Adress: INRAE - MaIAGE Unit
              Domaine de Vilvert - Bat 233
              78352 JOUY-EN-JOSAS CEDEX
Phone: +33 1 34 65 22 36

Research interest

I am interested in the development of new methods to study microbial ecosystem with metagenomic sequencing.



On-going projects


Bioinformatics working groups

  • Board member of PEPI IBIS since 2015
  • Co-organiser of metagenomics working group of PEPI IBIS since 2013
  • In charge of the Workpackage ANNOT of the CATI BOOM since 2019

Supervising and co-supervising

  • Solène Pety (Septembre 2021-January 2023) M2 internship -  Master of Bioinformatics - Rouen University.
    Development of methods for strain and genes fluxes from metagenomic datasets along an food production chain

  • Nathan Godart (May - July 2021) L3 internship, Poitiers University 
    Test of Antobiotic Resistance Gene haplotype reconstructions methods in metagenomic datasets

  • Anne-Carmen Sanchez (February - July 2020 and Sept 2020-July 2021). M2 internship - Paris 6 University - Engineer
    Analysis of microbial diversity in metagenomic datasets - Analysis of genes and strains fluxes in chicken metagenomes

  • Benoit Goutorbe (September 2019 - August 2022). Ph. D student - Paris Saclay University 
    Developement & implementation of a precise method for human microbiota study with a clinical application

  • Yassin El Djoudi (June - July 2019). L3 internship, Poitiers University 
    Intraspecific polymorphism study on gut microbiota prevalent species from sequenced genomes.

  • Daniel de Murat (March - July 2018). M1 Internship - Master of Bioinformatics, Paris 7 University
    Comparative analysis of metagenomic analysis tools.

  • Quentin Cavaillé (October 2017- March 2019). Web and databases engineer.
    Development of a tool for cheese ecosystem analysis with metagenomic datasets.

  • Thibaut Guirimand (October 2015 - August 2017). Web and databases engineer.
    Development of a tool for cheese ecosystem analysis with metagenomic datasets.

  • Charlie Pauvert (April 2014 - August 2016): M1 and M2 internship (2 years apprenticeship) -  Master of Bioinformatics - Rouen University.
    Cheese ecosystems metagenomics - Explorations & improvements around a bioinformatics tool

  • Amira Hamdi (February - June 2012). M2 internship - Master of Bioinformatics - Evry Universty  Cheese ecosystem analyses



Since 2017 : Research engineer in bioinformatics in MaIAGE Unit, team StatInfOmics

2011- 2016 : Research engineer in bioinformatics in Micalis, teams FME, Fine, IFE

2010 - 2011 : Post-Doc at IBENS (12 months) - Supervisor: Lionel Navarro

2009 - 2010 : Post Doc at ENS-Lyon (18 months) - Supervisor: Gaël Yvert

2005 - 2009 : Ph. D in bioinformatics in Atelier de Bioinformatique de Paris 6 - Supervisors: Eduardo Rocha and Joël Pothier

Recent publications

All my publications and communications are available on prodinra and google schoolar


  • Falentin, H., Auer, L., Mariadassou, M., Pascal, G., Rué, O., Dugat-Bony, E., ... & Abraham, AL. (2019). Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’ initier aux analyses métabarcoding.
  • Burz, S. D., Abraham, A. L., Fonseca, F., David, O., Chapron, A., Béguet-Crespel, F., ... & Schwintner, C. (2019). A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation. Scientific Reports, 9(1), 8897.
  • Mkaouar, H., Akermi, N., Kriaa, A., Abraham, A. L., Jablaoui, A., Soussou, S., ... & Rhimi, M. (2019). Serine protease inhibitors and human wellbeing interplay: new insights for old friends. PeerJ, 7, e7224.


  • Couvigny B, Kulakauskas S, Pons N, Quinquis B, Abraham AL, Meylheuc T, Delorme C, Renault P, Briandet R, Lapaque N,  Nicolas, Guédon E. Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius. Frontiers in microbiology. 2018


  • 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. PubMed PMID: 28281695; PubMed Central PMCID: PMC5345009.
  • Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc, M, Klopp C, Terrapon N, Henrissat B, Blottière HM, Doré J, Béra-Maillet C. A, fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Sci Rep. 2017 Jan 16;7:40248. doi: 10.1038/srep40248. PubMed PMID: 28091525; PubMed Central PMCID: PMC5238381.


  • 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. eCollection 2016. PubMed PMID: 27416027; PubMed Central PMCID: PMC4945068.
  • Alard J, Lehrter V, Rhimi M, Mangin I, Peucelle V, Abraham AL, Mariadassou M, Maguin E, Waligora-Dupriet AJ, Pot B, Wolowczuk I, Grangette C. Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota. Environ Microbiol. 2016 May;18(5):1484-97. doi: 10.1111/1462-2920.13181. Epub 2016 Jan 26. PubMed PMID: 26689997.