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Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements
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Document Title
Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements
Author
Kruasuwan W. Jenjaroenpun P. Arigul T. Chokesajjawatee N. Leekitcharoenphon P. Foongladda S. Wongsurawat T.
Affiliations
Division of Medical Bioinformatics Research Department Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand; Siriraj Long-Read Lab (Si-LoL) Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC) 113 Thailand Science Park Phahonyothin Road Khlong Nueng Pathum Thani Khlong Luang Thailand; Research Group for Genomic Epidemiology National Food Institute Technical University of Denmark Kgs. Lyngby 2800 Denmark; Department of Microbiology Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand; Department of Biomedical Informatics University of Arkansas for Medical Sciences Little Rock AR United States
Type
Article
Source Title
Scientific Reports
ISSN
20452322
Year
2023
Volume
13
Issue
1
Open Access
All Open Access Gold Green
Publisher
Nature Research
DOI
10.1038/s41598-023-31626-4
Abstract
The market for the application of probiotics as a livestock health improvement supplement has increased in recent years. However most of the available products are quality-controlled using low-resolution techniques and un-curated databases resulting in misidentification and incorrect product labels. In this work we deployed two workflows and compared results obtained by full-length 16S rRNA genes (16S) and metagenomic (Meta) data to investigate their reliability for the microbial composition of both liquid and solid forms of animal probiotic products using Oxford Nanopore long-read-only (without short-read). Our result revealed that 16S amplicon data permits to detect the bacterial microbiota even with the low abundance in the samples. Moreover the 16S approach has the potential to provide species-level resolution for prokaryotes but not for assessing yeast communities. Whereas Meta data has more power to recover of high-quality metagenome-assembled genomes that enables detailed exploration of both bacterial and yeast populations as well as antimicrobial resistance genes and functional genes in the population. Our findings clearly demonstrate that implementing these workflows with long-read-only monitoring could be applied to assessing the quality and safety of probiotic products for animals and evaluating the quality of probiotic products on the market. This would benefit the sustained growth of the livestock probiotic industry. ? 2023 The Author(s).
Industrial Classification
License
CC BY
Rights
Authors
Publication Source
WOS