Mapping Global Biodiversity and Habitat Distribution of Lactobacillaceae Using NCBI Sequence Metadata

The Lactobacillaceae family encompasses microorganisms of exceptional ecological and biotechnological importance, serving as central agents in food fermentations, health applications, and nutrient cycling across diverse environments. Despite their broad functional and phylogenetic diversity, the global distribution and ecological specialization of Lactobacillaceae are not yet fully understood. In this study, we performed a comprehensive analysis of over 2 million records from the NCBI database to survey and trace the ecological landscape of Lactobacillaceae across thousands of distinct habitats. Our results reveal that food products and animal hosts represent the primary ecological niches for members of this family. The examined taxa exhibit a broad spectrum of ecological strategies, ranging from generalists with wide environmental adaptability to specialists with strict niche preferences. Notably, our findings highlight a profound geographical and ecological sampling bias, with unclassified taxids frequent in animal gastrointestinal tracts, soils, and especially in living plant tissues—habitats identified as promising frontiers for discovering novel biodiversity. The obtained results emphasize the urgent need for expanded sampling efforts in underexplored geographic regions such as Africa, Antarctica, the Arctic, South America, and Central Asia to capture a more complete picture of Lactobacillaceae diversity. The study underscores the necessity of implementing standardized, metadata-rich data deposition practices to enable unbiased, large-scale ecological and evolutionary analyses. Ultimately, these insights not only deepen our fundamental knowledge of Lactobacillaceae diversity but also provide a strategic framework for future bioprospecting, fostering the discovery of novel strains and expanding the biotechnological potential of this influential bacterial family.