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Akkermansia Muciniphila for Its Future Application Paranymphs Steven Aalvink E a P L I C [email protected]

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Akkermansia Muciniphila for Its Future Application Paranymphs Steven Aalvink E a P L I C Steven.Aalvink@Wur.Nl M e t a b Invitation o l i c c h You are kindly invited to a r a attend the public defense c t e of my PhD thesis r i z a t i o n a Metabolic n d v characterization i a b l e and viable delivery of d e l Akkermansia i v e r y muciniphila o f A for its future application k k e r m Monday, January 22, 2018 a n at 4 pm in the Aula of s i a Wageningen University m Generaal Foulkesweg 1A, u c Metabolic characterization Wageningen i n i p h and viable delivery of i Kees C. H. van der Ark l a f [email protected] o r Akkermansia muciniphila i t s f u Paranymphs t for its future application u r Steven Aalvink e a [email protected] p p l i c a Hugo de Vries t i o [email protected] n 2 0 Kees C. H. van der Ark 1 8 Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application Kees C.H. van der Ark Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application Kees C.H. van der Ark Thesis committee Promotor Prof. Dr Willem M. de Vos Professor of Microbiology Wageningen University & Research Thesis Co-promotor Dr Clara Belzer submitted in fulfilment of the requirements for the degree of doctor Assistant professor, Laboratory of Microbiology at Wageningen University Wageningen University & Research by the authority of the Rector Magnificus, Other members Prof. Dr A.P.J. Mol, Prof. Dr E.J. Smid, Wageningen University & Research in the presence of the Dr N. Juge, Institute of Food Research, Norwich, United Kingdom Thesis Committee appointed by the Academic Board Dr H.J.M. Harmsen, University of Groningen to be defended in public Dr M. Derrien, Danone, Paris, France on Monday 22 January 2018 at 4 p.m. in the Aula. This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences) Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application Kees C.H. van der Ark Thesis committee Promotor Prof. Dr Willem M. de Vos Professor of Microbiology Wageningen University & Research Thesis Co-promotor Dr Clara Belzer submitted in fulfilment of the requirements for the degree of doctor Assistant professor, Laboratory of Microbiology at Wageningen University Wageningen University & Research by the authority of the Rector Magnificus, Other members Prof. Dr A.P.J. Mol, Prof. Dr E.J. Smid, Wageningen University & Research in the presence of the Dr N. Juge, Institute of Food Research, Norwich, United Kingdom Thesis Committee appointed by the Academic Board Dr H.J.M. Harmsen, University of Groningen to be defended in public Dr M. Derrien, Danone, Paris, France on Monday 22 January 2018 at 4 p.m. in the Aula. This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences) Table of content Chapter 1. General introduction and thesis outline................................................................ 7 Chapter 2. More than just a gut feeling: Constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes.............................................................. 39 Chapter 3. Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation. ................................................................................................................ 69 Chapter 4. The influence of an animal component free medium on cell morphology and therapeutic efficacy of Akkermansia muciniphila................................................................ 97 Chapter 5. Adaptation of Akkermansia muciniphila to the oxic-anoxic interface of the mucus layer ................................................................................................................................... 125 Chapter 6. Encapsulation of the therapeutic microbe Akkermansia muciniphila in a double emulsion enhances survival in simulated gastric conditions.............................................. 171 Chapter 7. General Discussion........................................................................................... 199 Summary............................................................................................................................ 225 Samenvatting ..................................................................................................................... 228 About the author ................................................................................................................ 231 Acknowledgements............................................................................................................ 232 Kees C.H. van der Ark List of Publications............................................................................................................ 234 Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application, Overview of Completed training activities ........................................................................ 235 236 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2018) With references, with summaries in English and Dutch DOI: 10.18174/427507 ISBN: 978-94-6343-825-4 Table of content Chapter 1. General introduction and thesis outline................................................................ 7 Chapter 2. More than just a gut feeling: Constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes.............................................................. 39 Chapter 3. Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation. ................................................................................................................ 69 Chapter 4. The influence of an animal component free medium on cell morphology and therapeutic efficacy of Akkermansia muciniphila................................................................ 97 Chapter 5. Adaptation of Akkermansia muciniphila to the oxic-anoxic interface of the mucus layer ................................................................................................................................... 125 Chapter 6. Encapsulation of the therapeutic microbe Akkermansia muciniphila in a double emulsion enhances survival in simulated gastric conditions.............................................. 171 Chapter 7. General Discussion........................................................................................... 199 Summary............................................................................................................................ 225 Samenvatting ..................................................................................................................... 228 About the author ................................................................................................................ 231 Acknowledgements............................................................................................................ 232 Kees C.H. van der Ark List of Publications............................................................................................................ 234 Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application, Overview of Completed training activities ........................................................................ 235 236 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2018) With references, with summaries in English and Dutch DOI: 10.18174/427507 ISBN: 978-94-6343-825-4 CHAPTER 1 GENERAL INTRODUCTION AND THESIS OUTLINE Chapter 1. General Introduction cells per gram of faeces for that of Archaea. The amount of eukaryotic cells is approximately General Introduction 100-1000 fold lower than bacteria and includes protozoa, fungi and multicellular helminths This thesis deals with the physiology, growth and application strategy of Akkermansia (Berg, 1996, Sender, et al., 2016, Hugon, et al., 2017). It is estimated that the amount of muciniphila (Figure 1). This intestinal bacterium lives in the colon of most humans and bacteria is similar to the amount of cells in an average human body (Sender, et al., 2016). mammals, and degrades the mucus that is produced by the specialised epithelial goblet cells of the host. A. muciniphila is highly specialised in degrading mucus, hence the species name The number of cultured microbial species from the gut has been reviewed and found to reach muciniphila, which loosely translates as ‘loving mucin’. The genus name Akkermansia over 1000 (Rajilic-Stojanovic and de Vos, 2014). This number will rapidly increase by the derives from Dr. Antoon Akkermans, who was leading the Microbial Ecology group of the recent isolation of hundreds of new candidate species by high throughput methods (Browne, Laboratory of Microbiology at Wageningen University at the time A. muciniphila was et al., 2016, Lagier, et al., 2016). The number of prokaryotic species in the gut based on isolated and published (Derrien, et al., 2004). Here an introduction is provided into the role systematic mining of 16S rRNA gene libraries was recently estimated to amount to of the intestinal microbiota in health and disease with specific attention for A. muciniphila, approximately 2500 (Ritari, et al., 2015). This would suggest that over half of the bacterial its properties and impact. In addition, an overview is provided of approaches
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