Approaches for in silico finishing of microbial genome sequences

Abstract The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.

Application of Molecular Microbiology Techniques in Bioremediation of Hydrocarbons and Other Pollutants.

Molecular microbiology techniques have revolutionized microbial ecology by paving the way for rapid, high-throughput methods for culture-independent assessment and exploitation of microbial communities present in complex ecosystems like crudeoil/ hydrocarbon polluted soil. The soil microbial community is relatively diverse with a high level of prokaryotic diversity. This soil species pool represents a gold mine for genes involved in the biodegradation of different classes of pollutants. Currently, less than 1% of this diversity is culturable by traditional cultivation techniques. The application of molecular microbiology techniques in studying microbial populations in polluted sites without the need for culturing has led to the discovery of novel and unrecognized microorganisms and as such complex microbial diversity and dynamics in contaminated soil offer a resounding opportunity for bioremediation strategies. The combination of PCRamplification of metagenomic DNA, microbial community profiling techniques and identification of catabolic genes are ways to elucidate the composition, functions and interactions of microbial communities during bioremediation. In this review, an overview of the different applications of molecular methods in bioremediation of hydrocarbons and other pollutants in environmental matrices and an outline of the recent advances in this fast-developing field are given.

Revolutionising Bacteriology to Improve Treatment Outcomes and Antibiotic Stewardship / 감염과화학요법

Laboratory investigation of bacterial infections generally takes two days: one to grow the bacteria and another to identify them and to test their susceptibility. Meanwhile the patient is treated empirically, based on likely pathogens and local resistance rates. Many patients are over-treated to prevent under-treatment of a few, compromising antibiotic stewardship. Molecular diagnostics have potential to improve this situation by accelerating precise diagnoses and the early refinement of antibiotic therapy. They include: (i) the use of 'biomarkers' to swiftly distinguish patients with bacterial infection, and (ii) molecular bacteriology to identify pathogens and their resistance genes in clinical specimens, without culture. Biomarker interest centres on procalcitonin, which has given good results particularly for pneumonias, though broader biomarker arrays may prove superior in the future. PCRs already are widely used to diagnose a few infections (e.g. tuberculosis) whilst multiplexes are becoming available for bacteraemia, pneumonia and gastrointestinal infection. These detect likely pathogens, but are not comprehensive, particularly for resistance genes; there is also the challenge of linking pathogens and resistance genes when multiple organisms are present in a sample. Next-generation sequencing offers more comprehensive profiling, but obstacles include sensitivity when the bacterial load is low, as in bacteraemia, and the imperfect correlation of genotype and phenotype. In short, rapid molecular bacteriology presents great potential to improve patient treatments and antibiotic stewardship but faces many technical challenges; moreover it runs counter to the current nostrum of defining resistance in pharmacodynamic terms, rather than by the presence of a mechanism, and the policy of centralising bacteriology services.