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Intestinal Microbiology


These are exiting times to study gut bacteria. The microbes in our gut might have a tremendous impact on our health and well-being: Multiple studies have shown that different diseases are associated with changes in the composition of this microbiota. At the same time, astonishing progress in molecular and cellular biology – strongly driven by the advancement of molecular and omics techniques – has given us for the first time a more comprehensive understanding how a single bacterial cell functions and growths.  Building on this knowledge, we are studying the growth physiology of different gut bacteria. We aim to understand how the growth behaviors of different strains affect composition of the gut microbiota and couple into the interactions of the microbiota with the human host. We are doing this by combining a set of different tools, including state of the art anaerobic cultivation techniques to quantify bacterial growth and inter-species interactions, in-vitro setups to emulate intestinal flow and its effect on growth, and simulation techniques to integrate the specifics of human intestinal physiology when studying host-microbe interactions.

Figure summarizing the ecological context of gut bacteria and their physiology


As part of the Talks in English seminar series by the Bio-X this talk introduces our view: "Grow with the flow" - an introduction to our gut microbiota research. 


Intestinal flow and pH shape the human gut microbiota

In published studies we focused primarily on the growth dynamics of primary fermenters in the gut which can degrade starch and fibers. To understand the growth dynamics of these strains, one has to consider intestinal flow dynamics. Local acidity and varying pH values are also important in determining the growth of different bacterial strains. 

Markus Arnoldini*, Jonas Cremer*, Terence Hwa: Bacterial growth, flow, and mixing shape human gut microbiota density and compositionIn: Gut Microbes, (6), pp. 559–566, 2018.
Jonas Cremer*, Markus Arnoldini*, Terence Hwa: Effect of water flow and chemical environment on microbiota growth and composition in the human colonIn: Proceedings of the National Academy of Science of the United States of America, 114 (25), pp. 6438–6443, 2017.
Jonas Cremer*, Igor Segota*, Chih-yu Yang, Markus Arnoldini, John T Sauls, Zhongge Zhang, Edgar Gutierrez, Alex Groisman, Terence Hwa: Effect of flow and peristaltic mixing on bacterial growth in a gut-like channelIn: Proceedings of the National Academy of Science of the United States of America, 113 (41), pp. 11414–11419, 2016.