| Title: | Application of MinION Amplicon Sequencing to Buccal Swab Samples for Improving Resolution and Throughput of Rumen Microbiota Analysis |
| Authors: | Miura, Hiroto Browse this author |
| Takeda, Masayuki Browse this author |
| Yamaguchi, Megumi Browse this author |
| Ohtani, Yoshihisa Browse this author |
| Endo, Go Browse this author |
| Masuda, Yasuhisa Browse this author |
| Ito, Kaede Browse this author |
| Nagura, Yoshio Browse this author |
| Iwashita, Kunihiro Browse this author |
| Mitani, Tomohiro Browse this author →KAKEN DB |
| Suzuki, Yutaka Browse this author →KAKEN DB |
| Kobayashi, Yasuo Browse this author →KAKEN DB |
| Koike, Satoshi Browse this author →KAKEN DB |
| Keywords: | rumen microbiota |
| buccal swab |
| MinION |
| amplicon sequencing |
| 16S rRNA gene |
| Issue Date: | 2022 |
| Publisher: | Frontiers Media |
| Journal Title: | Frontiers in microbiology |
| Volume: | 13 |
| Start Page: | 783058 |
| Publisher DOI: | 10.3389/fmicb.2022.783058 |
| Abstract: | The Illumina MiSeq platform has been widely used as a standard method for studying the rumen microbiota. However, the low resolution of taxonomic identification is the only disadvantage of MiSeq amplicon sequencing, as it targets a part of the 16S rRNA gene. In the present study, we performed three experiments to establish a high-resolution and high-throughput rumen microbial profiling approach using a combination of MinION platform and buccal swab sample, which is a proxy for rumen contents. In experiment 1, rumen contents and buccal swab samples were collected simultaneously from cannulated cattle (n = 6) and used for microbiota analysis using three different analytical workflows: amplicon sequencing of the V3-V4 region of the 16S rRNA gene using MiSeq and amplicon sequencing of near full-length 16S rRNA gene using MinION or PacBio Sequel II. All reads derived from the MinION and PacBio platforms were classified at the species-level. In experiment 2, rumen fluid samples were collected from beef cattle (n = 28) and used for 16S rRNA gene amplicon sequencing using the MinION platform to evaluate this sequencing platform for rumen microbiota analysis. We confirmed that the MinION platform allowed species-level taxa assignment for the predominant bacterial groups, which were previously identified at the family- and genus-level using the MiSeq platform. In experiment 3, buccal swab samples were collected from beef cattle (n = 30) and used for 16S rRNA gene amplicon sequencing using the MinION platform to validate the applicability of a combination of the MinION platform and buccal swab samples for rumen microbiota analysis. The distribution of predominant bacterial taxa in the buccal swab samples was similar to that in the rumen samples observed in experiment 2. Based on these results, we concluded that the combination of the MinION platform and buccal swab samples may be potentially applied for rumen microbial analysis in large-scale studies. |
| Type: | article |
| URI: | http://hdl.handle.net/2115/86226 |
| Appears in Collections: | 農学院・農学研究院 (Graduate School of Agriculture / Faculty of Agriculture) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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