This intricate interplay of transporters and dietary factors reflects the complex nature of nutrient absorption in farmed fish. Phosphorus retention can be influenced by several dietary parameters, such as the raw materials used as protein and phosphorus sources, and the ratio of phosphorus to other minerals, such as calcium [
30,
63,
65,
66,
67,
69,
70,
71]. The development of new fish feed formulations allows aquaculture to tailor the nutritional composition of the feed to meet the specific requirements of different fish species and use alternative protein sources to reduce the reliance of aquaculture on fish meal and fish oil. However, efforts to replace fish meal with plant proteins in fish diets face challenges related to the impact on the functional integrity of farmed fish intestines [
10,
64]. Plant natural defense mechanisms, such as protease inhibitors, phytates, glucosinolates, saponins, tannins, lectins, oligosaccharides, and non-starch polysaccharides, can induce intestinal inflammation [
74]. This inflammation is linked to changes in gene expression within the intestine, including the absorption of phosphorus. Furthermore, anti-nutritional factors, such as phytate, can affect how efficiently aquacultured species absorb phosphorus. Phytate is a type of phosphorus present in plant-based feed ingredients commonly used in aquaculture diets. However, many aquatic species have limited ability to digest phytate because they lack the necessary enzyme, called phytase, which is responsible for breaking it down [
6]. To mitigate the negative effects of these anti-nutritional factors, fish feed processing methods are employed to neutralize harmful compounds present in plant ingredients and prevent adverse effects on fish. This includes techniques to destroy or reduce the presence of plant natural defense mechanisms. Phytase, for example, an enzyme that can break down phytic acid, is a useful tool that can help fish make the best use of phosphorus available in plant-protein-based feeds. Studies have shown that its addition, can increase the availability of phosphorus in fish diets, leading to improved growth and health [
75,
76,
77,
78,
79,
80]. Interestingly, the commonly used soybean meal (SBM) in fish diets has been found to impact nutrient absorption, down-regulating the expression of fabp2, a fatty-acid binding protein responsible for lipid absorption in the gut. This disruption in fabp2 expression can interfere with the transport and absorption of lipids, leading to reduced lipid intestinal uptake [
81]. Decreased fabp2 expression has been particularly observed in fish experiencing SBM-induced inflammation in the distal portion of the intestine [
82,
83]. Overall, when fed plant proteins, farmed fish often exhibit intestinal inflammation, which can be addressed by incorporating functional feed additives or employing processing techniques for plant proteins [
84,
85]. This becomes especially important given the growing trend of substituting fish meal with plant protein in aquafeed.
Dietary phosphorus levels can also affect phosphorus absorption in farmed fish, influencing the expression of phosphate transporters like NaPi-IIb and Pit-1 with the highest expression observed in the anterior intestine, followed by the posterior and middle intestines [
12,
86,
87]. Increasing the dietary levels of calcium and vitamin D has been shown to enhance phosphorus absorption by upregulating the expression of sodium-phosphate co-transporters in the fish intestine, particularly in the anterior segment [
37,
55].