MALDI-TOF MS Classification of Formosan Thraustochytrids and Their Use in Shrimp Farming

Thraustochytrids are emerging marine protists for the sustainable production of high-value bioactives, particularly ω-3 polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA) and carotenoids like astaxanthin. We established a MALDI-TOF MS Biotyper database for 33 Formosan thraustochytrid strains isolated from Taiwanese mangroves and compared it with 18S rRNA gene-based phylogenetic analysis. Biotyper-based classification provided enhanced taxonomic resolution and, when integrated with PCA and K-means clustering of biochemical traits, enabled functional grouping of the strains. HPLC quantification revealed diverse DHA and astaxanthin yields, leading to the selection of two strains for Litopenaeus vannamei aquaculture trials: DHA-rich Schizochytrium sp. W1.2 and astaxanthin-rich Aurantiochytrium sp. YA7.1. W1.2 enhanced postlarval survival and growth, while YA7.1 improved feed conversion and adult size. These findings highlight the usefulness of integrated biochemical and proteomic classification to select strains effectively. They also reveal the dual benefits of thraustochytrids in microbial taxonomy and functional nutrition, supporting sustainable shrimp aquaculture.