The human gut acts as a host to vast populations of microorganisms such as bacteria, viruses, archaea, and fungi. All these microorganisms together residing in the human gut are called the Human Gut Microbiome (HGM). Years of attention and research have already elucidated that the health of the HGM is tightly correlated with the overall health of the individual. Especially the commensal bacteria have shown to influence the food metabolism, nutrient uptake, energy homeostasis, epithelial barrier integrity, host immunological response, and the protection against colonization of pathogens.
The functional role of other key microorganisms in the HGM has, however, not been studied in as much detail, if at all. Fungi are often overlooked yet repeatedly found in observational studies. In this research, we aim to elucidate the functional role that some of the most common yeasts have in the HGM and how it affects the other microorganisms by using a synthetic consortium of HGM bacteria. Furthermore, to investigate the effect of these yeasts when combined with the synthetic consortium on the host, a novel gut on a chip model is used.
To understand the functional roles and interactions of the species in the synthetis consortium, we use both species interactions models and genome-scale metabolic models in addition to in vitro experiments. With species interaction model we identify complex structures from data of pairwise interactions. The genome-scale metabolic models are used to identify the metabolic potential of the different species, both to identify their nutrient requirements as to identify potential interactions.
Scientist involved in this project
Pim van Leeuwen
- Thesis: Analyzing and visualizing molecular events in bacterial spore germination
J. Wen, 7 October 2020, UvA-DARE (Digital Academic Repository)
- Artificial Sporulation Induction (ASI) by kinA Overexpression Affects the Proteomes and Properties of Bacillus subtilis Spores
Tu, Z.; R. Abhyankar, W.; N. Swarge, B.; van der Wel, N.; Kramer, G.; Brul, S.; J. de Koning, L. Int. J. Mol. Sci. 2020, 21, 4315.
- A live-cell super-resolution technique demonstrated by imaging germinosomes in wild-type bacterial spores
Breedijk, R.M.P., Wen, J., Krishnaswami, . et al. Sci Rep 10, 5312 (2020). https://doi.org/10.1038/s41598-020-62377-1
- Fungal-Bacterial Interactions in Health and Disease
Krüger W, Vielreicher S, Kapitan M, Jacobsen ID, Niemiec MJ. Pathogens (Basel, Switzerland). 2019 May;8(2).
- Interspecies Interactions between Clostridium difficile and Candida albicans
van Leeuwen PT, van der Peet JM, Bikker FJ, et al. mSphere. 2016;1(6):e00187-16. Published 2016 Nov 9.
- The gut microbiome
- Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
Kevin D’hoe, Stefan Vet, Karoline Faust, Frédéric Moens, Gwen Falony, Didier Gonze, Verónica Lloréns-Rico, Lendert Gelens, Jan Danckaert, Luc De Vuyst, Jeroen Raes, eLife 2018;7:e37090