LactoTypeDB: a regenerable, type-anchored 16S rRNA gene reference for species-level identification of the Lactobacillaceae in foods
Amplicon surveys of fermented and spoiled foods routinely resolve Lactobacillaceae, the lactic acid bacteria responsible for many food and beverage fermentations, only to genus, whereas registers such as the Inventory of Microbial Food Cultures require species-level identification. This shortfall arises from the 16S rRNA genes limited, region-dependent resolution and from incomplete,…
LactoTypeDB is a type-anchored reference for the 16S rRNA gene, designed to enable species-level identification of Lactobacillaceae in foods. This reference covers 434 of the family's 441 species and all 37 genera, addressing a gap in current amplicon surveys that only resolve Lactobacillaceae to the genus level. By integrating LactoTypeDB into the Living Tree Project release LTP 08_2023, researchers were able to eliminate species-level misidentification in all tested regions and reduce misidentification of other sequences from 1,374 errors to just 3 using the full-length 16S rRNA gene.
When applied to a survey of 11,612 V3-V4 sequences from two meat production lines, LactoTypeDB returned a species identification for 213 sequences and a genus identification for 5,926, while flagging 3,495 as potential new species. The remaining ambiguity lies in the reduced resolution of the V3-V4 markers, which groups 417 of the 434 species into 27 categories, making it difficult to distinguish between them.
For food microbiology laboratories, the practical impact of LactoTypeDB is that species calls can now be trusted where applicable, and sequences that do not match can be flagged as candidates for isolation, rather than being seen as an obstacle to overcome.
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