Wyniki wyszukiwania

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Evaluation of direct metagenomics and target enriched approaches for high-throughput sequencing of field rabies viruses

100%

Orlowska A., Iwan E., Smreczak M., Rola J.

Journal of Veterinary Research

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2019

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tom 63

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nr 4

2

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The importance of metagenomics research in human ecological niches and their role in the diagnosis of noninfectious diseases

86%

Weiner M., Kubajka M.

Health Problems of Civilization

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2015

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tom 09

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nr 2

Human body is a complex system that is affected by a significant number of microscopic organisms called the microbiomes. The dynamic development of science has led to innovative discoveries in the field of microbiology. This in turn has extracted new field, metagenomics, thanks to which it became possible to perform detailed analysis of individual groups of bacteria and to determine their effects on preserving a good health. One of the biggest scientific projects that would investigate the influence of microbiomes on humans is HMP (Human Microbiome Project). As part of it the research is being conducted leading to characterize human microbiome at the level of nucleotide sequence of the entire genomic DNA. The microflora of the skin, oral cavity, respiratory tract, digestive tract (intestines), genitourinary system has an essential role in the homeostasis. In the last year the carried research proved that it is a vital part of the human organism in preserving a good health. Any changes in its composition may lead to systemic diseases. Pathological changes affect the outcome of the interaction within the microflora that includes species of commensal and pathogenic bacteria, as well as immunology and genetics of the host. Metagenomics research will contribute not only to the recognition of new, so far unidentified by the bacteriological methods microorganisms, but most of all they will serve as a basis to understand the relationships between the human organism and in-dwelling microorganisms. Thanks to the development of the metagenomics or the NGS (Next Generation Sequencing) it will be possible to discover new metabolic pathways and bidirectional links of bacteria with human metabolism. This will help in finding new therapeutic methods in the treatment of many noninfectious diseases so far considered as civilization diseases or genetically conditioned.

3

An improved procedure of the metagenomic DNA extraction from saline soil, sediment and salt

86%

Kashi F. J.

International Letters of Natural Sciences

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2016

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tom 60

4

Life in extreme habitats: diversity of endolithic microorganisms from cold desert ecosystems of Eastern Pamir

72%

Khomutovska N., Jerzak M., Kostrzewska-Szlakowska I., Kwiatkowski J., Suska-Malawska M., Syczewski M., Jasser I.

Polish Journal of Ecology

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2017

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tom 65

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nr 4

The aim of this study was to identify cyanobacteria diversity in rock communities from the cold desert ecosystem in Eastern Pamir Mountains (Tajikistan) and assess if the rock type and rock`s porosity can be indicators of microbial diversity in this extreme environment. Seven samples were collected in July 2015 from hillsides (ca 4000–4500 m a.s.l.) of the Eastern Pamir Mountains. Petrographic and scanning microscopy (SEM) allowed for the characterization of the rocks inhabited by endolithic communities as granite, gneiss and limestone with variable porosity. Based on next-generation sequencing (NGS) of amplicon of V3–V4 hypervariable region of 16S rRNA gene, we established that Actinobacteria,Proteobacteria and Cyanobacteria dominated the endolithic communities of microorganisms in the rocks studied, which distinguishes these communities from those described for other cold arid regions. Chroococcidiopsis and Leptolyngbya were dominant genera in the cyanobacterial communities according to culture-dependent analysis, as well as microscopic analyses of endoliths scraps from the rocks. Culture-independent metagenomic analyses revealed that Microcoleus, Acaryochloris, Chroococcidiopsis and Thermosynechococcus reads were the most abundant from all reads and dominated interchangeably in the samples. Endolithic communities of microorganisms in the rocks from the cold desert shrubland of Eastern Pamir Mts. appear to be diverse and different from communities described for other cold deserts.

5

Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library

58%

Cieslinski H., Bialkowska A., Tkaczuk K., Dlugolecka A., Kur J., Turkiewicz M.

Polish Journal of Microbiology

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2009

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tom 58

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nr 3

199-204

In this work, we present the construction of a metagenomic library in Escherichia coli using pUC19 vector and environmental DNA directly isolated from Antarctic topsoil and screened for lipolytic enzymes. Screening on agar supplemented with olive oil and rhodamine B revealed one clone with lipolytic activity (Lip 1) out of 11000 E. coli clones. This clone harbored a plasmid, pLip 1, which has an insert of 4722 bp that was completely sequenced from both directions. Further analysis of the insert showed three open reading frames (ORFs). ORF2 encoded a protein (Lip 1) of 469 amino acids with 93% identity to the uncultured Pseudomonas sp. lipase LipJ03. Amino acid sequence comparison and phylogenetic analysis indicated that Lip 1 lipase was closely related to family I subfamily 3. Furthermore, we present a three-dimensional model of lipase Lip 1 which was generated based on the two known structures of mesophilic lipases from Pseudomonas sp. MIS 38 (PML lipase, PDB; 2Z8X) and Seiratia marcescens (SML lipase, PDB: 2QUB). Finally, we report the results of comparisons between lipase Lip 1 and mesophilic lipases and point out similarities and differences in the catalytic site and in other parts of the analyzed structures.

6

Metagenomics study of the microbes in constructed wetland system treating sewage

58%

Usharani B.

International Letters of Natural Sciences

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2019

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tom 74

Constructed wetlands are eco-friendly, cost-effective technology involved in treatment of wastewaters. The goal of this study is focused on characterization of microbial community existing in a constructed wetland system planted with Cyperus alternifolius treating sewage contaminated with heavy metals. The characteristics of effluent met the standards of discharge for inland use and irrigation. Microbes in constructed wetland apparently play a pivotal role in the efficiency of system for removal of organics, nutrients, suspended solids and heavy metal. To expose the active players in the lime light, a representative soil sample from the reed bed was collected and characterized for microbial community analysis. Metagenomic studies of the bacterial and fungal flora were identified. Results revealed that the phylum Proteobacteria (38.27%) and Ascomycota (77.47%) dominated in the bacterial and fungal kingdom respectively. However, in the bacterial kingdom at species level major portion remain unclassified except Pseudomonas alcaligenes but in the fungal kingdom at species level only 3.1% remain unclassified. The role of bacteria in wastewater treatment is exemplified in previous reports but the role of fungi in the wastewater system needs exploration. However, the findings reveal that the identified microbes might have definitely played a vital role in wastewater treatment. The database available for the identification of bacterial species remain undiscovered for a major portion and requires upgradation. Next generation sequence being a high-end technology in microbial ecology decodes the entire community in environmental samples but lack of database limits the identification. Implementation of improvements in the paucity of databases is essential.

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Analiza mikroflory regionalnych serów gołka

44%

Sip A., Olejnik-Schmidt A., Wieckowicz M., Grajek W.

Acta Scientiarum Polonorum. Biotechnologia

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2010

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tom 09

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nr 4

Celem pracy było zbadanie stanu mikrobiologicznego wędzonych serów regionalnych gołka wywarzanych z niepasteryzowanego mleka owczo-krowiego w rejonie Karpat oraz dokonanie wstępnej identyfikacji występujących w nich bakterii fermentacji mlekowej. Stan mikrobiologiczny gołek określano na podstawie wyników oznaczeń liczebności tlenowych bakterii mezofilnych, bakterii fermentacji mlekowej (LAB), Staphylococcus aureus oraz drożdży i pleśni. W gołkach badano też obecność bakterii Salmonella i Listeria. Liczebność poszczególnych grup drobnoustrojów oznaczano metodą posiewo- wą, a obecność bakterii będących wskaźnikiem bezpieczeństwa mikrobiologicznego wykrywano metodą ELFA. Skład rodzajowy LAB gołek określano na podstawie wyników analizy metagenomowej. Analizę tę prowadzono metodą PCR z zastosowaniem specyficznych rodzajowo starterów. Dominujące LAB identyfikowano ponadto na poziomie gatunku metodą PCR-RFLP i sekwencjonowania. Przeprowadzone badania wykazały, że mikroflora gołek wytwarzanych przez różnych producentów miała zbliżony skład ilościowy. Najbardziej liczna była w niej populacja kwasolubnych LAB. W badanych gołkach było ich średnio 6,9x109 jtk*g-1. We wszystkich gołkach znajdowało się też od 1,2x106 do 1,6x107jtk'g-1 drożdży. W żadnej gołce nie wykryto obecności bakterii Salmonella, Listeria, enterotoksycznych S. aureus oraz pleśni. W gołkach występowały natomiast LAB z rodzaju Enterococcus, Lactococcus, Lactobacillus i Leuconostoc. Wśród 166 szczepów LAB wyizolowanych z gołek dominowały bakterie Lb. casei.

Ograniczanie wyników

Evaluation of direct metagenomics and target enriched approaches for high-throughput sequencing of field rabies viruses

The importance of metagenomics research in human ecological niches and their role in the diagnosis of noninfectious diseases

An improved procedure of the metagenomic DNA extraction from saline soil, sediment and salt

Life in extreme habitats: diversity of endolithic microorganisms from cold desert ecosystems of Eastern Pamir

Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library

Metagenomics study of the microbes in constructed wetland system treating sewage

Analiza mikroflory regionalnych serów gołka