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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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| Acceso al texto completo restringido a Biblioteca INIA La Estanzuela. Por información adicional contacte bib_le@inia.org.uy. |
Registro completo
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Biblioteca (s) : |
INIA La Estanzuela. |
Fecha actual : |
21/02/2014 |
Actualizado : |
25/06/2021 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Circulación / Nivel : |
A - 2 |
Autor : |
COZZOLINO, D.; FASSIO, A.; FERNANDEZ, E.; RESTAINO, E.; LA MANNA, A. |
Afiliación : |
DANIEL COZZOLINO GÓMEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ALBERTO SANTIAGO FASSIO ARAUJO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ENRIQUE GENARO FERNANDEZ RODRIGUEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ERNESTO ANGEL RESTAINO GALUP, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ALEJANDRO FRANCISCO LA MANNA ALONSO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
Título : |
Measurement of chemical composition in wet whole maize silage by visible and near infrared reflectance spectroscopy. |
Fecha de publicación : |
2006 |
Fuente / Imprenta : |
Animal Feed Science and Technology, 2006, 129 (3-4): 329-336 |
DOI : |
10.1016/j.anifeedsci.2006.01.025 |
Idioma : |
Inglés |
Notas : |
Article history:Received 10 June 2005 /Received in revised form 16 January 2006/ Accepted 25 January 2006. |
Contenido : |
Abstract: Visible (Vis) and near infrared reflectance (NIR) spectroscopy were used to predict dry matter(DM), acid and neutral detergent fibre (ADFom and aNDFom), ash, crude protein (CP) and pHin wet whole maize (WWM) silage samples. Samples were analysed by reference methods andspectra collected using a NIR spectrophotometer in reflectance (400?2500 nm). Predictive equa-tions were developed using modified partial least squares (MPLS) with full cross validation usingraw spectra or second derivative. Two scatter corrections were also used, namely standard normalvariate and detrend (SNVD) and multiplicative scatter correction (MSC). Coefficient of determina-tion in calibrationR2caland standard error of cross validation (SECV) were 0.91 (SECV: 6.5 g kg?1DM) for CP, 0.85 (SECV: 27.4 g kg?1) for DM using SNVD, and 0.86 (SECV: 22.1 g kg?1DM) using raw spectra. Poor correlations between the reference methods and NIR werefound for aNDFom, ash, OMD and pH. It was concluded that NIR spectroscopy might be a suit-able method to predict DM, CP and ADFom on WWM silage samples with minimal sample preparation. |
Palabras claves : |
MODIFIED PARTIAL LEAST SQUARES; NIR; NIR (NEAR INFRARED REFLECTANCE); SAMPLE PRESENTATION; SILAGE; WET WHOLE MAIZE. |
Asunto categoría : |
-- |
Marc : |
LEADER 02071naa a2200265 a 4500 001 1049572 005 2021-06-25 008 2006 bl uuuu u00u1 u #d 024 7 $a10.1016/j.anifeedsci.2006.01.025$2DOI 100 1 $aCOZZOLINO, D. 245 $aMeasurement of chemical composition in wet whole maize silage by visible and near infrared reflectance spectroscopy. 260 $c2006 500 $aArticle history:Received 10 June 2005 /Received in revised form 16 January 2006/ Accepted 25 January 2006. 520 $aAbstract: Visible (Vis) and near infrared reflectance (NIR) spectroscopy were used to predict dry matter(DM), acid and neutral detergent fibre (ADFom and aNDFom), ash, crude protein (CP) and pHin wet whole maize (WWM) silage samples. Samples were analysed by reference methods andspectra collected using a NIR spectrophotometer in reflectance (400?2500 nm). Predictive equa-tions were developed using modified partial least squares (MPLS) with full cross validation usingraw spectra or second derivative. Two scatter corrections were also used, namely standard normalvariate and detrend (SNVD) and multiplicative scatter correction (MSC). Coefficient of determina-tion in calibrationR2caland standard error of cross validation (SECV) were 0.91 (SECV: 6.5 g kg?1DM) for CP, 0.85 (SECV: 27.4 g kg?1) for DM using SNVD, and 0.86 (SECV: 22.1 g kg?1DM) using raw spectra. Poor correlations between the reference methods and NIR werefound for aNDFom, ash, OMD and pH. It was concluded that NIR spectroscopy might be a suit-able method to predict DM, CP and ADFom on WWM silage samples with minimal sample preparation. 653 $aMODIFIED PARTIAL LEAST SQUARES 653 $aNIR 653 $aNIR (NEAR INFRARED REFLECTANCE) 653 $aSAMPLE PRESENTATION 653 $aSILAGE 653 $aWET WHOLE MAIZE 700 1 $aFASSIO, A. 700 1 $aFERNANDEZ, E. 700 1 $aRESTAINO, E. 700 1 $aLA MANNA, A. 773 $tAnimal Feed Science and Technology, 2006, 129 (3-4): 329-336
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