A5023134115- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Microbial metabolism and enzyme function
- Legume Nitrogen Fixing Symbiosis
- Protist diversity and phylogeny
- Plant-Microbe Interactions and Immunity
- Biofuel production and bioconversion
- Plant Pathogens and Fungal Diseases
- Polar Research and Ecology
- Methane Hydrates and Related Phenomena
- Plant Pathogenic Bacteria Studies
- Bacteriophages and microbial interactions
- Metal Extraction and Bioleaching
- Anaerobic Digestion and Biogas Production
- Microbial bioremediation and biosurfactants
- Mycorrhizal Fungi and Plant Interactions
- Microbial Fuel Cells and Bioremediation
- Microbial Metabolic Engineering and Bioproduction
- Wastewater Treatment and Nitrogen Removal
- Microbial Natural Products and Biosynthesis
- Plant and fungal interactions
- Enzyme-mediated dye degradation
- Infant Development and Preterm Care
- Yeasts and Rust Fungi Studies
- Molecular Biology Techniques and Applications
Joint Genome Institute
2014-2024
Lawrence Berkeley National Laboratory
2011-2024
United States Department of Energy
2022
Los Alamos National Laboratory
2015-2017
Service Interdisciplinaire sur les Systèmes Moléculaires et les Matériaux
2016
University of Illinois Chicago
2012-2013
Health and Human Development (2HD) Research Network
2013
Comer Children's Hospital
2013
University of Pennsylvania
2013
Lawrence Livermore National Laboratory
2004-2009
The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking software for metagenome assembly, binning and taxonomic profiling. Methods profiling are key to interpreting data, but lack consensus about complicates performance assessment. challenge has engaged the global developer benchmark their programs on highly complex realistic data sets, generated ∼700 newly sequenced microorganisms ∼600 novel viruses...
The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing complete open reading frame (ORF) for every human mouse gene. initially used random strategy select clones from large number libraries diverse tissues. Candidate were chosen based on 5′-EST sequences, then fully sequenced high accuracy analyzed by algorithms developed this project. Currently, more than 11,000 10,000 genes are...
Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic non-symbiotic strains from very wide range of environmental (soil, water, plants, fungi) clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis 16S rRNA sequences, concantenated 4⁻7 housekeeping gene lately by genome sequences. Currently, division this group into Burkholderia, Caballeronia, Paraburkholderia, Robbsia strongly supported...
Summary Pseudomonas is a large and diverse genus of Gammaproteobacteria . To provide framework for discovery evolutionary taxonomic relationships these bacteria, we compared the genomes type strains 163 species 3 additional subspecies , including 118 sequenced herein. A maximum likelihood phylogeny 166 based on protein sequences 100 single‐copy orthologous genes revealed thirteen groups composed two to sixty three each. Pairwise average nucleotide identities alignment fractions were...
Abstract Marine algae convert a substantial fraction of fixed carbon dioxide into various polysaccharides. Flavobacteriia that are specialized on algal polysaccharide degradation feature genomic clusters termed utilization loci (PULs). As knowledge extant PUL diversity is sparse, we sequenced the genomes 53 North Sea and obtained 400 PULs. Bioinformatic annotations suggest usage large array polysaccharides, including laminarin, α-glucans, alginate as well mannose-, fucose-, xylose-rich...
Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, 6200 rat genes. The MGC cloning effort initially relied on random expressed tag screening of libraries. Here, we summarize our recent progress using directed RT-PCR DNA synthesis. now contains clones entire protein-coding 92% 89% genes curated (NM-accession) transcripts, 97% 96% transcripts that have or more...
Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding generic boundaries and composition this large heterogeneous taxon. Here we used amino acid nucleotide sequences 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which investigate structure sensu lato. These data unambiguously supported five distinct lineages, four correspond stricto newly introduced genera Paraburkholderia, Caballeronia...
Neutrophilic microaerophilic iron-oxidizing bacteria (FeOB) are thought to play a significant role in cycling of carbon, iron and associated elements both freshwater marine iron-rich environments. However, the roles neutrophilic FeOB still poorly understood due largely difficulty cultivation lack functional gene markers. Here, we analyze genomes two stalk-forming FeOB, Ferriphaselus amnicola OYT1 strain R-1. Phylogenetic analyses confirm that these distinct species within Betaproteobacteria;...
Abstract There is a need to clarify relationships within the actinobacterial genus Micromonospora , type of family Micromonosporaceae given its biotechnological and ecological importance. Here, draft genomes 40 strains two non-type are made available through Genomic Encyclopedia Bacteria Archaea project used generate phylogenomic tree which showed they could be assigned well supported phyletic lines that were not evident in corresponding trees based on single concatenated sequences conserved...
The permafrost soils of the high elevation McMurdo Dry Valleys are most cold, desiccating and oligotrophic on Earth. Rhodococcus sp. JG3 is one very few bacterial isolates from Antarctic Valley permafrost, displays subzero growth down to −5°C. To understand how able survive extreme conditions be metabolically active at temperatures, we sequenced its genome compared it genomes 14 mesophilic rhodococci. possessed a higher copy number genes for general stress response, UV protection cold shock,...
The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae renowned producers of secondary metabolites commercial interest, yet only a small part its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context phylum-wide analysis 6,700 including public isolates metagenome-assembled (MAGs). We estimate that 30%–50% projected phylogenetic possesses genomic representation...
Abstract Dinitrogen (N2)-fixation by cyanobacteria in symbiosis with feathermosses is the primary pathway of biological nitrogen (N) input into boreal forests. Despite its significance, little known about cyanobacterial gene repertoire and regulatory rewiring needed for establishment maintenance symbiosis. To determine acquisitions changes allowing to form maintain this symbiosis, we compared genomically closely related symbiotic-competent -incompetent Nostoc strains using a proteogenomics...
Three strains of methylotrophic Rhodocyclaceae (FAM1(T), RZ18-153 and RZ94) isolated from Lake Washington sediment samples were characterized. Based on phylogenetic analysis 16S rRNA gene sequences the should be assigned to genus Methyloversatilis. Similarly other members family, show broad metabolic capabilities are able utilize a number organic acids, alcohols aromatic compounds in addition methanol methylamine. The main fatty acids 16:1ω7c (49-59%) 16:0 (32-29%). Genomes all isolates...
Cyanobacteria belonging to the genus Nostoc comprise free-living strains and also facultative plant symbionts. Symbiotic can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated evolutionary transition from symbiont. Here, we compared genomes derived 11 symbiotic isolated different plants infer phylogenetic relationships between strains. Phylogenetic reconstructions 89 Nostocales showed that a broad range, entering epiphytic...
Abstract Background Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar differ all other cold by experiencing 24-h sunlight in summer no winter. The Vestfold Hills East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years ago. Ace Lake is meromictic (stratified) lake this region has been intensively studied since 1970s. Here, total...
ABSTRACT The genomes of Methylosarcina lacus LW14 T (=ATCC BAA-1047 = JCM 13284 ), Methylobacter sp. strain 21/22, 31/32, Methylomonas LW13, MK1, and 11b were sequenced are reported here. All the strains obligately methanotrophic bacteria isolated from sediment Lake Washington.
Abstract In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets evaluation metrics complicates proper performance assessment. The Critical Assessment Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on unprecedented complexity realism. Benchmark metagenomes were...
Serratia plymuthica WS3236 was selected for whole genome sequencing based on preliminary genetic and chemical screening indicating the presence of multiple natural product pathways. This led to identification a putative sodorifen biosynthetic gene cluster (BGC). The is volatile organic compound (VOC) with an unusual polymethylated hydrocarbon bicyclic structure (C16H26) produced by strains S. plymuthica. BGC encoding consists four genes, two which (sodA, sodB) are homologs genes enzymes...
PURPOSE: To identify infant and maternal characteristics associated with the pace of progression from first oral feeding to complete feeding. SUBJECTS: One hundred forty-two stable premature infants who were fully or partially gavage immediately after birth (29 34 weeks gestational age at birth). DESIGN: Exploratory secondary analysis. METHODS: Data are an ongoing randomized clinical trial a developmental maternally administered intervention (Hospital Home Transition–Optimizing Premature...
The genus Trichococcus currently contains nine species: T. flocculiformis, pasteurii, palustris, collinsii, patagoniensis, ilyis, paludicola, alkaliphilus, and shcherbakoviae. In general, species can degrade a wide range of carbohydrates. However, only pasteurii non-characterized strain Trichococcus, ES5, have the capacity converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis provides opportunity further explore physiological potential uncover novel properties this...
Abstract The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii , 57 saccharobutylicum 4 saccharoperbutylacetonicum 5 butyricum 7 acetobutylicum 3...
ABSTRACT Genome sequences of Methylobacter luteus , whittenburyi Methylosarcina fibrata Methylomicrobium agile and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.
Abstract Thiobacillus thioparus DSM 505 T is one of first two isolated strains inorganic sulfur-oxidising Bacteria . The original strain T. was lost almost 100 years ago and the working type Culture C (=DSM = ATCC 8158 ) by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It an obligate chemolithoautotroph that conserves energy oxidation reduced sulfur compounds using Kelly-Trudinger pathway uses it to fix carbon dioxide not capable heterotrophic or mixotrophic...
Summary We sequenced the genomes of 19 methylotrophic isolates from L ake W ashington, which belong to nine genera within eight families A lphaproteobacteria , two being newly proposed families. Comparative genomic analysis with a focus on methylotrophy metabolism classifies these strains into heterotrophic and obligately or facultatively autotrophic methylotrophs. The most persistent metabolic modules enabling this group are N ‐methylglutamate pathway, types methanol dehydrogenase ( MxaFI...