Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing
IntroductionMicrobes 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,...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1164632/full |
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| author | Annie Wing-Tung Lee Chloe Toi-Mei Chan Lily Lok-Yee Wong Cheuk-Yi Yip Wing-Tung Lui Kai-Chun Cheng Jake Siu-Lun Leung Lam-Kwong Lee Ivan Tak-Fai Wong Timothy Ting-Leung Ng Hiu-Yin Lao Gilman Kit-Hang Siu |
| author_facet | Annie Wing-Tung Lee Chloe Toi-Mei Chan Lily Lok-Yee Wong Cheuk-Yi Yip Wing-Tung Lui Kai-Chun Cheng Jake Siu-Lun Leung Lam-Kwong Lee Ivan Tak-Fai Wong Timothy Ting-Leung Ng Hiu-Yin Lao Gilman Kit-Hang Siu |
| author_sort | Annie Wing-Tung Lee |
| collection | DOAJ |
| description | IntroductionMicrobes 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.MethodsHere, 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.ResultsAccording 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.DiscussionIn 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. |
| first_indexed | 2024-04-09T18:14:53Z |
| format | Article |
| id | doaj.art-b6a0d455b401437584883c2cf10b3f02 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-09T18:14:53Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-b6a0d455b401437584883c2cf10b3f022023-04-13T05:07:47ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-04-011410.3389/fmicb.2023.11646321164632Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencingAnnie Wing-Tung LeeChloe Toi-Mei ChanLily Lok-Yee WongCheuk-Yi YipWing-Tung LuiKai-Chun ChengJake Siu-Lun LeungLam-Kwong LeeIvan Tak-Fai WongTimothy Ting-Leung NgHiu-Yin LaoGilman Kit-Hang SiuIntroductionMicrobes 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.MethodsHere, 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.ResultsAccording 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.DiscussionIn 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.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1164632/fullurban microbiomenanopore sequencing16S rRNA gene sequencingtaxonomic classifiersconventional culture |
| spellingShingle | Annie Wing-Tung Lee Chloe Toi-Mei Chan Lily Lok-Yee Wong Cheuk-Yi Yip Wing-Tung Lui Kai-Chun Cheng Jake Siu-Lun Leung Lam-Kwong Lee Ivan Tak-Fai Wong Timothy Ting-Leung Ng Hiu-Yin Lao Gilman Kit-Hang Siu Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing Frontiers in Microbiology urban microbiome nanopore sequencing 16S rRNA gene sequencing taxonomic classifiers conventional culture |
| title | Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing |
| title_full | Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing |
| title_fullStr | Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing |
| title_full_unstemmed | Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing |
| title_short | Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing |
| title_sort | identification of microbial community in the urban environment the concordance between conventional culture and nanopore 16s rrna sequencing |
| topic | urban microbiome nanopore sequencing 16S rRNA gene sequencing taxonomic classifiers conventional culture |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1164632/full |
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