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Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges

A fatal bulking phenomenon was found to occur occasionally in the methanogenic granular sludge of a mesophilic ( 35 – 40 degrees C), full- scale upflow anaerobic sludge blanket ( UASB) reactor treating organic wastewater discharged from a sugar manufacturing factory. A vast number of filamentous cells were observed in the bulking sludge that were… [Read More]

Microbial genome data resources

Studies of the genomes of individual microbial organisms as well as aggregate genomes (metagenomes) of microbial communities are expected to lead to advances in various areas, such as healthcare, environmental cleanup, and alternative energy production. A variety of specialized data resources manage the results of different microbial genome data processing and interpretation stages, and represent… [Read More]

Comparative genome analysis in the integrated microbial genomes (IMG) system

Comparative genome analysis is critical for the effective exploration of a rapidly growing number of complete and draft sequences for microbial genomes. The Integrated Microbial Genomes (IMG) system (img.archive.jgi.doe.gov) has been developed as a community resource that provides support for comparative analysis of microbial genomes in an integrated context. IMG allows users to navigate the… [Read More]

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic… [Read More]

Accurate phylogenetic classification of variable-length DNA fragments

Metagenome studies have retrieved vast amounts of sequence data from a variety of environments leading to new discoveries and insights into the uncultured microbial world. Except for very simple communities, the encountered diversity has made fragment assembly and the subsequent analysis a challenging problem. A taxonomic characterization of metagenomic fragments is required for a deeper… [Read More]

Integrating ecology into biotechnology

New high-throughput culture-independent molecular tools are allowing the scientific community to characterize and understand the microbial communities underpinning environmental biotechnology processes in unprecedented ways. By creatively leveraging these new data sources, microbial ecology has the potential to transition from a descriptive to a predictive framework, in which ecological principles are integrated and exploited to engineer… [Read More]

Continuous molecular evolution of protein-domain structures by single amino acid changes

Protein structures cluster into families of folds that can result from extremely different amino acid sequences [11]. Because the enormous amount of genetic information generates a limited number of protein folds [2], a particular domain structure often assumes numerous functions. How new protein structures and new functions evolve under these limitations remains elusive. Molecular evolution… [Read More]

Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana

Diatoms are unicellular brown algae that likely arose from the endocytobiosis of a red alga into a single-celled heterotroph and that constitute an algal class of major importance in phytoplankton communities around the globe. The first whole-genome sequence from a diatom species, Thalassiosira pseudonana Hasle et Heimdal, was recently reported, and features that are central… [Read More]