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Biblioteca (s) : |
INIA Treinta y Tres. |
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Fecha : |
21/02/2014 |
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Actualizado : |
13/09/2018 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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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. |
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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. |
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Título : |
Enrichment allows identification of diverse, rate elements in metagenomic resistome-virulome sequencing. |
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Fecha de publicación : |
2017 |
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Fuente / Imprenta : |
Microbiome, 2017, 5, p. 142 |
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Páginas : |
13 p. |
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DOI : |
10.1186/s40168-017-0361-8 |
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Idioma : |
Inglés |
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Notas : |
Article History: Received: 29 May 2017, Accepted: 5 October 2017, Published: 17 October 2017 |
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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 |
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Palabras claves : |
ANTIMICROBIAL RESISTANCE; METAGENÓMICA; MICROBIAL ECOLOGY; MOLECULAR ENRICHMENT; RARE MICROBIOME; RESISTOME. |
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Thesagro : |
ANALISIS BIOLOGICO; ECOLOGIA MICROBIANA; RESISTENCIA A AGENTES DANINOS. |
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Asunto categoría : |
U30 Métodos de investigación |
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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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Registro original : |
INIA Treinta y Tres (TT) |
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha actual : |
17/05/2022 |
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Actualizado : |
17/05/2022 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
Internacional - -- |
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Autor : |
PACHECO-ROMERO, M.; VALLEJOS, M.; PARUELO, J.; ALCARAZ-SEGURA, D.; TORRES-GARCÍA, M. T.; SALINAS-BONILLO, M. J.; CABELLO, JAVIER |
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Afiliación : |
MANUEL PACHECO-ROMERO, Andalusian Center for the Assessment and Monitoring of Global Change (CAESCG), Univ. of Almería, Spain; Dept. of Biology and Geology, Univ. of Almería, Spain; Faculty of Sustainability, Leuphana, Univ. Lüneburg, Germany.; MARÍA VALLEJOS, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; Cátedra de Métodos Cuantitativos y Sistemas de Información, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina; JOSÉ PARUELO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; Cátedra Métodos Cuantitativos y Sistemas de Información, Fac. Agronomía, Univ. de Buenos Aires, Bs.As., Argentina; Fac. de Ciencias, IECA, Universidad de la República, Mdeo, Uruguay.; DOMINGO ALCARAZ-SEGURA, Andalusian Center for the Assessment and Monitoring of Global Change (CAESCG), Univ. of Almería, Spain;Dept. of Botany, Univ. of Granada, Spain; Iecolab, Interuniversity Institute for Earth System Research (IISTA), Univ. of Granada, Spain; M. TRINIDAD TORRES-GARCÍA, Andalusian Center for the Assessment and Monitoring of Global Change (CAESCG), University of Almería, Almería, Spain Department of Biology and Geology, University of Almería, Almería, Spain; MARÍA J. SALINAS-BONILLO, Andalusian Center for the Assessment and Monitoring of Global Change (CAESCG), University of Almería, Almería, Spain Department of Biology and Geology, University of Almería, Almería, Spain; JAVIER CABELLO, Andalusian Center for the Assessment and Monitoring of Global Change (CAESCG), University of Almería, Almería, Spain Department of Biology and Geology, University of Almería, Almería, Spain. |
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Título : |
A data-driven methodological routine to identify key indicators for social-ecological system archetype mapping. |
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Fecha de publicación : |
2022 |
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Fuente / Imprenta : |
Environmental Research Letters, 2022, Volume 17, Issue 4, Article number 045019. OPEN ACCESS. doi: https://doi.org/10.1088/1748-9326/ac5ded |
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ISSN : |
1748-9318 |
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DOI : |
10.1088/1748-9326/ac5ded |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 2 July 2021; Revised 28 January 2022; Accepted for publication 15 March 2022; Published 30 March 2022.
License: Original content from this work may be used under the terms of the Creative Commons Attribution 4.0 licence. Any further distribution of this work must
maintain attribution to the author(s) and the title of the work, journal citation and DOI. -- Article: Gold Open Access, Green Open Access.
Corresponding author: Pacheco-Romero, M.; Andalusian Center for the Assessment and Monitoring of Global Change (CAESCG), University of Almería, Almería, Spain; email:manuel.pacheco@ual.es --
Funding text - We thank R Romero-Calcerrada and J M Requena-Mullor for helpful discussions, and three anonymous reviewers for their constructive suggestions to improve this paper. We also thank the Spanish Ministry of Economy and Business (Project CGL2014-61610-EXP) for the financial support, as well as the Spanish Ministry of Education for the FPU Predoctoral Fellowship of MPR (FPU14/06782) and MTTG (16/02214). MPR gratefully acknowledges funding from Universidad de Almería for a research stay at the Laboratory of Regional Analysis and Remote Sensing (LART) of University of Buenos Aires to develop this study. This research was done within the LTSER Platforms of the Arid Iberian South East—Spain (LTER_EU_ES_027) and Sierra Nevada/Granada (ES- SNE)—Spain (LTER_EU_ES_010), and contributes to the Global Land Programme. |
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Contenido : |
ABSTRACT.- The spatial mapping of social-ecological system (SES) archetypes constitutes a fundamental tool to operationalize the SES concept in empirical research. Approaches to detect, map, and characterize SES archetypes have evolved over the last decade towards more integrative and comparable perspectives guided by SES conceptual frameworks and reference lists of variables. However, hardly any studies have investigated how to empirically identify the most relevant set of indicators to map the diversity of SESs. In this study, we propose a data-driven methodological routine based on multivariate statistical analysis to identify the most relevant indicators for mapping and characterizing SES archetypes in a particular region. Taking Andalusia (Spain) as a case study, we applied this methodological routine to 86 indicators representing multiple variables and dimensions of the SES. Additionally, we assessed how the empirical relevance of these indicators contributes to previous expert and empirical knowledge on key variables for characterizing SESs. We identified 29 key indicators that allowed us to map 15 SES archetypes encompassing natural, mosaic, agricultural, and urban systems, which uncovered contrasting land sharing and land sparing patterns throughout the territory. We found synergies but also disagreements between empirical and expert knowledge on the relevance of variables: agreement on their widespread relevance (32.7% of the variables, e.g. crop and livestock production, net primary productivity, population density); relevance conditioned by the context or the scale (16.3%, e.g. land protection, educational level); lack of agreement (20.4%, e.g. economic level, land tenure); need of further assessments due to the lack of expert or empirical knowledge (30.6%). Overall, our data-driven approach can contribute to more objective selection of relevant indicators for SES mapping, which may help to produce comparable and generalizable empirical knowledge on key variables for characterizing SESs, as well as to derive more representative descriptions and causal factor configurations in SES archetype analysis.
© 2022 The Author(s). Published by IOP Publishing Ltd. MenosABSTRACT.- The spatial mapping of social-ecological system (SES) archetypes constitutes a fundamental tool to operationalize the SES concept in empirical research. Approaches to detect, map, and characterize SES archetypes have evolved over the last decade towards more integrative and comparable perspectives guided by SES conceptual frameworks and reference lists of variables. However, hardly any studies have investigated how to empirically identify the most relevant set of indicators to map the diversity of SESs. In this study, we propose a data-driven methodological routine based on multivariate statistical analysis to identify the most relevant indicators for mapping and characterizing SES archetypes in a particular region. Taking Andalusia (Spain) as a case study, we applied this methodological routine to 86 indicators representing multiple variables and dimensions of the SES. Additionally, we assessed how the empirical relevance of these indicators contributes to previous expert and empirical knowledge on key variables for characterizing SESs. We identified 29 key indicators that allowed us to map 15 SES archetypes encompassing natural, mosaic, agricultural, and urban systems, which uncovered contrasting land sharing and land sparing patterns throughout the territory. We found synergies but also disagreements between empirical and expert knowledge on the relevance of variables: agreement on their widespread relevance (32.7% of the variables, e.g. crop and livestock prod... Presentar Todo |
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Palabras claves : |
Coupled human and natural systems; Essential social-ecological system variables; Human-environment interactions; LONG-TERM SOCIAL-ECOLOGICAL RESEARCH; LTSER; Random forest; SOCIAL-ECOLOGICAL SYSTEM FRAMEWORK. |
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Asunto categoría : |
A50 Investigación agraria |
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URL : |
https://iopscience.iop.org/article/10.1088/1748-9326/ac5ded/pdf
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Marc : |
LEADER 04770naa a2200313 a 4500
001 1063148
005 2022-05-17
008 2022 bl uuuu u00u1 u #d
022 $a1748-9318
024 7 $a10.1088/1748-9326/ac5ded$2DOI
100 1 $aPACHECO-ROMERO, M.
245 $aA data-driven methodological routine to identify key indicators for social-ecological system archetype mapping.$h[electronic resource]
260 $c2022
500 $aArticle history: Received 2 July 2021; Revised 28 January 2022; Accepted for publication 15 March 2022; Published 30 March 2022. License: Original content from this work may be used under the terms of the Creative Commons Attribution 4.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. -- Article: Gold Open Access, Green Open Access. Corresponding author: Pacheco-Romero, M.; Andalusian Center for the Assessment and Monitoring of Global Change (CAESCG), University of Almería, Almería, Spain; email:manuel.pacheco@ual.es -- Funding text - We thank R Romero-Calcerrada and J M Requena-Mullor for helpful discussions, and three anonymous reviewers for their constructive suggestions to improve this paper. We also thank the Spanish Ministry of Economy and Business (Project CGL2014-61610-EXP) for the financial support, as well as the Spanish Ministry of Education for the FPU Predoctoral Fellowship of MPR (FPU14/06782) and MTTG (16/02214). MPR gratefully acknowledges funding from Universidad de Almería for a research stay at the Laboratory of Regional Analysis and Remote Sensing (LART) of University of Buenos Aires to develop this study. This research was done within the LTSER Platforms of the Arid Iberian South East—Spain (LTER_EU_ES_027) and Sierra Nevada/Granada (ES- SNE)—Spain (LTER_EU_ES_010), and contributes to the Global Land Programme.
520 $aABSTRACT.- The spatial mapping of social-ecological system (SES) archetypes constitutes a fundamental tool to operationalize the SES concept in empirical research. Approaches to detect, map, and characterize SES archetypes have evolved over the last decade towards more integrative and comparable perspectives guided by SES conceptual frameworks and reference lists of variables. However, hardly any studies have investigated how to empirically identify the most relevant set of indicators to map the diversity of SESs. In this study, we propose a data-driven methodological routine based on multivariate statistical analysis to identify the most relevant indicators for mapping and characterizing SES archetypes in a particular region. Taking Andalusia (Spain) as a case study, we applied this methodological routine to 86 indicators representing multiple variables and dimensions of the SES. Additionally, we assessed how the empirical relevance of these indicators contributes to previous expert and empirical knowledge on key variables for characterizing SESs. We identified 29 key indicators that allowed us to map 15 SES archetypes encompassing natural, mosaic, agricultural, and urban systems, which uncovered contrasting land sharing and land sparing patterns throughout the territory. We found synergies but also disagreements between empirical and expert knowledge on the relevance of variables: agreement on their widespread relevance (32.7% of the variables, e.g. crop and livestock production, net primary productivity, population density); relevance conditioned by the context or the scale (16.3%, e.g. land protection, educational level); lack of agreement (20.4%, e.g. economic level, land tenure); need of further assessments due to the lack of expert or empirical knowledge (30.6%). Overall, our data-driven approach can contribute to more objective selection of relevant indicators for SES mapping, which may help to produce comparable and generalizable empirical knowledge on key variables for characterizing SESs, as well as to derive more representative descriptions and causal factor configurations in SES archetype analysis. © 2022 The Author(s). Published by IOP Publishing Ltd.
653 $aCoupled human and natural systems
653 $aEssential social-ecological system variables
653 $aHuman-environment interactions
653 $aLONG-TERM SOCIAL-ECOLOGICAL RESEARCH
653 $aLTSER
653 $aRandom forest
653 $aSOCIAL-ECOLOGICAL SYSTEM FRAMEWORK
700 1 $aVALLEJOS, M.
700 1 $aPARUELO, J.
700 1 $aALCARAZ-SEGURA, D.
700 1 $aTORRES-GARCÍA, M. T.
700 1 $aSALINAS-BONILLO, M. J.
700 1 $aCABELLO, JAVIER
773 $tEnvironmental Research Letters, 2022, Volume 17, Issue 4, Article number 045019. OPEN ACCESS. doi: https://doi.org/10.1088/1748-9326/ac5ded
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