A5024108968- Microbial Community Ecology and Physiology
- Microbial Metabolic Engineering and Bioproduction
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Gut microbiota and health
- Algal biology and biofuel production
- Biofuel production and bioconversion
- Bacterial Genetics and Biotechnology
- Vibrio bacteria research studies
- Gene Regulatory Network Analysis
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Legume Nitrogen Fixing Symbiosis
- Microfluidic and Bio-sensing Technologies
- Studies on Chitinases and Chitosanases
- Ethics in Clinical Research
- Sex and Gender in Healthcare
- Marine and coastal ecosystems
- Enzyme Structure and Function
- Enzyme Catalysis and Immobilization
- Plant and fungal interactions
- Social Media in Health Education
- Microbial Fuel Cells and Bioremediation
- Biochemical and Molecular Research
ETH Zurich
2020-2025
VIB-KU Leuven Center for Microbiology
2025
University of Southern California
2024
IIT@MIT
2024
University of California, Los Angeles
2016-2022
Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders decompose complex forms organic matter. It is unclear, however, to what extent structure downstream assembly community follows polymer breakdown. Investigating a model marine degrades chitin, we show chitinases secreted different produce oligomers specific chain lengths not only select for consumers but also influence metabolites these into shared resource pool....
Abstract microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging curated database of >60,000 monocultures, users can known and unknown MS/MS spectra link them to their respective producers via fragmentation patterns. Identification microbe-derived metabolites relative without priori knowledge will vastly enhance the understanding microorganisms’ role ecology human health.
Abstract It has long been known that bacteria coordinate their physiology with nutrient environment, yet our current understanding offers little intuition for how respond to the second-to-minute scale fluctuations in concentration characteristic of many microbial habitats. To investigate effects rapid on bacterial growth, we couple custom microfluidics single-cell microscopy quantify growth rate E. coli experiencing 30 s 60 min fluctuations. Compared steady environments equal average...
Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving extensive needed to support coexistence free-living are poorly understood. Here we characterize bacterial physiology under self-acidification and establish that excretion key metabolites following growth arrest provides a collaborative, inter-species mechanism stress resistance. This collaboration occurs not only between...
Competition for and exchange of nutrients play crucial roles in shaping microbial community function dynamics. Although cross-feeding small metabolites is known to drive carbon among species, the importance self-produced extracellular polymeric substances (EPS), which include proteins, polysaccharides, DNA, humic-like substances, remains less understood. Utilizing chitin-degrading isolates natural seawater communities, we found that 4 7% from chitin degradation converted into EPS, accounting...
Abstract The ability of marine bacteria to direct their movement in response chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While many are chemotactic towards small metabolites, organic matter is predominantly composed large molecules polymers. Yet, the signalling role these largely unknown. Using situ laboratory-based chemotaxis assays, we show that strongly attracted abundant algal polysaccharides laminarin alginate. Unexpectedly,...
In many natural environments, microorganisms decompose microscale resource patches made of complex organic matter. The growth and collapse populations on these unfold within spatial ranges a few hundred micrometers or less, making such ecosystems hotspots heterotrophic metabolism. Despite the potential importance patch-level dynamics for large-scale functioning microbial communities, we have not yet been able to delineate ecological processes that control at microscale. Here, address this...
Abstract Bacteria in nature encounter substrates at widely varying concentrations, yet studies of bacterial physiology have focused more on nutrient type than concentration, partly due to challenges maintaining low concentrations. We developed a Millifluidic Continuous Culture Device (MCCD) culture bacteria under precisely controlled conditions, including very manner suitable for proteomic analysis. Using the MCCD, we cultured Escherichia coli with mixture amino acids as sole carbon source...
Polysaccharide quantification plays a vital role in understanding ecological and nutritional processes microbes, plants, animals. Traditional methods typically hydrolyze these large molecules into monomers using chemical methods, but such approaches do not work for all polysaccharides. Enzymatic degradation is promising alternative requires the use of characterized recombinant enzymes or microbial isolates that secrete enzymes. In this study, we introduce versatile method employs undefined...
Abstract Contamination susceptibility, water usage and inability to utilize 5-carbon sugars disaccharides are among the major obstacles in industrialization of sustainable biorefining. Extremophilic thermophiles acidophiles being researched combat these problems, but organisms which answer all above problems have yet emerge. Here, we present engineering unexplored, extreme alkaliphile Bacillus marmarensis as a platform for new bioprocesses meet challenges. With newly developed transformation...
Microbiology conferences can be powerful places to build collaborations and exchange ideas, but for queer transgender (trans) scientists, they also become sources of alienation isolation. Many conference organizers would like create welcoming inclusive events feel ill-equipped make this vision a reality, historical lack representation trans folks in microbiology means we rarely occupy these key leadership roles ourselves. Looking more broadly, scientists are systematically marginalized...
Most of Earth’s biomass is composed polysaccharides. During decomposition, polysaccharides are degraded by heterotrophic bacteria as a nutrient and energy source thereby partly remineralized into CO 2 . As heterogeneously distributed in nature, following the colonization degradation polysaccharide hotspot cells need to reach new hotspots. Even though many studies indicate that these degradation-dispersal cycles contribute carbon flow marine systems, we know little about how alternate between...
ABSTRACT Cyanobacteria fix carbon dioxide and release carbon-containing compounds into the wider ecosystem, yet they are sensitive to small metabolites that may impact their growth physiology. Several cyanobacteria can grow mixotrophically, but we currently lack a molecular understanding of how specific nutrients alter release, limiting our knowledge environmental factors might primary producers ecosystems support. In this study, develop high-throughput phytoplankton culturing platform...
Abstract Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, forces driving the extensive needed to support coexistence free-living are poorly understood. Here we characterize bacterial physiology under self-acidification, and establish that excretion key metabolites following acidification provides a collaborative, inter-species mechanism stress resistance. This collaboration occurs not only...
Identifying and quantifying metabolites secreted by microbial isolates can aid in understanding the physiological traits of diverse species their interaction with environment. Mass spectrometry-based metabolomics has potential to provide a holistic view exometabolism marine isolates, but high salt content such samples interferes chromatography ionization during measurement polar exometabolites. The most common desalting methods are faced major limitations, including limited separation small...
Abstract MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging curated database of >60,000 monocultures, users can known and unknown MS/MS spectra link them to their respective producers via fragmentation patterns. Identification microbial-derived metabolites relative producers, without priori knowledge, will vastly enhance the understanding microorganisms’ role ecology...
Resource competition strongly shapes microbial community dynamics and function. In polysaccharide-degrading communities, primary degraders secrete monomer-releasing enzymes exploiters consume released products without investing in enzymes. By investigating competitive strategies between chitin N-acetylglucosamine (GlcNAc) exploiters, we uncover several interacting factors, including GlcNAc liberation rates, diffusive loss, resource partitioning competitors, which determine viability growth...
Abstract MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging curated database of >60,000 monocultures, users can known and unknown MS/MS spectra link them to their respective producers via fragmentation patterns. Identification microbial-derived metabolites relative producers, without priori knowledge, will vastly enhance the understanding microorganisms' role ecology...