High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts
| العنوان: | High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts |
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| المؤلفون: | Justina Medžiūnė, Arvydas Lubys, Gediminas Alzbutas, Laurynas Karpus, Žana Kapustina, Gytis Mackevičius, Karolis Matjošaitis, Simona Žeimytė, Irmantas Rokaitis |
| المصدر: | Microbial Genomics Microbial genomics, London : Microbiology Society, 2021, vol. 7, iss. 9, art. no. 000624, p. [1-16] |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | DNA, Bacterial, In silico, Locus (genetics), Bacterial genome size, Computational biology, Biology, RNA, Ribosomal, 16S, Methods, Microbiome, 16S rRNA, Gene, high-throughput microbiome profiling, semi-targeted sequencing, targeted DNA sequencing, Phylogeny, Genomic Methodologies, Bacteria, Base Sequence, Microbiota, Computational Biology, High-Throughput Nucleotide Sequencing, General Medicine, Genomics, Sequence Analysis, DNA, 16S ribosomal RNA, Hypervariable region, Metagenomics, Metagenome, Genome, Bacterial |
| الوصف: | Sequence-based characterization of bacterial communities has long been a hostage of limitations of both 16S rRNA gene and whole metagenome sequencing. Neither approach is universally applicable, and the main efforts to resolve constraints have been devoted to improvement of computational prediction tools. Here, we present semi-targeted 16S rRNA sequencing (st16S-seq), a method designed for sequencing V1–V2 regions of the 16S rRNA gene along with the genomic locus upstream of the gene. By in silico analysis of 13 570 bacterial genome assemblies, we show that genome-linked 16S rRNA sequencing is superior to individual hypervariable regions or full-length gene sequences in terms of classification accuracy and identification of gene copy numbers. Using mock communities and soil samples we experimentally validate st16S-seq and benchmark it against the established microbial classification techniques. We show that st16S-seq delivers accurate estimation of 16S rRNA gene copy numbers, enables taxonomic resolution at the species level and closely approximates community structures obtainable by whole metagenome sequencing. |
| وصف الملف: | application/pdf |
| تدمد: | 2057-5858 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eeddd6bf8c5eca61a434c172d693f0f0Test https://pubmed.ncbi.nlm.nih.gov/34473015Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....eeddd6bf8c5eca61a434c172d693f0f0 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 20575858 |
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