A5005596786- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Gene Regulatory Network Analysis
- Microbial Community Ecology and Physiology
- Pharmacological Effects of Natural Compounds
- Microbial Metabolic Engineering and Bioproduction
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- Innovative Microfluidic and Catalytic Techniques Innovation
- Diet and metabolism studies
- 3D Printing in Biomedical Research
- Genomics and Phylogenetic Studies
- Molecular Communication and Nanonetworks
- Single-cell and spatial transcriptomics
- Metabolomics and Mass Spectrometry Studies
- Gastrointestinal motility and disorders
- Microfluidic and Capillary Electrophoresis Applications
- Probiotics and Fermented Foods
- Bacterial biofilms and quorum sensing
- Evolutionary Game Theory and Cooperation
- Bacterial Genetics and Biotechnology
- Ecosystem dynamics and resilience
- Fungal and yeast genetics research
Duke University
2024-2025
University of Wisconsin–Madison
2017-2024
Great Lakes Bioenergy Research Center
2021-2022
University of California, Berkeley
2015-2017
QB3
2014-2017
California Institute of Technology
2007-2015
University of California, San Francisco
2014-2015
Article21 June 2018Open Access Transparent process Deciphering microbial interactions in synthetic human gut microbiome communities Ophelia S Venturelli Corresponding Author [email protected] orcid.org/0000-0003-2200-1963 Department of Biochemistry, University Wisconsin-Madison, Madison, WI, USA Search for more papers by this author Alex V Carr Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, Garth Fisher Ryan H Hsu...
The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach synthetic human gut production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth butyrate separately, providing key insights into ecological mechanisms driving production. We use our explore vast community space using...
To survive in resource-limited and dynamic environments, microbial populations implement a diverse repertoire of regulatory strategies. These strategies often rely on anticipating impending environmental shifts, enabling the population to be prepared for future change conditions. It has long been known that cells optimize nutritional value from mixtures carbon sources, example glucose galactose, by sequential activation programs allow metabolizing preferred source first before secondary...
ABSTRACT The spatial organization of microbial communities arises from a complex interplay biotic and abiotic interactions, is major determinant ecosystem functions. Here we design microfluidic platform to investigate how the arrangement microbes impacts gene expression growth. We elucidate key biochemical parameters that dictate mapping between positioning patterns. show distance can establish low-pass filter periodic inputs enhance fidelity information processing. Positive negative...
An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar proteins differ substantially in their to mutations and capacity evolve new functions, it has remained unclear these differences might be due evolutionary selection for properties. Here we use laboratory experiments demonstrate protein if evolving population sufficiently...
Feedback loops are ubiquitous features of biological networks and can produce significant phenotypic heterogeneity, including a bimodal distribution gene expression across an isogenic cell population. In this work, combination experiments computational modeling was used to explore the roles multiple feedback in bimodal, switch-like response Saccharomyces cerevisiae galactose regulatory network. Here, we show that bistability underlies observed bimodality, as opposed stochastic effects, two...
Predicting the dynamics and functions of microbiomes constructed from bottom-up is a key challenge in exploiting them to our benefit. Current models based on ecological theory fail capture complex community behaviors due higher order interactions, do not scale well with increasing complexity considering multiple functions. We develop apply long short-term memory (LSTM) framework advance understanding assembly health-relevant metabolite production using synthetic human gut community. A...
Microbiomes interact dynamically with their environment to perform exploitable functions such as production of valuable metabolites and degradation toxic for a wide range applications in human health, agriculture, environmental cleanup. Developing computational models predict the key bacterial species factors build optimize are crucial accelerate microbial community engineering. However, there is an unknown web interactions that determine highly complex dynamic behavior these systems, which...
In the human gut, growth of pathogen Clostridioides difficile is impacted by a complex web interspecies interactions with members gut microbiota. We investigate contribution on antibiotic response C . to clinically relevant antibiotics using bottom-up assembly communities. identify 2 classes microbial that alter ’s susceptibility: resulting in increased ability grow at high concentrations (rare) and enhancement low (common). Based genome-wide transcriptional profiling data, we demonstrate...
The human gut pathogen Clostridioides difficile displays substantial inter-strain genetic variability and confronts a changeable nutrient landscape in the gut. We examined how microbiota inter-species interactions influence growth toxin production of various C. strains across different environments. Negative influencing are prevalent an environment containing single highly accessible resource sparse difficile-preferred carbohydrates. significant community-context dependent variation does not...
Synthetic circuits embedded in host cells compete with cellular processes for limited intracellular resources. Here we show how funnelling of resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity recoding gene sequence eliminate recognition sites, while preserving amino acid sequence. The expression fluorescent reporter and flux high-value metabolite...
Population heterogeneity can promote bacterial fitness in response to unpredictable environmental conditions. A major mechanism of phenotypic variability the human gut symbiont
DNA is a universal and programmable signal of living organisms. Here we develop cell-based sensors by engineering the naturally competent bacterium Bacillus subtilis (B. subtilis) to detect specific sequences in environment. The sensor strains can identify diverse bacterial species including major human pathogens with high specificity. Multiplexed detection genomic from different complex samples be achieved coupling sensing mechanism orthogonal fluorescent reporters. We also demonstrate that...
Microbial communities play a central role in transforming environments across Earth, driving both physical and chemical changes. By harnessing these capabilities, synthetic microbial communities, assembled from the bottom up, offer valuable insights into mechanisms that govern community functions. These can also be tailored to produce desired outcomes, such as synthesis of health-related metabolites or nitrogen fixation improve plant productivity. Widely used computational models predict...