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L'université De Nantes Comue Universite Bretagne Loire T HESE DE DOCTORAT DE L'UNIVERSITÉ DE NANTES COMUE UNIVERSITE BRETAGNE LOIRE ÉCOLE DOCTORALE N° 600 École doctorale : Écologie, Géosciences, Agronomie et Alimentation Spécialité : Microbiologie, virologie et parasitologie Par Nassima ILLIKOUD Caractérisation des mécanismes d’altération des produits carnés et de la mer par Brochothrix thermosphacta Approches phénotypique, génomique, transcriptomique et analyse du volatilome Thèse présentée et soutenue à Oniris, Nantes, le 9 juillet 2018 Unité de recherche : UMR 1014, INRA, Oniris, Université Bretagne-Loire Composition du Jury : Président Michel DION Professeur, Université de Nantes, France Rapporteurs Christophe CHASSARD Directeur de recherche, INRA, Clermont-Ferrand, France Marie-Christine CHAMPOMIER-VERGÈS Directrice de recherche, INRA, Jouy-en-Josas, France Examinateur Anne-Marie REVOL-JUNELLES Professeur, Université de Lorraine, France Directeur de thèse Monique ZAGOREC Directrice de Recherche, INRA, Nantes, France Co-encadrant de thèse Emmanuel JAFFRÈS Maître de conférences, Oniris, Nantes, France Invités Marie-France PILET Professeur, Oniris, Nantes, France Yves LE LOIR Directeur de recherche, INRA, Rennes, France « La réussite est l’accuulatio d’échecs, d’erreurs, de faux départs, de confusions, et la volonté de continuer malgré tout. » Nick Gleason Je ddie cette thse à ma me et ma sœu qui nous ont uitts top tôt… w w W W / / a/ / ! " W ! #a w W a 5 % & & ' W I t aC t '' + W a , -! W + ! ' ! ! , W ! . W'' a C t . , + , , ' aC t , , b W ! + ! w! 0 I C ' + ', ' a ! 1! /2 " 3 4 w#! ' . ! wt/w tCD. W+ ! ' ! , 7 a 5 8 w 9 D :# 1 !; D/<a1 a ! ' , , , W ! 0 / w / :. ' & a ! h ; ! a#&540hC W ' aD 5 w ! ! .' t ' 5 . + , " ! W / a! , a Wa / ! ! > # w aD 1 , " " a + tCD. w :, ' 0 + ??; a ! #! . + ! > ! 4 / , 1 a ! t , ! W ! >aw + W ! , , 1 , @ ! W 1 b & , ! > 7 . A 1 a w ' #2 w b . 5 b # D ! ! W 0 , > w ! a 9 @ W # &+ ' ! a D ! '' #05 .' W ! .' ' ' B , , , + , > , ! 0 w 0 & & + + & '! + 4 ! C / C 1 !, D CC & D CCC D CCE t F CE # !, '! G CEC & G CEE 3 ', H CEI 4' CC CI . !, CD CIC 4 CJ CIE 0+ CK CII / ! ' . CH CIIC I CH CIIE D ' EC CID C '' ! ! L ' . EE CIF 4 ' EE CIJ 1 ! ' . EF CIJC t ' EF CIJE t ' . ! :.# ; ID CIG 1 ! ' '! ! . ' ! ID CIGC . ID CIGE t IJ CIGI t IJ CIK D ' . IG CIH / IH CD 1 ! 2 . DE CDC # ! , , DD CDE # ! , DD CDI # ' DF / E 5 ! , , . DK EC t DK EE D 2 ' ' ! . DH EEC 4 FM EEE a FE EEEC . ! L FE EEEE 1! L . FF EEEI 5b# + FF EEED . ' ! t/w FF EEEF CJ1 5b# ,! FJ EEEJ a#&540hC FJ EEEG wt/w FG EEEK tCD. FG EEEH # < FK EEECM 1 FH EEI w JM EEIC / ' . JM EEIE . ' t/w JM EEII / 2 ' ! JC EEID # JD EED 5 JG EEF / GM EI / , ' GF / I / ! . GG IC t GG IE h ' ! , ' ' . /5 IIG 0#t CGF .1#1C I ..t IMGM GG IEC # GK IEE 4 GH IEI h! 4' KM IEIC / ' ' KM IEIE .+ ' KF IED D ,! ' KF IEDC D KF IEDE D L ! 5b# KJ IEDI D ,! KG IEDD D KG IEF D t KK IEJ 4 ! ' ! , HE IEG / CMC II w CCF ID / , ' CCJ / D # ' . CCK DC t CCK DE 0 ' ' ! . CEM DEC 4 CEM DEE a CEC DEEC . ! L CEC DEEE a CEE DEEI /! CEE DEED h! / : h/ ; CEE DEEF wb# ,! CEI DEEJ 0 CED DEI w CEF DEIC . ! L ' CEF DEIE I ! ! CEJ DEII ! CEG DEID / 2 ' '' + ! CEK DEIF D ' ! CIM DEIJ D ' ! CIJ DED / CIH DI / , ' CDG 5 ! CDK + CFI w' !, CFF ! & #5b # 5 + , #b4 #! b 4 #bh # # ' #wb # w , #L 8 # .# . ! # .I4 . I 4' .&#10 . & #! 1 0 5b# 5 + # /51 / ! 5b# 1, /C> / C ! > /hD / ' h ! D ' /w41tw / w! 4 1 t w 5. 5'' + .a.& . a . ! & .b# . b # C#h C #! h!2 C/ ' ! D/<a1 D / ! a 1 4/CaI 4 / ' C a ! I! 4Cw.a.w 4 CN w .+ a 4bw# 4 b w #! , 41h 4 h!2 ' 1 2 O.DD O . ' D D &#. & # . <. &. & . a#&540hC a +# & 5 <4 2 0 ' C! a#t a ' # t9!!<t9! a51 a 1! ! a4/C#a a 1 C a&10 a & 1, 0! b#5 b # 5 b#5t b # 5 t b/.4 b / ' . ! 4' h./5 h!2 ' . / 5 t. t' . 1 t t/# t / #! t/w t / w tCD. t C D . I t ! t9D5. t 9 D 5 . t01 t ' 1 wt/w w . t/w wb# , wb# 1,! wb# w wb# 15 1 5 11h 1' 1 ! h! 10## 1 0 # #! 0#. 0 . .50# t t 0.. 0 . .50# 0 0 ., / 0a# 0 wb# 0 ' wb# >C/ > C / >aw > a+ w >tDa# >L! tD a ! #! h/ h! / t t9!! & + 0 CC / ,, D 0 CE # ' ' ! L ' . EI 0 CI a '' . ' ! ! EI 0 CD h! / : h/ ; . EG 0 CF D L ' . . IH 0 EC . FD 0 IC / ' ! ' ' . /5 IIG 0#t CGF .1#1C CI ..t IMGM KC 0 IE t ' KJ 0 II D HM 0 ID b ' ! L ! /hD ' ! HC 0 IF & ' . /5 IIG ' ! CMI 0 IJ & ' . .4 ' ! CCC 0 IG & ' . .44 ' ! CCI 0 IK & ' /w41tw ! ' /5 IIG .1#1C I 0#t CGF CCD 0 DC h/ ' : ; ' ! L ' . /5 IIG 0#t CGF CEK 0 DE 1 ' wb# , CEH 0 DI D ! /5 IIG 0#t CGF CDM 0 DD D ! /5IIG 0#t CGF CDI + & '! C! CC . + :CHJC P EMCI; F C! CE . ! ! ' B' ! J C! CI 3 ' ', 9! H C! CD w , '' ' CM C! CF t ! ' . ! ' . . CH C! CJ 1 ! ' . DC C! CG 5 + + . DI C! EC 1' ' ' t/w JC C! EE a ! ' t/w tCD. JD C! EI # .
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