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:

YearTitle & DetailsCitations
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
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
7
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)
3
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
1
2023 Food and gut microbiome modelizations to sustain health
J Tap
NutrEvent
0
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
37
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
35
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
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
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
30
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
1
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
Webinar MetaGenoPolis
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
15
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
9
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
151
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
102
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
44
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
17
2019 Alternative stable states of a holobiont: the intestinal microbiota-host relationship.
M Van De Guchte, SD Burz, J Tap, J Cadiou, J Wu, A Cotillard, C Mayeur, ...
The Second International Conference on Holobionts
0
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, MP del Río, FP Batet, ...
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
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
18
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
13
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
604
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
338
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
3
2017 Mikrobiom und entzündliche Darmerkrankungen
DM Autenrieth, DC Baumgart
DMW-Deutsche Medizinische Wochenschrift
142 (04), 261-266
1
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
42
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
0
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
369
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
19
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, ...
Digestive Disease Week
148 (4), S-142-S-143
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
2026
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
1083
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
1058
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
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
4760
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
938
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
499
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
456
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
351
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
8188
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
975
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
90
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
13053
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
1477
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
109
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
1150
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
451
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 Phylogenetic and Functional Specificities of Crohn’s Disease Microbiota
S Mondot, J Tap, JP Furet, P Lepage, J Doré, P Marteau, M Leclerc

0
2004 Caractérisation moléculaire des Escherichia coli O111 et diversité des souches isolées en France
J Tap
Centre national de référence des Escherichia coli et Shigella. Institut Pasteur
1
2003 Les mycotoxines
G Royer, J TAP
Université Paris XII Année
2004
2
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
NA Structure génétique de Mycobacterium prototuberculosis et origine de M. tuberculosis.
J Tap

0