A5002596998- Microbial Community Ecology and Physiology
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Genomics and Phylogenetic Studies
- Biofuel production and bioconversion
- Microbial Metabolic Engineering and Bioproduction
- Metabolomics and Mass Spectrometry Studies
- Gut microbiota and health
- Fullerene Chemistry and Applications
- Analytical Chemistry and Chromatography
- Microbial Fuel Cells and Bioremediation
- Chromium effects and bioremediation
- Methane Hydrates and Related Phenomena
- Metal Extraction and Bioleaching
- Ion-surface interactions and analysis
- Climate change and permafrost
- Probiotics and Fermented Foods
- Enzyme Production and Characterization
- Atmospheric and Environmental Gas Dynamics
- Advanced Chemical Physics Studies
- RNA and protein synthesis mechanisms
- Enzyme Catalysis and Immobilization
- Photosynthetic Processes and Mechanisms
- Anaerobic Digestion and Biogas Production
- Enzyme Structure and Function
Oak Ridge National Laboratory
2016-2025
University of Tennessee at Knoxville
2013-2023
Bioenergy Life Science (United States)
2010-2022
Dartmouth Hospital
2020
Dartmouth College
2020
St. Jude Children's Research Hospital
2020
Knoxville College
2019
Oak Ridge Associated Universities
2018
Joint Institute for Computational Sciences
2017
Lawrence Berkeley National Laboratory
2010-2016
The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and Bacteroidetes. Little known about factors that govern interactions between their members. Here, we examine niches of representatives both in vivo. Finished genome sequences were generated from Eubacterium rectale E. eligens, which belong to Clostridium Cluster XIVa, one most common Firmicute clades. Comparison these 25 other Bacteroidetes indicated possess smaller...
Bacterial PERegrinations Many branches of the bacterial domain life are only known from sequences that turn up in metagenomic analyses and still named by acronym—for example, phylum-level groups BD1-5, OP11, OD1, PERs. The parent organisms probably widespread, but they have not been cultured, very little is about their metabolisms or contributions functions natural environment. Wrighton et al. (p. 1661 ) pumped acetate into an aquifer Colorado to prompt naturally occurring bacteria action...
Using genomic and mass spectrometry–based proteomic methods, we evaluated gene expression, identified key activities, examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species biofilm, including 48% predicted dominant organism, Leptospirillum group II. Proteins involved protein refolding response to oxidative stress appeared be highly expressed, which suggests that damage...
In the biogeochemical nitrogen cycle, microbial respiration processes compete for nitrate as an electron acceptor. Denitrification converts into nitrogenous gas and thus removes fixed from biosphere, whereas ammonification ammonium, which is directly reusable by primary producers. We combined multiple parallel long-term incubations of marine nitrate-respiring communities with isotope labeling metagenomics to unravel how specific environmental conditions select either process. Microbial...
Recent studies have revealed a relationship between protein abundance and sampling statistics, such as sequence coverage, peptide count, spectral in label-free liquid chromatography−tandem mass spectrometry (LC−MS/MS) shotgun proteomics. The use of statistics offers promising method measuring relative detecting differentially expressed or coexpressed proteins. We performed systematic analysis various approaches to quantifying differential expression eukaryotic Saccharomyces cerevisiae...
Crohn's disease (CD) is an inflammatory bowel of complex etiology, although dysbiosis the gut microbiota has been implicated in chronic immune-mediated inflammation associated with CD. Here we combined shotgun metagenomic and metaproteomic approaches to identify potential functional signatures CD stool samples from six twin pairs that were either healthy, or had ileum (ICD) colon (CCD). Integration these omics revealed several genes, proteins, pathways primarily differentiated ICD healthy...
Malnutrition and dietary repair Childhood malnutrition is accompanied by growth stunting immaturity of the gut microbiota. Even after therapeutic intervention with standard commercial complementary foods, children may fail to thrive. Gehrig et al. Raman monitored metabolic parameters in healthy Bangladeshi those recovering from severe acute malnutrition. The authors investigated interactions between diet, microbiota development, recovery. Diets were then designed using pig mouse models nudge...
Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, there are gaps our knowledge—particularly for Archaea—that occur at relatively low abundance and extreme environments. Ultrasmall cells (<500 nm diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected a variety acidic ecosystems. We reconstructed composite, near-complete ~1-Mb three lineages, referred ARMAN...
A variety of quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling using iTRAQ or TMT. Here, these were compared in terms the depth proteome coverage, quantification accuracy, precision, reproducibility a high-performance hybrid mass spectrometer, LTQ Orbitrap Velos. Our results show that (1) spectral counting method provides deepest coverage for identification, but its performance is worse than labeling-based...
Artificial human gut microbial communities implanted into germ-free mice provide insights how species-level responses to changes in diet give rise community-level structural and functional reconfiguration types of bacteria prioritize use available nutrients vivo.
Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by intersecting activities of microbial community members, yet organisms responsible largely unknown. Metagenomic methods can identify functions, but genome recovery is often precluded data complexity. To address this limitation, we developed subsampling assembly to re-construct high-quality draft genomes from complex samples. We applied these evaluate interlinked roles most abundant biogeochemical cycling...
Vitamin and mineral (micronutrient) deficiencies afflict 2 billion people. Although the impact of these imbalances on host biology has been studied extensively, much less is known about their effects gut microbiota developing or adult humans. Therefore, we established a community cultured, sequenced human gut-derived bacterial species in gnotobiotic mice fed animals defined micronutrient-sufficient diet, followed by derivative diet devoid vitamin A, folate, iron, zinc, return to sufficient...
Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important characterizing an organism's physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer conditions the isolation of ectosymbiotic Nanoarchaeota ('Nanopusillus acidilobi') host (Acidilobus, a crenarchaeote) from terrestrial geothermal environment. The cells 'Nanopusillus' are among smallest known cellular...
By means of high-resoluton transmission electron microscopy, both C(60) and C(70) fullerenes have been found in a, carbon-rich Precambrian rock from Russia The were confirmed by Fourier transform mass spectrometry with laser desorption thermal desorption/electron-capture methods to verify that the indeed present geological sample not generated ionization event. spectra measured under conditions sufficient resolve (13)C/(12)C isotopic ratios for indicate these correspond normal range values.
Using genomic and mass spectrometry–based proteomic methods, we evaluated gene expression, identified key activities, examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species biofilm, including 48% predicted dominant organism, Leptospirillum group II. Proteins involved protein refolding response to oxidative stress appeared be highly expressed, which suggests that damage...
We report the observation of long-lived (\ensuremath{\tau}>${10}^{\mathrm{\ensuremath{-}}3}$ sec) doubly charged negative ions ${\mathrm{C}}_{60}$ in gas phase. ${\mathrm{C}}_{60}^{\mathrm{\ensuremath{-}}}$ and ${\mathrm{C}}_{60}^{2\mathrm{\ensuremath{-}}}$ are produced by laser desorption from a surface covered with molecules believed to be ionization laser-heated surface. Pseudopotential calculations indicate that is slightly bound (electron affinity...
Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead ecological divergence. To address this relationship ecosystem context, we investigated links between genotype ecology of two genotypic groups Leptospirillum group II bacteria comprehensively characterized, natural acidophilic biofilm communities. These share 99.7% 16S rRNA identity 95% average amino acid their orthologs. One predominates during early...
Temporal genomic profiling and whole-cell proteomic analyses were performed to characterize the dynamic molecular response of metal-reducing bacterium Shewanella oneidensis MR-1 an acute chromate shock. The complex dynamics cellular processes demand integration methodologies that describe biological systems at levels regulation, gene protein expression, metabolite production. Genomic microarray analysis transcriptome midexponential phase cells subjected 1 mm potassium (K2CrO4) exposure time...