A5065046552- Gut microbiota and health
- Evolution and Genetic Dynamics
- Evolutionary Game Theory and Cooperation
- Tryptophan and brain disorders
- Microbial Community Ecology and Physiology
- Clostridium difficile and Clostridium perfringens research
- Single-cell and spatial transcriptomics
- Immune cells in cancer
- T-cell and B-cell Immunology
- interferon and immune responses
- RNA modifications and cancer
- Metabolomics and Mass Spectrometry Studies
- Cancer Genomics and Diagnostics
- Probiotics and Fermented Foods
- Microbial Metabolic Engineering and Bioproduction
- Genetics, Bioinformatics, and Biomedical Research
- Adolescent and Pediatric Healthcare
- Cancer-related molecular mechanisms research
Stanford University
2021-2024
Westlake University
2024
Bioengineering Center
2022
Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show many macroecological can be quantitatively recapitulated by a simple class consumer-resource models, which metabolic capabilities different are randomly drawn from common distribution. Our model parametrizes properties community using only small number global parameters,...
Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, use thousands of microbial communities cultured in vitro from human feces uncover simple assembly rules develop a predictive model community composition upon addition single nutrients central carbon metabolism complex medium. Community membership was largely determined by donor feces, whereas relative abundances were...
Abstract Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models resource competition to investigate responses species-specific death rates, as induced by antibiotic activity or other growth-inhibiting factors such bacteriophages. Our analyses highlight complex dependence species coexistence that can arise from interplay and activity, independent...
ABSTRACT Members of microbial communities interact via a plethora mechanisms, including resource competition, cross-feeding, and pH modulation. However, the relative contributions these mechanisms to community dynamics remain uncharacterized. Here, we develop framework distinguish effects competition from other interaction by integrating data growth measurements in spent media, synthetic assembly, metabolomics with consumer-resource models. When applied human gut commensals, our revealed...
Human gut commensal bacteria are routinely exposed to various stresses, including therapeutic drugs, and collateral effects difficult predict. To systematically interrogate community-level of drug perturbations, we screened stool-derived
Abstract Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show many can be quantitatively recapitulated by a simple class resource-competition models, which metabolic capabilities different are randomly drawn from common ensemble. Our coarse-grained model parametrizes intrinsic consumer-resource properties community using small...
ABSTRACT Microbiomes can exhibit large variations in species abundances but high reproducibility of functional units, an observation often considered evidence for redundancy. Based on such reduction variability, selection is hypothesized to act units these ecosystems. However, the link between redundancy and remains unclear. Here, we show that variability does not always imply profiles. We propose empirical null models account confounding effects statistical averaging bias toward...
Abstract Perturbations such as dietary shifts and drug treatment can reduce gut microbiome diversity, with negative health effects on the host, but predicting changes to community diversity is challenging due many mechanisms by which species interact. While both nutrient competition cross-feeding play major roles in microbiota assembly, effect of environmental stresses antibiotics typically studied experimentally monoculture, most theoretical studies have focused communities that interact...
ABSTRACT Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models resource competition to investigate responses antibiotic-induced species-specific death rates. Our analyses highlight complex dependence species coexistence that can arise from interplay and antibiotic activity, independent other biological mechanisms. We show cause richness change...