Derrien, A Gupta, B Leneve, R Brazeilles, ... Neurogastroenterology And Motility 28, 30-30	0
2016	NEW INSIGHTS ON RELATIONSHIPS BETWEEN FODMAPS INTAKE, GUT MICROBIOTA AND SEVERITY OF SYMPTOMS IN IRRITABLE BOWEL SYNDROME J Tap, M Derrien, H Törnblom, N Pons, S Cools-Portier, J Doré, B Le Neve, ...	0
2016	Metagenomics exploration of the gut microbiome in irritable bowel syndrome J Tap	0
2016	It's all in the mix: diagnosis and management of food intolerance reply B Le Neve, R Brazeilles, M Derrien, J Tap, D Guyonnet, L Ohman, ... Clinical Gastroenterology and Hepatology 14 (8), 1222-1223	0
2015	Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults J Tap, JP Furet, M Bensaada, C Philippe, H Roth, S Rabot, O Lakhdari, ... Environmental microbiology 17 (12), 4954-4964	387
2015	Metagenomics of the human intestinal tract: from who is there to what is done there A Cultrone, J Tap, N Lapaque, J Doré, HM Blottière Current Opinion in Food Science 4, 64-68	20
2015	The gut microbiota for health experts exchange: an online network for sharing knowledge P Enck, K Campbell, J Tap, PY Arnoux, JM Antoine The FASEB Journal 29, 909.4	1
2015	Identification of a Gut Microbial Signature Linked to Severity of Irritable Bowel Syndrome J Tap, L Ohman, H Törnblom, B Le Nevé, R Brazeilles, J Doré, M Derrien, ... < bound method Organization. get_name_with_acronym of< Organization: INRAE …	0
2015	Le microbiote intestinal comme marqueur potentiel du cancer colorectal J Tap, G Zeller, AY Voigt, A Amiot, J van Nhieu, P Schrotz-King, M Kloor, ...	0
2014	An integrated catalog of reference genes in the human gut microbiome J Li, H Jia, X Cai, H Zhong, Q Feng, S Sunagawa, M Arumugam, ... Nature biotechnology 32 (8), 834-841	2158
2014	Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes HB Nielsen, M Almeida, AS Juncker, S Rasmussen, J Li, S Sunagawa, ... Nature biotechnology 32 (8), 822-828	1137
2014	Potential of fecal microbiota for early‐stage detection of colorectal cancer G Zeller, J Tap, AY Voigt, S Sunagawa, JR Kultima, PI Costea, A Amiot, ... Molecular systems biology 10 (11), 766	1130
2014	Gut Microbiota Variations Correlate with Disease Activity in Spondyloarthritis (SpA) and Rheumatoid Arthritis (RA). J Tap, J Abou-Ghantous, A Leboime, RS Nahal, P Langella, HJ Garchon, ... ARTHRITIS & RHEUMATOLOGY 66, S273-S273	1
2014	Method for diagnosing adenomas and/or colorectal cancer (CRC) based on analyzing the gut microbiome P Bork, J Tap, G Zeller, A Voigt, JR Kultima, PI Costea, D Mende, ... EP Patent EP P2955232A1	0
2014	Procédé de diagnostic d'adénomes et/ou du cancer colorectal (CRC) basé sur l'analyse du microbiome intestinal P Bork, J Tap, G Zeller, AY Voigt, JR Kultima, PI Costea, D Mende, ...	0
2013	Richness of human gut microbiome correlates with metabolic markers E Le Chatelier, T Nielsen, J Qin, E Prifti, F Hildebrand, G Falony, ... Nature 500 (7464), 541-546	4960
2013	Genomic variation landscape of the human gut microbiome S Schloissnig, M Arumugam, S Sunagawa, M Mitreva, J Tap, A Zhu, ... Nature 493 (7430), 45-50	978
2013	Metagenomic species profiling using universal phylogenetic marker genes S Sunagawa, DR Mende, G Zeller, F Izquierdo-Carrasco, SA Berger, ... Nature methods 10 (12), 1196-1199	522
2013	Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes LC Kong, J Tap, J Aron-Wisnewsky, V Pelloux, A Basdevant, JL Bouillot, ... The American journal of clinical nutrition 98 (1), 16-24	466
2013	Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis P Supply, M Marceau, S Mangenot, D Roche, C Rouanet, V Khanna, ... Nature genetics 45 (2), 172-179	358
2013	Individuality and temporal stability of the human gut microbiome S Sunagawa, S Schloissnig, M Arumugam, K Forslund, M Mitreva, J Tap, ... Central Asian Journal of Global Health 2 (Suppl)	7
2013	Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes. KLC Kong LingChun, J Tap, J Aron-Wisnewsky, V Pelloux, A Basdevant, ...	0
2011	Enterotypes of the human gut microbiome M Arumugam, J Raes, E Pelletier, D Le Paslier, T Yamada, DR Mende, ... nature 473 (7346), 174-180	8555
2011	Microbial dysbiosis in colorectal cancer (CRC) patients I Sobhani, J Tap, F Roudot-Thoraval, JP Roperch, S Letulle, P Langella, ... PloS one 6 (1), e16393	1003
2011	Identification of NF‐κB Modulation Capabilities within Human Intestinal Commensal Bacteria O Lakhdari, J Tap, F Béguet-Crespel, K Le Roux, T De Wouters, ... BioMed Research International 2011 (1), 282356	96
2011	Research Article Identification of NF-κB Modulation Capabilities within Human Intestinal Commensal Bacteria O Lakhdari, J Tap, F Béguet-Crespel, K Le Roux, T de Wouters, ...	0
2010	A human gut microbial gene catalogue established by metagenomic sequencing J Qin, R Li, J Raes, M Arumugam, KS Burgdorf, C Manichanh, T Nielsen, ... nature 464 (7285), 59-65	13561
2010	Differential adaptation of human gut microbiota to bariatric surgery–induced weight loss: links with metabolic and low-grade inflammation markers JP Furet, LC Kong, J Tap, C Poitou, A Basdevant, JL Bouillot, D Mariat, ... Diabetes 59 (12), 3049-3057	1499
2010	Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes L Tasse, J Bercovici, S Pizzut-Serin, P Robe, J Tap, C Klopp, BL Cantarel, ... Genome research 20 (11), 1605-1612	282
2010	Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut O Lakhdari, A Cultrone, J Tap, K Gloux, F Bernard, SD Ehrlich, F Lefevre, ... PloS one 5 (9), e13092	110
2010	Adaptation of intestinal microbiota after weight loss: Effects of gastric bypass (GBP) in massively obese subjects. LC Kong, JP Furet, J Tap, C Poitou, A Basdevant, JL Bouillot, G Corthier, ... Diabetes & Metabolism 36, A7-A8	3
2010	Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammatory markers LC Kong, JP Furet, J Tap, C Poitou-Bernert, A Basdevant, JL Bouillot, ... Diabetes 59, A486-A486	1
2009	Towards the human intestinal microbiota phylogenetic core J Tap, S Mondot, F Levenez, E Pelletier, C Caron, JP Furet, E Ugarte, ... Environmental microbiology 11 (10), 2574-2584	1182
2009	Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR JP Furet, O Firmesse, M Gourmelon, C Bridonneau, J Tap, S Mondot, ... FEMS microbiology ecology 68 (3), 351-362	471
2009	Towards the healthy human intestinal microbiota phylogenetic core? J Tap, S Mondot, F Levenez, E Pelletier, C Caron, JP Furet, E Ugarte, ... Microbial Ecology 57 (3), 580-581	5
2009	Impact du régime alimentaire sur la dynamique structurale et fonctionnelle du microbiote intestinal humain J Tap Université Pierre et Marie Curie	4
2009	Vers le noyau phylogenetique du microbiote intestinal human J Tap, S Mondot, F Levenez, E Pelletier, C Caron, J Furet, JP Pierre, ...	0
2009	Impact du régime alimentaire sur la dynamique structurale et fonctionnelle du microbiote intestinal humain\| Theses. fr J Tap Paris 6	0
2009	Phylogenetic and Functional Specificities of Crohn’s Disease Microbiota S Mondot, J Tap, JP Furet, P Lepage, J Doré, P Marteau, M Leclerc	0
2006	Structure génétique de Mycobacterium prototuberculosis et origine de M. tuberculosis. J Tap < bound method Organization. get_name_with_acronym of< Organization: INRAE …	0
2004	Caractérisation moléculaire des Escherichia coli O111 et diversité des souches isolées en France J Tap Rapport de stage. Unité Biodiversité Bactéries Pathogènes Emergentes. Centre …	2
2003	Les mycotoxines G Royer, J TAP Université Paris XII Année 2004	3
NA	Genome analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of the etiologic agent of tuberculosis P Supply, M Marceau, S Mangenot, D Roche, C Rouanet, V Khanna, ...	0