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<p>This study aimed to reconstruct and characterise metagenome-assembled genomes (MAGs) from the healthy human oral microbiome to identify both culturable and unculturable probiotic bacterial lineages. Special emphasis was placed on exploring microbial diversity, probiotic potential, and functional traits related to vitamin biosynthesis. Shotgun metagenomic datasets of healthy oral samples were retrieved from the European Nucleotide Archive. Using the metaWRAP pipeline, quality-filtered paired-end reads were assembled and binned, followed by bin refinement and quality assessment against MIMAG standards. High-quality (HQ) and medium-quality (MQ) MAGs were dereplicated using dRep and taxonomically classified with GTDB-Tk. Z-score statistics were used to identify enriched and underrepresented genera. Functional annotation was performed using Prokka and COGclassifier to identify vitamin biosynthesis genes. Probiotic potential was assessed using MetaProbiotics and the Probio-Ichnos database. Genome novelty was validated using FastANI and TYGS. A total of 423 MAGs were reconstructed, comprising 114 HQ and 309 MQ genomes across 8 bacterial phyla. <i>Bacillota</i> and <i>Bacteroidota</i> were the dominant phyla, with notable proportions of both culturable and unculturable members. Z-score analysis identified 31 statistically enriched genera, with <i>Prevotella</i> being the most abundant. Of the recovered genomes, 153 were identified as culturable, 158 as unculturable with references, and 112 as potentially novel uncultured taxa. Functional annotation revealed key probiotic traits, including vitamin biosynthesis capabilities, in several uncultured MAGs. This study highlights the untapped potential within the uncultivable fraction of the oral microbiome and provides a genome-resolved framework for advancing microbiome-based health interventions.</p>

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Analysis of healthy oral shotgun metagenomic datasets reveals hidden microbial diversity and vitamin biosynthetic potential in culturable and unculturable taxa through genome-centric analysis

  • 期刊论文

  • 发表日期：

    2025年9月17日

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  • Arunmozhi Bharathi Achudhan,
  • Aadhith Raj Prakash,
  • Lilly M. Saleena

摘要

This study aimed to reconstruct and characterise metagenome-assembled genomes (MAGs) from the healthy human oral microbiome to identify both culturable and unculturable probiotic bacterial lineages. Special emphasis was placed on exploring microbial diversity, probiotic potential, and functional traits related to vitamin biosynthesis. Shotgun metagenomic datasets of healthy oral samples were retrieved from the European Nucleotide Archive. Using the metaWRAP pipeline, quality-filtered paired-end reads were assembled and binned, followed by bin refinement and quality assessment against MIMAG standards. High-quality (HQ) and medium-quality (MQ) MAGs were dereplicated using dRep and taxonomically classified with GTDB-Tk. Z-score statistics were used to identify enriched and underrepresented genera. Functional annotation was performed using Prokka and COGclassifier to identify vitamin biosynthesis genes. Probiotic potential was assessed using MetaProbiotics and the Probio-Ichnos database. Genome novelty was validated using FastANI and TYGS. A total of 423 MAGs were reconstructed, comprising 114 HQ and 309 MQ genomes across 8 bacterial phyla. Bacillota and Bacteroidota were the dominant phyla, with notable proportions of both culturable and unculturable members. Z-score analysis identified 31 statistically enriched genera, with Prevotella being the most abundant. Of the recovered genomes, 153 were identified as culturable, 158 as unculturable with references, and 112 as potentially novel uncultured taxa. Functional annotation revealed key probiotic traits, including vitamin biosynthesis capabilities, in several uncultured MAGs. This study highlights the untapped potential within the uncultivable fraction of the oral microbiome and provides a genome-resolved framework for advancing microbiome-based health interventions.