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Escherichia coli O104:H4 outbreak - have we learnt a lesson from it?

100%
Bloch S. K., Felczykowska A., Nejman-Faleńczyk B.
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2012
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vol. 59
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issue 4
483-488
EN
Shiga toxin-producing Escherichia coli (STEC) strains belong to the group of pathogens that cause bloody diarrhea and hemorrhagic colitis with often severe complications. The main problem with human pathogenic E. coli strains, including STEC, is a wide spectrum of phenotypes and clinical manifestations. It is related to a variety of exchangeable genetic elements, like plasmids, bacteriophages, transposons and pathogenicity islands, that take part in horizontal gene transfer which influences creation of new dangerous bacterial strains. A good example of this phenomenon is a novel Shiga toxin-producing E. coli O104:H4 serotype that was associated with a widespread and severe foodborne disease outbreak in Germany in 2011. The O104:H4 strain was created by a number of horizontal gene transfer events between two distinct pathogens, resulting in the emergence of the new, atypical strain. That outbreak proved that also rare and unusual serotypes of STEC may be a significant risk factor and that the procedures recommended for STEC detection were not suitable to deal with this kind of pathogens. With respect to new combinations of chromosomal and extrachromosomal elements in susceptible bacterial hosts, epidemics and frequent human infections caused by STEC strains, we suggest that more attention should be paid to the development and improvement of diagnostic methods. It is difficult to determine STEC bacteria by general microbiological, biochemical and immunological assays, because strains can vary dramatically in their phenotypic and serotypic properties. It is postulated that standardized genetic tests, based on detection of features most frequently presented by STEC, particularly those located on easily exchangeable elements (such as Shiga toxin-encoding phages), can be more adequate for STEC detection.
2
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Sampling, metadata and DNA extraction - important steps in metagenomic studies

100%
Felczykowska A., Krajewska A., Zielińska S., Łoś J.
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2015
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vol. 62
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issue 1
151-160
EN
Metagenomic studies have become increasingly popular. They allow for the estimation of biodiversity in complex populations. This diversity presents an enormous but largely unexpected genetic and biological pool and can be exploited for the recovery of novel genes, entire metabolic pathways and their products. Generally metagenomic study is a genomic analysis of organisms by direct extraction and cloning of DNA from their natural environment. The most common problems of modern metagenomics are as follows: majority of the microorganisms present in the environment cannot be cultivated by standard techniques, DNA extraction methods are not very effective, isolated DNA is contaminated with various compounds, a choice for a screening method is not obvious.
3
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Metagenomic approach in the investigation of new bioactive compounds in the marine environment

100%
Felczykowska A., Bloch S. K., Nejman-Faleńczyk B., Barańska S.
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2012
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vol. 59
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issue 4
501-505
EN
The marine environment is estimated to be one of the most significant sources of biological activity in the world. In the last few decades an increase in the research intensity conducted on marine microorganisms has been observed, which confirms the great potential of these organisms in the field of bioactive compounds' production. In order to efficiently use the natural resources of the marine environment, metagenomics can be applied. This powerful technique allows for efficient screening of microbial biodiversity for bioactive compounds. The primary aim of this review is to present some aspects of the construction of metagenomic libraries, and strategies of screening for novel bioactives in the marine surrounding. This paper also illustrates several examples of the application of metagenomic methods in the discovery of novel enzymes and drugs in various marine environments.
4
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The most widespread problems in the function-based microbial metagenomics

76%
Felczykowska A., Krajewska A., Zielińska S., Łoś J., Bloch S., Nejman-Faleńczyk B.
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2015
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vol. 62
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issue 1
161-166
EN
Metagenomics is a powerful tool to better understand the microbial niches, especially these from extreme habitats like oceans and seas, hot springs or deserts. However, one who is going to face the metagenomic studies should realize the challenges which might occur in the course of experiments. This manuscript indicates common problems in function-driven metagenomics, especially factors that influence gene expression are taken into account. Codon usage bias, internal cell accumulation, correct protein folding or presence of proper initiation factors are discussed and possible ways to overcome these problems are proposed. Finally, the annotation process is described, including possible limitations that one should take under consideration. What is more, the most popular databases for metagenomic data are mentioned and discussed.
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