Please use this identifier to cite or link to this item:
http://hdl.handle.net/10397/105771
DC Field | Value | Language |
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dc.contributor | Department of Health Technology and Informatics | - |
dc.creator | Lee, AWT | - |
dc.creator | Chan, CTM | - |
dc.creator | Wong, LLY | - |
dc.creator | Yip, CY | - |
dc.creator | Lui, WT | - |
dc.creator | Cheng, KC | - |
dc.creator | Leung, JSL | - |
dc.creator | Lee, LK | - |
dc.creator | Wong, ITF | - |
dc.creator | Ng, TTL | - |
dc.creator | Lao, HY | - |
dc.creator | Siu, GKH | - |
dc.date.accessioned | 2024-04-23T04:31:09Z | - |
dc.date.available | 2024-04-23T04:31:09Z | - |
dc.identifier.uri | http://hdl.handle.net/10397/105771 | - |
dc.language.iso | en | en_US |
dc.publisher | Frontiers Research Foundation | en_US |
dc.rights | © 2023 Lee, Chan, Wong, Yip, Lui, Cheng, Leung, Lee, Wong, Ng, Lao and Siu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) (http://creativecommons.org/licenses/by/4.0/). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. | en_US |
dc.rights | The following publication Lee AW-T, Chan CT-M, Wong LL-Y, Yip C-Y, Lui W-T, Cheng K-C, Leung JS-L, Lee L-K, Wong IT-F, Ng TT-L, Lao H-Y and Siu GK-H (2023) Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing. Front. Microbiol. 14:1164632 is available at https://doi.org/10.3389/fmicb.2023.1164632. | en_US |
dc.subject | 16S rRNA gene sequencing | en_US |
dc.subject | Conventional culture | en_US |
dc.subject | Nanopore sequencing | en_US |
dc.subject | Taxonomic classifiers | en_US |
dc.subject | Urban microbiome | en_US |
dc.title | Identification of microbial community in the urban environment : the concordance between conventional culture and nanopore 16S rRNA sequencing | en_US |
dc.type | Journal/Magazine Article | en_US |
dc.identifier.volume | 14 | - |
dc.identifier.doi | 10.3389/fmicb.2023.1164632 | - |
dcterms.abstract | Introduction: Microbes in the built environment have been implicated as a source of infectious diseases. Bacterial culture is the standard method for assessing the risk of exposure to pathogens in urban environments, but this method only accounts for <1% of the diversity of bacteria. Recently, full-length 16S rRNA gene analysis using nanopore sequencing has been applied for microbial evaluations, resulting in a rise in the development of long-read taxonomic tools for species-level classification. Regarding their comparative performance, there is, however, a lack of information. | - |
dcterms.abstract | Methods: Here, we aim to analyze the concordance of the microbial community in the urban environment inferred by multiple taxonomic classifiers, including ARGpore2, Emu, Kraken2/Bracken and NanoCLUST, using our 16S-nanopore dataset generated by MegaBLAST, as well as assess their abilities to identify culturable species based on the conventional culture results. | - |
dcterms.abstract | Results: According to our results, NanoCLUST was preferred for 16S microbial profiling because it had a high concordance of dominant species and a similar microbial profile to MegaBLAST, whereas Kraken2/Bracken, which had similar clustering results as NanoCLUST, was also desirable. Second, for culturable species identification, Emu with the highest accuracy (81.2%) and F1 score (29%) for the detection of culturable species was suggested. | - |
dcterms.abstract | Discussion: In addition to generating datasets in complex communities for future benchmarking studies, our comprehensive evaluation of the taxonomic classifiers offers recommendations for ongoing microbial community research, particularly for complex communities using nanopore 16S rRNA sequencing. | - |
dcterms.accessRights | open access | en_US |
dcterms.bibliographicCitation | Frontiers in microbiology, 2023, v. 14, 1164632 | - |
dcterms.isPartOf | Frontiers in microbiology | - |
dcterms.issued | 2023 | - |
dc.identifier.scopus | 2-s2.0-85153773282 | - |
dc.identifier.eissn | 1664-302X | - |
dc.identifier.artn | 1164632 | - |
dc.description.validate | 202404 bcch | - |
dc.description.oa | Version of Record | en_US |
dc.identifier.FolderNumber | OA_Scopus/WOS | en_US |
dc.description.fundingSource | Self-funded | en_US |
dc.description.pubStatus | Published | en_US |
dc.description.oaCategory | CC | en_US |
Appears in Collections: | Journal/Magazine Article |
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File | Description | Size | Format | |
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fmicb-14-1164632.pdf | 6.6 MB | Adobe PDF | View/Open |
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