A5042605429- Gut microbiota and health
- Aquaculture disease management and microbiota
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Nutrition, Genetics, and Disease
- Food Industry and Aquatic Biology
- SARS-CoV-2 detection and testing
- Environmental DNA in Biodiversity Studies
- Spaceflight effects on biology
- COVID-19 diagnosis using AI
- Molecular Biology Techniques and Applications
- Pharmaceutical and Antibiotic Environmental Impacts
- Coral and Marine Ecosystems Studies
- Space Exploration and Technology
- Coastal wetland ecosystem dynamics
- Indoor Air Quality and Microbial Exposure
- Respiratory viral infections research
- Fish Ecology and Management Studies
- Aquaculture Nutrition and Growth
- Isotope Analysis in Ecology
- Ocean Acidification Effects and Responses
- Marine and coastal plant biology
- Marine Biology and Ecology Research
- Marine Bivalve and Aquaculture Studies
Salk Institute for Biological Studies
2021-2025
University of California, San Diego
2016-2024
Scripps Institution of Oceanography
2018-2024
SeaWorld Entertainment
2022
Hubbs-Sea World Research Institute
2022
University of Konstanz
2022
SUNY College of Environmental Science and Forestry
2020
State University of New York
2020
York University
2020
University of San Diego
2020
The International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. To date, mandatory microbial monitoring observational studies of spacecraft space stations have been conducted traditional culture methods, although it known many microbes cannot be cultured with standard techniques. fully appreciate the true number diversity survive in ISS, molecular...
Microbial sequences inferred as belonging to one sample may not have originated from that sample. Such contamination arise laboratory or reagent sources physical exchange between samples. This study seeks rigorously assess the behavior of this often-neglected between-sample contamination. Using unique bacteria, each assigned a particular well in plate, we frequency at which source appear other wells. We evaluate effects different DNA extraction methods performed two laboratories using...
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure function microbial communities multiple habitats on a planetary scale. Here we present multi-omics analysis diverse set 880 community samples collected for Earth Microbiome Project. We include amplicon (16S, 18S, ITS) shotgun metagenomic sequence data, untargeted metabolomics data (liquid chromatography-tandem mass spectrometry gas chromatography...
Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass represent a niche that is often understudied because technical constraints. Many studies attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results typically false positive signals obtained during the sampling process. We have investigated various kits methods determine limit detection pipelines. Here we present KatharoSeq, high-throughput protocol...
Many tools for dealing with compositional ' 'omics' data produce feature-wise values that can be ranked in order to describe features' associations some sort of variation. These include differentials (which specified covariates) and feature loadings variation along a given axis biplot). Although prior work has discussed the use these 'rankings' as starting point exploring log-ratios particularly high- or low-ranked features, such exploratory analyses have previously been done using custom...
Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week incubation experiment, tested independent combined effects of temperature partial pressure carbon dioxide (pCO2), microbiomes foundation species, giant kelp Macrocystis pyrifera, surrounding water column. The microbiome responded differently to each stressors. microbiome, condition caused an...
Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) require more water than recirculating systems (RAS), which enable up to 99% their be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological physical microbiome interactions three Atlantic salmon (RAS n = 2, FT 1). Gill, skin, digesta from six juvenile along with...
Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries increasing stress and disease. To understand how environment host biology drives mucosal microbiomes in marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], pyloric ceca) from 229 Pacific chub mackerel,
Abstract Fish are the most diverse and widely distributed vertebrates, yet little is known about microbial ecology of fishes nor biological environmental factors that influence fish microbiota. To identify explain diversity patterns in a geographical subset marine fish, we analyzed microbiota (gill tissue, skin mucus, midgut digesta hindgut digesta) from 101 species Southern California fishes, spanning 22 orders, 55 families 83 genera, representing ~25% local diversity. We compare alpha,...
Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems potentially members human microbiome, beyond those that can cause disease. To expand our analysis microbial to include data from fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against standardized protocol for archaea using 16S rRNA gene amplicon-...
Reduced costs of sequencing have tremendously impacted the field microbial ecology, allowing scientists to design more studies with larger sample sizes that often exceed 10,000 samples. Library preparation not kept pace prices, although automated liquid handling robots provide a unique opportunity bridge this gap while also decreasing human error. Here, we take advantage an acoustic robot develop high-throughput miniaturized library method highly cited and broadly used 16S rRNA gene amplicon...
Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to length time required generate analyze omics data. Here, we applied a novel integrated pipeline for analysis human environmental samples under 48 h. Human subjects that ferment their own foods provided swab from skin, feces, oral cavity, fermented foods, household surfaces assess impact home...
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from assembly abundant microbes in many rather than exhaustive fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for metagenomics real we introduce a benchmark library prep and sequencing using internal references generated by synthetic long-read technology, allowing us evaluate high-throughput preparation methods against...
Abstract Background Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration longitudinal microbial and chemical data is necessary illuminate how gut supplement energetic nutritional requirements animals. Although mammalian systems are well-studied this capacity, role microbes breakdown utilization recalcitrant marine macroalgae herbivorous fish relatively understudied an emerging priority for bioproduct...
Next-generation sequencing sample preparation requires nanogram to microgram quantities of DNA; however, many relevant samples are comprised only a few cells. Genomic analysis these whole genome amplification method that is unbiased and free exogenous DNA contamination. To address challenges we have developed protocols for the production DNA-free consumables including reagents improved upon multiple displacement (iMDA). A specialized ethylene oxide treatment was renders present within Gram...
One goal of microbial ecology researchers is to capture the maximum amount information from all organisms in a sample. The recent COVID-19 pandemic, caused by RNA virus SARS-CoV-2, has highlighted gap traditional DNA-based protocols, including high-throughput methods authors previously established as field standards. To enable simultaneous SARS-CoV-2 and community profiling, compared relative performance two total nucleic acid extraction protocols with authors' benchmarked protocol. included...
ABSTRACT Sorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a stratified soil microbiome plays crucial role plant health, growth, carbon storage. Microbiome studies on agricultural soils, particularly fields growing S. bicolor , have been mostly limited surface soils (<30 cm). Here we investigated the abiotic factors of properties, field location, depth, biotic sorghum type across 38 genotypes...
Abstract The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial productivity as a natural feed source fish. To understand if pond fertilization livestock manure induces probiotic or prebiotic effect, we communally reared tilapia ( Oreochromis shiranus ), and North African catfish Clarias gariepinus for 4 weeks under seven treatments including layer chicken, broiler guinea fowl, quail, pig, cow, vs. commercial...
Abstract Background Determining the role of fomites in transmission SARS-CoV-2 is essential hospital setting and will likely be important outside medical facilities as governments around world make plans to ease COVID-19 public health restrictions attempt safely reopen economies. Expanding testing include environmental surfaces would ideally performed with inexpensive swabs that could transported without concern being a source new infections. However, CDC-approved clinical-grade sampling...