Below you can find a list of the group’s publications in reverse chronological order. In case you have trouble getting one of them, don’t hesitate to contact Markus. You can also find an up-to-date list on Markus’ Google Scholar page.
Gut microbiota restricts intestinal lipid uptake via modulation of bile phosphatidylcholine metabolism in mice. S Brunner, J Plagge, M Zimmermann-Kogadeeva, M Höring, G Liebisch, M Basic, S Bolsega, K-P Janssen, E Slack, S von Gamm, A Viehof-Beckmann, T Clavel, M Zimmermann, J Heeren, P Giansanti, AS Weiss, S Hermeling, A Dupont, A-L Ullrich, F Jokisch, C Seeliger, A Bleich, M Hidrobo, B Stecher, OI Coleman, C Moresi, G Greter, M Arnoldini, J Scheiber, S Matysik, M Klingenspor, B Küster, D Haller, R Burkhardt, F Kuipers, J Ecker. Nature Microbiology (2026)
Interspecies interaction controls Escherichia coli growth in human gut microbiome samples. M Boumasmoud, R Léon-Sampedro, V Beusch, F Benz, M Arnoldini, AR Hall. PNAS (2026)
Emergent spatial structure in the gut microbiota is driven by bacterial growth and gut contractions. G Greter, S Hummel, D Künzli, N Dünki, N Ruoho, P Burkhardt, S Ganguillet, M Radiom, C Moresi, L Laganenka, W-D Hardt, S Geisel, S Jordi, B Misselwitz, B Yilmaz, J Slomka, E Secchi, R Stocker, E Slack, M Arnoldini. PLOS Biology (2026)
Abundance-weighted pathway mapping demonstrates family-level structure of butyrate and propionate production across the human gut microbiome. R Christensen, YHD Wang, M Arnoldini, J Cremer, ISME Communications (2026)
Quantifying the daily harvest of fermentation product from the human gut microbiota. M Arnoldini, R Sharma, C Moresi, G Chure, J Chabbey, E Slack, J Cremer, Cell (2025)
Acute targeted induction of gut-microbial metabolism disrupts host circadian rhythm. G Greter, S Oswald, D Künzli, J Lan, E Slack, M Arnoldini, reviewed preprint at Elife (2024)
Experimental in vitro microfluidic calorimetric chip data towards the early detection of infection on implant surfaces. SLK Vehusheia, CI Roman, M Arnoldini, C Hierold. Sensors (2024)
Non-invasive monitoring of microbiota and host metabolism using secondary electronspray ionization mass spectrometry. J Lan, G Greter, B Streckenback, M Arnoldini, R Zenobi, E Slack. Cell Reports Methods (2023)
Enabling direct microcalorimetric measurement of metabolic activity and exothermic reactions onto microfluidic platforms via heat flux sensor integration. SLK Vehusheia, C Roman, O Braissant, M Arnoldini, C Hierold. Microsystems & Nanoengineering (2023)
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota. D Hoces, G Greter, M Arnoldini, ML Stäubli, C Moresi, A Sintsova, S Berent, I Kolinko, F Bansept, A Woller, J Häfliger, E Martens, W-D Hardt, S Sunagawa, C Loverdo, E Slack. eLife (2023)
Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle. D Hoces, J Lan, W Sun, T Geiser, ML Stäubli, E Cappio Barrazone, M Arnoldini, TD Challa, M Klug, A Kellenberger, S Nowok, E Faccin, AJ Macpherson, B Stecher, S Sunagawa, R Zenobi, W-D Hardt, C Wolfrum, E Slack. PLOS Biology (2022)
Smart investment of virus RNA testing resources to enhance Covid-19 mitigation. H Gorji, M Arnoldini, DF Jenny, W-D Hardt, P Jenny. PLOS ONE (2021)
A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. M Diard, E Bakkeren, V Lentsch, A Rocker, NA Bekele, D Hoces, S Aslani, M Arnoldini, F Böhi, K Schumann-Moor, J Adamcik, L Piccoli, A Lanzavecchia, BM Stadtmueller, N Donohue, MW van der Woude, A Hockenberry, PH Viollier, L Falquet, D Wüthrich, F Bonfiglio, C Loverdo, A Egli, G Zandomeneghi, R Mezzenga, O Holst, BH Meier, W-D Hardt, E Slack. Nature Microbiology (2021)
Dynamic modeling to identify mitigation strategies for the COVID-19 pandemic. H Groji, M Arnoldini, DF Jenny, W-D Hardt, P Jenny. Swiss Medical Weekly (2021)
How the gut microbiota influences our health and how we can influence it. M Arnoldini, V Lentsch, D Latorre, G Greter, E Slack, A Giorgetti, A Groppo, L Kha. Frontiers for Young Minds (2021) (review)
Growing, evolving and sticking in a flowing environment: understanding IgA interactions with bacteria in the gut. D Hoces, M Arnoldini, M Diard, C Loverdo, E Slack. Immunology (2020) (review)
Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. SY Wotzka, M Kreuzer, L Maier, M Arnoldini, BD Nguyen, AO Brachmann, DL Berthold, M Zünd, A Hausmann, E Bakkeren, D Hoces, E Gül, M Beutler, T Dolowschiak, M Zimmermann, T Fuhrer, K Moor, U Sauer, A Typas, J Piel, M Diard, AJ Macpherson, B Stecher, S Sunagawa, E Slack, W-D Hardt. Nature Microbiology (2019)
Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy. C Gil-Cruz, C Perez-Shibayama, A De Martin, F Ronchi, K Van Der Borght, R Niederer, L Onder, M Lütge, M Novkovic, V Nindl, G Ramos, M Arnoldini, EMC Slack, V Boivin-Jahns, R Jahns, M Wyss, C Mooser, BN Lambrecht, MT Maeder, H Rickli, L Flatz, U Eriksson, MB Geuking, KD McCoy, B Ludewig. Science (2019)
Why is measles vaccination so important. E Slack, M Arnoldini, D Latorre, S Aslani, V Biagioli, T Cruz, NE Dünki, ACJ Eichelberg, M Goldiger, N Howald, G Marastoni, T Marti, V Peterhans, L Slevakumar, A Winterberg. Frontiers for Young Minds (2019) (review)
Bacterial growth, flow, and mixing shape human gut microbiota density and composition. M Arnoldini, J Cremer, T Hwa. Gut Microbes (2018) (review)
Effect of water flow and chemical environment on microbiota growth and composition in the human colon. J Cremer, M Arnoldini, T Hwa. PNAS (2017)
High-avidity IgA protects the intestine by enchaining growing bacteria. K Moor, M Diard, ME Sellin, B Felmy, SY Wotzka, A Toska, E Bakkeren, M Arnoldini, F Bansept, A Dal Co, T Völler, A Minola, B Fernandez-Rodriguez, G Agatic, S Barbieri, L Piccoli, C Casiraghi, D Corti, A Lanzavecchia, RR Regoes, C Loverdo, R Stocker, DR Brumley, W-D Hardt, E Slack. Nature (2017)
Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel. J Cremer, I Segota, C Yang, M Arnoldini, J T Sauls, Z Zhang, A Groisman, T Hwa. PNAS (2016)
Genetic manipulation of glycogen allocation affects replicative lifespan in E. coli. A Böhm, M Arnoldini, T Bergmiller, C Bigosch, T Röösli, M Ackermann. PLOS Genetics (2016)
How type 1 fimbriae help Escherichia coli to evade extracellular antibiotics. IA Vizcarra, V Hosseini, P Kollmannsberger, S Meier, SS Weber, M Arnoldini, M Ackermann, V Vogel. Scientific Reports (2016)
Antibiotic treatment selects for cooperative virulence of Salmonella typhimurium. M Diard, M E Sellin, T Dolowschiak, M Arnoldini, M Ackermann, W-D Hardt. Current Biology (2014)
Bistable expression of virulence genes in Salmonella leads to the formation an antibiotic tolerant subpopulation. M Arnoldini, I A Vizcarra, R Peña-Miller, N Stocker, M Diard, V Vogel, R E Beardmore, W-D Hardt, M Ackermann. PLOS Biology (2014)
Antagonism between bacteriostatic and bactericidal antibiotics is prevalent. PS Ocampo, V Lázár, B Papp, M Arnoldini, P Abel zur Wiesch, R Busa-Fekete, G Fekete, C Pál, M Ackermann, S Bonhoeffer. Antimicrobial Agents & Chemotherapy (2014)
Monitoring of dynamic microbiological processes using real-time flow cytometry. M Arnoldini, T Heck, A Blanco, F Hammes. PLOS ONE (2013)
Evolution of stress response in the face of unreliable environmental signals. M Arnoldini, R Mostowy, S Bonhoeffer, M Ackermann. PLOS Comp Biol (2012)
The cost of virulence: retarded growth of Salmonella Typhimurium cells expressing type III secretion system 1. A Sturm, M Heinemann, M Arnoldini, A Benecke, M Ackermann, M Benz, J Dormann, W-D Hardt. PLOS Pathogens (2011)
Arnoldini Lab 