Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization
Abstract Bacteria often exist and function as a community, known as the bacterial microbiota, which consists of vast numbers of bacteria belonging to many bacterial species (taxa). Characterizing the bacterial microbiota needs high‐throughput approaches that enable the identification and quantificat...
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| Format: | Article |
| Language: | English |
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Wiley
2024-09-01
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| Series: | iMetaOmics |
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| Online Access: | https://doi.org/10.1002/imo2.9 |
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| author | Jianshi Jin Xiongduo Liu Katsuyuki Shiroguchi |
| author_facet | Jianshi Jin Xiongduo Liu Katsuyuki Shiroguchi |
| author_sort | Jianshi Jin |
| collection | DOAJ |
| description | Abstract Bacteria often exist and function as a community, known as the bacterial microbiota, which consists of vast numbers of bacteria belonging to many bacterial species (taxa). Characterizing the bacterial microbiota needs high‐throughput approaches that enable the identification and quantification of many bacterial cells, and such approaches have been under development for more than 30 years. In this review, we describe the history of high‐throughput technologies based on 16S ribosomal RNA (rRNA) gene‐amplicon sequencing for the characterization of bacterial microbiotas. Then, we summarize the features and applications of current 16S rRNA gene‐amplicon sequencing approaches, including a recent achievement that enables the identification of individual cells with single‐base accuracy for 16S rRNA genes and the quantification of many identified cells. Furthermore, we present the prospects for further technical development, including the combined use of high‐throughput methods and other informative analyses, such as whole‐genome sequencing in the common unit of the cell, which enables bacterial microbiota characterization based on both the number of cells and their functions. |
| format | Article |
| id | doaj-art-bc818eef983444de9cef21eb5bade813 |
| institution | Kabale University |
| issn | 2996-9506 2996-9514 |
| language | English |
| publishDate | 2024-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | iMetaOmics |
| spelling | doaj-art-bc818eef983444de9cef21eb5bade8132025-01-31T16:15:20ZengWileyiMetaOmics2996-95062996-95142024-09-0111n/an/a10.1002/imo2.9Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterizationJianshi Jin0Xiongduo Liu1Katsuyuki Shiroguchi2State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology Chinese Academy of Sciences Beijing ChinaState Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology Chinese Academy of Sciences Beijing ChinaLaboratory for Prediction of Cell Systems Dynamics RIKEN Center for Biosystems Dynamics Research (BDR) Osaka JapanAbstract Bacteria often exist and function as a community, known as the bacterial microbiota, which consists of vast numbers of bacteria belonging to many bacterial species (taxa). Characterizing the bacterial microbiota needs high‐throughput approaches that enable the identification and quantification of many bacterial cells, and such approaches have been under development for more than 30 years. In this review, we describe the history of high‐throughput technologies based on 16S ribosomal RNA (rRNA) gene‐amplicon sequencing for the characterization of bacterial microbiotas. Then, we summarize the features and applications of current 16S rRNA gene‐amplicon sequencing approaches, including a recent achievement that enables the identification of individual cells with single‐base accuracy for 16S rRNA genes and the quantification of many identified cells. Furthermore, we present the prospects for further technical development, including the combined use of high‐throughput methods and other informative analyses, such as whole‐genome sequencing in the common unit of the cell, which enables bacterial microbiota characterization based on both the number of cells and their functions.https://doi.org/10.1002/imo2.916S rRNA‐amplicon sequencingabsolute quantificationbacterial microbiotahigh‐throughput measurementsingle cell analysis |
| spellingShingle | Jianshi Jin Xiongduo Liu Katsuyuki Shiroguchi Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization iMetaOmics 16S rRNA‐amplicon sequencing absolute quantification bacterial microbiota high‐throughput measurement single cell analysis |
| title | Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization |
| title_full | Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization |
| title_fullStr | Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization |
| title_full_unstemmed | Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization |
| title_short | Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization |
| title_sort | long journey of 16s rrna amplicon sequencing toward cell based functional bacterial microbiota characterization |
| topic | 16S rRNA‐amplicon sequencing absolute quantification bacterial microbiota high‐throughput measurement single cell analysis |
| url | https://doi.org/10.1002/imo2.9 |
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