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| Registros recuperados: 42 | |
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| 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 |
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| PANDOLFI, J. R. C.; SILVA, V. S.; KRAMER, B.; PEIXOTO, J. de O.; CANTAO, M. E.; LOYOLA, W.; COLDEBELLA, A.; RECH, D. V.; TREVISOL, I. M.; ESTEVES, P. A.; JAENISCH, F. R. F.; KLEIN, T. A. P.; VAZ, C. S. L.; CARON, L.; SCHIOCHET, M. F.; LOPES, L. dos S.; IBELLI, A. M. G.; TESSMANN, A. L.; MORES, N.; BRENTANO, L.; SANTOS, F. B. de O.; LEDUR, M. C.; IANISKI, F.; SILVA, M. L. B. da. |
| Projeto/Plano de Ação: 11.11.11.111. |
| Tipo: Separatas |
Palavras-chave: Microbiologia; Produção Animal.; Metagenomics; Broiler chickens; Poultry production. |
| Ano: 2012 |
URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/953157 |
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| FLORES, S. W. S.; CHIARAMONTE, J. B.; ROSSMANN, M.; MENDES, R.. |
| Abstract: Plants rely on their rhizosphere microbiome for specific functions, such as, nutrient acquisition and protection against diseases. The domestication and subsequent plant breeding neglected the important role of the rhizosphere microbiome on plant performance. Here, we tested the hypothesis that ancestor materials have higher ability to host beneficial microorganisms in the rhizosphere when compared to modern cultivars. For this, we assessed the composition and functionality of the rhizosphere microbiome associated with a wild (Wild Mex) and with a cultivated (IAC Alvorada) common bean grown in highly biodiverse soil (Amazonian Dark Earth). Antagonistic bacteria were isolated from common bean rhizosphere and total rhizosphere DNA was extracted for... |
| Tipo: Separatas |
Palavras-chave: Wild common bean; Metagenome; Rhizobacteria; Metagenomics; Microbial communities. |
| Ano: 2015 |
URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1036667 |
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| 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 |
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| SILVA, J. P.; TICONA, A. R. P.; HAMANN, P. R. V.; QUIRINO, B. F.; NORONHA, E. F.. |
| Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches... |
| Tipo: Artigo de periódico |
Palavras-chave: Lignina; Biodegradação; Lignin; Biodegradation; Metagenomics; Proteomics; Transcriptomics. |
| Ano: 2021 |
URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1131423 |
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| BELTRAME, L. C.; ZAMPARETTE, C. P.; FELTRIN, C.; CUNHA, C. R. da; COLTRO, E. P.; ATHAYDE, G. S. da S.; BENETTI FILHO, V.; TÁPPARO, D. C.; MONTEIRO, J.; KICH, J. D.; PALMEIRO, J. K.; WAGNER, G.; FONGARO, G.; ZÁRATE-BLADÉS, C. R.; SINCERO, T. C. M.. |
| Tipo: Artigo de periódico |
Palavras-chave: Resistência antimicrobiana; Resistência aos antibióticos; Sequenciamento; Metagênomica; Resistoma; Antimicrobial resistance; MinION nanopore device®; Swine manure; NGS-next-generation sequencing; Chorume; Suíno; Dejeto; Esterco; Sus Domesticus; Animal husbandry; Pig manure; Metagenomics; One Health initiative. |
| Ano: 2022 |
URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1144728 |
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| ROMAGNOLI, E. M.. |
| Considerando a dieta como um fator modulador do microbioma ruminal, neste trabalho objetivou-se investigar o impacto do bagaço da cana-de-açúcar sobre a composição e funcionalidade das espécies microbianas residentes no rúmen de carneiros (Ovis aries). Foram utilizados seis animais machos fistulados de O. aries, dos quais três foram alimentados com uma dieta composta por 70% de volumoso e 30% de concentrado (tratamento controle) e outros três animais alimentados com uma dieta similar a anterior, mas com 14% do volumoso substituído por bagaço de cana-de-açúcar (tratamento bagaço). O conteúdo ruminal (líquido e fibra) foram amostrados quinzenalmente durante 60 dias. A partir dessas amostras foram acessadas a estrutura e a composição da comunidade microbiana... |
| Tipo: Teses |
Palavras-chave: Metagenômica; Metatranscriptômica 165 rRNA; Cana-de-açúcar.; Bagaço; Rúmen.; Metagenomics; Sugarcane bagasse. |
| Ano: 2016 |
URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1065429 |
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| 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 |
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| SOUTO, B. de M.; ARAÚJO, A. C. B. de; HAMANN, P. R. V.; BASTOS, A. de R.; CUNHA, I. de S.; PEIXOTO, J.; KRUGER, R. H.; NORONHA, E. F.; QUIRINO, B. F.. |
| Functional screening of metagenomic libraries is an effective approach for identification of novel enzymes. A Caatinga biome goat rumen metagenomic library was screened using esculin as a substrate, and a gene from an unknown bacterium encoding a novel GH3 enzyme, BGL11, was identified. None of the BGL11 closely related genes have been previously characterized. Recombinant BGL11 was obtained and kinetically characterized. Substrate specificity of the purified protein was assessed using seven synthetic aryl substrates. Activity towards nitrophenyl-beta-D-glucopyranoside (pNPG), 4-nitrophenyl- beta -D-xylopyranoside (pNPX) and 4-nitrophenyl- beta -D-cellobioside (pNPC) suggested that BGL11 is a multifunctional enzyme with beta-glucosidase, beta-xylosidase,... |
| Tipo: Artigo de periódico |
Palavras-chave: Enzima; Clonagem; Programa de Computador; Peptídeo; Metagenomics; Enzymes; Cloning (animals); Signal peptide; Prevotella; Computer software; Screening. |
| Ano: 2021 |
URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1129624 |
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| 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 |
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| 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 |
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| LIU,Xiao-Feng; LIU,Chen-Jian; ZENG,Xue-Qin; ZHANG,Hai-Yan; LUO,Yi-Yong; LI,Xiao-Ran. |
| Abstract Traditional fermented soybean contains a variety of microflora. To obtain a comprehensive and accurate understanding of the microbial community structure and metabolic potential of fermented soybean, comparative metagenomics and metatranscriptomics were performed on a sample of fermented soybean in Yunnan Province. Metagenomic DNA and metatranscriptomic RNA were sequenced using Illumina HiseqTM2500, which yielded a total of 92,192,276 reads, with an average read length of 150 bp and 38,798,262 paired-end sequences, with an average length of 151 bp. The results show that Providencia stuartii was the most abundant species and the genes of carbohydrates (2296, 13.30%), protein metabolism (1530, 8.86%), and amino acids and amino acid derivatives... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Fermented soybean; Metagenomics; Metatranscriptomics; Microbial community. |
| Ano: 2019 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0101-20612019005000301 |
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| LIU,Xiao-Feng; LIU,Chen-Jian; ZENG,Xue-Qin; ZHANG,Hai-Yan; LUO,Yi-Yong; LI,Xiao-Ran. |
| Abstract Traditional fermented soybean contains a variety of microflora. To obtain a comprehensive and accurate understanding of the microbial community structure and metabolic potential of fermented soybean, comparative metagenomics and metatranscriptomics were performed on a sample of fermented soybean in Yunnan Province. Metagenomic DNA and metatranscriptomic RNA were sequenced using Illumina HiseqTM2500, which yielded a total of 92,192,276 reads, with an average read length of 150 bp and 38,798,262 paired-end sequences, with an average length of 151 bp. The results show that Providencia stuartii was the most abundant species and the genes of carbohydrates (2296, 13.30%), protein metabolism (1530, 8.86%), and amino acids and amino acid derivatives... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Fermented soybean; Metagenomics; Metatranscriptomics; Microbial community. |
| Ano: 2020 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0101-20612020000100018 |
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| 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 (< 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 |
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| Registros recuperados: 42 | |
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