A5054108248- Gut microbiota and health
- Calibration and Measurement Techniques
- Microbial Community Ecology and Physiology
- Colorectal Cancer Screening and Detection
- Marine Biology and Ecology Research
- Bacteriophages and microbial interactions
- Spacecraft and Cryogenic Technologies
- Genetics, Bioinformatics, and Biomedical Research
- Engineering Applied Research
- Soil Moisture and Remote Sensing
- Genomics and Phylogenetic Studies
- Mycorrhizal Fungi and Plant Interactions
- Environmental DNA in Biodiversity Studies
- Methane Hydrates and Related Phenomena
- Plant Virus Research Studies
- Vibrio bacteria research studies
- Scientific Computing and Data Management
- Cancer survivorship and care
- Plant Pathogens and Fungal Diseases
- Food Allergy and Anaphylaxis Research
- Isotope Analysis in Ecology
- Energy, Environment, Agriculture Analysis
- Parasite Biology and Host Interactions
- Marine Bivalve and Aquaculture Studies
- Environmental and Sediment Control
University of South Florida
2020-2025
College of Marin
2022-2025
Florida College
2021-2025
University of South Florida St. Petersburg
2023-2025
University of Miami
2020-2024
NOAA Atlantic Oceanographic and Meteorological Laboratories
2021-2023
National Oceanic and Atmospheric Administration
2021-2023
Clemson University
2018-2022
Vanderbilt University
2019-2020
National University of Singapore
2008-2013
Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as ‘microbial community relationships that recapitulate phylogeny their host’, we review relevant literature and data last decade, emphasizing frequently used methods regular patterns observed analyses. Quantitative is provided by statistical evaluating higher microbiome variation between host species than...
Abstract Lucinidae clams harbor gammaproteobacterial thioautotrophic gill endosymbionts that are environmentally acquired. Thioautotrophic lucinid symbionts related to metabolically similar associated with diverse marine host taxa and fall into three distinct phylogenetic clades. Most studies on the lucinid–bacteria chemosymbiosis have been done seagrass-dwelling hosts, whose belong largest clade. In this study, we examined taxonomy functional repertoire of bacterial at an unprecedented...
Improved RNA virus understanding is critical to studying animal and plant health, environmental processes. However, the continuous rapid evolution makes their identification characterization challenging. While recent sequence-based advances have led extensive discovery, there growing variation in how viruses are identified, analyzed, characterized, reported. To this end, an RdRp Summit was organized a hybrid meeting took place Valencia, Spain May 2023 convene leading experts with emphasis on...
Lysogens, bacteria that contain viruses (prophages) integrated into their genomes, are abundant in the gut of animals. Prophages often influence bacterial traits; however, prophages on microbiota-host immune axis animals remains poorly understood.Here, we investigate prophage SfPat Shewanella fidelis 3313, a persistent member microbiome model marine tunicate, Ciona robusta . Establishment deletion mutant (ΔSfPat) reveals this physiology vitro and during colonization gut. In , reduces S. 3313...
Lysogens, bacteria that contain viruses (prophages) integrated into their genomes, are abundant in the gut of animals. Prophages often influence bacterial traits; however, prophages on microbiota-host immune axis animals remains poorly understood.Here, we investigate prophage SfPat Shewanella fidelis 3313, a persistent member microbiome model marine tunicate, Ciona robusta . Establishment deletion mutant (ΔSfPat) reveals this physiology vitro and during colonization gut. In , reduces S. 3313...
Harmful algal blooms (HABs) caused by the dinoflagellate Karenia brevis frequently occur in eastern Gulf of Mexico, where they negatively impact environment, human health, and economy. Very little is known about viruses associated with K. blooms, although viral infection other HAB-forming phytoplankton species can play an important role bloom dynamics. We used metagenomics to identify 11 pooled seawater samples collected from Southwest Florida, USA 2021 during a severe, spatiotemporally...
Lucinidae are the most specious family of extant chemosymbiotic bivalves and occupy a wide range habitats worldwide. All lucinids examined to date house chemosynthetic endosymbionts within their gill tissues. Fossil evidence suggests Silurian origin for family, with associations dating back at least Late Jurassic. Previous systematics work indicates that shell characters contain limited phylogenetic signal, when they do carry it is typically more derived, genus-level positions. Instead using...
ABSTRACT Harmful algal blooms (HABs) caused by the dinoflagellate Karenia brevis frequently occur in eastern Gulf of Mexico, where they negatively impact environment, human health, and economy. Very little is known about viruses associated with K. blooms, although viral infection other HAB-forming phytoplankton species can play an important role bloom dynamics. We used metagenomics to identify 11 pooled seawater samples collected from southwest Florida, USA, 2021 during a severe,...
The development of high throughput experimental technologies have given rise to the "-omics" era where terabyte-scale datasets for systems-level measurements various cellular and molecular phenomena pose considerable challenges in data processing extraction biological meaning. Moreover, it has created an unmet need effective integration these achieve insights into systems. While increased demand bioinformatics experts who can interface with biologists, also raised requirement biologists...
To examine a) whether there are significant differences in the severity of symptoms fatigue, sleep disturbance, or depression between patients with rectal cancer who develop co-occurring and those no before at end chemotherapy radiation therapy (CRT); b) gut microbial diversity symptoms; c) before-treatment measurements taxa abundances can predict co-occurrence symptoms.
Abstract Background Amplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby single genetic locus amplified and sequenced from the DNA whole or partial organisms, organismal traces (e.g., skin, mucus, feces), microbes in an sample. Several software packages exist for analyzing amplicon data, among which QIIME 2 has emerged as popular option because its broad functionality, plugin architecture, provenance tracking, interactive...
Epigenetics has recently emerged as a critical field for studying how non-gene factors can influence the traits and functions of an organism.At core this new wave research is use computational tools that play roles not only in directing selection key experiments, but also formulating testable hypotheses through detailed analysis complex genomic information achievable using traditional approaches alone.Epigenomics, which combines genomics with computer science, mathematics, chemistry,...
Abstract Fish eDNA metabarcoding is a nonintrusive, time‐ and cost‐effective way to detect biodiversity, with potential applications in ecosystem‐based management fisheries assessment. Nevertheless, fish‐specific resources are currently not well‐developed, many fish species yet sequenced reference databases. We developed Mitohelper, Python‐based command line tool annotate align mitochondrial sequences available the existing MitoFish database. Mitohelper improves annotations by adding gene...
Turtlegrass virus X, which infects the seagrass Thalassia testudinum , is only potexvirus known to infect marine flowering plants. We investigated distribution in seagrasses using a degenerate reverse transcription polymerase chain reaction (RT-PCR) assay originally designed capture diversity terrestrial The assay, implements Potex-5 and Potex-2RC primers, successfully amplified 584 nt RNA-dependent RNA (RdRp) fragment from TVX-infected seagrasses. Following validation, we screened 74...
The rapid advancement of computer and information technology in recent years has resulted the rise e-learning technologies to enhance complement traditional classroom teaching many fields, including bioinformatics. This paper records experience implementing support problem-based learning (PBL) two undergraduate bioinformatics classes National University Singapore.Survey results further established efficiency suitability tools supplement PBL education. 63.16% year three students showed a...
Small bioinformatics databases, unlike institutionally funded large are vulnerable to discontinuation and many reported in publications no longer accessible. This leads irreproducible scientific work redundant effort, impeding the pace of progress. We describe a Web-accessible system, available online at http://biodb100.apbionet.org , for archival future on demand re-instantiation small databases within minutes. Depositors can rebuild their by downloading Linux live operating system (...
Background. The role of alterations in gut microbiota composition (termed dysbiosis) has been implicated the pathobiology depressive symptoms; however, evidence remains limited. This cross-sectional pilot study is aimed at exploring whether symptom scores changed during neoadjuvant chemotherapy and radiation therapy to treat rectal cancer, if microbial taxa abundances predicted functional pathways correlate with symptoms end therapy. Methods. 40 newly diagnosed cancer patients (ages 28-81;...
Seagrass-dwelling members of the bivalve family Lucinidae harbor environmentally acquired gill endosymbionts. According to previous studies, lucinid symbionts potentially represent multiple strains from a single thioautotrophic gammaproteobacterium species. This study utilized genomic- and transcriptomic-level data resolve symbiont taxonomic, genetic, functional diversity
Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate phylogeny their host”, we review relevant literature and data last decade, emphasizing frequently used methods regular patterns observed analyses. Quantitative is provided by statistical evaluating higher microbiome variation between host species than...
ABSTRACT Microbial communities play key roles in ocean ecosystems through regulation of biogeochemical processes such as carbon and nutrient cycling, food web dynamics, gut microbiomes invertebrates, fish, reptiles, mammals. Assessments marine microbial diversity are therefore critical to understanding spatiotemporal variations community structure function ecosystems. With recent advances DNA shotgun sequencing for metagenome samples computational analysis, it is now possible access the...
Abstract SAR11 is a dominant bacterial clade in marine oligotrophic ecosystems. can also be estuarine systems, where they are not well-studied. We examined the effects of season, nutrient concentrations, and salinity shaping subclade abundance, diversity, function, growth two Mid-Atlantic estuaries, Delaware Chesapeake Bays. Using metagenome-assembled genomes, we identified twelve distinct genomospecies within Ia, II, IIIa, V subclades, which made up to 60% total community. The functional...
Abstract Background Bioinformatics tools are commonly used for assessing potential protein allergenicity. While these methods have achieved good accuracies highly conserved sequences, they less effective when the overall similarity is low. In this study, we assessed feasibility of using position-specific scoring matrices as a basis predicting allergenicity in proteins. Results Two simple proteins, based on general and group-specific allergen profiles, presented. Testing results indicate that...