A5016666109- Scientific Computing and Data Management
- Research Data Management Practices
- Plant Pathogens and Fungal Diseases
- Microbial Community Ecology and Physiology
- Mycorrhizal Fungi and Plant Interactions
- Gut microbiota and health
- Mycotoxins in Agriculture and Food
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Antifungal resistance and susceptibility
- Bioinformatics and Genomic Networks
- Spaceflight effects on biology
- Diet and metabolism studies
- Plant-Microbe Interactions and Immunity
- High Altitude and Hypoxia
- Biomedical Text Mining and Ontologies
- Metabolomics and Mass Spectrometry Studies
- Plant and Biological Electrophysiology Studies
- SARS-CoV-2 detection and testing
- Helicobacter pylori-related gastroenterology studies
- Barrier Structure and Function Studies
- Biosensors and Analytical Detection
- Bacterial biofilms and quorum sensing
- Fungal and yeast genetics research
- Bacillus and Francisella bacterial research
Los Alamos National Laboratory
2019-2025
Michigan State University
2025
New Mexico Consortium
2025
Bioscience (Slovakia)
2020
Abstract Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number diversity examinations have increased, but current knowledge is predominantly limited to a small taxa partners. Here, we screened for potential over 700 phylogenetically diverse isolates, representing 366 genera, or tenfold increase compared with previously examined including isolates from several unexplored phyla. Both 16 S rDNA-based exploration four...
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...
The ISS rodent habitat has provided crucial insights into the impact of spaceflight on mammals, inducing symptoms characteristic liver disease, insulin resistance, osteopenia, and myopathy. Although these physiological responses can involve microbiome Earth, host-microbiota interactions during are still being elucidated. We explore murine gut microbiota host gene expression in colon after 29 56 days using multiomics. Metagenomics revealed significant changes 44 species, including relative...
Bacterial-fungal interactions (BFIs) play an integral role in shaping microbial community composition, biogeochemical functions, spatial dynamics, and dispersal. Mycelial networks created by filamentous fungi or other microorganisms (e.g., Oomycetes) act as 'fungal highways' that can be utilized bacteria for transport throughout heterogeneous environments, greatly facilitating their mobility granting them access to regions may challenging impossible reach on own due air pockets within the...
The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used interrogate diverse samples. However, due lagging awareness and implementation standards data stewardship, many datasets are produced that not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes community-learning model annually train cohort early-career researchers in stewardship best...
Aspergillus fungi are opportunistic pathogens that affect millions of people worldwide. Aspergilli produce organic acids to optimize the environmental pH and match needs their enzymatic machinery. In this study, we tested hypothesis also occurs during infection. By producing oxalic acid (OA), would manipulate lung infection thus, interfering with process could control pathogen. To test hypothesis, assessed in silico potential for OA production a wide range Aspergilli. A genetic marker AO was...
Microbiome research is becoming a mature field with wealth of data amassed from diverse ecosystems, yet the ability to fully leverage multi-omics for reuse remains challenging. To provide view into researchers' behavior and attitudes towards reuse, we surveyed over 700 microbiome researchers evaluate sharing challenges. We found that many are impeded by difficulties metadata records, challenges processing bioinformatics, problems repository submissions. also explored cost constraints at each...
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...
Bacteria-fungi interactions (BFIs) are essential in ecosystem functioning. These modulated not only by local nutritional conditions but also the physicochemical constraints and 3D structure of environmental niche. In soils, unsaturated complex nature substrate restricts dispersal activity bacteria. Under conditions, some bacteria engage with filamentous fungi an interaction (fungal highways) which they use fungal hyphae to disperse. Based on a previous experimental device enrich pairs...
Crohn's disease (CD) is a chronic inflammatory bowel (IBD) of the digestive tract in humans. There evidence that Parabacteroides distasonis could contribute to IBD. Here, we present complete genome sequence strain designated CavFT-hAR46, which was isolated from gut intramural cavernous fistulous (CavFT) microlesion CD patient.
Several bacteria have long been known to interact intimately with fungi, but molecular approaches only recently uncovered how cosmopolitan these interactions are in nature. Currently, bacterial-fungal (BFI) inferred based on patterns of co-occurrence amplicon sequencing investigations. However, determining the nature interactions, whether internally or externally associated, remains a grand challenge BFI research. Fluorescence situ hybridization (FISH) is robust method that targets unique...
Yersinia pestis is a category A infective agent that causes bubonic, septicemic, and pneumonic plague. Notably, the acquisition of antimicrobial or multidrug resistance through natural purposed means qualifies Y. as potential biothreat agent. Therefore, high-quality antibodies designed for accurate sensitive diagnostics, therapeutics potentiating replacing traditional antibiotics are utmost need national security public health preparedness.Here, we describe set human monoclonal...
Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well the curation and maintenance of such large collections can be challenging. Genomes eukaryotic organelles, chloroplasts other plastids, particularly susceptible assembly errors misrepresentations in these due their close evolutionary relationships with bacteria, which may co-occur within same environment, case when plants. Here, based on sequence similarities bacterial genomes,...
Members of the fungal genus Morchella are widely known for their important ecological roles and significant economic value. In this study, we used amplicon genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well vegetative mycelium sclerotia obtained isolates grown in vitro . These investigations included diverse representatives both Elata Esculenta clades. Unique community compositions were observed across various...
<title>Abstract</title> The rodent habitat on the International Space Station has provided crucial insights into impact of spaceflight mammals, inducing symptoms characteristic liver disease, insulin resistance, osteopenia, and myopathy. Although these physiological responses can involve microbiome when observed Earth, changes in host-microbiota interactions during are still being elucidated. Here, we explore murine gut microbiota host gene expression colon after 29 56-days using multiomic...