Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing.

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.

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, u

SUBMITTER: Lee AW 

PROVIDER: S-EPMC10133568 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature