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Registro completo
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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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 | Acceso al texto completo restringido a Biblioteca INIA Las Brujas. Por información adicional contacte bibliolb@inia.org.uy. |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha actual : |
02/06/2022 |
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Actualizado : |
02/12/2022 |
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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 : |
AMORÓS, M. E.; LAGARDE, L.; DO CARMO, H.; HEGUABURU, V.; MONNÉ, M.; BUENAHORA, J.; GONZÁLEZ, A. |
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Afiliación : |
MARÍA EUGENIA AMORÓS, Laboratorio de Ecología Química, Facultad de Química, Univ de La República, Udelar, Avda. Gral. Flores 2124, Montevideo, CP 11800, Uruguay; LAUTARO LAGARDE, Laboratorio de Ecología Química, Facultad de Química, Univ de La República, Udelar, Avda. Gral. Flores 2124, Montevideo, CP 11800, Uruguay; HUGO DO CARMO, Centro Universitario de Paysandú, Universidad de La República, Paysandú, Uruguay; VIVIVANA HEGUABURU, Centro Universitario de Paysandú, Universidad de La República, Paysandú, Uruguay; MARCELA MONNÉ, Museu Nacional, Univ Federal Do Rio de Janeiro, Rio de Janeiro, Brazil; JOSE HERMES BUENAHORA ACOSTA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ANDRÉS GONZÁLEZ, Laboratorio de Ecología Química, Facultad de Química, Univ de La República, Udelar, Avda. Gral. Flores 2124, Montevideo, CP 11800, Uruguay. |
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Título : |
Trapping of retrachydes thoracicus thoracicus (Olivier) and other neotropical cerambycid beetles in pheromone- and kairomone-baited traps. |
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Fecha de publicación : |
2022 |
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Fuente / Imprenta : |
Neotropical Entomology, 2022, volume 51, Issue 3, pages 386-396. doi: https://doi.org/10.1007/s13744-022-00955-w |
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ISSN : |
1519-566X |
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DOI : |
10.1007/s13744-022-00955-w |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 18 October 2021; Accepted 21 March 2022; Published online 11 May 2022.
Corresponding author: Amorós, M.E.; Laboratorio de Ecología Química, Facultad de Química, Univ de La RepúblicaUdelar, Avda. Gral. Flores 2124, Montevideo, Uruguay; email:eamoros@fq.edu.uy ; González, A.; Laboratorio de Ecología Química, Facultad de Química, Univ de La RepúblicaUdelar, Avda. Gral. Flores 2124, Montevideo, Uruguay; email:agonzal@fq.edu.uy -- The authors wish to thank financial support from CSIC (Comisión Sectorial de Investigación Científica) Universidad de la República, PEDECIBA (Programa para el Desarrollo de las Ciencias Básicas, Uruguay), and INIA (Instituto Nacional de Investigación Agropecuaria). |
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Contenido : |
ABSTRACT - The subfamily Cerambycinae, one of the most diverse in longhorn beetles, is well known for its remarkable chemical parsimony in male-emitted pheromones. Conserved shared structural motifs have been reported in numerous species, sometimes working in combination with plant volatile kairomones. Among other compounds, the most ubiquitous male pheromone in cerambycine species is 3-hydroxyhexan-2-one. We conducted field trials using intercept traps baited with 3-hydroxyhexan-2-one and observed abundant captures of several Neotropical cerambycine species. These were Retrachydes thoracicus thoracicus (Olivier), Megacyllene acuta (Germar), Compsocerus violaceus (White), and Cotyclytus curvatus (Germar) in high numbers, as well as Chydarteres striatus striatus (Fabricius) and Odontocroton flavicauda (Bates) in smaller numbers. When ethanol was added to the traps, a remarkable increase in the attractiveness of 3-hydroxyhexan-2-one was observed for R. thoracicus thoracicus and M. acuta. Adding ethanol also resulted in the capture of Chrysoprasis aurigena (Germar). Finally, incidental catches in pheromone-baited traps of Trachelissa maculicollis (Audinet-Serville), Neoclytus pusillus (Laporte & Gory), Achryson unicolor (Bruch, 1908) and Achryson surinamum (Linnaeus), Megacyllene mellyi (Chevrolat) and Thelgetra adustus (Burmeister) were also observed. Pheromone chemistry has been reported for C. curvatus, M. acuta and N. pusillus, all three producing 3-hydroxyhexan-2-one, and for C. aurigena and A. surinamum, which produce other compounds. Our findings suggest that the captured species probably produce 3-hydroxyhexan-2-one for their pheromone communication system. Alternatively, they might be ?eavesdropping? on the pheromones of other cerambycine species. The probable synergistic effect of ethanol is likely explained from its kairomonal role as a volatile cue for plant stress or ripeness.
© 2022, Sociedade Entomológica do Brasil. MenosABSTRACT - The subfamily Cerambycinae, one of the most diverse in longhorn beetles, is well known for its remarkable chemical parsimony in male-emitted pheromones. Conserved shared structural motifs have been reported in numerous species, sometimes working in combination with plant volatile kairomones. Among other compounds, the most ubiquitous male pheromone in cerambycine species is 3-hydroxyhexan-2-one. We conducted field trials using intercept traps baited with 3-hydroxyhexan-2-one and observed abundant captures of several Neotropical cerambycine species. These were Retrachydes thoracicus thoracicus (Olivier), Megacyllene acuta (Germar), Compsocerus violaceus (White), and Cotyclytus curvatus (Germar) in high numbers, as well as Chydarteres striatus striatus (Fabricius) and Odontocroton flavicauda (Bates) in smaller numbers. When ethanol was added to the traps, a remarkable increase in the attractiveness of 3-hydroxyhexan-2-one was observed for R. thoracicus thoracicus and M. acuta. Adding ethanol also resulted in the capture of Chrysoprasis aurigena (Germar). Finally, incidental catches in pheromone-baited traps of Trachelissa maculicollis (Audinet-Serville), Neoclytus pusillus (Laporte & Gory), Achryson unicolor (Bruch, 1908) and Achryson surinamum (Linnaeus), Megacyllene mellyi (Chevrolat) and Thelgetra adustus (Burmeister) were also observed. Pheromone chemistry has been reported for C. curvatus, M. acuta and N. pusillus, all three producing 3-hydroxyhexan-2-one, and ... Presentar Todo |
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Palabras claves : |
3-hydroxy-2-hexanone; Cerambycinae; Ethanol; Kairomone-pheromone synergism; Longhorn beetles. |
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Asunto categoría : |
A50 Investigación agraria |
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Marc : |
LEADER 03635naa a2200289 a 4500
001 1063200
005 2022-12-02
008 2022 bl uuuu u00u1 u #d
022 $a1519-566X
024 7 $a10.1007/s13744-022-00955-w$2DOI
100 1 $aAMORÓS, M. E.
245 $aTrapping of retrachydes thoracicus thoracicus (Olivier) and other neotropical cerambycid beetles in pheromone- and kairomone-baited traps.$h[electronic resource]
260 $c2022
500 $aArticle history: Received 18 October 2021; Accepted 21 March 2022; Published online 11 May 2022. Corresponding author: Amorós, M.E.; Laboratorio de Ecología Química, Facultad de Química, Univ de La RepúblicaUdelar, Avda. Gral. Flores 2124, Montevideo, Uruguay; email:eamoros@fq.edu.uy ; González, A.; Laboratorio de Ecología Química, Facultad de Química, Univ de La RepúblicaUdelar, Avda. Gral. Flores 2124, Montevideo, Uruguay; email:agonzal@fq.edu.uy -- The authors wish to thank financial support from CSIC (Comisión Sectorial de Investigación Científica) Universidad de la República, PEDECIBA (Programa para el Desarrollo de las Ciencias Básicas, Uruguay), and INIA (Instituto Nacional de Investigación Agropecuaria).
520 $aABSTRACT - The subfamily Cerambycinae, one of the most diverse in longhorn beetles, is well known for its remarkable chemical parsimony in male-emitted pheromones. Conserved shared structural motifs have been reported in numerous species, sometimes working in combination with plant volatile kairomones. Among other compounds, the most ubiquitous male pheromone in cerambycine species is 3-hydroxyhexan-2-one. We conducted field trials using intercept traps baited with 3-hydroxyhexan-2-one and observed abundant captures of several Neotropical cerambycine species. These were Retrachydes thoracicus thoracicus (Olivier), Megacyllene acuta (Germar), Compsocerus violaceus (White), and Cotyclytus curvatus (Germar) in high numbers, as well as Chydarteres striatus striatus (Fabricius) and Odontocroton flavicauda (Bates) in smaller numbers. When ethanol was added to the traps, a remarkable increase in the attractiveness of 3-hydroxyhexan-2-one was observed for R. thoracicus thoracicus and M. acuta. Adding ethanol also resulted in the capture of Chrysoprasis aurigena (Germar). Finally, incidental catches in pheromone-baited traps of Trachelissa maculicollis (Audinet-Serville), Neoclytus pusillus (Laporte & Gory), Achryson unicolor (Bruch, 1908) and Achryson surinamum (Linnaeus), Megacyllene mellyi (Chevrolat) and Thelgetra adustus (Burmeister) were also observed. Pheromone chemistry has been reported for C. curvatus, M. acuta and N. pusillus, all three producing 3-hydroxyhexan-2-one, and for C. aurigena and A. surinamum, which produce other compounds. Our findings suggest that the captured species probably produce 3-hydroxyhexan-2-one for their pheromone communication system. Alternatively, they might be ?eavesdropping? on the pheromones of other cerambycine species. The probable synergistic effect of ethanol is likely explained from its kairomonal role as a volatile cue for plant stress or ripeness. © 2022, Sociedade Entomológica do Brasil.
653 $a3-hydroxy-2-hexanone
653 $aCerambycinae
653 $aEthanol
653 $aKairomone-pheromone synergism
653 $aLonghorn beetles
700 1 $aLAGARDE, L.
700 1 $aDO CARMO, H.
700 1 $aHEGUABURU, V.
700 1 $aMONNÉ, M.
700 1 $aBUENAHORA, J.
700 1 $aGONZÁLEZ, A.
773 $tNeotropical Entomology, 2022, volume 51, Issue 3, pages 386-396. doi: https://doi.org/10.1007/s13744-022-00955-w
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