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Pathobiome 2018

Preliminary program

Preliminary program


18 March 2018   


   16:00-17:00     Registration of Attendees  
17:00-19:00 Welcoming and introduction
Joël Doré (INRA, Jouy en Josas, France)

Science-Society interaction

Public lecture on the role of the microbiota in infectious diseases.


19 March 2018













08:30-08:45 Welcoming introduction  
08:45-09:30 Opening lecture
Anna-Liisa LAINE (Helsinki University, Finland)

Within host pathogen diversity - causes and consequences

Session 1: From pathogens to pathobiome

9:30-10:30 Keynote lecture
Muriel Vayssier (INRA, France)

From tick borne pathogens to tick borne pathobiome

10:30-11:30 Posters & Coffee Break  
11:30 -12:30 Oral presentations

James Doonan (Bangor University, UK)

Distinguishing pathogen from symbiont in the acute oak decline pathobiome.

Kari Saikkonen (Natural Resources Institute Finland, Finland)

The outlook for plant pathobiome research.               

Emilie Lejal (INRA, Maisons-Alfort, France)

Dynamics and co-occurrences of Ixodes ricinus-borne pathogens.

12:45-14:00 Lunch break  

Session 2: From the host to pathobiome

14:00-15:00 Keynote lecture
Brett Finlay (University of British Columbia, Canada)

The role of the microbiome in enteric infections

15:00-16:00 Oral presentations

Shaynoor Dramsi (Institut Pasteur, France)

Competitive advantage of Streptococcus gallolyticus in colon cancer microbiota 

Pascale Serror (INRA, Jouy-en-Josas, France)

Lactobacillus paracasei CNCM I-3689 reduces level of vancomycin-resistance Enterococcus and promotes Bacteroidetes resilience following antibiotic challenge.

Philippe Velge (INRA, Nouzilly, France)

Salmonella carrier state in chicken: role of gut microbiota in the Super-shedder and Resistant phenotypes.

16:00-17:00 Posters & Coffee Break  
17:00 -18:20
Oral presentations

Nicolas Barnich (Université Clermont Auvergne, Inserm, INRA, France)                           

Adaptation of the pathobiont adherent-invasive E. coli to gut environment in the context of Crohn’s disease.

Yannick Tremblay (Institut Pasteur, Paris, France)

Role of deoxycholate in induction of Clostridium difficile biofilm formation.       

Biet Franck (INRA, Nouzilly, France)

Mycobacterium avium subsp. paratuberculosis hosted by free-living amoebae.

Derek Lundberg (Max Planck Institute for Developmental Biology, Germany)

Are strong natural ACD6 alleles in A. thaliana microbial paranoia?


20 March 2018










Stéphane Hacquard  (Max Planck Institute for Plant Breeding, Germany)

Microbial interactions and community assembly at the root-soil interface

Session 3: The pathobiome as a driver of pathogen adaptation and diversification

09:15-10:15 Keynote lecture
Fabrice Roux (INRA/CNRS, Toulouse, France)

A genomic map of local adaptation to microbiota and potential pathobiota in Arabidopsis thaliana.

10:15-11:15 Posters & Coffee Break   
11:15-12:35  Oral presentations

Talia Karasov (Max Planck Institute, Germany)

Long-term maintenance and expansions of dozens of pathogenic Pseudomonas strains within A. thaliana populations.

Tania V. Fort (INRA,  Pessac, France)

Vertical transmission of microbiota is influenced by maternal and environmental effects in sessile oak (Quercus petraea).              

Philippe Roumagnac (CIRAD, France)

Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.

Rosanna Wright (University of York, UK)

The structure and genetics of cross-resistance evolution in bacteria-phage interactions.

12:45-14:00  Lunch break  

Session 4: Statistical and Mathematical modeling to unravel interactions

14:00-15:00 Keynote lecture
Otso Ovaskainen (University of Helsinki , Finland)

How to make more out of community data? A conceptual framework and its

implementation as models and software.

15:00-16:00 Oral presentations

Julien Chiquet (AgroParitech/INRA, Paris, France)

Network Reconstruction from Ecological Count Data with a Sparse Poisson Lognormal Model.

Arnaud Cougoul (INRA, Theix, France)

Limits of statistical detection of microbial associations from metagenomic data.

PAUVERT Charlie (INRA, Bordeaux, France)

Cropping system shapes foliar fungal networks of grapevine.

16:00-16:30 Young scientific awards for oral and Poster presentation