A5037094479- Bacteriophages and microbial interactions
- Plant-Microbe Interactions and Immunity
- Microbial Metabolic Engineering and Bioproduction
- Nematode management and characterization studies
- Fungal and yeast genetics research
- Microbial Community Ecology and Physiology
- Insect symbiosis and bacterial influences
- Genomics and Phylogenetic Studies
- Mycorrhizal Fungi and Plant Interactions
- Cell Image Analysis Techniques
- Gut microbiota and health
- Spectroscopy Techniques in Biomedical and Chemical Research
- Plant pathogens and resistance mechanisms
- Clostridium difficile and Clostridium perfringens research
- Bacterial Identification and Susceptibility Testing
- Parasite Biology and Host Interactions
- Protein purification and stability
- RNA and protein synthesis mechanisms
- Marine Invertebrate Physiology and Ecology
- Biofuel production and bioconversion
- Reproductive tract infections research
- Bacterial Genetics and Biotechnology
- Pancreatitis Pathology and Treatment
- CRISPR and Genetic Engineering
- Plant Pathogenic Bacteria Studies
Fred Hutch Cancer Center
2020-2025
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2025
University of California, Berkeley
2016-2019
Institute of Plant and Microbial Biology, Academia Sinica
2016
Occidental College
2012-2013
There is increasing interest in the plant microbiome as it relates to both health and agricultural sustainability. One key unanswered question whether we can select for a that robust after colonization of target hosts. We used successive passaging experiment address this by selecting upon tomato phyllosphere microbiome. Beginning with diverse microbial community generated from field-grown plants, inoculated replicate plants across 5 genotypes 4 45-d passages, sequencing at each passage....
Interactions between bacteria and bacteriophage viruses (phages) are known to influence pathogen growth virulence, microbial diversity even biogeochemical cycling. Lytic phages in particular infect lyse their host cells, can therefore have significant effects on cell densities as well competitive dynamics within communities. Despite the impacts of lytic ecology evolution free-living communities, little is about role host-associated microbiomes. We set out characterize impact tomato...
The plant microbiome is known to benefit host health in numerous ways, including providing protection against pathogens. Here, we provide evidence that tomato seed-associated microbiota play an important role early seedling health. To test the importance of seed epiphytic communities for susceptibility common bacterial pathogen, Pseudomonas syringae pv. tomato, transplanted naturally occurring microbial back onto seeds prior germination and compared disease those were not reinoculated after...
COVID-19 (coronavirus disease 2019) patients exhibiting gastrointestinal symptoms are reported to have worse prognosis. Ace2 (angiotensin-converting enzyme 2), the gene encoding host protein which SARS-CoV-2 spike proteins bind, is expressed in gut and therefore may be a target for preventing or reducing severity of COVID-19. Here we test hypothesis that expression respiratory tracts modulated by microbiome. We used quantitative PCR profile germ-free mice, conventional raised specific...
Success of phage therapies is limited by bacterial defenses against phages. While a large variety anti- defense mechanisms has been characterized, how expression these systems distributed across individual cells and their combined activities translate into protection from phages not studied. Using single-cell RNA sequencing, we profiled the transcriptomes ∼50,000 cultures human pathobiont, Bacteroides fragilis, infected with lytic bacteriophage. We quantified asynchronous progression...
Colorectal cancer (CRC) is a globally prevalent cancer. Emerging research implicates the gut microbiome in CRC pathogenesis. Bacteria such as Clostridium scindens can produce carcinogenic bile acid deoxycholic (DCA). It unknown whether imaging methods differentiate DCA-producing and DCA-non-producing C. cells. Light microscopy images of anaerobically cultured four conditions were acquired at 100× magnification using Tissue FAX system: media alone (DCA-non-producing state), with cholic...
Virus-like particles are used to encapsulate drugs, imaging agents, enzymes, and other biologically active molecules in order enhance their function. However, the size of most virus-like is inflexible, precluding design appropriately sized containers for different applications. Here, we describe a chromatographic selection particle assembly. Using this selection, identified single amino acid substitution coat protein bacteriophage MS2 that mediates uniform switch geometry from T = 3 1...
Abstract Recent investigations have demonstrated that unusually ‘hairy’ yeti crabs within the family Kiwaidae associate with two predominant filamentous bacterial families, Epsilon and Gammaproteobacteria. These analyses, however, were based on samples collected from a single body region, setae of pereopods. To more thoroughly investigate microbiome associated Kiwa puravida , crab species Costa Rica, we utilized barcoded 16S rRNA amplicon pyrosequencing, as well microscopy terminal...
Leeches within the Piscicolidae are of great numerical and taxonomic importance, yet little is known about bacteria that associate with this diverse group blood-feeding marine parasites fish elasmobranchs. We focused primarily on from a deep-sea leech species unknown identity, collected at ∼ 600 m depth in Monterey Canyon, CA, along two shallow-living genera, Austrobdella Branchellion, Los Angeles Harbor, CA. Molecular analysis all five revealed dominance gammaproteobacteria, which were...
Abstract There is increasing interest in the plant microbiome as it relates to both health and agricultural sustainability. One key unanswered question whether we can select for a that robust after colonization of target hosts. We used successive passaging experiment address this by selecting upon tomato phyllosphere microbiome. Beginning with diverse microbial community generated from field-grown plants, inoculated replicate plants across five genotypes four eight-week long passages,...
Abstract Background Despite the latest advancements in metabolic engineering for genome editing and characterization of host performance, successful development robust cell factories used industrial bioprocesses accurate prediction behavior microbial systems, especially when shifting from laboratory-scale to conditions, remains challenging. To increase probability success a scale-up process, data obtained thoroughly performed studies mirroring cellular responses typical large-scale stimuli...
The eukaryote immune system evolved and continues to evolve within a microbial world, as such is critically shaped by - in some cases even reliant upon the presence of host-associated species. There are clear examples adaptations that allow host simultaneously tolerate and/or promote growth symbiotic microbiota whilst protecting itself against pathogens, but relationship between immunity microbiome reaches far beyond simple recognition includes complex cross-talk microbe well direct...
Here, we describe the isolation and genomic annotation of two novel siphovirus species bacteriophages that infect Bacteroides uniformis: phage EMB1 EMB2. has a 34,204-bp genome with 48 coding sequences, EMB2 34,008-bp 47 sequences.
Abstract To understand the genetic basis of changes in strain physiology during industrial fermentation, and corresponding roles these genes play performance, we employed a barcoded yeast deletion library to assess genome-wide fitness across simulated fermentation regime. Our results demonstrate utility Bar-seq associated stresses populations under conditions. We find that mutant population diversity is maintained through multiple seed trains, enabling for large scale selective pressures act...