A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities
ABSTRACT Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identificati...
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| Language: | English |
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American Society for Microbiology
2024-10-01
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| Series: | mSystems |
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| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00859-24 |
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| author | Julian Dommann Jakob Kerbl-Knapp Diana Albertos Torres Adrian Egli Jennifer Keiser Pierre H. H. Schneeberger |
| author_facet | Julian Dommann Jakob Kerbl-Knapp Diana Albertos Torres Adrian Egli Jennifer Keiser Pierre H. H. Schneeberger |
| author_sort | Julian Dommann |
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| description | ABSTRACT Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cramér’s V = 0.857, and Theil’s U = 0.316). For species-level community profiling, we found strong correlations (rs > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average rs = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.IMPORTANCEA quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline. |
| format | Article |
| id | doaj-art-7a14a9cb5b8f4bdb8e9ca3d5d4ae79b4 |
| institution | OA Journals |
| issn | 2379-5077 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | American Society for Microbiology |
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| series | mSystems |
| spelling | doaj-art-7a14a9cb5b8f4bdb8e9ca3d5d4ae79b42025-08-20T02:09:01ZengAmerican Society for MicrobiologymSystems2379-50772024-10-0191010.1128/msystems.00859-24A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communitiesJulian Dommann0Jakob Kerbl-Knapp1Diana Albertos Torres2Adrian Egli3Jennifer Keiser4Pierre H. H. Schneeberger5Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, SwitzerlandDepartment of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, SwitzerlandInstitute of Medical Microbiology, University of Zurich, Zurich, SwitzerlandInstitute of Medical Microbiology, University of Zurich, Zurich, SwitzerlandDepartment of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, SwitzerlandDepartment of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, SwitzerlandABSTRACT Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cramér’s V = 0.857, and Theil’s U = 0.316). For species-level community profiling, we found strong correlations (rs > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average rs = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.IMPORTANCEA quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.https://journals.asm.org/doi/10.1128/msystems.00859-24DNA sequencinggut microbiomebioinformatics |
| spellingShingle | Julian Dommann Jakob Kerbl-Knapp Diana Albertos Torres Adrian Egli Jennifer Keiser Pierre H. H. Schneeberger A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities mSystems DNA sequencing gut microbiome bioinformatics |
| title | A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities |
| title_full | A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities |
| title_fullStr | A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities |
| title_full_unstemmed | A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities |
| title_short | A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities |
| title_sort | novel barcoded nanopore sequencing workflow of high quality full length bacterial 16s amplicons for taxonomic annotation of bacterial isolates and complex microbial communities |
| topic | DNA sequencing gut microbiome bioinformatics |
| url | https://journals.asm.org/doi/10.1128/msystems.00859-24 |
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