Mukesh K Jogi, Sristy Shikha, Pushpendra Singh, Shreyansh, Aranya Paul, Vijay Nema, Akshay Shankar, Mohammad Sajid, Anil Kumar, Brijendra K Kashayap, Mausumi Bharadwaj, Shalini Singh, Pramod Kumar
{"title":"利用 ion Torrent 平台对 16s rRNA 基因扩增子进行短线次世代测序,以确定扩增子序列变异(ASV)的特征并确定基因拷贝数。","authors":"Mukesh K Jogi, Sristy Shikha, Pushpendra Singh, Shreyansh, Aranya Paul, Vijay Nema, Akshay Shankar, Mohammad Sajid, Anil Kumar, Brijendra K Kashayap, Mausumi Bharadwaj, Shalini Singh, Pramod Kumar","doi":"10.1080/15257770.2025.2479620","DOIUrl":null,"url":null,"abstract":"<p><p>The short-amplicon sequencing of hypervariable regions of 16S rRNA gene is the widely used method for bacterial identification and microbiota profiling. Bacteria possess multiple copies of 16S rRNA gene and may contain single nucleotide variations (SNPs) or amplicon sequence variants (ASVs). The ASVs based determination of microbial taxa can be better representation over operational taxonomic units (OTUs). Illumina based NGS platforms are mostly used to define the ASVs whereas Ion-torrent platform is commonly used for diagnostic purposes. We aimed to identify bacterial isolates having ASVs and infer the copy numbers of16S rRNA gene using short read sequencing performed on the Ion Gene Studio S5 NGS platform. The V2-V3 regions of 16S rRNA gene were amplified from the bacterial isolates and subjected to NGS. Further, the sequences produced by NGS were compared with those generated from Sanger sequencing. The bacterial isolates were identified and characterize during ASVs. The copy number of the 16S rRNA gene was established in Gram-negative isolates. Assigning bacterial taxa based on ASVs would provide a more accurate representation of the variant data.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-14"},"PeriodicalIF":1.1000,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Short-read next-generation sequencing of 16s rRNA gene amplicons for characterizing amplicon sequence variants (ASVs) and determination of gene copy numbers using ion Torrent platform.\",\"authors\":\"Mukesh K Jogi, Sristy Shikha, Pushpendra Singh, Shreyansh, Aranya Paul, Vijay Nema, Akshay Shankar, Mohammad Sajid, Anil Kumar, Brijendra K Kashayap, Mausumi Bharadwaj, Shalini Singh, Pramod Kumar\",\"doi\":\"10.1080/15257770.2025.2479620\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The short-amplicon sequencing of hypervariable regions of 16S rRNA gene is the widely used method for bacterial identification and microbiota profiling. Bacteria possess multiple copies of 16S rRNA gene and may contain single nucleotide variations (SNPs) or amplicon sequence variants (ASVs). The ASVs based determination of microbial taxa can be better representation over operational taxonomic units (OTUs). Illumina based NGS platforms are mostly used to define the ASVs whereas Ion-torrent platform is commonly used for diagnostic purposes. We aimed to identify bacterial isolates having ASVs and infer the copy numbers of16S rRNA gene using short read sequencing performed on the Ion Gene Studio S5 NGS platform. The V2-V3 regions of 16S rRNA gene were amplified from the bacterial isolates and subjected to NGS. Further, the sequences produced by NGS were compared with those generated from Sanger sequencing. The bacterial isolates were identified and characterize during ASVs. The copy number of the 16S rRNA gene was established in Gram-negative isolates. Assigning bacterial taxa based on ASVs would provide a more accurate representation of the variant data.</p>\",\"PeriodicalId\":19343,\"journal\":{\"name\":\"Nucleosides, Nucleotides & Nucleic Acids\",\"volume\":\" \",\"pages\":\"1-14\"},\"PeriodicalIF\":1.1000,\"publicationDate\":\"2025-03-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Nucleosides, Nucleotides & Nucleic Acids\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1080/15257770.2025.2479620\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nucleosides, Nucleotides & Nucleic Acids","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1080/15257770.2025.2479620","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Short-read next-generation sequencing of 16s rRNA gene amplicons for characterizing amplicon sequence variants (ASVs) and determination of gene copy numbers using ion Torrent platform.
The short-amplicon sequencing of hypervariable regions of 16S rRNA gene is the widely used method for bacterial identification and microbiota profiling. Bacteria possess multiple copies of 16S rRNA gene and may contain single nucleotide variations (SNPs) or amplicon sequence variants (ASVs). The ASVs based determination of microbial taxa can be better representation over operational taxonomic units (OTUs). Illumina based NGS platforms are mostly used to define the ASVs whereas Ion-torrent platform is commonly used for diagnostic purposes. We aimed to identify bacterial isolates having ASVs and infer the copy numbers of16S rRNA gene using short read sequencing performed on the Ion Gene Studio S5 NGS platform. The V2-V3 regions of 16S rRNA gene were amplified from the bacterial isolates and subjected to NGS. Further, the sequences produced by NGS were compared with those generated from Sanger sequencing. The bacterial isolates were identified and characterize during ASVs. The copy number of the 16S rRNA gene was established in Gram-negative isolates. Assigning bacterial taxa based on ASVs would provide a more accurate representation of the variant data.
期刊介绍:
Nucleosides, Nucleotides & Nucleic Acids publishes research articles, short notices, and concise, critical reviews of related topics that focus on the chemistry and biology of nucleosides, nucleotides, and nucleic acids.
Complete with experimental details, this all-inclusive journal emphasizes the synthesis, biological activities, new and improved synthetic methods, and significant observations related to new compounds.