Consulta: subjectFacets:"Metagenomics"
Registros recuperados: 13
Data/hora: 01/06/2024 10:09:00

Holobionts and their hologenomes: Evolution with mixed modes of inheritance
Provedor de dados: 74
Autores: Haag,Karen Luisa.
Abstract Symbioses are ubiquitous and have played an influential role in the evolution of life on Earth. Genomic studies are now revealing a huge diversity of associations among hosts and their microbiotas, allowing us to characterize their complex ecological and evolutionary dynamics. The different transmission modes and the asynchronous cell proliferation of the numerous symbionts associated with one host generate a genomic conflict ought to be solved. Two disputing views have been used to model and predict the outcome of such conflicts. The traditional view is based on community ecology, and considers that selection at the level of individuals is sufficient to explain longstanding associations among species. A new perspective considers that the host and...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genomics; Metagenomics; Microbiota; Symbiosis; Holobiont.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200189

A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks
Provedor de dados: 5
Autores: Desdouits, Marion; Wacrenier, Candice; Ollivier, Joanna; Schaeffer, Julien; Le Guyader, Soizick.
Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability...
Tipo: Text
Palavras-chave: Norovirus; Foodborne virus; Metagenomics; Amplicon deep sequencing; Viral diversity.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00646/75831/76818.pdf

Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula
Provedor de dados: 5
Autores: Cowart, Dominique; Murphy, Katherine R.; Cheng, C. -h. Christina.
The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods. We collected water samples from four WAP shallow (≤ 300 m) shelf regions, recovered the eDNA therein, and performed metagenomic shotgun sequencing and analyses to determine the effectiveness of this method to assess marine benthic...
Tipo: Text
Palavras-chave: EDNA; Antarctica; Metagenomics; King crabs; Benthic invertebrates.
Ano: 2018
URL: http://archimer.ifremer.fr/doc/00413/52490/53278.pdf

The ocean sampling day consortium
Provedor de dados: 5
Autores: Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Z.; Sonnenschein, Eva C.; Cariou, Thierry; O'Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Cacador, Isabel; Canning-clode, Joao; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhaes; Luna, Gian Marco; Quero, Grazia Marina; Loescher, Carolin R.; Kremp, Anke; Delorenzo, Marie E.; Ovreas, Lise; Tolman, Jennifer; Laroche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P.; Ramos, Sandra; Magalhaes, Catarina; Jude-lemeilleur, Florence; Leopoldina Aguirre-macedo, Ma; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A.; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M.; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion M. F.; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C.; Kandil, Mahrous M.; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-ezpeleta, Naiara; Berteaux-lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; Ten Hoopen, Petra; Cochrane, Guy; L'Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M.; Martin, Patrick; Jensen, Rachelle M.; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; Dos Santos, Antonina; Villar, Emilie; Pesant, Stephane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Silveira, Jorge A. Herrera; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J.; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Nyhus, Paul Anders Fronth; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N.; Gasol, Josep M.; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S.; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M.; Collins, R. Eric; Ducluzeau, Anne-lise; Martinez, Jonathan; Costello, Mark J.; Amaral-zettler, Linda A.; Gilbert, Jack A.; Davies, Neil; Field, Dawn; Gloeckner, Frank Oliver.
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
Tipo: Text
Palavras-chave: Ocean sampling day; OSD; Biodiversity; Genomics; Health Index; Bacteria; Microorganism; Metagenomics; Marine; Micro B3; Standards.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00371/48262/48647.pdf

Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean
Provedor de dados: 5
Autores: Sun, Ying; Debeljak, Pavla; Obernosterer, Ingrid.
Marine microbes are major drivers of all elemental cycles. The processing of organic carbon by heterotrophic prokaryotes is tightly coupled to the availability of the trace element iron in large regions of the Southern Ocean. However, the functional diversity in iron and carbon metabolism within diverse communities remains a major unresolved issue. Using novel Southern Ocean meta-omics resources including 133 metagenome-assembled genomes (MAGs), we show a mosaic of taxonomy-specific ecological strategies in naturally iron-fertilized and high nutrient low chlorophyll (HNLC) waters. Taxonomic profiling revealed apparent community shifts across contrasting nutrient regimes. Community-level and genome-resolved metatranscriptomics evidenced a moderate...
Tipo: Text
Palavras-chave: Metagenomics; Microbial biooceanography; Microbial ecology.
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00693/80483/83626.pdf

Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean
Provedor de dados: 5
Autores: Pereira, Olivier; Hochart, Corentin; Auguet, Jean-christophe; Debroas, Didier; Galand, Pierre E.
Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re‐analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co‐occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more...
Tipo: Text
Palavras-chave: 16S rRNA; Euryarchaeota; Global ocean; Metagenomics; Poseidoniales; Proteorhodopsin.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00505/61676/65607.pdf

Selective elimination of chloroplastidial DNA for metagenomics of bacteria associated with the green alga Caulerpa Taxifolia (bryopsidophyceae)
Provedor de dados: 5
Autores: Aires, Tania; Marba, Nuria; Serrao, Ester A.; Duarte, Carlos M.; Arnaud-haond, Sophie.
Molecular analyses of bacteria associated with photosynthetic organisms are often confounded by coamplification of the chloroplastidial 16S rDNA with the targeted bacterial 16S rDNA. This major problem has hampered progress in the characterization of bacterial communities associated to photosynthetic organisms and has limited the full realization of the potential offered by the last generation of metagenomics approaches. A simple and inexpensive method is presented, based on ethanol and bleach treatments prior to extraction, to efficiently discard a great part of chloroplastidial DNA without affecting the characterization of bacterial communities through pyrosequencing. Its effectiveness for the description of bacterial lineages associated to the green...
Tipo: Text
Palavras-chave: 16S; Chloroplasts; Elimination; Green algae; Metagenomics.
Ano: 2012
URL: http://archimer.ifremer.fr/doc/00076/18739/16464.pdf

Novel opportunities for NGS-based one health surveillance of foodborne viruses
Provedor de dados: 5
Autores: Desdouits, Marion; De Graaf, Miranda; Strubbia, Sofia; Oude Munnink, Bas B.; Kroneman, Annelies; Le Guyader, Soizick; Koopmans, Marion P. G.
Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application
Tipo: Text
Palavras-chave: Next-generation sequencing; Metagenomics; Foodborne virus; Food virology; Human enteric virus; Norovirus.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00641/75330/75988.pdf

Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia
Provedor de dados: 5
Autores: Mei, Nan; Postec, Anne; Monnin, Christophe; Pelletier, Bernard; Payri, Claude E.; Menez, Benedicte; Frouin, Eleonore; Ollivier, Bernard; Erauso, Gael; Quemeneur, Marianne.
High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (similar to 11), low-temperature (&lt; 40 degrees C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling...
Tipo: Text
Palavras-chave: Hydrogen; Microbial diversity; Hydrogen producers; Serpentinization; HydA genes; [FeFe]-hydrogenase; Metagenomics.
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00467/57913/60308.pdf

Construction and characterization of a metagenomic DNA library from the rhizosphere of wheat (Triticum aestivum)
Provedor de dados: 85
Autores: Hernández-León,R; Martínez-Trujillo,M; Valencia-Cantero,E; Santoyo,G.
Rhizospheric soil of wheat plants contains a high diversity of microorganisms, and therefore, comprises a large reservoir for discovering genes with diverse agro-biotechnological applications. In this work, we constructed an E. coli metagenomic library based on bacterial artificial chromosome (BAC) clones with large genomic inserts from metagenomic DNA from the rhizosphere of wheat plants. The average of the DNA cloned segments varies from 5 to 80 kb, with an average size of 38 kb. Random clones were end-sequenced and homology results showed that the clonation of metagenomic DNA codes mainly for metabolic and catalytic functions (40%), including amidohydrolase, hydrolase, peptidase, serine protease, endonuclease and exonuclease. Another interesting...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Metagenomics; Rhizosphere; Wheat.
Ano: 2012
URL: http://www.scielo.org.ar/scielo.php?script=sci_arttext&pid=S1851-56572012000100018

Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation
Provedor de dados: 90
Autores: Paixão,Douglas Antonio Alvaredo; Dimitrov,Mauricio Rocha; Pereira,Rodrigo Matheus; Accorsini,Fábio Raphael; Vidotti,Maria Benincasa; Lemos,Eliana Gertrudes de Macedo.
Diesel oil is a compound derived from petroleum, consisting primarily of hydrocarbons. Poor conditions in transportation and storage of this product can contribute significantly to accidental spills causing serious ecological problems in soil and water and affecting the diversity of the microbial environment. The cloning and sequencing of the 16S rRNA gene is one of the molecular techniques that allows estimation and comparison of the microbial diversity in different environmental samples. The aim of this work was to estimate the diversity of microorganisms from the Bacteria domain in a consortium specialized in diesel oil degradation through partial sequencing of the 16S rRNA gene. After the extraction of DNA metagenomics, the material was amplified by...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: PCR; Cloning; 16S rRNA; Metagenomics; Soil; Biosurfactants.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-06832010000300019

The insect reservoir of biodiversity for viruses and for antiviral mechanisms
Provedor de dados: 42
Autores: OLMO,ROENICK P.; MARTINS,NELSON EDUARDO; AGUIAR,ERIC ROBERTO G.R.; MARQUES,JOÃO T.; IMLER,JEAN-LUC.
Abstract: Insects are the most diverse group of animals. They can be infected by an extraordinary diversity of viruses. Among them, arthropod-borne viruses (arboviruses) can be transmitted to humans. High-throughput sequencing of small RNAs from insects provides insight into their virome, which may help understand the dynamics of vector borne infectious diseases. Furthermore, investigating the mechanisms that restrict viral infections in insects points to genetic innovations that may inspire novel antiviral strategies.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Antiviral immunity; Insects; Metagenomics; Restriction factors; RNA interference; Virome.
Ano: 2019
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652019000600604

Functional Genes of Microorganisms, Comprehending the Dynamics of Agricultural Ecosystems
Provedor de dados: 52
Autores: Reali,Catiusca; Pilz Júnior,Harry Luiz; Meile,Jean Christophe; Galindo,Sabine Shorr; Fiuza,Lidia Mariana.
ABSTRACT The microbial composition of different types,in ecosystems (including agro-ecosystems), has been investigated in a rapidly growing number of studies in the past few years. The importance of microorganisms, regarding the maintenance and stability of nutrients in agroecosystems, is a key to maintain the sustainability of a crop. Molecular tools to study microbial communities are possible through many methods such as RISA, DGGE, TGGE, clone libraries, T-RFLP, RAPD, SSCP and more recently NGS (Next-Generation Sequencing). DGGE is widely employed to characterize the diversity and the community dynamics of microorganisms in the environment, making possible to find out specific groups through functional genes, allowing access to data that cannot be...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Agroecosystems; Functional genes; Bacteria; DGGE; Metagenomics; Microbial ecology.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132017000100201