A5087166268- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Microbial Community Ecology and Physiology
- SARS-CoV-2 and COVID-19 Research
- Molecular Biology Techniques and Applications
- Plant Virus Research Studies
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Medical Imaging and Pathology Studies
- Viral gastroenteritis research and epidemiology
- SARS-CoV-2 detection and testing
- Gut microbiota and health
- Scientific Computing and Data Management
- COVID-19 diagnosis using AI
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Plant Pathogenic Bacteria Studies
- RNA and protein synthesis mechanisms
- Salmonella and Campylobacter epidemiology
- Plant and Fungal Interactions Research
- Mycorrhizal Fungi and Plant Interactions
- Zoonotic diseases and public health
- Environmental DNA in Biodiversity Studies
- Vibrio bacteria research studies
Los Alamos National Laboratory
2017-2024
Dartmouth College
2016-2019
Kerala Veterinary and Animal Sciences University
2018
Bioscience (Slovakia)
2017
Los Alamos National Security (United States)
2017
University of Tennessee at Knoxville
2012-2014
Oak Ridge National Laboratory
2012-2013
In the last 5 years, rapid pace of innovations and improvements in sequencing technologies has completely changed landscape metagenomic metagenetic experiments. Therefore, it is critical to benchmark various methodologies for interrogating composition microbial communities, so that we can assess their strengths limitations. The most common phylogenetic marker community diversity studies 16S ribosomal RNA gene 10 years field moved from a small number amplicons samples more complex where...
Bacterial and fungal communities associated with plant roots are central to the host health, survival growth. However, a robust understanding of root-microbiome factors that drive microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships bacterial rhizosphere root endosphere riparian tree species Populus deltoides, influence soil parameters, environmental properties (host phenotype aboveground...
Summary Next‐generation sequencing has dramatically changed the landscape of microbial ecology, large‐scale and in‐depth diversity studies being now widely accessible. However, determining accuracy taxonomic quantitative inferences comparing results obtained with different approaches are complicated by incongruence experimental computational data types also lack knowledge true ecological diversity. Here we used highly diverse bacterial archaeal synthetic communities assembled from pure...
Abstract There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate construction standardized and robust for disparate types projects, we have developed a complete bioinformatic workflow, with web-based component to perform phylogenetic molecular evolutionary (PhaME) analysis reads, draft assemblies completed genomes closely Furthermore, ability incorporate raw...
The assembly of high-quality genomes from mixed microbial samples is a long-standing challenge in genomics and metagenomics. Here, we describe the application ProxiMeta, Hi-C-based metagenomic deconvolution method, to deconvolve human fecal metagenome. This method uses intra-cellular proximity signal captured by Hi-C as direct indicator which sequences originated same cell, enabling culture-free de novo without any reliance on priori information. We show that ProxiMeta provides results...
To date, the potential impact of viral communities on biogeochemical cycles in soil has largely been inferred from correlational evidence, such as virus-driven changes microbial abundances, auxiliary metabolic genes, and links with physiochemical properties. more directly test viruses carbon cycling during plant litter decomposition, we added concentrated community suspensions to complex decomposer 40-day microcosm experiments. Microbial two New Mexico alpine soils, Pajarito (PJ) Santa Fe...
Diverse microbial communities thrive on and in deep-sea hydrothermal vent mineral deposits. However, our understanding of the inter-field variability these is poor, as limited sampling sequencing efforts have hampered most previous studies. To explore communities, we used barcoded pyrosequencing variable region 4 (V4) 16S rRNA gene to characterize archaeal bacterial over 30 deposit samples from six fields located along Eastern Lau Spreading Center. Overall, Center are similar other active...
Gene transfer agents (GTAs) are phage-like particles that can package and a random piece of the producing cell's genome, but unable to all genes required for their own production. As such, GTAs represent an evolutionary conundrum: they selfish genetic elements propagating through unknown mechanism, defective viruses, or viral structures "repurposed" by cells gene exchange, as name implies? In Rhodobacter capsulatus, production R. capsulatus GTA (RcGTA) is associated with cluster resembling...
Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most contain apparently random pieces of the host genome. Since these elements can deliver packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized ancestor was a virus. Whether GTAs represent an atypical virus, defective or virus co-opted by prokaryotes for...
The National Microbiome Data Collaborative (NMDC) Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed framework aligned with the FAIR (Findable, Accessible, Interoperable Reusable) principles (1). NMDC currently hosts 10.2 terabytes of data, spanning five types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, natural organic matter characterizations), generated at two Department Energy User...
Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies pathogen genome enrichment sequencing are being used by laboratories worldwide, together with different, sometimes ad hoc, analytical procedures generating sequences. fully integrated process raw sequence to consensus determination, suited outbreaks such as the ongoing COVID-19 pandemic, is critical provide a solid genomic basis epidemiological analyses...
ABSTRACT We present the genome assemblies of two similar Paeniglutamicibacter strains, ORCA_105 and MACA_103, isolated from Mammoth Oregon Cave systems, respectively. These closely related, but distinct genomes will provide a resource for those studying genomic adaptation to caves.
Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, reuse, applications of machine learning model biological processes. To broad accessibility workflows, the National Microbiome Data Collaborative (NMDC) has developed Empowering Development Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web...
Despite over three decades of progress, extraction high molecular weight (HMW) DNA from clay soils or iron oxide cemented has remained challenging. HMW is desirable for next generation sequencing as it yields the most comprehensive coverage. Several procedures were compared samples that exhibit strong nucleic acid adsorption. pH manipulation use alternative ion solutions offered no improvement in recovery. Lysis by liquid N2 grinding concentrated guanidine followed sodium phosphate supported...
Many of the sequenced bacterial and archaeal genomes encode regions viral provenance. Yet, not all these bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that now maintained in some bacteria archaea hypothesized enable exchange DNA within populations. In Alphaproteobacteria, genes homologous "head-tail" gene cluster encodes structural components Rhodobacter capsulatus GTA (RcGTA) found many taxa, even if they only distantly related capsulatus. most available...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists sample acquisition, library preparation, whole sequencing. This necessitated a classification scheme detailing Variants Concern (VOC) Interest (VOI), rapid expansion bioinformatics tools for sequence analysis. These bioinformatic are means major actionable results: maintaining...
Microbiology can greatly help in the quest for a sustainable solution to problem of iron corrosion, which causes important economic losses wide range fields, including protection cultural heritage and building materials. Using bacteria transform reactive unstable corrosion products into more-stable compounds represents promising approach. The overall aim this study was develop method conservation restoration corroded items, starting from isolation iron-reducing natural environments. This...
A wealth of viral data sits untapped in publicly available metagenomic sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work this complexity and scale could done hackathon setting. Ten teams comprised over 40 participants from six countries, assembled crowd-sourced set analysis processing pipelines complex biological three-day event on San Diego State University campus starting 9 January 2019. Prior hackathon, 141,676...
Genomic sequencing of clinical samples to identify emerging variants SARS-CoV-2 has been a key public health tool for curbing the spread virus. As result, an unprecedented number genomes were sequenced during COVID-19 pandemic, which allowed rapid identification genetic variants, enabling timely design and testing therapies deployment new vaccine formulations combat variants. However, despite technological advances deep sequencing, analysis raw sequence data generated globally is neither...
Next-generation sequencing (NGS) offers unparalleled resolution for untargeted organism detection and characterization. However, the majority of NGS analysis programs require users to be proficient in programming command-line interfaces. EDGE bioinformatics was developed offer scientists with little no expertise a point-and-click platform analyzing data rapid reproducible manner. (Empowering Development Genomics Expertise) v1.0 released January 2017, is an intuitive web-based engineered...
Abstract During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and support rapid experimental examination genome-informed vaccine therapeutic designs. Given broad range methods applied generate new genomes, it is critical that consensus variant calling tools yield consistent results across disparate pipelines. Here we examine impact technologies (Illumina Oxford Nanopore) 7 different downstream...
Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based will continue detect all known viral strains. To enable continuous monitoring of assays, have developed a web-based assay validation algorithm that checks against ever-expanding genome databases using both thermodynamic edit-distance metrics. The assay-screening results displayed heatmap, showing...
Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. In pathogens, persisters able antibiotic treatment and reinfect patients frustrating cycle of chronic infection. To better define core persistence mechanisms for therapeutics development, we performed transcriptomics analyses Burkholderia thailandensis populations enriched via three methods: flow sorting low proton motive force,...