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TABLE OF CONTENTS

1 Towards an understanding of microbial ecosystems 1

1.1 Introduction . . . 1

1.2 Reconstructing microbial networks . . . 3

1.3 Dynamics and stability of microbiota . . . 10

1.4 Aim of our research . . . 20

References . . . 21

2 Modeling microbial populations: a toolbox 33 2.1 Growth of a microbial population . . . 35

2.2 Interspecies interactions and community dynamics . . . 48

2.3 Spatially extended models . . . 59

2.4 Other approaches . . . 64

References . . . 66

3 Construction of a predictive model for microbial growth in a synthetic gut community 75 3.1 Problem statement . . . 75

3.2 Summary . . . 76

References . . . 78

3.3 Publication 1: Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community . . . 80

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4 Reduction of nutrient-explicit equations 111

4.1 Problem statement . . . 111

4.2 Summary . . . 113

4.3 Manuscripts . . . 116

5 A spatial model of cooperation 145 5.1 Problem statement . . . 145

5.2 Reduction of the spatial mutualistic system to the Nagumo equation . . . 147

5.3 The Nagumo equation predicts long-term behavior of the mutualistic system 153 5.4 Length and time scales determine the dynamics . . . 157

5.5 Numerical simulations confirm theoretical predictions . . . 159

5.6 Discussion . . . 160

References . . . 162

6 Conclusions 167 References . . . 171 Appendices

Appendix A Supplementary material of Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations (section 4.3.1) 177 Appendix B Supplementary material of Mutualistic cross-feeding in

mi-crobial systems generates bistability via an Allee effect (section 4.3.2) 185 Appendix C Supplementary material of A spatial model of cooperation 201 Appendix D Excitable dynamics through toxin-induced mRNA cleavage

in bacteria 211

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