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<p>The selection of probiotic candidates has historically relied on empirical screening for gastrointestinal survival, structurally narrowing the exploration of functional diversity by preferentially selecting strains that pass early-stage survival assays through validation pipelines centred on survival-related traits. This study integrates genomic mining with bibliometric analysis of publications associated with strains from the Probio-Ichnos database to test whether genomic functional potential is reflected in current research priorities. Analysis of 757 high-quality genomes revealed a a highly conserved Survival Core comprising stress adaptation genes present in over 90% of the dataset, reflecting convergent selection for host persistence. A taxonomic functional divide was observed: <i>Bacillus</i> displayed a generalist profile with high functional density, in contrast with the genome-reduced specialisation of <i>Lactobacillaceae</i>. However, the bibliometric analysis of 871 primary publications shows that research focus remains concentrated on a limited set of canonical traits, creating a partial context-dependent discrepancy between genomic potential and experimental attention. Studies remain concentrated around a standard validation consensus dominated by antimicrobial activity, adhesion, and immunomodulation. While safety remains central, survival traits like acid and bile resistance are less cited than functional effectors, and genetically ubiquitous traits such as thermal stress tolerance are underexplored. Significant taxonomic discrepancies were also found for immunomodulation, where some genera with rich genetic repertoires remain understudied. These findings suggest that current validation pipelines may contribute to a survivorship bias that limits functional discovery. We propose a shift toward reverse probiotics and in silico prediction to better harness unconventional traits and expand the biotechnological potential beyond the survival-centric model.</p>

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Bridging the gap between probiotic genomic potential and research priorities beyond the survival core

  • 期刊论文

  • 发表日期：

    2026年4月22日

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  • Mohamed Amine Gomri,
  • Mohamed El Hadef El Okki,
  • Nour ElHouda Ounissi,
  • Nadia Bachtarzi,
  • Meriem Meradji

摘要

The selection of probiotic candidates has historically relied on empirical screening for gastrointestinal survival, structurally narrowing the exploration of functional diversity by preferentially selecting strains that pass early-stage survival assays through validation pipelines centred on survival-related traits. This study integrates genomic mining with bibliometric analysis of publications associated with strains from the Probio-Ichnos database to test whether genomic functional potential is reflected in current research priorities. Analysis of 757 high-quality genomes revealed a a highly conserved Survival Core comprising stress adaptation genes present in over 90% of the dataset, reflecting convergent selection for host persistence. A taxonomic functional divide was observed: Bacillus displayed a generalist profile with high functional density, in contrast with the genome-reduced specialisation of Lactobacillaceae. However, the bibliometric analysis of 871 primary publications shows that research focus remains concentrated on a limited set of canonical traits, creating a partial context-dependent discrepancy between genomic potential and experimental attention. Studies remain concentrated around a standard validation consensus dominated by antimicrobial activity, adhesion, and immunomodulation. While safety remains central, survival traits like acid and bile resistance are less cited than functional effectors, and genetically ubiquitous traits such as thermal stress tolerance are underexplored. Significant taxonomic discrepancies were also found for immunomodulation, where some genera with rich genetic repertoires remain understudied. These findings suggest that current validation pipelines may contribute to a survivorship bias that limits functional discovery. We propose a shift toward reverse probiotics and in silico prediction to better harness unconventional traits and expand the biotechnological potential beyond the survival-centric model.