Intestinal microbiota opportunities and scientific challenges. Prof. V. Delcenserie Food Science Department Veterinary Medicine Faculty

Transcription

1 Intestinal microbiota opportunities and scientific challenges Prof. V. Delcenserie Food Science Department Veterinary Medicine Faculty

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4 Plan Introduction What is intestinal microbiota? What is its function? Opportunities links between microbiota and health Challenges modelisation of intestinal microbiota Laboratory applications Discussion/conclusion ULg Faculté de Médecine Vétérinaire - FARAH 4

5 Plan Introduction What is intestinal microbiota? What is its function? Opportunities links between microbiota and health Challenges modelisation of intestinal microbiota Laboratory applications Discussion/conclusion ULg Faculté de Médecine Vétérinaire - FARAH 5

6 Intestinal microbiota?

7 Stomach < 10 3 cells/g Titre de ma présentation Intestinal microbiota? Small intestine cells/g Proximal colon cells/g Transverse colon cells/g Distal colon > cells/g G.Enders and J. Enders,

8 Intestinal microbiota? Arumugam et al., Nature May 12; 473(7346):

9 Metabolome? Metabolic important functions exerted by bacteria Vitamins production Short chain fatty acids (SCFAs) production Amino acid (Aas) synthesis Bile acid biotransformation Hydrolysis and fermentation of non-digestible substrates ULg Faculté de Médecine Vétérinaire - FARAH 9

10 SCFAs production: the main actors Lactic acid butyrate Titre de ma présentation One example Lactic acid LAB Firmicutes: Clostridial clusters IV, XIVa and Lactobacillus Firmicutes: clostridial cluster IX Lactic acid propionate Eubacterium Roseburia Faecalibacterium Coprococcus spp. SCFAs production Actinobacteria: bifidobacteria Acetate Butyrate Propionate Inulin Arabinoxylan Rivière et al., 2016 Vernocchi et al., 2016 Frontiers in Microbiology

11 Plan Introduction What is intestinal microbiota? What is its function? Opportunities links between microbiota and health Challenges modelisation of intestinal microbiota Laboratory applications Discussion/conclusion ULg Faculté de Médecine Vétérinaire - FARAH 11

12 Opportunities Vernocchi et al., 2016 In Frontiers in Microbiology

13 Opportunities Studies linking intestinal microbiota and diseases Croh n disease Ulcerative colitis Irritable bowel syndrome Celiac disease Clostridium difficile infection Colorectal cancer Allergy/ato py Obesity Diabete ULg Faculté de Médecine Vétérinaire - FARAH 13

14 Plan Introduction What is intestinal microbiota? What is its function? Opportunities links between microbiota and health Challenges modelisation of intestinal microbiota Laboratory applications Discussion/conclusion ULg Faculté de Médecine Vétérinaire - FARAH 14

15 Intestinal modeling Titre de ma présentation Challenge G.Enders and J. Enders,

16 Evolution of the Titre different de ma présentation models

17 Example: Chemostat (Dworkin 2006) ULg Faculté de Médecine Vétérinaire - FARAH 17

18 Evolution of the Titre different de ma présentation models Mc Donald, 2013

19 Example: Robogut ULg Faculté de Médecine Vétérinaire - FARAH 19

20 Evolution of the Titre different de ma présentation models Mc Donald, 2013

21 Example: TNO Intestinal Model 1 (TIM1) (McDonald thesis 2013) (Bioresource tech. 2010;101:7966) (Ouwehand. Gastrointestinal Microbiology 2006) ULg Faculté de Médecine Vétérinaire - FARAH 21

22 Example: TNO Intestinal Model 2 (TIM2) (Van Nuenen 2005) ULg Faculté de Médecine Vétérinaire - FARAH 22

23 Evolution of the Titre different de ma présentation models Mc Donald, 2013

24 SHIME model - 6 bioreactors controlled by informatics and able to mimic conditions found in: - Stomach - duodenum/jejunum - ileum, caecum - Ascending, transversal and descending colon (Van den Abbeele et al., 2010). - The collect and analysis of samples are possible at each stage of digestion (Ex: Microbiota analysis, short chain fatty acid, lactate, other biomarkers...) - Low restriction regarding ethical procedure compared to in vivo trials - Interaction with microbiota

25 Challenges: limitations of the model No mucus layer No epithelial cells or immune cells No absorption Human only? M- SHIME «HMI» module Dialysis Infant/a nimal Van den Abbeele et al., 2013 Marzorati et al., 2014 ULg Faculté de Médecine Vétérinaire - FARAH 25

26 Challenges: limitations of the model No mucus layer No epithelial cells or immune cells M-SHIME «HMI» module No absorption Dialysis Human only? Infant/animal ULg Faculté de Médecine Vétérinaire - FARAH 26

27 Plan Introduction What is intestinal microbiota? What is its function? Opportunities links between microbiota and health Challenges modelisation of intestinal microbiota Laboratory applications Discussion/conclusion ULg Faculté de Médecine Vétérinaire - FARAH 27

28 Applications Titre de ma présentation in the lab Project Babygut (V.Delcenserie, P. Bondue) Bifidobacterium infantis, B. mongoliense or B. crudilactis Possess genes encoding for: - sialidases - fucosidases Delcenserie et al., 2007 Lugli et al., 2014 Milani et al., 2014 Objective 1: bifidobacteria able to grow on media supplemented with BMO? Objective 2: Production of antimicrobial component in culture supernatant? (Virulence expression metatranscription) Objective 3: gastrointestinal model testing

29 Applications Titre de ma présentation in the lab Objective 1 Breastfed infant feces Raw milk cheese B. bifidum B. crudilactis Delcenserie et al., 2007 Lugli et al., 2014 Milani et al., 2014 Fermentation 48 h at 37 C 10 % H 2, 10 % Co 2, 80 % N 2 Media supplemented in 3 siallylactose 0 h, 24 h et 48 h D.O. Counting

30 Applications Titre de ma présentation in the lab Objective 2 Breastfed infant feces Raw milk cheese B. bifidum B. crudilactis Fermentation 48 h at 37 C 10 % H 2, 10 % Co 2, 80 % N 2 Media supplemented in 3 siallylactose Centrifugation and filtration to collect the Cell-Free Spent Media Challenge against E. coli O157:H7 and Salmonella Typhimurium Medellin-Pena et al., 2007 Bayoumi and Griffiths, 2010 Zeinhom et al., 2012 Measure effects on virulence gene expression

31 Applications Titre de ma présentation in the lab Effect on E. coli O157:H7 Relative gene expression ratio ler A flic luxs stxb2 qsea Relative gene expression ratio ler flic luxs stxb2 qsea B Relative gene expression ratio ler flic luxs stxb2 qsea -25 C Relative gene expression ratio D ** * * ** ler flic luxs stxb2 qsea Bondue et al., 2016 Frontiers in Microbiology Effect of CFSM MRS2 G (A), MRS2 (B), MRS2 Wh (C), MRS2 3 SL (D) on virulence expression of E. coli O157:H7 Light grey: B. bifidum Dark grey: B. crudilactis

32 Applications Titre de ma présentation in the lab Effect on S. Typhimurium Expression relative des gènes de virulence 0,0-5,0-10,0-15,0 * * hila ssrb2 sopd Bifidobacterium bifidum * Expression relative des gènes de virulence 5,0 0,0-5,0-10,0 * * hila ssrb2 sopd Bifidobacterium bifidum Bifidobacterium crudilactis Bifidobacterium crudilactis Effect of CFSM MRS2 G on virulence expression of S. Typhimurium Effect of CFSM MRS2-3 SL on virulence expression of S. Typhimurium Bondue et al., 2016 Frontiers in Microbiology

33 Applications Titre de ma présentation in the lab Objective 3 Model adaptation: - Small volumes - Diet + bifidobacteria - Effect on intestinal microbiota (NGS, Arisa) - Production of SCFA - Effect on virulence expression of E. coli O157:H7 and S. Typhimurium

34 Applications Titre de ma présentation in the lab Project Copropig Effect of apple by-product on piglet intestinal health during weaning (FARAH, GxABT and CRAw) Model adaptation: - Before weaning - After weaning Apple byproduct in piglet feeding Testing in gastrointestinal model «Piglet SHIME» - Effect on intestinal microbiota (NGS, Arisa) - Effect on intestinal biomarkers - Production of SCFA

35 Applications Titre de ma présentation in the lab First results... ULg Faculté de Médecine Vétérinaire - FARAH 35

36 Applications Titre de ma présentation in the lab First results... - Same trend than litterature for ascending colon - Opposite for ileon ULg Faculté de Médecine Vétérinaire - FARAH 36

37 Discussion and conclusion ULg Faculté de Médecine Vétérinaire - FARAH 37

38 Discussion and conclusion Gastrointestinal model: biomarkers identification Stability and repeatability of the models Continuous improvement of the model Omics Whole Genome Sequencing ULg Faculté de Médecine Vétérinaire - FARAH 38

39 Acknowledgements SHIME team!! 39