Microalgae are rich in biodiversity, with approximately 50,000 species discovered to date. They play a crucial role in natural ecosystem by facilitating material cycling. Their extensive genetic diversity and metabolic versatility enable them to thrive in a wide range of habitats, even high temperatures and salinity environments. Many species of microalgae are rich in proteins and lipids, including polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), as well as carotenoids and their derivatives (e.g. astaxanthin and lutein). They also produce other biologically active compounds (e.g. sulfated polysaccharides and phlorotannins) (Gupta et al., 2023). These properties make them widely applied in food, pharmaceuticals, bioenergy, immune function enhancement, cardiovascular disease prevention, and biodiesel production. Microalgae are major primary producers in aquatic environments and can rapidly synthesize PUFAs, particularly omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs) of which EPA and DHA are essential fatty acids.

Microalgal DHA is a crucial polyunsaturated fatty acid (PUFA) known for its significant anti-inflammatory and immunomodulatory effects. It activates anti-inflammatory pathways, enhances liver protection, and supports the vitality of immune cells. These properties make it effective in alleviating inflammatory conditions such as rheumatoid arthritis. Additionally, DHA regulates metabolism by improving blood lipid and glucose profiles, reducing fat accumulation induced by high-fat diets, and increasing HDL levels, thereby helping to mitigate cardiovascular diseases and obesity-related complications. Squalene also shows promise in enhancing tolerance to low-oxygen conditions and is emerging as a new area of research (Khan et al., 2021). In addition to DHA, microalgal lipids contain valuable compounds such as squalene, a triterpene recognized for its anti-inflammatory, antitumor, and cardioprotective properties. Squalene shows potential in enhancing tolerance to low-oxygen and is becoming a new research focus. Other PUFAs, such as linoleic and arachidonic acids, exhibit therapeutic potential for various health issues, including hypertension, respiratory problems, digestive ulcers, skin disorders, and schizophrenia. This versatility makes microalgal lipids valuable as nutritional supplements and health product ingredients.

Microalgae present several advantages for the production of PUFA compared to traditional fish-based sources. These advantages include simple nutrient requirements, rapid growth rates, low pollutant content, and a lack of fishy odor (Mao et al., 2022). The high nutritional value and safety of microalgal oils have been confirmed through toxicological and genotoxicity assessments, supporting their widespread application in food and nutritional supplements. Additionally, the physicochemical properties of microalgal DHA meet national standards, making it a reliable raw material (Chen et al., 2016).

Microalgae are highly nutritious, containing significant amounts of proteins, amino acids, and carbohydrates. Some species, such as Chlorella and Dunaliella salina, have carbohydrate content exceeding 40% of their dry weight. In terms of protein, red algae and Spirulina contain up to 60% and 60∼71%, respectively, which is much higher than traditional crops such as soybeans (38%) and eggs (13.2%) (Churchward-Venne et al., 2017). The advantage of microalgal protein extend beyond its content; it also boasts a well-balanced amino acid composition. Microalgae can synthesize 20 different amino acids, including 8 essential ones. For example, Chlorella has a high concentration of essential amino acids that meets or exceeds the standard set by World Health Organization (WHO) and Food and Agriculture Organization (FAO). Therefore, microalgal protein is considered an ideal sustainable protein and has been widely applied in food formulations and animal feed.

Microalgae protein is not only an extremely nutritious food but is also intriguing due to its diverse biological activities. Microalgal proteins and their hydrolysates or peptides have significant potential in providing antioxidant, anticancer, antihypertensive, anti-inflammatory, and anti-atherosclerotic effects. These bioactivities are attributed to the involvement of enzyme proteins, peptides, and protein complexes (Wang et al., 2022b). Phycobiliproteins include phycoerythrin, phycoerythrocyanin, phycocyanin (PC), and allophycocyanin (APC).

Natural pigments derived from microalgae, such as chlorophyll, carotenoids, astaxanthin, and fucoxanthin, play a vital role in photosynthesis and possess exceptional antioxidant, anti-inflammatory, and antimicrobial properties (Aditi et al., 2025). Consequently, these pigments are regarded as highly valuable natural functional ingredients in the food industry. Compared to synthetic colorants, microalgae-derived pigments better align with the increasing demand for "natural, healthy, and sustainable" food trends. They serve as excellent alternatives to artificial dyes while also enabling for nutrient fortification and the creation of functional foods (Siladji et al., 2024). These pigments mainly consist of carotenoids, phycobilins, chlorophylls, and fucoxanthin. In addition to their essential role in algae photosynthesis, they also exhibit significant antioxidant, anti-inflammatory, and antibacterial biological activities. They are intensely studied for their ability to scavenge free radicals, which can damage cells and enhance immune function.

Microalgal chlorophylls and carotenoids are naturally occurring compounds with a wide range of applications in many fields. These pigments play a crucial role in photosynthesis by capturing light energy to support microalgal growth. Microalgae reproduce rapidly and require minimal resources, making carotenoids valuable bioactive substances with sustainability advantages. As a result, they are considered a sustainable alternative to synthetic dyes and animal-derived compounds. Chlorophyll is the main pigment involved in photosynthesis. In addition to its role in absorbing and converting light energy, it also possesses some physiologically beneficial properties, including antioxidant, anti-inflammatory, and intestinal regulatory effects. The chlorophyll content in microalgae generally ranges from 0.5% to 1.5% of their body weight, while Chlorella vulgaris contains up to 7% (Megawati et al., 2022). Besides, fucoxanthin is one of the typical brown algal carotenoids. Due to its special molecular structure, it offers multiple health benefits, such as anti-tumor, anti-obesity, and blood sugar regulation effects.

In recent years, advancements in genetic engineering, metabolic regulation, and artificial intelligence algorithm have led to a more in-depth study of synthetic pathways for bioactive compounds in microalgae. These developments have significantly improved the yield of bioactive compounds. The application of these technologies not only broadens the applications of microalgal bioactive substances in food, medicine, and bioenergy but also provide new approaches for the sustainable development of biological resources. This paper reviews the application of CRISPR/Cas9 technology to enhance the biosynthesis and regulation of bioactive compounds in microalgae (Fig. 1).