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. 2023 Nov 21;14:1307440. doi: 10.3389/fmicb.2023.1307440

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Copyright © 2023 Ghielmetti, Loubser, Kerr, Stuber, Thacker, Martin, O’Hare, Mhlophe, Okunola, Loxton, Warren, Moseley, Miller and Goosen.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). 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.

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Overview of the culture-independent targeted amplicon sequencing approach using Oxford Nanopore Technologies (ONT) sequencing platform. After DNA extraction directly from tissue samples, ONT library preparation, including DNA ends repair, native barcoding and adapter ligation, was performed. The prepared library was loaded on the flow cell (R10.4.1) and inserted in the sequencer (MinION). Basecalling was carried out real-time, storing the data in FASTQ format. Raw reads were subsequently used for downstream bioinformatic analysis and enabled characterization and quantification of the bacterial community present in the samples.