Consulta: subjectFacets:"Metagenomic"
Registros recuperados: 7
Data/hora: 08/06/2024 09:38:13

Metagenomic to evaluate norovirus genomic diversity in oysters: Impact on hexamer selection and targeted capture-based enrichment
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Strubbia, Sofia; Schaeffer, Julien; Besnard, Alban; Wacrenier, Candice; Le Mennec, Cecile; Garry, Pascal; Desdouits, Marion; Le Guyader, Soizick.
Human virus transmission through food consumption has been identified since many years and the international trade increases the risk of dissemination of viral pathogens. The development of metagenomic approach holds many promises for the surveillance of viruses in food and water. This work aimed to analyze norovirus diversity and to evaluate strain-dependent accumulation patterns in three oyster types by using a metagenomic approach. Different hexamer sets to prime cDNA were evaluated before capture-based approach to enhance virus reads recovery during deep sequencing. The study includes the use of technical replicates of artificially contaminated oysters and the analysis of multiple negatives controls. Results showed a clear impact of the hexamer set...
Tipo: Text
Palavras-chave: Norovirus; Oysters; Metagenomic; Human enteric viruses.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00614/72575/71535.pdf

Approche métagénomique de la chimiosynthèse en système hydrothermal océanique profond : cas particulier des symbioses bactériennes associées à la crevette Rimicaris exoculata
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Jan, Cyrielle.
The hydrothermal shrimp Rimicaris exoculata is an endemic species of the Mid-Atlantic Ridge (MAR).This species lives in dense aggregates on the walls of active chimneys and dominates the megafauna of most of these sites. This shrimp has two distinct microbial communities whose roles remain almost unknown. One of these communities is associated with the cephalothorax and hypertrophied mouthparts.These are covered by a dense community of bacteria affiliated to chemoautotrophic epibionts associated with mineral deposits. To deepen our knowledge on the symbiotic community in the context of the thesis, a metagenomic approach was undertaken. This helped highlighting the microbial diversity present with a dominant phylum, the Proteobacteria. Two classes are...
Tipo: Text
Palavras-chave: Epibiontes; Métagénomique; Rimicaris exoculata; Symbiose; Zetaproteobacteria; Symbiosis; Epibionts; Metagenomic.
Ano: 2012
URL: https://archimer.ifremer.fr/doc/00498/60954/64357.pdf

Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Strubbia, Sofia; Phan, My V. T.; Schaeffer, Julien; Koopmans, Marion; Cotten, Matthew; Le Guyader, Soizick.
This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was...
Tipo: Text
Palavras-chave: Human enteric viruses; Norovirus; Sewage; Metagenomic; Virome.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00512/62332/66592.pdf

Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Bastaraud, Alexandra; Cecchi, Philippe; Handschumacher, Pascal; Altmann, Mathias; Jambou, Ronan.
A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could...
Tipo: Text
Palavras-chave: Waterborne diseases; Drug resistance; Urbanization; Surface water; Plastics; Metagenomic.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00601/71328/69758.pdf

Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis
Provedor de dados: Pesquisa Agropecuária Brasileira
Autores: Silveira,Érico Leandro da; Pereira,Rodrigo Matheus; Scaquitto,Denilson César; Pedrinho,Eliamar Aparecida Nascimbém; Val-Moraes,Silvana Pómpeia; Wickert,Ester; Carareto-Alves,Lúcia Maria; Lemos,Eliana Gertrudes de Macedo.
Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity....
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genetic diversity; Metagenomic; Microbial communities.
Ano: 2006
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2006001000008

A broad pH range and processive chitinase from a metagenome library
Provedor de dados: Brazilian Journal of Medical and Biological Research
Autores: Thimoteo,S.S.; Glogauer,A.; Faoro,H.; de Souza,E.M.; Huergo,L.F.; Moerschbacher,B.M.; Pedrosa,F.O.
Chitinases are hydrolases that degrade chitin, a polymer of N-acetylglucosamine linked β(1-4) present in the exoskeleton of crustaceans, insects, nematodes and fungal cell walls. A metagenome fosmid library from a wastewater-contaminated soil was functionally screened for chitinase activity leading to the isolation and identification of a chitinase gene named metachi18A. The metachi18A gene was subcloned and overexpressed in Escherichia coli BL21 and the MetaChi18A chitinase was purified by affinity chromatography as a 6xHis-tagged fusion protein. The MetaChi18A enzyme is a 92-kDa protein with a conserved active site domain of glycosyl hydrolases family 18. It hydrolyses colloidal chitin with an optimum pH of 5 and temperature of 50°C. Moreover, the enzyme...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Chitinase; Metagenomic; Aeromonas; Kinetics.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2017000100602

Comparative metagenome of a stream impacted by the urbanization phenomenon
Provedor de dados: Brazilian Journal of Microbiology
Autores: Medeiros,Julliane Dutra; Cantão,Maurício Egídio; Cesar,Dionéia Evangelista; Nicolás,Marisa Fabiana; Diniz,Cláudio Galuppo; Silva,Vânia Lúcia; Vasconcelos,Ana Tereza Ribeiro de; Coelho,Cíntia Marques.
Abstract Rivers and streams are important reservoirs of freshwater for human consumption. These ecosystems are threatened by increasing urbanization, because raw sewage discharged into them alters their nutrient content and may affect the composition of their microbial community. In the present study, we investigate the taxonomic and functional profile of the microbial community in an urban lotic environment. Samples of running water were collected at two points in the São Pedro stream: an upstream preserved and non-urbanized area, and a polluted urbanized area with discharged sewage. The metagenomic DNA was sequenced by pyrosequencing. Differences were observed in the community composition at the two sites. The non-urbanized area was overrepresented by...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Aquatic environment; Urbanization; Microbial community; Metagenomic.
Ano: 2016
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000400835