Recent advances in computational biology have provided powerful tools for analyzing, modeling, and optimizing probiotic microorganisms, thereby supporting their development as promising agents for improving human health. The essential role of the microbiota in regulating physiological processes and preventing disease has driven interest in the rational design of next-generation probiotics. This review highlights progress in in silico approaches for enhancing the functionality of probiotic strains. Particular attention is given to genome-scale metabolic models, advanced simulation algorithms, and AI-driven tools that provide deeper insight into microbial metabolism and enable precise probiotic optimization. The integration of these methods with multi-omics data has greatly improved our ability to predict strain behavior and design probiotics with specific health benefits. Special focus is placed on modeling probiotic–prebiotic interactions and host–microbiome dynamics, which are essential for the development of functional food products. Despite these achievements, key challenges remain, including limited model accuracy, difficulties in simulating complex host–microbe systems, and the absence of unified standards for validating in silico-optimized strains. Addressing these gaps requires the development of integrative modeling platforms and clear regulatory frameworks. This review provides a critical overview of current advances, identifies existing barriers, and outlines future directions for the application of computational strategies in probiotic research.

Cyanobacterial pigments have attracted considerable attention in industry due to their bioactive potential and natural origin. In the present study, the growth dynamics and pigment composition, in terms of chlorophyll a, total carotenoids and phycobiliprotein content, of four cyanobacterial strains isolated from thermal springs, namely Oscillatoria subbrevis CZS 2201, Phormidium ambiguum CZS 2205, Nostoc calcicola TSZ 2203, and Synechococcus sp. CZS 2204, were investigated. The analysis revealed that the maximum quantity of chlorophyll a and total carotenoids was observed in Oscillatoria subbrevis CZS 2201 (26.49 and 3.44 µg mL⁻¹), followed by Phormidium ambiguum CZS 2205 (18.64 and 2.32 µg mL⁻¹), whereas a minimum amount was detected in Synechococcus sp. CZS 2204 (12.13 and 1.24 µg mL⁻¹), respectively. In addition, Oscillatoria subbrevis CZS 2201 showed higher quantity of phycobiliproteins, especially C-phycocyanin (45.81 mg g⁻¹), C-phycoerythrin (64.17 mg g⁻¹) and C-allophycocyanin (27.45 mg g⁻¹). Moreover, carotenoid derivatives of Oscillatoria subbrevis CZS 2201 were also identified, among which β-carotene was the dominant form (1.94 µg mL⁻¹), while the accumulation of zeaxanthin and myxoxanthophyll was relatively high (0.53 and 0.41 µg mL⁻¹, respectively) compared with echinenone and cryptoxanthin (0.34 and 0.23 µg mL⁻¹, respectively). The study revealed that Oscillatoria subbrevis CZS 2201 was a potent producer of secondary carotenoids, including myxoxanthophyll.

Photosynthetic prokaryotes known as cyanobacteria produce an extensive range of primary and secondary metabolites that serve multiple biotechnological and biomedical purposes. The non-model filamentous Phormidium species capture researchers’ attention through their biotechnological potentials from diverse metabolites and their ability to thrive in tough environments while producing bioactive compounds. In this study, a thermotolerant strain of Phormidium ambiguum was isolated from the Chundzha thermal springs in southeastern Kazakhstan and characterized morphologically, physiologically, and biochemically. This cyanobacterium demonstrated fast growth in its culture media along with significant accumulation of proteins (44.8% DM), carbohydrates (45% DM), and photosynthetic pigments like chlorophyll a and valuable carotenoids, including b-carotene, myxoxantophyll and zeaxanthin. The LC-ESI-MS/MS analysis of cyanobacterial non-polar extract identified 150 potential metabolites which include fatty acid derivatives, terpenoids and carotenoid-related compounds known for their antioxidant and antimicrobial properties, as well as immune system stimulation. Biological assays confirmed a weak antioxidant capacity in the DPPH test, while in immunological assays, the extract of P. ambiguum stimulated T lymphocyte proliferation and activation, as well as NK cell proliferation in vitro. It also exhibited moderate antibacterial activity towards tested Gram-negative and Gram-positive bacterial strains. While additional studies are required to address environmental robustness, biosynthetic regulation, and practical scalability, the present findings indicate that P. ambiguum represents a valuable non-model cyanobacterium for exploratory bioprospecting. Its metabolite profile and observed bioactivities support further investigation of this thermotolerant strain as a potential source of immunomodulatory, antioxidant, and antimicrobial compounds under controlled conditions.