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| Acceso al texto completo restringido a Biblioteca INIA Treinta y Tres. Por información adicional contacte bibliott@inia.org.uy. |
Registro completo
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Biblioteca (s) : |
INIA Treinta y Tres. |
Fecha : |
21/02/2014 |
Actualizado : |
13/09/2018 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Autor : |
NOYES, N.R.; WEINROTH, M.E.; PARKER, J.K.; DEAN, C.J.; LAKIN, S.M.; RAYMOND, R.A.; ROVIRA, P.J.; DOSTER, E.; ABDO, Z.; MARTIN, J.N.; JONES, K.L.; RUIZ, J.; BOUCHER, C.A.; BELK, K.E.; MORLEY, P.S. |
Afiliación : |
NOELLE R. NOYES; MAGGIE E. WEINROTH; JENNIFER K. PARKER; CHRIS J. DEAN; STEVEN M. LAKIN; ROBERT A. RAYMOND; PABLO JUAN ROVIRA SANZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ENRIQUE DOSTER; ZAID ABDO; JENNIFER N. MARTIN; KENNETH L. JONES; JAIME RUIZ; CHRISTINA A. BOUCHER; KEITH E. BELK; PAUL S. MORLEY. |
Título : |
Enrichment allows identification of diverse, rate elements in metagenomic resistome-virulome sequencing. |
Fecha de publicación : |
2017 |
Fuente / Imprenta : |
Microbiome, 2017, 5, p. 142 |
Páginas : |
13 p. |
DOI : |
10.1186/s40168-017-0361-8 |
Idioma : |
Inglés |
Notas : |
Article History: Received: 29 May 2017, Accepted: 5 October 2017, Published: 17 October 2017 |
Contenido : |
Background: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.
Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional
metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins.
Conclusions: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistomevirulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of
microbiome-resistome dynamics. MenosBackground: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.
Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional
metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistan... Presentar Todo |
Palabras claves : |
ANTIMICROBIAL RESISTANCE; METAGENÓMICA; MICROBIAL ECOLOGY; MOLECULAR ENRICHMENT; RARE MICROBIOME; RESISTOME. |
Thesagro : |
ANALISIS BIOLOGICO; ECOLOGIA MICROBIANA; RESISTENCIA A AGENTES DANINOS. |
Asunto categoría : |
U30 Métodos de investigación |
Marc : |
LEADER 03225naa a2200433 a 4500 001 1032862 005 2018-09-13 008 2017 bl uuuu u00u1 u #d 024 7 $a10.1186/s40168-017-0361-8$2DOI 100 1 $aNOYES, N.R. 245 $aEnrichment allows identification of diverse, rate elements in metagenomic resistome-virulome sequencing.$h[electronic resource] 260 $c2017 300 $a13 p. 500 $aArticle History: Received: 29 May 2017, Accepted: 5 October 2017, Published: 17 October 2017 520 $aBackground: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. Conclusions: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistomevirulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics. 650 $aANALISIS BIOLOGICO 650 $aECOLOGIA MICROBIANA 650 $aRESISTENCIA A AGENTES DANINOS 653 $aANTIMICROBIAL RESISTANCE 653 $aMETAGENÓMICA 653 $aMICROBIAL ECOLOGY 653 $aMOLECULAR ENRICHMENT 653 $aRARE MICROBIOME 653 $aRESISTOME 700 1 $aWEINROTH, M.E. 700 1 $aPARKER, J.K. 700 1 $aDEAN, C.J. 700 1 $aLAKIN, S.M. 700 1 $aRAYMOND, R.A. 700 1 $aROVIRA, P.J. 700 1 $aDOSTER, E. 700 1 $aABDO, Z. 700 1 $aMARTIN, J.N. 700 1 $aJONES, K.L. 700 1 $aRUIZ, J. 700 1 $aBOUCHER, C.A. 700 1 $aBELK, K.E. 700 1 $aMORLEY, P.S. 773 $tMicrobiome, 2017, 5, p. 142
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121. | | MARQUES, C. B.; DE BARBIERI, I.; VELAZCO, J.I.; NAVAJAS, E.; CIAPPESONI, G. Genetic parameters for feed efficiency, gas emissions, oxygen consumption and wool traits in Australian Merino. [28] Part 5 - Novel traits: environment and greenhouse gas. In: Proceedings of the World Congress on Genetics Applied to Livestock Production (WCGALP), 12., Rotterdam, the Netherlands, 3-8 July 2022. doi: https://doi.org/10.3920/978-90-8686-940-4_28 160-163. Article history: Published online: February 9, 2023. -- Corresponding authors: Camila Barconi Marques, email: cbalconi@inia.org.uy ; Gabriel Ciappesoni, email: gciappesoni@inia.org.uy -- Acknowledgements: This project has received...Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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124. | | GODWIN, I.; LI, L.; LUIJBEN, K.; OELBRANDT, N.; VELAZCO, J.I.; MILLER, J.; HEGARTY, R. The effects of chronic nitrate supplementation on erythrocytic methaemoglobin reduction in cattle. Animal Production Science, 2015, v. 55(5), p. 611-616. Article history: Received 2 September 2013, accepted 6 February 2014, published online 8 May 2014.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - B |
Biblioteca(s): INIA Treinta y Tres. |
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125. | | ROVIRA, P.J.; VELAZCO, J.I.; EZQUIVEL, J.E.; BRITO, G.; MONTOSSI, F. Effect of shade on fecal shedding of bacteria in grazing cattle during summer in teperate climates ln: International Congress of Meat Science and Technology, 53. 2007, Beijing, China Zhou, Guanghoung; Zhang, Weili, eds. Proceedings of 53th international congress of meat science and technology. Beijing, (China): China Agricultural University Press, 2007. p. 607-608 China Agricultural University PressBiblioteca(s): INIA Treinta y Tres. |
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127. | | FERREIRA, G.; CIAPPESONI, G.; NAVAJAS, E.; GIORELLO, D.; VELAZCO, J.I.; BANCHERO, G.; DE BARBIERI, I. Evaluación de días de medición necesarios para estimar el consumo residual del alimento en ovinos. [Resumen]. Congreso de la Asociación Latinoamericana de Especialistas en Pequeños Rumiantes y Camélidos Sudamericanos (ALEPRyCS), 11., 4-7 de junio, Querétaro, 2019. Rev. Acad. Ciênc. Anim., v. 17(Supl 1):249, 2019. p. 249Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Tacuarembó. |
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129. | | MACEDO, I.; TERRA, J.A.; SIRI-PRIETO, G.; VELAZCO, J.I.; CARRASCO-LETELIER, L. La intensificación del agrosistema arroz pastura afecta la eficiencia de uso de la energía. In: Terra, J. A.; Martínez, S.; Saravia, H.; Mesones, B.; Álvarez, O. (Eds.) Arroz 2020. Montevideo (UY): INIA, 2020. p. 105-108. (INIA Serie Técnica; 257)Tipo: Capítulo en Libro Técnico-Científico |
Biblioteca(s): INIA Treinta y Tres. |
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130. | | VELAZCO, J.I.; BONILLA, O.; SAN JULIÁN, R.; LUZARDO, S.; BRITO, G.; MONTOSSI, F. Intensificación de la producción de carne ovina en laboreos de verano en sistemas de arroz-ganadería: suplementación con concentrados en corderos pesados Trabajos analíticos en ovinos. In: DEAMBROSI, E.; MONTOSSI, F.; SARAVIA, H.; BLANCO, P.H.; AYALA, W. (Eds.). 10 años de la Unidad de Producción Arroz-Ganadería. Montevideo (Uruguay): INIA, 2009. p. 137-146 (INIA Serie Técnica ; 180)Tipo: Capítulo en Libro Técnico-Científico |
Biblioteca(s): INIA Las Brujas; INIA Tacuarembó; INIA Treinta y Tres. |
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131. | | MACEDO, I.; CARRASCO-LETELIER, L.; VELAZCO, J.I.; SIRI-PRIETO, G.; TERRA, J.A. Intensification alternatives to rice-pasture systems: energy use efficiency. [Abstract] + [Poster]. In: International Temperate Rice Conference (7., 2020, Pelotas, RS), Science & Innovation: feeding a world of 10 billion people: proceedings. Pelotas RS, Brasil, February 9-12, 2020. Brasília, DF : Embrapa, 2020.Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Treinta y Tres. |
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132. | | MACEDO, I.; ROEL, A.; VELAZCO, J.I.; BORDAGORRI, A.; TERRA, J.A.; PITTELKOW, C.M. Intensification of rice-pasture rotations with annual crops reduces the stability of sustainability across productivity, economic, and environmental indicators. Agricultural Systems, October 2022, volume 202, Article Number 103488. OPEN ACCESS. doi: https://doi.org/10.1016/j.agsy.2022.103488 Article history: Received 6 May 2022, Revised 17 August 2022, Accepted 19 August 2022, Available online 30 August 2022, Version of Record 30 August 2022.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Treinta y Tres. |
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136. | | QUINTANS, G.; SCARSI, M.; VELAZCO, J.I.; LÓPEZ-MAZZ, C.; VIÑOLES, C.; BANCHERO, G. Recientes avances en el conocimiento del manejo de los rodeos de cría: aportes desde INIA. In: Congreso Asociación Uruguaya de Producción Animal (AUPA), 4., 2012, Montevideo, UY). 2012. [Actas]. Veterinaria, v. 72, n. 48, supl. 1, p. 87-90, 2012. Congreso publicado en revista arbitrada: Veterinaria (Montevideo).Tipo: Artículos en Revistas Indexadas Nacionales | Circulación / Nivel : B - 5 |
Biblioteca(s): INIA La Estanzuela; INIA Treinta y Tres. |
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140. | | VELAZCO, J.I.; BREMNER, G.; LI, L.; LUIJBEN, K.; HEGARTY, R.S.; PERDOK, H. Short-term emission measurements in beef feedlot cattle to demonstrate enteric methane mitigation from dietary nitrate.[Poster]. In: Greenhouse Gas and Animal Agriculture (GGAA) scientific conference, (5º, Dublin, Irlanda), 23-26 Jun. 2013.Biblioteca(s): INIA Treinta y Tres. |
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