A5073638902- Antifungal resistance and susceptibility
- Advanced Proteomics Techniques and Applications
- Microbial Community Ecology and Physiology
- Infections and bacterial resistance
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Enterobacteriaceae and Cronobacter Research
- Metabolomics and Mass Spectrometry Studies
- Food composition and properties
- Polar Research and Ecology
- Genetics, Bioinformatics, and Biomedical Research
- Fungal Infections and Studies
- Advanced Biosensing Techniques and Applications
- Microbial Metabolites in Food Biotechnology
- Climate change and permafrost
- Bacteriophages and microbial interactions
- Polysaccharides and Plant Cell Walls
- Advanced Glycation End Products research
- Infant Nutrition and Health
- Clostridium difficile and Clostridium perfringens research
- Methane Hydrates and Related Phenomena
- RNA modifications and cancer
- Geophysics and Gravity Measurements
- Epigenetics and DNA Methylation
Oak Ridge National Laboratory
2019-2025
University of Tennessee at Knoxville
2020-2022
Knoxville College
2022
Abstract Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out community-driven, multi-laboratory comparison metaproteomics: critical assessment metaproteome investigation study (CAMPI). Based well-established workflows, evaluate effect sample preparation, mass spectrometry, and bioinformatic analysis using two...
Abstract Previous bioinformatic analyses of metagenomic data have indicated that bacteriophages can use genetic codes different from those their host bacteria. In particular, reassignment stop codon TAG to glutamine (a variation known as ‘genetic code 15’) has been predicted. Here, we LC-MS/MS-based metaproteomics human fecal samples provide experimental evidence the 15 in two crAss-like phages. Furthermore, proteomic several phage structural proteins supports late infection cycle. Thus, our...
Abstract Background Fecal samples are widely used as a proxy for studying gut microbiome composition in both human and animal research. metaproteomics provides valuable insights by tracking changes the relative abundance of microbial taxa their protein functions. To ensure reliable results, it is crucial to minimize alterations metaproteome occurring from sample collection extraction. Therefore, employing effective stabilization methods essential preserve integrity fecal laboratory analysis,...
Abstract. Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology biogeochemical studies. A blinded multi-laboratory intercomparison was conducted assess comparability reproducibility taxonomic functional results their sensitivity methodological variables. Euphotic zone samples from Bermuda Atlantic Time-series Study (BATS) in North Ocean collected by situ...
Abstract Background Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. has primarily studied pure culture, leaving gaps understanding its function microbiome context. Results Here, we compare five unique genomes assembled from premature infant fecal samples, three which are newly reconstructed, analyze their genome structure, population diversity, situ activity relative to reference...
Abstract Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carried out first community-driven, multi-laboratory comparison metaproteomics: critical assessment metaproteome investigation study (CAMPI). Based well-established workflows, evaluated effect sample preparation, mass spectrometry, and bioinformatic analysis using...
Abstract. Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology biogeochemical studies. A blinded multi-laboratory intercomparison was conducted assess comparability reproducibility taxonomic functional results their sensitivity methodological variables. Euphotic zone samples from Bermuda Atlantic Time-Series Study in North Ocean collected by situ pumps...
Abstract Numerous genetic codes developed during the evolution of Eukaryotes and three are known in Bacteria, yet no alternative code has been established for Archaea. Some bacterial archaeal proteins include selenocysteine or pyrrolysine, 21 st 22 nd amino acids, but evidence establishes adoption a which stop codon universally encodes either acid. Here, we used proteomics to confirm prediction that certain Archaea consistently incorporate pyrrolysine at TAG codons, supporting new designate...
Methods for measuring gut microbiota biochemical activities in vivo are needed to characterize its functional states health and disease. To illustrate one approach, an arabinan-containing polysaccharide was isolated from pea fiber, structure defined, forward genetic proteomic analyses used compare effects, versus unfractionated fiber sugar beet arabinan, on a human bacterial strain consortium gnotobiotic mice. We produced ‘Microbiota Functional Activity Biosensors’ (MFABs) consisting of...
The human gut microbiome produces a complex mixture of biomolecules that interact with physiology and play essential roles in health disease. Crosstalk between micro-organisms host cells is enabled by different direct contacts, but also the export molecules through secretion systems extracellular vesicles. resulting molecular network, comprised various biomolecular moieties, has so far eluded systematic study. Here we present methodological framework, optimized for extraction...
Informatic Intercomparison MethodologiesLab 109: The raw files were searched against the metagenomic database employing a 2 round search using PEAKS Studio X.The initial was performed to focus for protein sequences with peptide sequence matches at 5% FDR.The focused further used second search, which allowed parent mass error tolerance of 10.0 ppm and fragment 0.6 Da.The considered up 3 missed cleavages, carbamidomethylation as fixed methionine oxidation N-terminal acetylation variable...
Abstract Metagenomic findings suggesting that bacteriophages (phages) can use genetic codes different from those of their host bacteria reveal a new dimension phage-host interaction dynamics. Whereas reassignment stop codons to code for amino acids has been predicted, there no proteomic validation alternative coding in phages. In fact, one where the codon TAG is reassigned glutamine (code 15) never experimentally validated any biological system. Here, we characterized two crAss-like phages...
The human gut microbiome, which develops and stabilizes during the early stages of infant life, plays an essential role in host health through production metabolic resources stimulation training immune system. To study colonization community functional dynamics microbiota based on responses to processes normal dysbiotic establishment gut, metaproteomics was conducted 91 fecal samples collected over first 90 days life from 17 hospitalized premature infants. Microbial antibiotic administration...
ABSTRACT Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. has primarily studied pure culture, leaving gaps understanding its function microbiome context. Here, we reconstructed five unique genomes from premature infant fecal samples analyzed their genome structure, population diversity situ activity relative to reference strains culture. All contain hotspots single nucleotide...
Abstract Methods for measuring gut microbiota biochemical activities in vivo are needed to characterize its functional states health and disease. To illustrate one approach, an arabinan-containing polysaccharide was purified from pea fiber, structure defined, forward genetic proteomic analyses used compare effects, versus unfractionated fiber sugar beet arabinan, on a human bacterial strain consortium gnotobiotic mice. We produced ‘Microbiota Functional Activity Biosensors’ (MFABs)...