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# MEM Days - The phyllosphere is a microbial jungle at the plant-climate interface

Corinne Vacher

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## To cite this version:

Corinne Vacher. MEM Days - The phyllosphere is a microbial jungle at the plant-climate interface. Journées du Métaprogramme MEM, Jan 2017, Paris, France. hal-01603163

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Submitted on 5 Jun 2020

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INRA
SCIENCE & IMPACT

MEM Metaprogramme

Microbial Ecosystems & Metaomics

2017 Scientific MEM days

January 18-20, Paris (Porte de la Villette)

Programme

List of posters

List of participants

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## Wednesday January 18th afternoon

### Introduction

<table><tr><td>12:30-14:00</td><td>1h30</td><td>Lunch</td></tr><tr><td>14:00-15:00</td><td>1h</td><td>Emmanuelle MAGUIN (Director of MEM Metaprogramme)<br/>Introduction and general presentation of MEM and thematic groups.</td></tr><tr><td>15:00-15:30</td><td>25 + 5 = 30</td><td>Tom CURTIS (Newcastle University)<br/>The Numbers Game</td></tr><tr><td>15:30-16:30</td><td>1h</td><td>Coffee-break / Posters</td></tr></table>

### Session 1) Taxonomic and functional diversity of microbial communities

<table><tr><td rowspan="5">16:30-18:10<br/>Chairpersons:<br/>Corinne VACHER</td><td>16:30-16:50<br/>15 + 5 = 20</td><td>Christophe MOUGEL (IGEPP, Rennes)<br/>MetaT - Metatranscriptomics &amp; functional diversity</td></tr><tr><td>16:50-17:10<br/>15 + 5 = 20</td><td>Fanny CALENGE (GABI, Jouy-en-Josas) &amp; Olivier ZEMB (GenPhyse, Toulouse)<br/>Preliminary catalogues of the rabbit and chicken gut metagenomes</td></tr><tr><td>17:10-17:30<br/>15 + 5 = 20</td><td>Sophie GAUDRIAULT (DGIMI, Montpellier)<br/>Development of methodology for a taxonomic assignation at the species level in the pathobiome of entomopathogenic nematodes from the Steinernema genus</td></tr><tr><td>17:30-17:50<br/>15 + 5 = 20</td><td>Jean-François COSSON (BIPAR, Maisons-Alfort)<br/>Standardization of the use of bacterial metagenomic approaches for epidemiological studies</td></tr><tr><td>17:50-18:10<br/>15 + 5 = 20</td><td>Aurélie DEVEAU (IAM, Nancy)<br/>Taxonomic and functional characterization of the truffle microbiome</td></tr><tr><td>18:10-20:00<br/>19:00-20:00</td><td>2h<br/>1h</td><td>Aperitif / Posters [Espace Meliès-Newton-Archimède]<br/>Speed-dating, animated by Christophe Chassard (UMRF, Aurillac), Stéphanie-Marie Deutsch et Hélène Falentin (STLO, Rennes) [Salles Edison-Ampère et Pascal-Descartes]</td></tr><tr><td>20:00</td><td></td><td>Dinner</td></tr></table>

## Thursday January 19th morning

### Session 2) Microbial interactions and community response to disturbances

<table><tr><td rowspan="4">8:30-10:00<br/>Chairpersons:<br/>Aurélie DEVEAU &amp; Moez RHIMI</td><td>8:30-9:00<br/>25 + 5 = 30</td><td>Anna-Liisa LAINE (Helsinki University)<br/>Variation in within-host pathogen communities: causes and consequences</td></tr><tr><td>9:00-9:20<br/>15 + 5 = 20</td><td>Mathieu BARRET (IRHS, Angers)<br/>Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms</td></tr><tr><td>9:20-9:40<br/>15 + 5 = 20</td><td>Eric DUGAT-BONY (GMPA, Grignon)<br/>FORTRESS Impact of microbial diversity on the barrier effect against an exogenous species.</td></tr><tr><td>9:40-10:00<br/>15 + 5 = 20</td><td>Philippe VELGE (ISP, Tours)<br/>Recontaminations between chicks and gut microbiota are required to induce homogeneous levels of Salmonella infection and excretion at the flock level</td></tr><tr><td>10:00-11:00</td><td>1h</td><td>Coffee-break / Posters</td></tr><tr><td rowspan="5">Chairpersons:<br/>Mahendra MARIADASSOU &amp; Sandra PLANCADE</td><td>11:00-11:20<br/>15 + 5 = 20</td><td>Julien CHIQUET (MIA, Paris)<br/>Sparse reconstruction of graphical models: application to ecological systems</td></tr><tr><td>11:20-11:40<br/>15 + 5 = 20</td><td>Delphine SICARD (SPO, Montpellier)<br/>Complexity of bacteria-yeasts interactions: perspectives from the point of view of mathematics and biology</td></tr><tr><td>11:40-12:00<br/>15 + 5 = 20</td><td>Béatrice LAROCHE (MAIAGE, Jouy-en-Josas)<br/>METAFUN - Metagenomic data integration to evaluate and model the functional potential of fiber metabolism in the human gut microbiota.</td></tr><tr><td>12:00-12:20<br/>15 + 5 = 20</td><td>Corinne VACHER (Biogeco, Bordeaux)<br/>The phyllosphere: microbial jungle at the plant-climate interface</td></tr><tr><td>12:20-12:35<br/>10</td><td>3 flash posters presentations (3 min each): see titles page 4<br/>P12 – Sandrine ELLERO-SIMATOS (TOXALIM, Toulouse)<br/>P13 – Sergine EVEN (STLO, Rennes) &amp; Xavier NOUVEL (IHAP, Toulouse)<br/>P18 – Valentin LOUX &amp; Olivier RUÉ (MAIAGE, Jouy)</td></tr><tr><td>12:30-14:00</td><td>1h30</td><td>Lunch</td></tr></table>
## Thursday January 19th afternoon

### Session 3) Steering and engineering of microbial communities

<table><tbody><tr><td>14:00-15:30</td><td>14:00-14:20<br>15 + 5 = 20</td><td><strong>Anne THIERRY (STLO, Rennes) & Francoise IRLINGER (GMPA, Grignon)</strong><br>Assembly of communities for the fermentation of cereals and protein crops</td></tr><tr><td rowspan="5"><strong>Chairpersons:</strong><br><strong>Matthias LAVIERICHARD & Matthieu BARRET</strong></td><td>14:20-14:40<br>15 + 5 = 20</td><td><strong>Olivier ZEMB (GenPhyse, Toulouse)</strong><br>PhageSoutract - Use of bacteriophages to perform knock-out in a bacterial community</td></tr><tr><td>14:40-15:00<br>15 + 5 = 20</td><td><strong>Kim MILFERSTEDT (LBE, Narbonne)</strong><br>Enigme - Engineering interactions in methanogenic communities at the ecosystem level</td></tr><tr><td>15:00-15:20<br>15 + 5 = 20</td><td><strong>Guillermina HERNANDEZ-RAQUET (LISBP, Toulouse)</strong><br>Integrating meta-omics data to elucidate the functioning of lignocellulolytic microbial consortia</td></tr><tr><td>15:20-15:30<br>10</td><td>3 flash posters presentations (3 min each): see titles page 4<br>P7 - Stéphane CHAILLOU (MICALIS, Jouy)<br>P14 - Hélène FALENTIN (STLO, Rennes) & Claire NÉDELLEC (MAIAGE, Jouy)<br>P20 - Elisa MICHEL (SPO, Montpellier)</td></tr><tr><td>15:30-16:30<br>1h</td><td>Coffee-break / Posters</td></tr><tr><td>16:30-18:00</td><td colspan="2"><strong>3 simultaneous round-tables animated by:</strong></td></tr><tr><td></td><td>1) <strong>Culturomics</strong><br>[Salle plénière Louis Lumière]</td><td>Marion LECLERC (MICALIS, Jouy), Pascale MOSONI (MEDIS, Clermont), Pascale SERROR (MICALIS, Jouy)</td></tr><tr><td></td><td>2) <strong>Modelling interactions for ecosystem understanding and steering</strong> [Salle Edison-Ampère]</td><td>Thibault NIDELET (SPO, Montpellier), Simon LABARTHE (MAIAGE, Jouy)</td></tr><tr><td></td><td>3) <strong>Phytobiome</strong><br>[Salle Pascal-Descartes]]</td><td>Corinne VACHER (BIOGECO, Bordeaux), Matthieu BARRET (IRHS, Angers)</td></tr><tr><td>18:00-20:00<br>19:00-20:00</td><td>2h<br>1h</td><td>Aperitif / Posters [Espace Meliès-Newton-Archimède]<br>Speed-dating, animated by Christophe Chassard (UMRF, Aurillac), Stéphanie-Marie Deutsch et Hélène Falentin (STLO, Rennes) [Salles Edison-Ampère et Pascal-Descartes]</td></tr><tr><td>20:00</td><td></td><td>Dinner</td></tr></tbody></table>

## Friday January 20th morning

### Session 4) White Session

<table><tbody><tr><td>8:30-10:00</td><td>8:30-9:00<br>25 + 5 = 30</td><td><strong>Mark MORRISON (University of Queensland Diamantina Institute)</strong><br>How can we shine more light on microbial dark matter...or, is there a culture gap in microbiome research?</td></tr><tr><td rowspan="4"><strong>Chairpersons:</strong><br><strong>Julie RÉVEILLAUD & Samuel MONDY</strong></td><td>9:00-9:20<br>15 + 5 = 20</td><td><strong>Marianne de PAEPE (MICALIS, Jouy)</strong><br>Temperate phages in the gastro-intestinal tract</td></tr><tr><td>9:20-9:40<br>15 + 5 = 20</td><td><strong>Roland MARMEISSE (LME, Lyon)</strong><br>The soil mycobiome, insight into the process of organic matter degradation in situ</td></tr><tr><td>9:40-9:55<br>15</td><td>3 flash posters presentations (3 min each): see titles page 4<br>P8 - Nathalie CHARBONNEL (CBGP, Montpellier)<br>P17 - Jean LEGEAY (IAM, Nancy)<br>P26 - Jean-Michel SAVOIE (MYCSA, Bordeaux)</td></tr><tr><td>10:00-11:00<br>1h</td><td>Coffee-break / Posters</td></tr><tr><td rowspan="5"><strong>Chairpersons:</strong><br><strong>Sandrine ELLERO-SIMATOS & Eric DUGAT-BONY</strong></td><td>11:00-11:20<br>15 + 5 = 20</td><td><strong>Catherine JUSTE (MICALIS, Jouy)</strong><br>OBOMICS - Integration of meta-omics datasets in the context of human obesity.</td></tr><tr><td>11:20-11:40<br>15 + 5 = 20</td><td><strong>Céline DELBÈS (UMRF, Aurillac)</strong><br>Milk fat composition as key driver of microbial dynamics in Cantal cheese rind</td></tr><tr><td>11:40-12:00<br>15 + 5 = 20</td><td><strong>Cyrielle GASC (MEDIS, Clermont)</strong><br>Microbial community profiling and targeted genome reconstruction through hybridization capture</td></tr><tr><td>12:00-12:10<br>10</td><td><strong>Emmanuelle Maguin</strong><br>Conclusion</td></tr><tr><td>12:15<br>1h30</td><td>Lunch</td></tr><tr><td colspan="3" style="text-align: center;">End of the MEM Days</td></tr></tbody></table>
## Posters

in alphabetical order of the presenting author(s)

<table><thead><tr><td>N°</td><td>Name</td><td>First name</td><td>Unit</td><td>MEM Thematic Group</td><td>Title</td><td>MEM Key action or project</td></tr></thead><tbody><tr><td>P1</td><td>ANDRÉ-LEROUX</td><td>Gwenaëlle</td><td>MalAGE UR1404</td><td>Maths-Bioinfo</td><td>MetaFoldScan: Work in Progress</td><td>AMI 2016</td></tr><tr><td>P2</td><td>BADAWI & HERNANDEZ-RAQUET</td><td>Myriam Guillermina</td><td>LISBP UMR0792</td><td>Digesters; Maths-Bioinfo</td><td>Dynamic analysis of glycoside hydrolase expression in enriched microbial consortia for the valorization of lignocellulosic biomass</td><td>AMI 2016</td></tr><tr><td>P3</td><td>BERA-MAILLET</td><td>Christel</td><td>MICALIS UMR1319</td><td>Digesters; Food</td><td>Functional metagenomics to explore food deconstruction and intestinal immunity mediated by the human gut microbiota</td><td></td></tr><tr><td>P4</td><td>BUEE</td><td>Marc</td><td>IAM UMR1136</td><td>Agri</td><td>MetaBAR - Microbial meta-community: MetaBARcoding approach</td><td>Action 2015</td></tr><tr><td>P5</td><td>CALENGE</td><td>Fanny</td><td>GABI UMR1313</td><td>Digesters</td><td>Looking for a caecal metagenomic signature of digestive efficiency in chicken</td><td>Action 2015</td></tr><tr><td>P6</td><td>CANDRESSE & MOUGEL</td><td>Thierry Christophe</td><td>BFP UMR1332 IGEPP UMR1349</td><td>Agri; Pathobiome</td><td>BrassicaDivPatho - Microbial diversity and microbial networks associated to Brassica napus and its pathogens</td><td>Action 2016</td></tr><tr><td>P7</td><td>CHAILLOU</td><td>Stéphane</td><td>MICALIS UMR1319</td><td>Digesters; Food; Maths-Bioinfo; Maths-Modél</td><td>Virome Access - Accessing virus genomes out of metagenomics data: improving statistical and bio-informatics analytic tools to better assess the contribution of phages on microbial ecosystems.</td><td>AMI 2016</td></tr><tr><td>P8</td><td>CHARBONNEL</td><td>Nathalie</td><td>CBGP UMR1062</td><td>Pathobiome</td><td>HANTAGULUMIC: Spatio-temporal analyses of Hantavirus, GUt and LUng MICrobiota interactions</td><td>AMI 2016</td></tr><tr><td>P9</td><td>COSSON</td><td>Jean-François</td><td>BIPAR UMR0956</td><td>Pathobiome</td><td>Toward an efficient strategy combining different High-Throughput Sequencing (HTS) technologies for the characterization of microbiota in wildlife</td><td>Action 2015</td></tr><tr><td>P10</td><td>DEVEAU</td><td>Aurélie</td><td>IAM UMR1136</td><td>Agri</td><td>Regulation of the tree microbiome by the host: from community to functions</td><td>AMI 2016</td></tr><tr><td>P11</td><td>DRIDI</td><td>Bedis</td><td>MICALIS UMR1319</td><td>Food</td><td>Food microbiome-transfer: a new graphical interface for investigating cheese metagenome</td><td></td></tr><tr><td>P12</td><td>ELLERO-SIMATOS</td><td>Sandrine</td><td>ToxAlim UMR1331</td><td>Digesters</td><td>Interactions between the gut microbiota and the xenobiotic receptors CAR and PXR</td><td></td></tr><tr><td>P13</td><td>EVEN & NOUVEL</td><td>Sergine Xavier</td><td>STLO UMR1253 IHAP UMR1225</td><td>Pathobiome</td><td>MICROCOSM: a multi-site exploration of MICRObiome in COws in relation to genetic Susceptibility to Mastitis</td><td>Action 2016</td></tr><tr><td>P14</td><td>FALENTIN & NEDELLEC</td><td>Hélène Claire</td><td>STLO UMR1253 MalAGE UR1404</td><td>Food Math-Bioinfo</td><td>Florilège: a database gathering microbial phenotypes of food interest</td><td>Action 2016</td></tr><tr><td>P15</td><td>LAROCHE</td><td>Béatrice</td><td>MalAGE UR1404</td><td>Math-Modelling & all TG</td><td>MIND - Modelling INteraction Dynamics in microbial communities</td><td>Action 2016</td></tr></tbody></table>
<table><tr><td>P16</td><td>LE LOIR</td><td>Yves</td><td>STLO UMR1253</td><td>Pathobiome</td><td>Microbiota of bovine udder and susceptibility to mastitis in dairy cows.</td><td></td></tr><tr><td>P17</td><td>LEGEAY</td><td>Jean</td><td>IAM UMR1136</td><td>Agri; Maths-Bioinfo</td><td>Ecology of Phytophthora in neo-tropical forests</td><td>Thèse 2015</td></tr><tr><td>P18</td><td>LOUX & RUÉ</td><td>Valentin Olivier</td><td>MalAGE UR1404</td><td>Maths-Bioinfo</td><td>New -omics data analysis activity on Migale platform for MEM community</td><td></td></tr><tr><td>P19</td><td>MADZAK</td><td>Catherine</td><td>GMPA UMR0782</td><td>Food</td><td>MicroFit project: developing a Tn-seq system in Yarrowia lipolytica to study the adaptation of this yeast to cheese ecosystem.</td><td>AMI 2016</td></tr><tr><td>P20</td><td>MICHEL</td><td>Elisa</td><td>SPO UMR1083</td><td>Food</td><td>Terroir, baker's practices, wheat varieties and their influence on sourdough microbial diversity</td><td>Thèse 2015</td></tr><tr><td>P21</td><td>MOSONI</td><td>Pascale</td><td>MEDIS UMR0454</td><td>Digesters</td><td>Poster 20: Impact of procyanidin-plant cell wall interactions within apple matrices on the metabolism of procyanidins by the human gut microbiota. Poster 21: Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level</td><td></td></tr><tr><td>P22</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>P23</td><td>NIDELET</td><td>Thibault</td><td>SPO UMR1083</td><td>Food; Maths-Modél</td><td>Ecology and diversity of yeasts in fermented food ecosystems</td><td></td></tr><tr><td>P24</td><td>PETIT</td><td>Marie-Agnès</td><td>MICALIS UMR1319</td><td>Pathobiome; Digesters</td><td>Metaviral Catalogues</td><td>Action 2016</td></tr><tr><td>P25</td><td>RAZZAUTI</td><td>Maria</td><td>CBGP UMR1062</td><td>Pathobiome</td><td>NGS as a regular tool for viral epidemiologic studies</td><td>Action 2015</td></tr><tr><td>P26</td><td>SAVOIE</td><td>Jean-Michel</td><td>MycSA UR1264</td><td>Agri; Pathobiome</td><td>Microbiome evolution during moist corn grain silage</td><td></td></tr><tr><td>P27</td><td>SICARD</td><td>Delphine</td><td>SPO UMR1083</td><td>Food</td><td>METABAR-FOOD - Metabarcoding and shot-gun of food microbiota</td><td>Action 2016</td></tr></table>
Participants

<table><thead><tr><td>NAME</td><td>FIRST Name</td><td>Unit</td><td>INRA Division</td><td>MEM Thematic Group</td><td>Keywords</td></tr></thead><tbody><tr><td>ACHILLEOS</td><td>Christine</td><td>URTAL UR0342</td><td>CEPIA</td><td>Food</td><td>Dairy technology, cheese microbiota, molecular biology, sensory quality, impact of technology</td></tr><tr><td>AL-SHIKHLEY</td><td>Liza</td><td>BIPAR UMR0956</td><td>SA</td><td>Math-Bioinfo; Pathobiome</td><td>Vector microbiome, pathobiome, interactions between pathogens and microbiome</td></tr><tr><td>ANDRÉ-LEROUX</td><td>Gwenaëlle</td><td>MalAGE UR1404</td><td>MICA</td><td>Math-Bioinfo</td><td>Micobial ecosystem, 3D screening, structural bioinformatics, target proteins</td></tr><tr><td>AUBERT</td><td>Julie</td><td>MIA UMR0518</td><td>MIA</td><td>Math-Bioinfo; Math-Modelling</td><td>Statistics, meta(transcriptomics) data analysis, metabarcoding data analysis, statistical modelling</td></tr><tr><td>BADAWI</td><td>Myriam</td><td>LISBP UMR0792</td><td>CEPIA</td><td>Digesters; Math-Bioinfo</td><td>Statistics, microarray, data analysis, bacterial consortia, lignocellulosic degradation</td></tr><tr><td>BARRET</td><td>Matthieu</td><td>IRHS UMR1345</td><td>SPE</td><td>Pathobiome</td><td>Seed microbiome, transmission of plant pathogens, community ecology, microbial interactions, metagenomics</td></tr><tr><td>BERA-MAILLET</td><td>Christel</td><td>MICALIS UMR1319</td><td>MICA</td><td>Digesters; Food</td><td>Human intestinal microbiota, fiber enzymatic disruption, anaerobic cultures and functional metagenomics</td></tr><tr><td>BESSIÈRES</td><td>Philippe</td><td>MalAGE UR1404</td><td>MICA</td><td>Food; Math-Bioinfo</td><td>Microbial genomics, bioinformatics, text mining, databases, knowledge integration</td></tr><tr><td>BOISRAMÉ-BAUDEVIN</td><td>Anita</td><td>MICALIS UMR1319</td><td>MICA</td><td>Food</td><td>Yeast, biodiversity, genetic and genomic</td></tr><tr><td>BROUDISCOU</td><td>Laurent</td><td>MoSAR UMR0791</td><td>PHASE</td><td>Digesters</td><td>Rumen, host-microbiome interaction, ruminant nutrition, microbial ecology, fementers</td></tr><tr><td>BUCHIN</td><td>Solange</td><td>URTAL UR0342</td><td>CEPIA</td><td>Food</td><td>Cheese, flavour, bacterial metabolism, bacterial interactions</td></tr><tr><td>BUEE</td><td>Marc</td><td>IAM UMR1136</td><td>EFPA</td><td>Agri</td><td>Fungal community ecology, tree microbiome, organic matter decomposition, N / C mobilisation, meta-omics</td></tr><tr><td>BUSSIERE</td><td>Francoise</td><td>ISP UMR1282</td><td>SA</td><td>Digesters; Pathobiome</td><td>Host response, immunology, intestine, parasitology, host/parasite interactions, microbiota</td></tr><tr><td>CALENGE</td><td>Fanny</td><td>GABI UMR1313</td><td>GA</td><td>Digesters</td><td>Genetics, digestibility, innate immunity, Gallus gallus, gut microbiota</td></tr><tr><td>CANCEILL</td><td>Danielle</td><td>DPT MICA UAR1194</td><td>MICA</td><td></td><td>Mem project manager</td></tr><tr><td>CANDRESSE</td><td>Thierry</td><td>BFP UMR1332</td><td>SPE</td><td>Pathobiome</td><td>Plant virus, phytobiome, fungal virus, viral ecology, pathogenicity</td></tr><tr><td>CHAILLOU</td><td>Stéphane</td><td>MICALIS UMR1319</td><td>MICA</td><td>Digesters; Food; Math-Bioinfo; Math-Modelling</td><td>Food microbial ecology, food spoilage, Microbial metabolism, Microbial interactions, Genome sequencing and annotation</td></tr><tr><td>CHAMPOMMIER-VERGÈS</td><td>Marie-Christine</td><td>MICALIS UMR1319</td><td>MICA</td><td>Food</td><td>Food microbiology/microbial ecology/fermented foods/spoilage/biopreservation</td></tr><tr><td>CHARBONNEL</td><td>Nathalie</td><td>CBGP UMR1062</td><td>EFPA</td><td>Pathobiome</td><td>Rodent borne zoonoses, interactions, community ecology, pathobiome and microbiome, disease emergence</td></tr><tr><td>CHASSARD</td><td>Christophe</td><td>UMRF UMR0545</td><td>MICA</td><td>Food</td><td>Food microbiology, Gut microbiology, Microbial interactions, human nutrition and health</td></tr><tr><td>CHIQUET</td><td>Julien</td><td>MIA UMR0518</td><td>MIA</td><td>Math</td><td>Network reconstruction, statistical learning, graphical model, high dimensional data, sparse methods</td></tr><tr><td>CITTI</td><td>Christine</td><td>IHAP UMR1225</td><td>SA</td><td>Pathobiome</td><td>Pathobiome, infectious diseases, microbial genomics, horizontal gene transfer, animal health</td></tr><tr><td>COSSON</td><td>Jean-François</td><td>BIPAR UMR0956</td><td>EFPA</td><td>Pathobiome</td><td>Health ecology, zoonoses, molecular epidemiology, ticks & rodents, microbiome</td></tr><tr><td>DE PAEPE</td><td>Marianne</td><td>MICALIS UMR1319</td><td>MICA</td><td>Digesters; Math-Modelling</td><td></td></tr><tr><td>DELBES</td><td>Céline</td><td>UMRF UMR0545</td><td>MICA</td><td>Food</td><td>Food microbiology, microbial ecology, farm pathobiome, microbe-microbe and microbe-matrix interactions</td></tr><tr><td>DELORME</td><td>Christine</td><td>MICALIS UMR1319</td><td>MICA</td><td>Food</td><td>Food microbiology, functional analysis, streptococci, bacteria-host interactions</td></tr></tbody></table>
<table><tr><td>DEQUIN</td><td>Sylvie</td><td>DPT MICA UAR1194</td><td>MICA</td><td>Head of MICA Division</td></tr><tr><td>DEUTSCH</td><td>Stéphanie</td><td>STLO UMR1253</td><td>MICA</td><td>Food</td><td>Food microbiology, cheese, genomics, functional analysis, physiology</td></tr><tr><td>DEVEAU</td><td>Aurélie</td><td>IAM UMR1136</td><td>EFPA</td><td>Agri</td><td>Microbial ecology, tree mirobiome, plant immunity, microbe-microbe interactions</td></tr><tr><td>DRIDI</td><td>Bedis</td><td>MICALIS UMR1319</td><td>MICA</td><td>Food</td><td>Food, cheese, microbial ecology, metagenomics, genomics</td></tr><tr><td>DUGAT-BONY</td><td>Eric</td><td>GMPA UMR0782</td><td>MICA</td><td>Food</td><td>Food microbiology, microbial ecology, interactions, functional analysis</td></tr><tr><td>ELLERO-SIMATOS</td><td>Sandrine</td><td>ToxAlim UMR1331</td><td>AlimH</td><td>Digesters</td><td>Gut microbiota, toxicology, host metabolism, xenobiotics, liver</td></tr><tr><td>EVEN</td><td>Sergine</td><td>STLO UMR1253</td><td>MICA</td><td>Pathobiome</td><td>Microbial ecology, pathobiome, mammary gland microbiota, barrier effect</td></tr><tr><td>FALENTIN</td><td>Hélène</td><td>STLO UMR1253</td><td>MICA</td><td>Food</td><td>Database, food, bacteria, yeast, phenotype</td></tr><tr><td>GASC</td><td>Cyrielle</td><td>UMR MEDIS (ex EA 4678 CIDAM)</td><td>MICA</td><td>Digesters</td><td>Microbial ecology, gene capture by hybridization, metagenomics</td></tr><tr><td>GAUDRIAULT</td><td>Sophie</td><td>DGIMI UMR1333</td><td>SPE</td><td>Digesters; Pathobiome</td><td>Bacteriology, Insect Pathology, Comparative genomics, Pathobiome</td></tr><tr><td>GODON</td><td>Jean-Jacques</td><td>LBE UR0050</td><td>MICA</td><td>Digesters</td><td>Microbial ecology, biodiversity, air microbiology, biomimicry</td></tr><tr><td>HAMELIN</td><td>Jérôme</td><td>LBE UR0050</td><td>MICA</td><td>Digesters</td><td>Microbial ecology, biodiversity, biotechnology, microbial engineering, biodiversity-functionning relationship</td></tr><tr><td>HELLOIN</td><td>Emmanuelle</td><td>ISP UMR1282</td><td>MICA</td><td>Pathobiome</td><td>Microbial Biological Resource Center, pathogenic bacteria</td></tr><tr><td>HERNANDEZ RAQUET</td><td>Guillermina</td><td>LISBP UMR0792</td><td>CEPIA</td><td>Digesters; Math-Bioinfo</td><td>Biotechnology, microbial ecology, biomass valorization, lignocellulose bioconversion, bioplastic production and degradation.</td></tr><tr><td>HERRERO CORRAL</td><td>Gema</td><td>DPT MICA UAR1194</td><td>MICA</td><td></td><td>Mem international cooperation</td></tr><tr><td>ILLIKOUD</td><td>Nassima</td><td>SECALIM UMR1014</td><td>MICA</td><td>Food</td><td>Meat, seafood, microbial communities, bacterial interactions, spoilage</td></tr><tr><td>IRLINGER</td><td>Françoise</td><td>GMPA UMR0782</td><td>MICA</td><td>Food</td><td></td></tr><tr><td>JUSTE</td><td>Catherine</td><td>MICALIS UMR1319</td><td>AlimH</td><td>Digesters</td><td>Gut microbicta, functional ecology, metaproteomics, risk markers, obesity</td></tr><tr><td>KEMPF</td><td>Florent</td><td>ISP UMR1282</td><td></td><td></td><td>Bioinformatics, metagenomics, chicken gut microbiota</td></tr><tr><td>LABARTHE</td><td>Simon</td><td>MAIAGE UR1404</td><td>MIA</td><td>Digesters; Math-Modelling; Pathobiome</td><td>Mathematical Modelling, microbial ecology, metagenomics</td></tr><tr><td>LALLES</td><td>Jean-Paul</td><td>DPT ALIM.H UAR1189</td><td>AlimH</td><td>Digesters</td><td>Nutrition and gut physiology</td></tr><tr><td>LAMANDE</td><td>Sonia</td><td>ISP UMR1282</td><td>SA</td><td>Pathobiome</td><td>Immunology, neonates, intestine, parasitology</td></tr><tr><td>LAO</td><td>Julie</td><td>MAIAGE UR1404</td><td>MIA</td><td>Math-Bioinfo</td><td>Statistics, bioinformatics</td></tr><tr><td>LAROCHE</td><td>Béatrice</td><td>MAIAGE UR1404</td><td>MIA</td><td>Math-Modelling</td><td>Modelling, microbial ecology, metagenomics</td></tr><tr><td>LAVAL</td><td>Valérie</td><td>BIOGER UMR 1290</td><td>SPE</td><td>Pathobiome</td><td>Pathobiom, fungi, taxonomy, r-syst systematic network, databases, metabarcoding</td></tr><tr><td>LAVIE-RICHARD</td><td>Mathias</td><td>MICALIS UMR1319</td><td>Mica</td><td>Digesters</td><td>Fungal microbiota, IBD, ahr, fungi - bacteria interaction, mouse model</td></tr><tr><td>LE LOIR</td><td>Yves</td><td>STLO UMR1253</td><td>MICA</td><td>Pathobiome</td><td>Mammary gland microbiota, bacterial interactions, S. Aureus, probiotics</td></tr></table>
<table><tr><td>LECLERC</td><td>Marion</td><td>MICALIS UMR1319</td><td>MICA</td><td>Digesters</td><td>Human gut microbiota, omics, anaerobic culture, math modelling</td></tr><tr><td>LEGEAY</td><td>Jean</td><td>IAM UMR1136</td><td>EFPA</td><td>Agri; Math-Bioinfo</td><td>Plant pathogens, soil microbial ecology, tropical forests, oomycetes, metabarcoding</td></tr><tr><td>LEJAL</td><td>Emilie</td><td>BIPAR UMR0956</td><td>SA</td><td>Pathobiome</td><td>Vector microbiome, pathobiome, interactions between pathogens and microbiome</td></tr><tr><td>LEPAGE</td><td>Patricia</td><td>MICALIS UMR1319</td><td>AlimH</td><td>Digesters</td><td>Gut microbiome, Inflammation, Meta-omics, Drugs and Xenobiotics bacterial metabolism</td></tr><tr><td>LOUX</td><td>Valentin</td><td>MalAGE UR1404</td><td>MIA</td><td>Math-Bioinfo</td><td>Bioinformatics</td></tr><tr><td>MADZAK</td><td>Catherine</td><td>GMPA UMR0782</td><td>MICA</td><td>Food</td><td>Cheese ecosystem, yeasts, Yarrowia lipolytica, heterologous expression, transposomics</td></tr><tr><td>MAGUIN</td><td>Emmanuelle</td><td>DPT MICA UAR1194</td><td>MICA</td><td></td><td>Head of MEM Metaprogram</td></tr><tr><td>MARIADASSOU</td><td>Mahendra</td><td>MalAGE UR1404</td><td>MIA</td><td>Math-Bioinfo</td><td>Statistics, microbial ecology, ecological modeling, phylogenetics</td></tr><tr><td>MARIE-ETANCELIN</td><td>Christel</td><td>GenPhySE UMR1388</td><td>GA</td><td>Digesters</td><td>Rumen microbiota, sheep genetics, host-microbiota interaction</td></tr><tr><td>MARMEISSE</td><td>Roland</td><td>LME UMR1418</td><td>EFPA</td><td>Agri</td><td>Fungi, metatranscriptomics, organic matter degradation, environmental biotechnology, microbial ecology</td></tr><tr><td>MICHEL</td><td>Elisa</td><td>SPO UMR1083</td><td>MICA</td><td>Food</td><td>Microbial ecology, food microbiology, bakery industry, bread</td></tr><tr><td>MILFERSTEDT</td><td>Kim</td><td>LBE UR0050</td><td>MICA</td><td>Digesters</td><td>Microbial ecology, complex communities, interactions, process engineering</td></tr><tr><td>MONDY</td><td>Samuel</td><td>Agroécologie UMR1347</td><td>SPE</td><td>Agri; Math-Bioinfo; Pathobiome</td><td>Bioinformatics, soil ecology, plant-microbe interaction</td></tr><tr><td>MORGAVI</td><td>Diego</td><td>UMRH UMR1213</td><td>PHASE</td><td>Dig</td><td>Microbial ecology, ruminant, methanogenesis, host-microbe interaction</td></tr><tr><td>MORIN</td><td>Emmanuelle</td><td>IAM UMR1136</td><td>EFPA</td><td>Agri; Math-Bioinfo</td><td>Comparative genomics, metagenomics, fungal genome annotation, interactions</td></tr><tr><td>MOSONI</td><td>Pascale</td><td>MEDIS UMR0454</td><td>MICA</td><td>Digesters</td><td>Human gut microbiota, metabolism, dietary fibres, polyphenols, cultural & omics approaches</td></tr><tr><td>MOUGEL</td><td>Christophe</td><td>IGEPP UMR1349</td><td>SPE</td><td>Agri</td><td>Rhizosphere, microbial diversity, microbial ecology</td></tr><tr><td>MUNOZ TAMAYO</td><td>Rafael</td><td>MoSAR UMR0791</td><td>PHASE</td><td>Digesters; Math-Modelling</td><td>Modelling, rumen, digestion, methanogenesis, thermodynamics</td></tr><tr><td>NEDELLEC</td><td>Claire</td><td>MalAGE UR1404</td><td>MIA</td><td>Math-Bioinfo</td><td>Text mining</td></tr><tr><td>NEUVÉGLISE</td><td>Cécile</td><td>MICALIS UMR1319</td><td>MICA</td><td>Food; Pathobiome</td><td>Yeast biodiversity, comparative genomics, food environments, insects</td></tr><tr><td>NICOLAS</td><td>Aurélie</td><td>STLO UMR1253</td><td>MICA</td><td>Digesters; Math-Bioinfo; Pathobiome</td><td>Bioinformatics, metagenomics, metratranstricptomics, molecular modeling</td></tr><tr><td>NIDELET</td><td>Thibault</td><td>SPO UMR1083</td><td>MICA</td><td>Food; Math-Modelling</td><td>Enology, modeling, ecosystem, data analyse</td></tr><tr><td>NOUVEL</td><td>Xavier</td><td>IHAP UMR1225</td><td>SA</td><td>Pathobiome</td><td>Infectious disease, Animal Health, Comparative genomics, Bacteriology, Pathobiome</td></tr><tr><td>OGLIASTRO</td><td>Mylene</td><td>DGIMI UMR1333</td><td>SPE</td><td>Pathobiome</td><td>Infectious diseases, viral diversity, insect viruses, pathobiome</td></tr><tr><td>ONESIME</td><td>Djamila</td><td>MICALIS UMR1319</td><td>MICA</td><td>Food</td><td>Yeast biodiversity, comparative genomics, food environments</td></tr><tr><td>PETIT</td><td>Marie-Agnès</td><td>MICALIS UMR1319</td><td>MICA</td><td>Pathobiome; Digesters</td><td>Bacteriophages, their evolution in natural ecosystems</td></tr><tr><td>PETITEAU</td><td>David</td><td>MGP US1367</td><td>MICA</td><td>Digesters</td><td>Business developer</td></tr></table>
<table><tr><td>PEYRET</td><td>Pierre</td><td>UMR MEDIS (ex EA 4678 CIDAM)</td><td>MICA</td><td>Digesters</td><td>Microbial ecology, xenobiotics, metagenomics and metatranscriptomics, gene capture by hybridization, bioinformatics</td></tr><tr><td>PLANCADE</td><td>Sandra</td><td>MalAGE UR1404</td><td>MICA</td><td>Digesters</td><td>Statistics, modelisation, repeated measurements, heterogeneous omics data, metaproteomics</td></tr><tr><td>POLLET</td><td>Thomas</td><td>BIPAR UMR0956</td><td>SA</td><td>Pathobiome</td><td>Vector microbiome, pathobiome, interactions between pathogens and microbiome</td></tr><tr><td>RAMA RAO</td><td>Nalini</td><td>MICALIS UMR1319</td><td>MICA</td><td>Digesters; Pathobiome</td><td>Innate immunity, host-pathogen interaction, Microbiology, Pathobiome, antimicrobials</td></tr><tr><td>RAZZAUTI</td><td>Maria</td><td>CBGP UMR1062</td><td>EFPA</td><td>Pathobiome</td><td>Health ecology, zoonoses, molecular epidemiology, virome, NGS screening</td></tr><tr><td>RENAULT</td><td>Pierre</td><td>MICALIS UMR1319</td><td>MICA</td><td>Digesters; Food</td><td>Food microbiology, shotgun metagenomics, genomics, database, microbial ecology</td></tr><tr><td>REVEILLAUD</td><td>Julie</td><td>CMAEE UMR1309</td><td>SA</td><td>Pathobiome</td><td>Metabarcoding, Shotgun metagenomics, pathobiome, bacterial and viral communities</td></tr><tr><td>RHIMI</td><td>Moez</td><td>MICALIS UMR1319</td><td>MICA</td><td>Digesters</td><td></td></tr><tr><td>ROUME</td><td>Hugo</td><td>MGP US1367</td><td>MICA</td><td>Digesters</td><td>Systems biology, microbial ecology, high-throuput sequencing, gut ecosystem, bacteria</td></tr><tr><td>RUÉ</td><td>Olivier</td><td>MalAGE UR1404</td><td>MICA</td><td>Math-Bioinfo</td><td>Bioinformatics</td></tr><tr><td>RUL</td><td>Françoise</td><td>MICALIS UMR1319</td><td>MICA</td><td>Food</td><td>Food microbiology, streptococci, bacterial physiology, bacteria/host interactions, proteomics</td></tr><tr><td>SANCHIS-BORJA</td><td>Vincent</td><td>Micalis UMR1319</td><td>MICA</td><td>Agri; Pathobiome</td><td>Pathobiome, host-parasite interactions; Gastrointestinal infections, gut ecosystem, Innate immunity</td></tr><tr><td>SARNIGUET</td><td>Alain</td><td>IGEPP UMR1349</td><td>SPE</td><td>Agri; Pathobiome</td><td>Rhizosphere microbiome, plant pathobiome and plant resistance, brassicacae, metatranscriptomics</td></tr><tr><td>SAVARY-AUZELOUX</td><td>Isabelle</td><td>UNH UMR1019</td><td>AlimH</td><td>Food</td><td>Food, nutrition, metabolic diseases</td></tr><tr><td>SAVOIE</td><td>Jean-Michel</td><td>MycSA UR1264</td><td>SPE</td><td>Agri; Pathobiome</td><td>Kernels and grain microbiome, fungal interactions, mycotoxins,</td></tr><tr><td>SCHBATH</td><td>Sophie</td><td>MAAGE UR1404</td><td>MIA</td><td>Math-Bioinfo;</td><td>Statistics, bioinformatics</td></tr><tr><td>SERROR</td><td>Pascale</td><td>MICALIS UMR1319</td><td>MICA</td><td>Pathobiome</td><td>Bacterial adaptation and pathogenesis, colonisation resistance, intestinal microbiota</td></tr><tr><td>SICARD</td><td>Delphine</td><td>SPO UMR1083</td><td>MICA</td><td>Food</td><td>Yeasts adaptation and evolution, food microbiota, microbial interactions, domestication, bakery</td></tr><tr><td>TAYEB</td><td>Jean</td><td>FARE UMR0614</td><td>CEPIA</td><td>Digesters</td><td>Biomass deconstruction, anaerobic consortia</td></tr><tr><td>THIERRY</td><td>Anne</td><td>STLO UMR1253</td><td>MICA</td><td>Food</td><td>Food microbiology, flavour chemistry, cheese ripening, metabolism, bacterial interactions</td></tr><tr><td>VACHER</td><td>Corinne</td><td>BIOGECO UMR1202</td><td>EFPA</td><td>Agri; Pathobiome</td><td>Plant microbiota, ecological networks, pathobiome, phyllosphere, metabarcoding</td></tr><tr><td>VALENCE-BERTEL</td><td>Florence</td><td>STLO UMR1253</td><td>MICA</td><td>Food</td><td>Biological Ressource Center, fermented food related bacteria, biodiversity, database, taxonomy</td></tr><tr><td>VAYSSIER-TAUSSAT</td><td>Muriel</td><td>BIPAR UMR0956</td><td>SA</td><td>Pathobiome</td><td>Vector microbiome, pathobiome, interactions between pathogens and microbiome</td></tr><tr><td>VELGE</td><td>Philippe</td><td>ISP UMR1282</td><td>MICA</td><td>Pathobiome</td><td>Salmonella, chicken, pathobiome, virulence, carrier state</td></tr><tr><td>ZAGOREC</td><td>Monique</td><td>SECALIM UMR1014</td><td>MICA</td><td>Food</td><td>Meat, microbial communities, bacterial interactions, spoilage, biopreservation</td></tr><tr><td>ZEMB</td><td>Olivier</td><td>GenPhySE UMR1388</td><td>PHASE</td><td>Digesters</td><td>Gut microbiota rabbit pig broiler</td></tr></table>
MEM Steering Committee: Management and Support

(January 2017)

<figure><img src="image_8.png" /><figcaption>**Emmanuelle MAGUIN**
Head of the MEM
metaprogramme
Jouy-en-Josas</figcaption></figure>

<figure><img src="image_9.png" /><figcaption>**Sylvie DEQUIN**
Head of the MICA
Division
Montpellier</figcaption></figure>

<figure><img src="image_10.png" /><figcaption>**Gema HERRERO CORRAL**
International Cooperation
Jouy-en-Josas</figcaption></figure>

<figure><img src="image_11.png" /><figcaption>**Danielle CANCEILL**
Project Manager
Jouy-en-Josas</figcaption></figure>

mem@inra.fr

Former members:
Sandrine Ayuso (2011-13)
Sophie Lebonvallet (2012-2016)

MEM Steering Committee: Members

(January 2017)

<figure><img src="image_12.png" /></figure>
MEM Scientific Advisory Board:

<figure><img src="image_13.png" /></figure>

✓

Headed by Christine Cherbut, INRA Scientific Director (Food, Nutrition & Bioeconomy)

International experts :

<table><thead><tr><td>Name</td><td>Institute</td><td>Research topics</td><td></td><td>Present at the MEM Days</td></tr></thead><tbody><tr><td>Graeme ATTWOOD</td><td>AgResearch (NZ)</td><td>Animal digesters. Rumen microbiology. Greenhouse gases.</td><td></td><td>✓</td></tr><tr><td>Tom CURTIS</td><td>Newcastle University (UK)</td><td>Biological Treatment Systems. Experimental and Theoretical Microbial Ecology. Artificial digesters, process, modelling.</td><td></td><td>✓</td></tr><tr><td>Denis DOCHAIN</td><td>Université catholique de Louvain (BE)</td><td>Maths. Modelling, analysis, design, monitoring and control of reaction systems.</td><td></td><td></td></tr><tr><td>Danilo ERCOLINI</td><td>University of Naples (IT)</td><td>Food microbiology. Microbial ecology of fermented foods.</td><td></td><td></td></tr><tr><td>Nikos KYRPIDES</td><td>DOE - Joint Genome Institute (USA)</td><td>Genome Biology. Bioinformatics. Sequencing.</td><td></td><td>✓</td></tr><tr><td>Anna-Liisa LAINE</td><td>University of Helsinki (FI)</td><td>Host-pathogen evolution. Evolutionary epidemiology. Trophic interactions.</td><td></td><td>✓</td></tr><tr><td>Vitor MARTINS DOS SANTOS</td><td>Wageningen University (NL)</td><td>Systems biology. Bacteria and ecosystems modelling.</td><td></td><td></td></tr><tr><td>Mark MORRISON</td><td>University of Queensland Diamantina Institute (AU)</td><td>Microbial Biology and Metagenomics. Human and animal microbiota (Flagship).</td><td></td><td>✓</td></tr><tr><td>Hans VAN VEEN</td><td>Netherlands Institute of Ecology, Wageningen (NL)</td><td>Microbial ecology of terrestrial ecosystems.</td><td></td><td></td></tr></tbody></table>

<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>

<figure><img src="image_19.png" /></figure>

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>

<figure><img src="image_22.png" /></figure>
Origin of the 112 participants at the 2017 MEM days:

<figure><img src="image_23.png" /></figure>

INRA Scientific Divisions represented at the MEM Days:

* AlimH: Nutrition, Chemical Food Safety and Consumer Behaviour

* CEPIA: Science and Process Engineering of Agricultural Products

* EFPA: Forest, Grassland and Freshwater Ecology

* GA: Animal Genetics

* MIA: Applied Mathematics and Informatics

* MICA: Microbiology and the Food Chain

* PHASE: Animal Physiology and Livestock Systems

* SA: Animal Health

* SPE: Plant Health and Environment

Scientific Committee of the 2017 MEM Days:

<table><thead><tr><th>MEM Project Manager</th><th>Danielle CANCEILL</th><th>DPT MICA (Jouy-en-Josas)</th></tr><tr><th>MEM Thematic Group</th><th>Name</th><th>Unit (City)</th><th>INRA Division</th></tr></thead><tbody><tr><td>Agri</td><td>Corinne VACHER</td><td>BIOGECO (Bordeaux)</td><td>EFPA</td></tr><tr><td>Agri</td><td>Aurélie DEVEAU</td><td>IAM (Nancy)</td><td>EFPA</td></tr><tr><td>Digesters</td><td>Mathias LAVIE-RICHARD</td><td>MICALIS (Jouy)</td><td>MICA</td></tr><tr><td>Digesters</td><td>Sandrine ELLERO-SIMATOS</td><td>TOXALIM (Toulouse)</td><td>AlimH</td></tr><tr><td>Food</td><td>Christophe CHASSARD</td><td>UMRF (Clermont)</td><td>MICA</td></tr><tr><td>Food</td><td>Hélène FALENTIN</td><td>STLO (Rennes)</td><td>MICA</td></tr><tr><td>Food/Math-Modelling</td><td>Thibault NIDELET</td><td>SPO (Montpellier)</td><td>MICA</td></tr><tr><td>Math-Modelling</td><td>Simon LABARTHE</td><td>MAIAGE (Jouy)</td><td>MIA</td></tr><tr><td>Math-Bioinfo Stats</td><td>Mahendra MARIADASSOU</td><td>MAIAGE (Jouy)</td><td>MIA</td></tr><tr><td>Pathobiome</td><td>Pascale SERROR</td><td>MICALIS (Jouy)</td><td>MICA</td></tr><tr><td>Pathobiome</td><td>Matthieu BARRET</td><td>IRHS (Angers)</td><td>SPE</td></tr><tr><td>Pathobiome</td><td>Julie REVEILLAUD</td><td>CMAEE (Montpellier)</td><td>SA</td></tr></tbody></table>

https://intranet.inra.fr/mem