A5046575171- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Legume Nitrogen Fixing Symbiosis
- Protist diversity and phylogeny
- Methane Hydrates and Related Phenomena
- Biofuel production and bioconversion
- Probiotics and Fermented Foods
- Metal Extraction and Bioleaching
- Bacteriophages and microbial interactions
- Plant nutrient uptake and metabolism
- Enzyme Production and Characterization
- Plant Disease Resistance and Genetics
- Wastewater Treatment and Nitrogen Removal
- Microbial metabolism and enzyme function
- Anaerobic Digestion and Biogas Production
- Microbial Fuel Cells and Bioremediation
- Plant Pathogenic Bacteria Studies
- Plant-Microbe Interactions and Immunity
- Microbial Metabolism and Applications
- Identification and Quantification in Food
- Laser-Plasma Interactions and Diagnostics
- Oral microbiology and periodontitis research
- Microbial Natural Products and Biosynthesis
- Mine drainage and remediation techniques
- Bacterial Identification and Susceptibility Testing
Los Alamos National Laboratory
2015-2024
The Christie NHS Foundation Trust
2023
University of Rochester
2020
Energetics (United States)
2020
Santa Fe Institute
2019
University of Michigan
2019
Joint Genome Institute
2009-2018
Cranfield University
2018
Lawrence Livermore National Laboratory
2010-2013
Lawrence Berkeley National Laboratory
2013
The bacterial and archaeal genomes that have been sequenced to date were chosen for sequencing based mainly on their physiology, which is fine but has resulted in a distinct phylogenetic bias. An alternative approach taken the Genomic Encyclopedia of Bacteria Archaea (GEBA) project, advocates choosing organism's position, with aim filling gaps along branches tree life. value this demonstrated by pilot study genome sequences 56 culturable species selected maximize coverage. Analysis provides...
The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth morphologies and ecologies; they play key roles in global carbon nitrogen cycles. chloroplasts all eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology biofuels. To explore the molecular basis different phenotypes biochemical capabilities, we sequenced genomes 54 phylogenetically phenotypically diverse strains....
Although Escherichia coli is the most widely studied bacterial model organism and often considered to be bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of G enomic E ncyclopedia B acteria A rchaea project, we here describe features E. DSM 30083T together with genome sequence annotation as well novel aspects phenotype. The 5,038,133 bp containing includes 4,762 protein-coding genes 175 RNA single plasmid. Affiliation set 250 genome-sequenced...
Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini), which uses fresh leaves cultivate a fungus for food specialized gardens. Using combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that garden microbiome ants composed diverse community bacteria high biomass-degrading capacity. Comparison...
The two microaerophilic, Fe-oxidizing bacteria (FeOB) Sideroxydans ES-1 and Gallionella ES-2 have single circular chromosomes of 3.00 3.16 Mb that encode 3049 3006 genes, respectively. Multi-locus sequence analysis (MLSA) confirmed the relationship these organisms to one another, indicated they may form a novel order, Gallionellalaes, within Betaproteobacteria. Both are adapted for chemolithoautotropy, including pathways CO2-fixation, electron transport growth at low O2-levels, an important...
Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which also one only two cultivated species in phylum, efficient and prolific degrader cellulose. Specifically, it has a particularly high activity against crystalline cellulose requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, does not degrade using cellulosome or producing...
Bacillus anthracis, cereus, and thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains anthracis reveal conspicuous sequence homogeneity, environmental isolates exhibit extensive genetic diversity. Here we report sequencing comparative analysis genomes two members group, 97-27 subsp. konkukian serotype H34, isolated from a necrotic human wound, E33L, which was swab zebra carcass in Namibia. These strains,...
Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation both biogenic compounds and anthropogenic contaminants. V. also engages in mutually beneficial interactions with bacteria plants. The complete genome sequence S110 composed 6,754,997 bp 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple features for autotrophic heterotrophic lifestyles. These...
ABSTRACT Sphingomonads comprise a physiologically versatile group within the Alphaproteobacteria that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, adaptations. Our multilocus phylogenetic average amino acid identity (AAI) analyses confirm Sphingomonas , Sphingobium Sphingopyxis Novosphingobium are well-resolved...
Background The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput data at low cost, while concomitantly creating a new set challenges. number available assembled microbial genomes continues to grow rapidly their quality reflects technology used, but also analysis software employed assembly annotation. Methodology/Principal Findings In this work, we have explored draft across various technologies. We compared finished assemblies 133 sequenced...
Plants represent a large reservoir of organic carbon comprised primarily recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants paradigmatic example. These use fresh foliar biomass as manure cultivate gardens composed Leucoagaricus gongylophorus, basidiomycetous fungus produces specialized hyphal swellings serve food source for the host ant colony....
ABSTRACT Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of model obligate methylamine utilizer, Methylobacillus flagellatus (strain KT) was sequenced. is represented by single circular chromosome approximately 3 Mbp, potentially encoding total 2,766 proteins. Based on analysis as well the results...
The complete and assembled genome sequences were determined for six strains of the alphaproteobacterial genus Methylobacterium, chosen their key adaptations to different plant-associated niches environmental constraints.
Abstract Background Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at genetic and phenotypic level present in natural populations this species, especially relation with promotion plant growth. AK83 BL225C are two nodule-isolated strains diverse phenotypes; more efficient promoting growth Medicago sativa plants than strain AK83. In order to investigate determinants diversification S. BL225C, we sequenced complete genomes...
Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of species, phylogenetic interest because its location in Dermacoccaceae, a poorly studied family within actinobacterial suborder Micrococcineae. known for production oligoketide antibiotics as well role an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, pitted keratolysis. It strictly aerobic can only grow when several amino acids are provided medium. The described this...
Methylosinus trichosporium OB3b (for "oddball" strain 3b) is an obligate aerobic methane-oxidizing alphaproteobacterium that was originally isolated in 1970 by Roger Whittenbury and colleagues. This has since been used extensively to elucidate the structure function of several key enzymes methane oxidation, including both particulate soluble monooxygenase (sMMO) extracellular copper chelator methanobactin. In particular, catalytic properties from M. have well characterized context with...
Odoribacter splanchnicus (Werner et al. 1975) Hardham 2008 is the type species of genus Odoribacter, which belongs to family Porphyromonadaceae in order ‘Bacteroidales’. The interest because members form an isolated cluster within Porphyromonadaceae. This first completed genome sequence a member and fourth from 4,392,288 bp long with its 3,672 protein-coding 74 RNA genes part Genomic Encyclopedia Bacteria Archaea project.
ABSTRACT Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for involving and production various biofuels other industrial products. To expand knowledge base clostridial relevant current biofuel efforts, we sequenced genomes 20 spanning multiple genera. The majority fall within class III cellulosome-encoding V saccharolytic Thermoanaerobacteraceae...
Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that member of the phylum Firmicutes. Here, we describe complete genome this microbe. This will be useful for rumen microbiology and cellulosome biology in biofuel production, as one its major fermentation products ethanol.
Carbon monoxide (CO) is commonly known as a toxic gas, yet both cultivation studies and emerging genome sequences of bacteria archaea establish that CO widely utilized microbial growth substrate. In this study, we determined the prevalence anaerobic carbon dehydrogenases ([Ni,Fe]-CODHs) in currently available genomic sequence databases. Currently, 185 out 2887, or 6% sequenced bacterial archaeal genomes possess at least one gene encoding [Ni,Fe]-CODH, key enzyme for utilization. Many encode...
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication forming buds directly spherical, ovoid or pear-shaped mother and a wall consisting of proteinaceous layer rather than peptidoglycan layer. The first strains P. brasiliensis, including type strain IFAM 1448T, were isolated water sample Lagoa Vermelha, salt pit near Rio de Janeiro,...