High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS
Abstract Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their rel...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2022-10-01
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| Series: | ISME Communications |
| Online Access: | https://doi.org/10.1038/s43705-022-00183-8 |
| _version_ | 1797227007965134848 |
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| author | Douglas B. Rusch Jie Huang Chris Hemmerich Matthew W. Hahn |
| author_facet | Douglas B. Rusch Jie Huang Chris Hemmerich Matthew W. Hahn |
| author_sort | Douglas B. Rusch |
| collection | DOAJ |
| description | Abstract Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their relative abundances at the greatest taxonomic resolution possible. Here, we describe a novel protocol (RoC-ITS) that uses the single-molecule Nanopore sequencing platform to assay the composition of microbial communities at the subspecies designation. Using rolling-circle amplification, this methodology produces long-read sequences from a circular construct containing the complete 16S ribosomal gene and the neighboring internally transcribed spacer (ITS). These long reads can be used to generate a high-fidelity circular consensus sequence. Generally, the ribosomal 16S gene provides phylogenetic information down to the species-level, while the much less conserved ITS region contains strain-level information. When linked together, this combination of markers allows for the identification of individual ribosomal units within a specific organism and the assessment of their relative stoichiometry, as well as the ability to monitor subtle shifts in microbial community composition with a single generic assay. We applied RoC-ITS to an artificial microbial community that was also sequenced using the Illumina platform, to assess its accuracy in quantifying the relative abundance and identity of each species. |
| first_indexed | 2024-04-24T14:33:58Z |
| format | Article |
| id | doaj.art-192691b3cf3e486e9788b1781b1e49b8 |
| institution | Directory Open Access Journal |
| issn | 2730-6151 |
| language | English |
| last_indexed | 2024-04-24T14:33:58Z |
| publishDate | 2022-10-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | ISME Communications |
| spelling | doaj.art-192691b3cf3e486e9788b1781b1e49b82024-04-03T01:25:11ZengOxford University PressISME Communications2730-61512022-10-012111310.1038/s43705-022-00183-8High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITSDouglas B. Rusch0Jie Huang1Chris Hemmerich2Matthew W. Hahn3Center for Genomics and Bioinformatics, Indiana UniversityCenter for Genomics and Bioinformatics, Indiana UniversityCenter for Genomics and Bioinformatics, Indiana UniversityCenter for Genomics and Bioinformatics, Indiana UniversityAbstract Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their relative abundances at the greatest taxonomic resolution possible. Here, we describe a novel protocol (RoC-ITS) that uses the single-molecule Nanopore sequencing platform to assay the composition of microbial communities at the subspecies designation. Using rolling-circle amplification, this methodology produces long-read sequences from a circular construct containing the complete 16S ribosomal gene and the neighboring internally transcribed spacer (ITS). These long reads can be used to generate a high-fidelity circular consensus sequence. Generally, the ribosomal 16S gene provides phylogenetic information down to the species-level, while the much less conserved ITS region contains strain-level information. When linked together, this combination of markers allows for the identification of individual ribosomal units within a specific organism and the assessment of their relative stoichiometry, as well as the ability to monitor subtle shifts in microbial community composition with a single generic assay. We applied RoC-ITS to an artificial microbial community that was also sequenced using the Illumina platform, to assess its accuracy in quantifying the relative abundance and identity of each species.https://doi.org/10.1038/s43705-022-00183-8 |
| spellingShingle | Douglas B. Rusch Jie Huang Chris Hemmerich Matthew W. Hahn High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS ISME Communications |
| title | High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS |
| title_full | High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS |
| title_fullStr | High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS |
| title_full_unstemmed | High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS |
| title_short | High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS |
| title_sort | high resolution phylogenetic and population genetic analysis of microbial communities with roc its |
| url | https://doi.org/10.1038/s43705-022-00183-8 |
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