Fast Identification Method for Screening Bacteria from Faecal Samples Using Oxford Nanopore Technologies MinION Sequencing

Most bacterial identification methods require extensive culturing, strain purification and DNA extraction protocols. This leads to additional expenses and time lags when isolating specific bacteria from complex microbiological ecosystems. This study aimed to develop a fast and robust method for iden...

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Bibliographic Details
Published in:Current microbiology 2023-03, Vol.80 (3), p.101-101, Article 101
Main Authors: Borges, Ana Sofia G., Basu, Meghna, Brinks, Erik, Bang, Corinna, Cho, Gyu-Sung, Baines, John F., Franke, Andre, Franz, Charles M. A. P.
Format: Article
Language:English
Subjects:
Bacteria
Bacteria - genetics
Biomedical and Life Sciences
Biotechnology
Colonies
Deoxyribonucleic acid
DNA
DNA, Bacterial - genetics
Ecosystem
Feces
High-Throughput Nucleotide Sequencing - methods
Humans
Identification methods
Lactobacilli
Life Sciences
Microbiology
Microorganisms
Nanopores
Polymerase chain reaction
Purification
RNA, Ribosomal, 16S - genetics
rRNA 16S
Screening
Selective media
Sequence analysis
Sequence Analysis, DNA - methods
Short Communication
Sonication
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Summary:Most bacterial identification methods require extensive culturing, strain purification and DNA extraction protocols. This leads to additional expenses and time lags when isolating specific bacteria from complex microbiological ecosystems. This study aimed to develop a fast and robust method for identification of lactobacilli, bifidobacteria and Bacteroides in human faecal samples. Bacteria from faecal samples were cultured anaerobically on selective media. Sonication-based DNA extraction was performed, followed by almost complete 16S rRNA gene polymerase chain reaction amplification and MinION sequencing with the Flongle adapter. Sequence analysis was performed using NanoCLUST, while RStudio was used for graphics. For 110 of the 125 colonies investigated, 100% of reads were attributed to a single species, while the remaining 15 colonies consisted of mixtures of up to three different species. The proposed bacterial identification method is advantageous for isolating particular bacteria for which there are no exclusively selective media, as it avoids lengthy colony purification and DNA purification methods, and yields a quick colony identification with high accuracy. Therefore, this method can be used for directly screening for pure cultures of target microorganisms and is suitable for the identification of bacteria in culturomics studies.
ISSN:0343-8651
1432-0991
DOI:10.1007/s00284-023-03201-7