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Biblioteca (s) : |
INIA Treinta y Tres. |
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Fecha : |
04/11/2019 |
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Actualizado : |
03/12/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
DOSTER, E.; ROVIRA, P.J.; NOYES, N.R.; BURGESS, B.A.; YANG, X.; WEINROTH, M.D.; LINKE, L.; MAGNUSON, R.; BOUCHER, C.; BELK, K.E.; MORLEY, P.S. |
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Afiliación : |
ENRIQUE DOSTER, Department in Microbiology, Immunology and Pathology, Colorado State University, USA.; PABLO JUAN ROVIRA SANZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; NOELLE R. NOYES, Department of Veterinary Population Medicine, University of Minnesota, USA.; BRANDY A. BURGESS, Department of Population Health, University of Georgia, USA.; XIANG YANG, Department of Animal Science, University of California, Davis, Davis, CA, USA.; MARGARET D. WEINROTH, Department of Animal Sciences, Colorado State University, USA.; LINDSEY LINKE, Department of Clinical Sciences, Colorado State University, USA.; ROBERTA MAGNUSON, Department of Clinical Sciences, Colorado State University, USA.; CHRISTINA BOUCHER, Department of Computer and Information Science and Engineering, University of Florida, Florida, USA.; KEITH E. BELK, Department of Animal Sciences, Colorado State University, Colorado, USA.; PAUL S. MORLEY, Veterinary Education, Research, and Outreach Center, West Texas A&M University, Texas, USA. |
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Título : |
A cautionary report for pathogen identification using shotgun metagenomics; a comparison to aerobic culture and polymerase chain reaction for Salmonella enterica identification. |
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Fecha de publicación : |
2019 |
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Fuente / Imprenta : |
Frontier in Microbiology, 2019, 10:2499. doi: 10.3389/fmicb.2019.02499 |
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Páginas : |
7 p. |
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DOI : |
10.3389/fmicb.2019.02499 |
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Idioma : |
Inglés |
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Notas : |
Article history: received: 8 July 2019 // Accepted 16 October 2019 // Published 01 November 2019.
Open Access Journal. www.frontiersin.org |
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Contenido : |
This study was conducted to compare aerobic culture, polymerase chain reaction (PCR), lateral flow immunoassay (LFI), and shotgun metagenomics for identification
of Salmonella enterica in feces collected from feedlot cattle. Samples were analyzed in parallel using all four tests. Results from aerobic culture and PCR were 100%
concordant and indicated low S. enterica prevalence (3/60 samples positive). Although low S. enterica prevalence restricted formal statistical comparisons, LFI and deep metagenomic sequencing results were discordant with these results. Specifically, metagenomic analysis using k-mer-based classification against the RefSeq database indicated that 11/60 of samples contained sequence reads that matched to the S. enterica genome and uniquely identified this species of bacteria within the sample. However, further examination revealed that plasmid sequences were often included with bacterial genomic sequence data submitted to NCBI, which can lead to incorrect taxonomic classification. To circumvent this classification problem, we separated all plasmid sequences included in bacterial RefSeq genomes and reassigned them to a unique taxon so that they would not be uniquely associated with specific bacterial species such as S. enterica. Using this revised database and taxonomic structure, we found that only 6/60 samples contained sequences specific for S. enterica, suggesting increased relative specificity. Reads identified as S. enterica in these six samples were further evaluated using BLAST and NCBI?s nr/nt database, which identified that only 2/60 samples contained reads exclusive to S. enterica chromosomal genomes. These two samples were culture- and PCR-negative, suggesting that even deep metagenomic sequencing suffers from lower sensitivity and specificity in comparison to more traditional pathogen detection methods. Additionally, no sample reads were taxonomically classified as S. enterica with two other metagenomic tools, Metagenomic Intra-species Diversity Analysis System (MIDAS) and Metagenomic Phylogenetic Analysis 2 (MetaPhlAn2). This study re-affirmed that the traditional techniques of aerobic culture and PCR provide similar results for S. enterica identification in cattle feces. On the other hand, metagenomic results are highly influenced by the classification method and reference database employed. These results highlight the nuances of computational detection of species-level sequences within short-read metagenomic sequence data, and emphasize the need for cautious interpretation of such results. MenosThis study was conducted to compare aerobic culture, polymerase chain reaction (PCR), lateral flow immunoassay (LFI), and shotgun metagenomics for identification
of Salmonella enterica in feces collected from feedlot cattle. Samples were analyzed in parallel using all four tests. Results from aerobic culture and PCR were 100%
concordant and indicated low S. enterica prevalence (3/60 samples positive). Although low S. enterica prevalence restricted formal statistical comparisons, LFI and deep metagenomic sequencing results were discordant with these results. Specifically, metagenomic analysis using k-mer-based classification against the RefSeq database indicated that 11/60 of samples contained sequence reads that matched to the S. enterica genome and uniquely identified this species of bacteria within the sample. However, further examination revealed that plasmid sequences were often included with bacterial genomic sequence data submitted to NCBI, which can lead to incorrect taxonomic classification. To circumvent this classification problem, we separated all plasmid sequences included in bacterial RefSeq genomes and reassigned them to a unique taxon so that they would not be uniquely associated with specific bacterial species such as S. enterica. Using this revised database and taxonomic structure, we found that only 6/60 samples contained sequences specific for S. enterica, suggesting increased relative specificity. Reads identified as S. enterica in these six samples were ... Presentar Todo |
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Palabras claves : |
CULTURE; PATHOGEN IDENTIFICATION; PCR; SALMONELLA ENTERICA; SHOTGUN METAGENOMICS. |
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Thesagro : |
CATTLE; FEEDLOT; VACAS. |
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Asunto categoría : |
L73 Enfermedades de los animales |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/13700/1/Rovira-arb-2019-Frontiers-Microbiology.pdf
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Marc : |
LEADER 03789naa a2200373 a 4500
001 1060378
005 2019-12-03
008 2019 bl uuuu u00u1 u #d
024 7 $a10.3389/fmicb.2019.02499$2DOI
100 1 $aDOSTER, E.
245 $aA cautionary report for pathogen identification using shotgun metagenomics; a comparison to aerobic culture and polymerase chain reaction for Salmonella enterica identification.$h[electronic resource]
260 $c2019
300 $a7 p.
500 $aArticle history: received: 8 July 2019 // Accepted 16 October 2019 // Published 01 November 2019. Open Access Journal. www.frontiersin.org
520 $aThis study was conducted to compare aerobic culture, polymerase chain reaction (PCR), lateral flow immunoassay (LFI), and shotgun metagenomics for identification of Salmonella enterica in feces collected from feedlot cattle. Samples were analyzed in parallel using all four tests. Results from aerobic culture and PCR were 100% concordant and indicated low S. enterica prevalence (3/60 samples positive). Although low S. enterica prevalence restricted formal statistical comparisons, LFI and deep metagenomic sequencing results were discordant with these results. Specifically, metagenomic analysis using k-mer-based classification against the RefSeq database indicated that 11/60 of samples contained sequence reads that matched to the S. enterica genome and uniquely identified this species of bacteria within the sample. However, further examination revealed that plasmid sequences were often included with bacterial genomic sequence data submitted to NCBI, which can lead to incorrect taxonomic classification. To circumvent this classification problem, we separated all plasmid sequences included in bacterial RefSeq genomes and reassigned them to a unique taxon so that they would not be uniquely associated with specific bacterial species such as S. enterica. Using this revised database and taxonomic structure, we found that only 6/60 samples contained sequences specific for S. enterica, suggesting increased relative specificity. Reads identified as S. enterica in these six samples were further evaluated using BLAST and NCBI?s nr/nt database, which identified that only 2/60 samples contained reads exclusive to S. enterica chromosomal genomes. These two samples were culture- and PCR-negative, suggesting that even deep metagenomic sequencing suffers from lower sensitivity and specificity in comparison to more traditional pathogen detection methods. Additionally, no sample reads were taxonomically classified as S. enterica with two other metagenomic tools, Metagenomic Intra-species Diversity Analysis System (MIDAS) and Metagenomic Phylogenetic Analysis 2 (MetaPhlAn2). This study re-affirmed that the traditional techniques of aerobic culture and PCR provide similar results for S. enterica identification in cattle feces. On the other hand, metagenomic results are highly influenced by the classification method and reference database employed. These results highlight the nuances of computational detection of species-level sequences within short-read metagenomic sequence data, and emphasize the need for cautious interpretation of such results.
650 $aCATTLE
650 $aFEEDLOT
650 $aVACAS
653 $aCULTURE
653 $aPATHOGEN IDENTIFICATION
653 $aPCR
653 $aSALMONELLA ENTERICA
653 $aSHOTGUN METAGENOMICS
700 1 $aROVIRA, P.J.
700 1 $aNOYES, N.R.
700 1 $aBURGESS, B.A.
700 1 $aYANG, X.
700 1 $aWEINROTH, M.D.
700 1 $aLINKE, L.
700 1 $aMAGNUSON, R.
700 1 $aBOUCHER, C.
700 1 $aBELK, K.E.
700 1 $aMORLEY, P.S.
773 $tFrontier in Microbiology, 2019, 10:2499. doi: 10.3389/fmicb.2019.02499
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Registro original : |
INIA Treinta y Tres (TT) |
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Registro completo
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Biblioteca (s) : |
INIA Tacuarembó. |
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Fecha actual : |
21/02/2014 |
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Actualizado : |
09/09/2020 |
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Autor : |
CARÁMBULA, M.; PIÑEIRO, D |
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Afiliación : |
M. CARÁMBULA, Becario del Proyecto IAI-SGP 004, IFEVA. Facultad de Agronomía UBA. Facultad de Agronomía. Universidad de la República. Uruguay.; D. PIÑEIRO, Facultad de Agronomía y Facultad de Ciencias Sociales. Universidad de la República. Uruguay. |
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Título : |
La forestación en Uruguay: cambio demográfico y empleo en tres localidades// [Afforestation in Uruguay: Demographic changes and employment in trhee villages]. |
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Fecha de publicación : |
2006 |
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Fuente / Imprenta : |
Agrociencia Uruguay, 2006, 10(2):63-73 |
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Idioma : |
Español |
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Notas : |
Article history: Recibido: 20/03/06 Aceptado: 04/09/06. AGRADECIMIENTOS: Agradecemos al equipo de investigación liderado por los Dres. José Paruelo y Esteban Jobbaggy del IFEVA,
Facultad de Agronomía de la Universidad de Buenos Aires por habernos invitado a participar del Proyecto IAISGP 004 "Climate and land use controls on ecosystem functioning". lo cual dió inicio a una productiva cooperación no solo entre equipos de distintos países sino también entre equipos de distintas disciplinas. También queremos agradecer a todas las nstituciones y a los pobladores de las tres localidades donde se llevó a cabo el estudio de caso, sus autoridades, líderes locales y vecinos por la disposición mostrada para colaborar con el mismo. |
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Contenido : |
RESUMEN: En el contexto de los grandes cambios a nivel societal que están ocurriendo en los últimas décadas del siglo XX en este artículo se analizan los impactos que tiene la forestación sobre los cambios demográficos y el empleo. La forestación parece haber incidido en retener y aun aumentar la población en los pequeños poblados estudiados. La forestación también ha aumentado el empleo pero por otro lado ha precarizado la relación laboral. El artículo también sugiere la existencia de dos modelos forestales distintos: uno con transformación de la materia prima en el lugar que da lugar aun desarrollo mas equilibrado, y otro modelo destinado a la producción de pasta de celulosa fuera de la localidad donde los desequilibrios poblacionales y la precarización del empleo parecen ser mayores. SUMMARY: In the context of the important social changes that are taking place in the last decades of the XXth. Century,
this paper explores the consequences of afforestation in local population changes and in employment. In the small rural villages that were studied, afforestation has increased population. It has also increased employment but creating low quality (precarious) jobs. The paper also suggests the existence of two different afforestation models: one in which timber is transformed in place resulting in a more balanced development, and another in which timber is exported to other regions to produce cellulose pulp where population changes and employment
precarization seem to be worse. |
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Palabras claves : |
AFFORESTATION; DESARROLLO TERRITORIAL; EMPLEO; EMPLEO PRECARIO; FORESTACIÓN; POBLACIÓN RURAL; PRECARIOUS EMPLOYMENT; RURAL POPULATION; RURALIDAD; SECTOR FORESTAL-MADERERO; URUGUAY. |
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Asunto categoría : |
K10 Producción forestal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/14631/1/Agrociencia2006v10n2p63-73.pdf
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Marc : |
LEADER 03098naa a2200277 a 4500
001 1026779
005 2020-09-09
008 2006 bl uuuu u00u1 u #d
100 1 $aCARÁMBULA, M.
245 $aLa forestación en Uruguay$bcambio demográfico y empleo en tres localidades// [Afforestation in Uruguay: Demographic changes and employment in trhee villages].$h[electronic resource]
260 $c2006
500 $aArticle history: Recibido: 20/03/06 Aceptado: 04/09/06. AGRADECIMIENTOS: Agradecemos al equipo de investigación liderado por los Dres. José Paruelo y Esteban Jobbaggy del IFEVA, Facultad de Agronomía de la Universidad de Buenos Aires por habernos invitado a participar del Proyecto IAISGP 004 "Climate and land use controls on ecosystem functioning". lo cual dió inicio a una productiva cooperación no solo entre equipos de distintos países sino también entre equipos de distintas disciplinas. También queremos agradecer a todas las nstituciones y a los pobladores de las tres localidades donde se llevó a cabo el estudio de caso, sus autoridades, líderes locales y vecinos por la disposición mostrada para colaborar con el mismo.
520 $aRESUMEN: En el contexto de los grandes cambios a nivel societal que están ocurriendo en los últimas décadas del siglo XX en este artículo se analizan los impactos que tiene la forestación sobre los cambios demográficos y el empleo. La forestación parece haber incidido en retener y aun aumentar la población en los pequeños poblados estudiados. La forestación también ha aumentado el empleo pero por otro lado ha precarizado la relación laboral. El artículo también sugiere la existencia de dos modelos forestales distintos: uno con transformación de la materia prima en el lugar que da lugar aun desarrollo mas equilibrado, y otro modelo destinado a la producción de pasta de celulosa fuera de la localidad donde los desequilibrios poblacionales y la precarización del empleo parecen ser mayores. SUMMARY: In the context of the important social changes that are taking place in the last decades of the XXth. Century, this paper explores the consequences of afforestation in local population changes and in employment. In the small rural villages that were studied, afforestation has increased population. It has also increased employment but creating low quality (precarious) jobs. The paper also suggests the existence of two different afforestation models: one in which timber is transformed in place resulting in a more balanced development, and another in which timber is exported to other regions to produce cellulose pulp where population changes and employment precarization seem to be worse.
653 $aAFFORESTATION
653 $aDESARROLLO TERRITORIAL
653 $aEMPLEO
653 $aEMPLEO PRECARIO
653 $aFORESTACIÓN
653 $aPOBLACIÓN RURAL
653 $aPRECARIOUS EMPLOYMENT
653 $aRURAL POPULATION
653 $aRURALIDAD
653 $aSECTOR FORESTAL-MADERERO
653 $aURUGUAY
700 1 $aPIÑEIRO, D
773 $tAgrociencia Uruguay, 2006, 10(2):63-73
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