A5030903484- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- Animal Virus Infections Studies
- Plant and Fungal Interactions Research
- Plant Parasitism and Resistance
- Legume Nitrogen Fixing Symbiosis
- Nematode management and characterization studies
- Microbial infections and disease research
- Zoonotic diseases and public health
- Photoreceptor and optogenetics research
- Animal Disease Management and Epidemiology
- Bacterial biofilms and quorum sensing
- Nicotinic Acetylcholine Receptors Study
- Microbial Community Ecology and Physiology
University of Wisconsin–Madison
2023-2025
University of Illinois Urbana-Champaign
2023-2024
Marine Biological Laboratory
2023
University of Chicago
2023
Abstract Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because the difficulty culturing them lack sufficient model systems. As a result, computational methods for identifying analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate screening enormous sequencing data sets originating various...
Abstract Background Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact community dynamics, ecology, and evolution. Efforts document diversity, host range, infection effects bacteriophage on cell metabolism extremely underexplored. Phages classified as virulent or temperate based their life cycles. Temperate phages adopt lysogenic mode infection, where genome integrates into...
Viruses, the majority of which are uncultivated, among most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses fundamental members microbiomes. While number studies leveraging viral metagenomics (viromics) for studying uncultivated is growing, standards viromics research lacking. Viromics can utilize computational discovery from total metagenomes all (hereafter metagenomes) or use physical separation virus-specific fractions...
Bacteriophages (phages), which are viruses that infect bacteria, the most abundant components of microbial communities and play roles in community dynamics host evolution. However, study phage-host interactions is hindered by a paucity model systems from natural environments. Here, we investigate "pink berry" consortia, naturally occurring, low-diversity, macroscopic bacterial aggregates found Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data comparative...
Bacteriophages (phages), viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics host evolution. The study phage-host interactions, however, is made difficult by a paucity model systems from natural environments known cultivable pairs. Here, we investigate interactions "pink berry" consortia, naturally-occurring, low-diversity, macroscopic aggregates bacteria found Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage...
ABSTRACT Background Viruses, the majority of which are uncultivated, among most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses fundamental members microbiomes. While number studies leveraging viral metagenomics (viromics) for studying uncultivated is growing, standards viromics research lacking. Viromics can utilize computational discovery from total metagenomes all (hereafter metagenomes) or use physical separation...
The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy legume Medicago truncatula Sinorhizobium meliloti in native soils. Our objectives...
The symbiotic relationship between the bioluminescent bacterium
Abstract As the most abundant and diverse biological entities, prokaryotic viruses play pivotal roles in ecological systems. Their taxonomic classification has been instrumental elucidating their diversity functions. However, determination of viral taxonomy remains a considerable challenge. Recently developed approaches succeed assignment at higher ranks, such as family level above, but struggle subfamily below to genus species resolutions. Here, we describe vClassifier toolkit,...
Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because difficulty culturing them the lack sufficient model systems. As a result, computational methods for identifying analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate screening enormous sequencing datasets originating various environments....
Viruses are key drivers of microbial diversity, nutrient cycling, and co-evolution in ecosystems, yet their study is hindered due to challenges culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much the viral genome, leaving proteins functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score VL-score, designed quantify virus-likeness protein families genomes create an open-access searchable database,...
<title>Abstract</title> Viruses are key drivers of microbial diversity, nutrient cycling, and co-evolution in ecosystems, yet their study is hindered due to challenges culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much the viral genome, leaving proteins functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score VL-score, designed quantify “virus-likeness” protein families genomes create an open-access...
The explosion in known microbial diversity the last two decades has made it abundantly clear that microbes environment do not exist isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed interactions between diverse groups community archaea, bacteria, and viruses (bacteriophage) common significant impacts on entire microbiomes. Thus, to a well-developed understanding naturally environment, biological entities all kinds must be studied...
ABSTRACT The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy legume Medicago truncatula Sinorhizobium meliloti in native soils. Our...