A5042068232- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Antifungal resistance and susceptibility
- Bacteriophages and microbial interactions
- Single-cell and spatial transcriptomics
- Infections and bacterial resistance
- Enterobacteriaceae and Cronobacter Research
- CRISPR and Genetic Engineering
- Microfluidic and Capillary Electrophoresis Applications
- Bacterial Genetics and Biotechnology
- Evolution and Genetic Dynamics
- Diet and metabolism studies
- Bioinformatics and Genomic Networks
- Neuroscience and Neural Engineering
- Dietary Effects on Health
- Methane Hydrates and Related Phenomena
- Environmental DNA in Biodiversity Studies
- Electrowetting and Microfluidic Technologies
- Semiconductor materials and devices
- Fungal Infections and Studies
- Innovative Microfluidic and Catalytic Techniques Innovation
- Inflammasome and immune disorders
Chan Zuckerberg Initiative (United States)
2018-2025
Arc Research Institute
2023-2025
Carnegie Institution for Science
2024-2025
Palo Alto Institute
2023-2025
Carnegie Department of Plant Biology
2024
Shanghai Dianji University
2023
Chan Zuckerberg Biohub San Francisco
2020-2023
Stanford University
2013-2022
Stanford Medicine
2019
Bioengineering Center
2017
More diversity at the top A detailed knowledge of cell differentiation hierarchies is important for understanding diverse biological processes such as organ development, tissue regeneration, and cancer. Single-cell RNA sequencing can help elucidate these hierarchies, but it requires reliable computational methods predicting lineage trajectories. Gulati et al. developed CytoTRACE, a framework based on simple observation that transcriptional diversity—the number genes expressed in...
Methanogenic archaea are major contributors to the global carbon cycle and were long thought belong exclusively euryarchaeal phylum. Discovery of methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in Bathyarchaeota, thereafter Verstraetearchaeota, led a paradigm shift, pushing back evolutionary origin predate that Euryarchaeota. The methylotrophic found non-Euryarchaota distinguished itself from predominantly hydrogenotrophic methanogens orders as former do not couple fixation...
Antibiotics alter microbiota composition and increase infection susceptibility. However, the generalizable effects of antibiotics on contribution environmental variables to gut commensals remain unclear. To address this, we tracked dynamics with high temporal taxonomic resolution during antibiotic treatment in a controlled murine system by isolating such as diet, history, housing co-inhabitants. Human microbiotas were remarkably resilient recovered treatment, transient dominance resistant...
Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process nonindustrialized populations. We deeply sequenced infant stool samples the Hadza hunter-gatherers of Tanzania and analyzed them a global meta-analysis. microbiomes develop along lifestyle-associated trajectories, with more than 20% genomes detected gut representing novel species. Industrialized infants-even those who are breastfed-have characterized by paucity
The gut microbiome modulates immune and metabolic health. Human data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers Tanzania comparative populations in Nepal California. We recovered 91,662 genomes bacteria, archaea, bacteriophages, eukaryotes, 44% which absent existing unified datasets. identified 124 gut-resident species...
Mechanistic insights into the role of human microbiome in predisposition to and treatment disease are limited by lack methods precisely add or remove microbial strains genes from complex communities. Here, we demonstrate that engineered bacteriophage M13 can be used deliver DNA Escherichia coli within mouse gastrointestinal (GI) tract. Delivery a programmable exogenous CRISPR-Cas9 system enables strain-specific depletion fluorescently marked isogenic during competitive colonization genomic...
From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing quantify transcript single Saccharomyces cerevisiae treated with and without salt explore population identify cellular covariates that influence stress-responsive transcriptome. Leveraging extensive knowledge yeast transcriptional regulation, uncovered regulatory...
Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics mini-metagenomics on soils Harvard Forest, leading to discovery of 16 novel viruses, chiefly recovered by mini-metagenomics. The candidate greatly expand phylogenetic known either represented lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis tupanviruses. One assembled genome a size 2.4...
Ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) expression correlates with poor prognosis in many cancers, and we previously discovered that ENPP1 is the dominant hydrolase of extracellular cGAMP: a cancer-cell-produced immunotransmitter activates anticancer stimulator interferon genes (STING) pathway. However, has other catalytic activities molecular cellular mechanisms contributing to its tumorigenic effects remain unclear. Here, using single-cell RNA-seq, show both cancer...
The appearance of jaws was a turning point in vertebrate evolution because it allowed primitive vertebrates to capture and process large, motile prey. jaw consists separate dorsal ventral skeletal elements connected by joint. How this structure evolved from the unjointed gill bar jawless ancestor is an unresolved question evolution. To understand developmental bases evolutionary transition, we examined expression 12 genes involved pharyngeal patterning modern fish lamprey. We find nested Dlx...
Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes complex mixtures metagenomic data can still be challenging represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method offers statistically rigorous approach to extract microbial while preserving resolution. We used this analyze two hot spring samples Yellowstone National Park...
Recent advances in flow-based microfluidics have led to the emergence of biochemistry-on-a-chip as a new paradigm clinical diagnostics and biomolecular recognition. However, potential roadblock deployment microfluidic biochips is lack test techniques screen defective devices before they are used for biochemical analysis. Defective chips lead repetition experiments, which undesirable due high reagent cost limited availability samples. Prior work on fault detection has been digital ("droplet")...
Abstract Hydrothermal vents have been key to our understanding of the limits life, and metabolic phylogenetic diversity thermophilic organisms. Here we used environmental metagenomics combined with analysis physicochemical data 16S rRNA gene amplicons characterize sediment-hosted microorganisms at recently discovered Auka in Gulf California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% those currently known, showing microbial community hydrothermal...
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...
Cyanobacteria are important agents in global carbon and nitrogen cycling hold great promise for biotechnological applications. Model organisms such as Synechocystis sp. Synechococcus have advanced our understanding of photosynthetic capacity circadian behavior, mostly using population-level measurements which the behavior individuals cannot be monitored. cells small divide slowly, requiring long-term experiments to track single cells. Thus, cumulative effects drift over long periods can...
Abstract Microbial community function depends on both taxonomic composition and spatial organization. While of the human gut microbiome has been deeply characterized, less is known about organization microbes between regions such as lumen mucosa microbial genes regulating this Using a defined 117 strain for which we generate high-quality genome assemblies, model mucosa/lumen with in vitro cultures incorporating mucin hydrogel carriers surfaces bacterial attachment. Metagenomic tracking...
Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by availability open niches, it remains unclear whether other ecological barriers limit commensal in natural settings. To disentangle these effects, we used a controlled perturbation with antibiotic ciprofloxacin to investigate dynamics microbiome transmission 22 households healthy, cohabiting adults. Colonization was rare...
Gut inflammation directly impacts the growth and stability of commensal gut microbes can lead to long-lasting changes in microbiota composition that prolong or exacerbate disease states. While mouse models are used extensively investigate interplay between inflamed state, paucity cultured has hindered efforts determine causal relationships. To address this issue, we assembling Collection Inflammation-Associated Mouse Intestinal Bacteria (CIAMIB). The initial release collection comprises 41...