Berkeley Lab

ENIGMA Researchers Uncover Factors in Microbial Community Collapse

Serdar Turkarslan, a Senior Research Scientist at the Institute for Systems Biology in Seattle, Washington; along with a team of researchers has developed a framework to quantify microbial community resilience in the face of environmental changes. This framework will be invaluable for observing the behavior of microbial communities under simulations of current and projected environmental conditions. Their […]

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Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

  A collaboration of researchers at Johns Hopkins University, Colorado State University, The University of Tennessee, The Lawrence Berkley National Laboratory, The Massachusetts Institute of Technology, The University of Oklahoma and the University of Georgia, Oak Ridge National Laboratory researchers in the Bioscience Division for the ENIGMA have released an article in Environmental Science and Technology. They have […]

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Predicting metabolic properties using dynamic substrate preference

Exometabolomic profiling was used to examine the time-varying substrate depletion from a mixture of 19 amino acids and glucose by two Pseudomonads and one Bacillus FRC isolates. ENIGMA researchers at Lawrence Berkeley National Lab examined if the first substrates depleted resulted in maximal growth rate, or related to growth medium or biomass composition and found […]

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Metabolizing Data in the Cloud

ENIGMA researchers at Scripps Research Institute have developed tools with available data to enable microbial and environmental research. ENIGMA’s XCMS Online systems biology data processing and the METLIN database represent a successful model of how community oriented cloud-computing can be implemented on a global scale. This free, cloud-based platform provides users with processing tools, data streaming, […]

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Uranium binding complex a potential tool for environmental sequestration of uranium

Widespread uranium contamination from industrial sources poses hazards to human health and the environment.  ENIGMA researchers from University of Georgia and Lawrence Berkeley National Lab identified a highly abundant uranium-binding complex (UBC) from Pelosinus sp. strain UFO1.  The complex makes up the primary protein component of the S-layer of strain UFO1 and binds 3.3 atoms of […]

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Stable protein interactome of the model sulfate reducing bacterium Desulfovibrio vulgaris Hildenborough

First demonstration of a highly accurate, genome-wide method for detecting stable protein-protein interactions, without the requirement for genetic manipulation of the organism (prior tagless methodologies have false discovery rates of >85%). Combined with our study of protein complexes published in February 2016, which was based on affinity purification coupled with mass spectroscopy (AP-MS), this experiment […]

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Benchmark properties for highly accurate bacterial protein interactions

SUMMARY Numerous affinity purification – mass-spectrometry (AP-MS) and yeast two hybrid (Y2H) screens have each defined thousands of pairwise protein-protein interactions (PPIs), most between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published […]

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Are free-living bacteria optimized by natural selection?

Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 1012 individuals and a typical level […]

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Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

Significant portions of natural groundwater reserves have been contaminated due to anthropogenic activities that result from by-products of industry, agricultural runoff, and human/animal waste. The contamination at the Department of Energy’s (DOE) Oak Ridge Integrated Field Research Challenge (OR-IFRC) includes radionuclides (e.g., uranium and technetium), nitrate, sulfide, and volatile organic compounds due to nuclear weapon […]

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Differences in diversity between extraction techniques

ENIGMA researchers at University of Tennessee Knoxville examined differences in diversity between extraction techniques. Lipid/DNA co-extraction from one sample is attractive in limiting biases associated with microbial community analysis from separate extractions. We sought to enhance established co-extraction methods and use high-throughput 16S rRNA sequencing to identify preferentially extracted taxa from co-extracted DNA. Co-extraction results […]

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Bacterial Communities As Precise Biosensors Of Environmental Damage

ENIGMA scientists show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate or oil. Bacterial communities yield a predictable response to environmental constraints. Bacterial systems can be used forensically to report the occurrence of environmental perturbations. Bacterial systems have the […]

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Metallomics of Two Microorganisms Featured on Metallomics Blog

Metallomics of Two Microorganisms Relevant to Heavy Metal Bioremediation Reveal Fundamental Differences in Metal Assimilation and Utilization was selected as a Hot Article and featured on the Metallomics blog.

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Desulfovibrio – Methanococcus Co-Evolution

Krona Website →

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Barcoded Transposon Mutant Library

A D. vulgaris Hildenborough barcoded transposon mutant library →

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DBC: Distribution-Based Clustering

Inferring operational taxonomic units (OTUs) by combining phylogenetic and ecological information.

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SLIME: Supervised Learning in Microbial Ecology

Machine learning tools for the analysis of 16S rRNA and shotgun metagenomics datasets.

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DOE Systems Biology Knowledgebase

DOE Systems Biology Knowledgebase Website →
ENIGMA data stored at KBase →

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ENIGMA 100-Well Survey Data Site

ENIGMA Field Sample Info Site →

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Network Portal

Network Portal Website →
Desulfovibrio Netowrk Portal →

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MicrobesOnline

MicrobesOnline Website →

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Gaggle

Gaggle Website →

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GLAMM: Genome-Linked Application for Metabolic Maps

GLAMM Website →

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METLIN: Metabolite and Tandem MS Database

METLIN Website →

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RegPrecise

RegPrecise Website →

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SIFTER: Statistical Inference of Function Through Evolutionary Relationships

SIFTER Website →

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RegTransBase

RegTransBase Website →

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XCMS Online: Scripps Center for Metabolomics

XCMS Online →

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RegPredict

RegPredict Website →

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Functional Gene Array Design and Microarray Data

Website →

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OpenMSI: Open Mass Spectrometry Imaging

OpenMSI Website →

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