Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes
The routine use of high-throughput sequencing to profile microbial communities necessitates improved protocols for detecting and adjusting for variation among sequencing runs for marker gene analysis. Although mock communities are widely used as a control among runs, the composition and diversity of...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
The American Phytopathological Society
2018-09-01
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| Series: | Phytobiomes Journal |
| Online Access: | https://doi.org/10.1094/PBIOMES-09-17-0041-R |
| _version_ | 1818853268143472640 |
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| author | Zewei Song Dan Schlatter Daryl M. Gohl Linda L. Kinkel |
| author_facet | Zewei Song Dan Schlatter Daryl M. Gohl Linda L. Kinkel |
| author_sort | Zewei Song |
| collection | DOAJ |
| description | The routine use of high-throughput sequencing to profile microbial communities necessitates improved protocols for detecting and adjusting for variation among sequencing runs for marker gene analysis. Although mock communities are widely used as a control among runs, the composition and diversity of mock communities, in most cases, are orders of magnitude lower than the actual samples. We demonstrated that replicated biological samples (“technical replicates”) are superior to a mock community in detecting variation and potential bias among sequencing runs. We present a case in which technical replicates of three soil samples were sequenced in three MiSeq runs containing samples from multiple experiments. The technical replicate samples revealed a potentially biased, outlier sequencing run, from which several Ascomycota taxa were substantially underestimated. Similar bias was seen in the other samples sequenced but was not detected using the mock community. Our study demonstrates that using technical replicates along with traditional mock communities provide additional quality control information and aid in detecting outlier sequencing runs. |
| first_indexed | 2024-12-19T07:34:07Z |
| format | Article |
| id | doaj.art-047ac9a9961e4468a75c5f716610f438 |
| institution | Directory Open Access Journal |
| issn | 2471-2906 |
| language | English |
| last_indexed | 2024-12-19T07:34:07Z |
| publishDate | 2018-09-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Phytobiomes Journal |
| spelling | doaj.art-047ac9a9961e4468a75c5f716610f4382022-12-21T20:30:36ZengThe American Phytopathological SocietyPhytobiomes Journal2471-29062018-09-012316517010.1094/PBIOMES-09-17-0041-RRun-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal MicrobiomesZewei SongDan SchlatterDaryl M. GohlLinda L. KinkelThe routine use of high-throughput sequencing to profile microbial communities necessitates improved protocols for detecting and adjusting for variation among sequencing runs for marker gene analysis. Although mock communities are widely used as a control among runs, the composition and diversity of mock communities, in most cases, are orders of magnitude lower than the actual samples. We demonstrated that replicated biological samples (“technical replicates”) are superior to a mock community in detecting variation and potential bias among sequencing runs. We present a case in which technical replicates of three soil samples were sequenced in three MiSeq runs containing samples from multiple experiments. The technical replicate samples revealed a potentially biased, outlier sequencing run, from which several Ascomycota taxa were substantially underestimated. Similar bias was seen in the other samples sequenced but was not detected using the mock community. Our study demonstrates that using technical replicates along with traditional mock communities provide additional quality control information and aid in detecting outlier sequencing runs.https://doi.org/10.1094/PBIOMES-09-17-0041-R |
| spellingShingle | Zewei Song Dan Schlatter Daryl M. Gohl Linda L. Kinkel Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes Phytobiomes Journal |
| title | Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes |
| title_full | Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes |
| title_fullStr | Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes |
| title_full_unstemmed | Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes |
| title_short | Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes |
| title_sort | run to run sequencing variation can introduce taxon specific bias in the evaluation of fungal microbiomes |
| url | https://doi.org/10.1094/PBIOMES-09-17-0041-R |
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