A5014507176- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Escherichia coli research studies
- Bacteriophages and microbial interactions
- Diet and metabolism studies
- Dietary Effects on Health
- Evolution and Genetic Dynamics
- Vibrio bacteria research studies
- Circadian rhythm and melatonin
- Viral gastroenteritis research and epidemiology
- Bacterial Genetics and Biotechnology
- Gastrointestinal motility and disorders
- COVID-19 epidemiological studies
- Gene Regulatory Network Analysis
- SARS-CoV-2 and COVID-19 Research
- thermodynamics and calorimetric analyses
- 3D Printing in Biomedical Research
- Salmonella and Campylobacter epidemiology
- Innovative Microfluidic and Catalytic Techniques Innovation
- SARS-CoV-2 detection and testing
- Metabolomics and Mass Spectrometry Studies
- Probiotics and Fermented Foods
- DNA Repair Mechanisms
- Thermal properties of materials
- Vaccine Coverage and Hesitancy
ETH Zurich
2014-2024
Department of Medical Sciences
2022-2024
Board of the Swiss Federal Institutes of Technology
2023
Collège de France
2022
Université Libre de Bruxelles
2022
École Polytechnique Fédérale de Lausanne
2021
Swiss Federal Institute of Aquatic Science and Technology
2012-2020
University of California, San Diego
2016-2018
Combination therapy is rarely used to counter the evolution of resistance in bacterial infections. Expansion use combination requires knowledge how drugs interact at inhibitory concentrations. More than 50 years ago, it was noted that, if bactericidal are most potent with actively dividing cells, then inhibition growth induced by a bacteriostatic drug should result an overall reduction efficacy when drug. Our goal here investigate this hypothesis systematically. We first constructed...
Virulence factors generally enhance a pathogen's fitness and thereby foster transmission. However, most studies of pathogen have been performed by averaging the phenotypes over large populations. Here, we analyzed costs virulence factor expression Salmonella enterica subspecies I serovar Typhimurium in simple culture experiments. The type III secretion system ttss-1, cardinal for eliciting diarrhea, is expressed just fraction S. population, yielding mixture cells that either express ttss-1...
Peptide mimicry breaks the heart Myocarditis, a prolonged chronic inflammation of muscle, can eventually progress to inflammatory cardiomyopathy, serious condition associated with failure. Activated T helper (T H ) cells that recognize myosin heavy chain 6–derived peptides are thought play central role in this pathogenesis. Using mouse model myocarditis, Gil-Cruz et al. found cardiac myosin–reactive initially primed by myosin-peptide mimics derived from commensal Bacteroides species gut (see...
Phenotypic heterogeneity can confer clonal groups of organisms with new functionality. A paradigmatic example is the bistable expression virulence genes in Salmonella typhimurium, which leads to phenotypically virulent and avirulent subpopulations. The two subpopulations have been shown divide labor during S. typhimurium infections. Here, we show that heterogeneous gene this organism also promotes survival against exposure antibiotics through a bet-hedging mechanism. Using microfluidic...
Significance The human colon is occupied by trillions of microbial cells. Recent sequencing studies have shown that many diseases lead to substantial changes in the composition this gut microbiota and suggest a strong influence on host physiology. However, not much known about underlying physiological factors shaping microbiota. Here, we focus role flow mixing colonic wall contractions. To grow proximal colon, microbes continuously overcome flow. Our vitro study suggests helps flow,...
Significance The human gut is populated by a dense microbial population, strongly impacting health and disease. Metagenomic sequencing has led to crucial insights into microbiota changes in response various perturbations, but mechanistic understanding of these largely missing. As the composition consequence bacterial growth, we propose an approach that focuses on growth large intestine physiological factors influencing it. Using combination experimental analysis quantitative simulations,...
Abstract To survive antibiotics, bacteria use two different strategies: counteracting antibiotic effects by expression of resistance genes or evading their e.g. persisting inside host cells. Since bacterial adhesins provide access to the shielded, intracellular niche and adhesin type 1 fimbriae increases survival chances macrophages, we asked if also influenced evasion. Combined gentamicin assays, flow cytometry, single cell microscopy kinetic modeling dose response curves showed that...
The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known greatly improve recovery energy from food. This has led hypothesis that increased digestive efficiency may underlie contribution obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat mass than germ-free (GF) or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, expenditure, and respiratory quotient using novel...
Most organisms live in ever-changing environments, and have to cope with a range of different conditions. Often, the set biological traits that are needed grow, reproduce, survive varies between As consequence, evolved sensory systems detect environmental signals, modify expression response. However, there limits ability such plastic responses changing environments. Sometimes, shifts might occur suddenly, without preceding so not time react. Other times, signals be unreliable, causing...
The human gut microbiota is highly dynamic, and host physiology diet exert major influences on its composition. In our recent study, we integrated new quantitative measurements bacterial growth with a reanalysis of published data to build comprehensive modeling framework. This can generate predictions how changes in different factors influence For instance, hydrodynamic forces the colon, along colonic water absorption that manifests as transit time, impact density be mechanistically...
Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. In this study, we used genetically barcoded Bacteroides thetaiotaomicron ( B. theta ) strains quantify population bottlenecks experienced by during colonization the mouse gut. As expected, reveals inverse relationship between microbiota complexity and probability that individual wildtype clone will colonize The polysaccharide capsule is important for resistance against...
We describe a straightforward approach to continuously monitor variety of highly dynamic microbiological processes in millisecond resolution with flow cytometry, using standard bench-top instrumentation. Four main experimental examples are provided, namely: (1) green fluorescent protein expression by antibiotic-stressed Escherichia coli, (2) labeling heat-induced membrane damage an autochthonous freshwater bacterial community, (3) the initial growth response late stationary E. coli cells...
Abstract Covid-19 mitigation commonly involves social distancing. Due to its high economic toll and impact on personal freedom, we need ease distancing deploy alternative measures, while preventing a second wave of infections. Bluetooth app-based contact tracing has been proposed, focusing symptomatic cases isolating their contacts. However, this approach would miss many transmissions by asymptomatic cases. To improve effectiveness mitigation, propose complement with Smart Testing relying...
Abstract Fermentation products released by the gut microbiota provide energy and important regulatory functions to host. Yet, little quantitative information is available on metabolite exchange between human host, thus effective doses of fermentation products. Here, we introduce an integrative framework combining experimental characterization major bacteria with a analysis digestive physiology put numbers this its dependence diet composition. From complex carbohydrates fueling growth, find...
Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters gastrointestinal tract, but micro-scale in lumen has not been extensively explored. In samples from mice humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid changes its viscoelastic properties under force contractions. This phenomenon sufficient explain clustering murine cecum, resulting...
Abstract All biological processes use or produce heat. Traditional microcalorimeters have been utilized to study the metabolic heat output of living organisms and production exothermic chemical processes. Current advances in microfabrication made possible miniaturization commercial microcalorimeters, resulting a few studies on activity cells at microscale microfluidic chips. Here we present new, versatile, robust microcalorimetric differential design based integration flux sensors top...
Relevant pandemic-spread scenario simulations can provide guiding principles for containment and mitigation policies. We devised a compartmental model to predict the effectiveness of different strategies with main focus on mass testing. The consists set simple differential equations considering population size, reported unreported infections, recoveries, number COVID-19-inflicted deaths. assumed that COVID-19 survivors are immune (e.g., mutations not considered) virus is primarily passed by...
The metabolic "handshake" between the microbiota and its mammalian host is a complex, dynamic process with major influences on health. Dissecting interaction microbial species metabolites found in tissues has been challenge due to requirement for invasive sampling. Here, we demonstrate that secondary electrospray ionization-mass spectrometry (SESI-MS) can be used non-invasively monitor activity of intestinal microbiome live, awake mouse. By comparing headspace metabolome individual gut...
Heat flux measurement shows potential for the early detection of infectious growth. Our research is motivated by possibility using heat sensors infection on aortic vascular grafts measuring onset bacterial Applying as an marker implant surfaces yet to be experimentally explored. We have previously shown exponential growth curve a population in thermally stabilized laboratory environment. In this work, we further explore limits microcalorimetric measurements via microfluidic chip fluctuating
In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded an mother with decreased potential for future and division, other rejuvenated daughter. Here, we aimed at investigating some of processes involved bacterium Escherichia coli, where types distinguished by age their poles. We found that certain changes regulation carbohydrate metabolism affect aging. A mutation carbon storage regulator gene,...