Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis
Abstract Objective Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-07-01
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| Series: | BMC Research Notes |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13104-018-3559-3 |
| _version_ | 1818109972309868544 |
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| author | Marie Cariou Céline Ribière Stéphanie Morlière Jean-Pierre Gauthier Jean-Christophe Simon Pierre Peyret Sylvain Charlat |
| author_facet | Marie Cariou Céline Ribière Stéphanie Morlière Jean-Pierre Gauthier Jean-Christophe Simon Pierre Peyret Sylvain Charlat |
| author_sort | Marie Cariou |
| collection | DOAJ |
| description | Abstract Objective Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pisum to compare the performances of two widely used PCR primer pairs with DNA capture, based on solution hybrid selection. Results All methods produced an exhaustive description of the 8 bacterial taxa known to be present in this sample. In addition, the methods yielded similar quantitative results, with the number of reads strongly correlating with quantitative PCR controls. Both methods can thus be considered as qualitatively and quantitatively robust on such a sample with low microbial complexity. |
| first_indexed | 2024-12-11T02:39:44Z |
| format | Article |
| id | doaj.art-e97768890bb748aeb814642dd112056d |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-11T02:39:44Z |
| publishDate | 2018-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-e97768890bb748aeb814642dd112056d2022-12-22T01:23:36ZengBMCBMC Research Notes1756-05002018-07-011111510.1186/s13104-018-3559-3Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysisMarie Cariou0Céline Ribière1Stéphanie Morlière2Jean-Pierre Gauthier3Jean-Christophe Simon4Pierre Peyret5Sylvain Charlat6Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université de Lyon, Université Lyon 1INRA, MEDIS, Université Clermont AuvergneINRA, UMR 1349 (IGEPP “Institut de Génétique, Environnement et Protection des Plantes”) INRA/Agrocampus Ouest/Université Rennes 1INRA, UMR 1349 (IGEPP “Institut de Génétique, Environnement et Protection des Plantes”) INRA/Agrocampus Ouest/Université Rennes 1INRA, UMR 1349 (IGEPP “Institut de Génétique, Environnement et Protection des Plantes”) INRA/Agrocampus Ouest/Université Rennes 1INRA, MEDIS, Université Clermont AuvergneLaboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université de Lyon, Université Lyon 1Abstract Objective Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pisum to compare the performances of two widely used PCR primer pairs with DNA capture, based on solution hybrid selection. Results All methods produced an exhaustive description of the 8 bacterial taxa known to be present in this sample. In addition, the methods yielded similar quantitative results, with the number of reads strongly correlating with quantitative PCR controls. Both methods can thus be considered as qualitatively and quantitatively robust on such a sample with low microbial complexity.http://link.springer.com/article/10.1186/s13104-018-3559-3Hybridization captureAmplicon sequencing16SPea aphidMicrobiota |
| spellingShingle | Marie Cariou Céline Ribière Stéphanie Morlière Jean-Pierre Gauthier Jean-Christophe Simon Pierre Peyret Sylvain Charlat Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis BMC Research Notes Hybridization capture Amplicon sequencing 16S Pea aphid Microbiota |
| title | Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis |
| title_full | Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis |
| title_fullStr | Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis |
| title_full_unstemmed | Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis |
| title_short | Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis |
| title_sort | comparing 16s rdna amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis |
| topic | Hybridization capture Amplicon sequencing 16S Pea aphid Microbiota |
| url | http://link.springer.com/article/10.1186/s13104-018-3559-3 |
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