This study aimed to investigate the bioaccessibility of carotenoids and chlorophylls from the biomass of microalgae Chaetoceros calcitrans. The samples were submitted to an in vitro digestion protocol, and the compounds were determined by HPLC-PDA-MS/MS. A total of 13 compounds were identified in all tests. After in vitro digestion, the relative bioaccessibility of carotenoids and chlorophylls ranged from 4 to 58%. The qualitative profile of carotenoids reflected the initial sample, with all-E-zeaxanthin (57.2%) being the most bioaccessible compound, followed by all-E-neochrome (31.26%), the latter being reported for the first time in the micellar fraction. On the other hand, among the chlorophylls only pheophytin a (15.01%) was bioaccessible. Furthermore, a chlorophyll derivative (Hydroxypheophytin a’) was formed after in vitro digestion. Considering all compounds, xanthophylls (12.03%) and chlorophylls (12.22%) were significantly (p < 0.05) more bioaccessible than carotenes (11.22%). Finally, the considerable individual bioaccessibilities found, especially for zeaxanthin, demonstrate the bioactive potential of this bioresource. However, the large reduction in the totality of compounds after in vitro digestion suggests that additional technological strategies should be explored in the future to increase the efficiency of micellarization and enhance its bioactive effects.
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