Our bodies obtain energy and nutrients by ingesting, digesting, and absorbing food. This process is carried out by the various organs of the digestive tract working in coordination, and behind the scenes, there is precise genetic control. This article will explain in detail the role of genes involved in the digestive system and how genetic information can be used to improve digestive function.
Development of the digestive tract and the role of genes
The digestive tract is composed of the esophagus, stomach, small intestine, and large intestine, each of which has a specific function. These organs differentiate and form from a single primitive intestinal tract during development. This differentiation is closely related to the expression of specific genes.
For example, research at Fukui University has revealed that the gene Id2, which regulates cell differentiation, plays an important role in the formation of stomach and intestinal cells. In mice lacking the Id2 gene, esophageal and stomach cells, which do not normally exist in the small intestine, appeared and tumor formation was observed. This suggests that Id2 promotes appropriate cell differentiation by suppressing the expression of specific genes.
Epigenetics (the mechanism that controls gene expression) also affects the function of the digestive tract. According to an explanation by the National Institute of Advanced Industrial Science and Technology, epigenetics controls the genetic switches of each cell type, such as turning on genes that produce neurotransmitters in nerve cells and turning off genes related to digestive enzymes.
The relationship between digestive enzymes and genes
Digestive enzymes play a role in breaking down food and converting it into a form that is easily absorbed by the body. The production and activity of these enzymes are also controlled by genes.
For example, the expression of digestion- and absorption-related genes in the intestinal tract is regulated by the presence of nutrients and the differentiation state of cells. Research has shown that the expression of digestion- and absorption-related genes increases as absorptive cells in the small intestine differentiate and mature.
Furthermore, studies using genetically modified mice suggest that certain genes are involved in the function of taste receptors in the gastrointestinal tract, which may alter food palatability and gastrointestinal responses, ultimately affecting the efficiency of digestion and absorption.
Relationship between genetic polymorphisms and vitamin absorption
Individual genetic polymorphisms (slight variations in genes) are known to affect vitamin absorption and metabolism. Biochemical studies have shown that people with certain genetic polymorphisms may require higher vitamin intakes than generally recommended, which may lead to an increased risk of vitamin deficiencies and related diseases.
For example, polymorphisms in the MTHFR gene, which is involved in folate metabolism, reduce the efficiency of folate metabolism, resulting in elevated blood homocysteine levels and an increased risk of cardiovascular disease. Based on this genetic information, individualized nutritional management and supplement intake may be recommended.
It has been revealed that the intestinal flora (microbiome) influences digestion and absorption, immune function, and even mental health. The composition and function of intestinal bacteria interact with the host’s genes, and the balance of these factors plays a major role in health.
A study at Waseda University analyzed the intestinal flora of healthy Japanese people and discovered approximately 5 million genes. This study suggested that the intestinal flora of Japanese people has a unique composition compared to other countries and contains many functions that are beneficial to the body. These characteristics may be related to the long average life expectancy and low obesity rate of Japanese people.
Utilizing genetic information to improve digestive function
1. Genetic testing for personalized optimization of digestive function
In recent years, the concept of personalized nutrition has been gaining attention. This involves using genetic testing to identify the characteristics of an individual’s digestive function and then adjusting their diet and supplements accordingly.
For example, people with a mutation in the LCT gene that causes lactose intolerance are prone to digestive upset when they consume dairy products. In this case, choosing lactose-free foods and taking lactase enzyme supplements can help alleviate the symptoms.
Additionally, people with more copies of the amylase (AMY1) gene tend to have a higher ability to digest carbohydrates, making them less likely to become obese even if they consume a moderate amount of sugar. On the other hand, people with fewer copies of AMY1 metabolize carbohydrates more slowly and are more likely to experience sudden spikes in blood sugar, so carbohydrate restriction may be more effective. ( ncbi.nlm.nih.gov )
Understanding the interactions between genes and gut bacteria can lead to more effective digestive improvements. Because the gut microbiome is determined in part by the host’s genes, it is important to know the type of gut bacteria you have.
For example, people with a high proportion of Firmicutes bacteria have a tendency to promote lipid absorption, so by limiting high-fat diets they can prevent obesity. On the other hand, people with a high proportion of Bacteroidetes bacteria have a high ability to metabolize carbohydrates, so the efficiency of energy intake from food differs.
Taking advantage of these differences in gut bacteria, it is effective to adopt a dietary strategy that combines probiotics (the intake of beneficial bacteria) and prebiotics (dietary fiber and oligosaccharides that serve as food for beneficial bacteria) (gut.bmj.com).
Epigenetics is a mechanism that regulates gene expression without changing the DNA sequence, allowing environmental and dietary influences to alter the function of digestive genes.
For example, it has been shown that calorie restriction activates the SIRT1 gene, which regulates metabolism and enhances antioxidant activity. SIRT1 improves the intestinal barrier function and suppresses inflammation in the digestive tract. ( nature.com )
Additionally, polyphenols (such as catechins in green tea and resveratrol in red wine) have been suggested to have the effect of regulating the intestinal environment through epigenetic modifications, and by regulating the expression of certain genes, contribute to improving digestive function.
4. Using genetic data to select digestive supplements
It is also important to choose supplements that are suited to each individual’s constitution based on genetic information. For example, the following methods of selecting supplements according to genotype are possible.
People with a mutation in the MTHFR gene: To compensate for the reduced metabolic efficiency, methylated folate (5-MTHF) is taken to improve the body’s utilization of the active ingredient.
People with a mutation in the PEMT gene: They have a low ability to synthesize choline, so taking egg yolk and lecithin supplements can support lipid metabolism.
People with an active CYP1A2 gene: They metabolize caffeine quickly and are less affected by coffee, but their performance needs to be adjusted depending on their caffeine intake. (genomebiology.biomedcentral.com)
Genetic information can be used to create an optimal diet plan, including specific dietary strategies such as:
People with poor carbohydrate metabolism (low AMY1 copy number): Focus on low-GI foods (brown rice, whole wheat bread, beans) to prevent blood sugar levels from rising.
People with high lipid absorption (FTO gene mutation): Focus on unsaturated fatty acids (olive oil, avocado, nuts) and limit your intake of saturated fatty acids.
People with good protein metabolism (UCP1 gene activated): Eat a high-protein diet (chicken, fish, soy products) to maximize metabolic efficiency。
In this way, genetic information can be used to create the optimal digestive strategy for you. Furthermore, dietary management apps and genetic testing kits allow for a more scientific approach. ( nature.com )
Further optimization of digestive function using genetic information
6. Risk of digestive diseases and genetic factors
Genetic information can also be used to assess the risk of digestive system diseases. For example, the following genetic factors are related to digestive function and disease risk:
1. Gastric cancer and genetic polymorphisms
The risk of developing stomach cancer is influenced not only by environmental factors (diet, Helicobacter pylori infection, etc.) but also by genetic factors. In particular, mutations in the PLCE1 gene have been suggested to increase the risk of developing stomach cancer and esophageal cancer. ( ncbi.nlm.nih.gov ) People who carry this gene may be able to reduce their risk by limiting their salt intake and actively undergoing Helicobacter pylori eradication treatment.
Inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn’s disease, are strongly associated with mutations in the NOD2 gene (gut.bmj.com). People with mutations in this gene are more likely to have an imbalance in their intestinal flora and an overactive immune system. Therefore, actively consuming anti-inflammatory omega-3 fatty acids and prebiotics can help manage symptoms.
3. Lactose intolerance and the LCT gene
Lactose intolerance is caused by a genetic mutation in the enzyme lactase (LCT), which breaks down lactose. If there is a mutation in the LCT gene, lactase activity decreases as people reach adulthood, making it difficult to digest lactose. ( nature.com ) In this case, indigestion can be prevented not only by avoiding dairy products but also by taking lactase supplements.
7. Genetic-Based Lifestyle Strategies for Improving Digestion
By optimizing your lifestyle using genetic information, you can expect to improve your digestive function.
① Match meal timing to genetic characteristics
Genes that regulate the body’s internal clock ( such as the CLOCK gene and PER1 gene ) also affect the rhythm of the digestive system. Research has shown that genetically predisposed people (those with a CLOCK gene mutation) are more likely to experience elevated blood sugar levels when eating late at night, so eating dinner earlier may improve metabolic efficiency. ( diabetesjournals.org )
② The relationship between fasting and genes
Fasting has the effect of resetting digestive function and improving the balance of intestinal bacteria. In particular, the FOXO3 gene promotes autophagy (the self-repair function of cells) and helps repair the intestines. For people whose genetic testing shows high FOXO3 activity, short-term fasting (12 to 16 hours) is effective in improving digestive function. ( cell.com )
8. Genetically tailored exercise for improved digestion
In addition to diet, exercise is also an important factor in improving digestive function, and by utilizing genetic information, more effective exercise plans can be created.
① Aerobic exercise and intestinal environment
Aerobic exercise (walking and jogging) is effective in increasing the diversity of intestinal bacteria and promoting intestinal peristalsis. It has been found that people with high PPARGC1A gene activity are particularly susceptible to the improved intestinal environment that comes with exercise. ( jphysiol.org )
② The effects of yoga and stretching
Yoga and stretching are effective in making the parasympathetic nervous system dominant and activating intestinal function. People with high BDNF gene activity tend to be more susceptible to indigestion caused by stress, so incorporating mindfulness and yoga into their daily routine can help maintain digestive function.
9. The relationship between digestion and stress: influence at the genetic level
Stress has a significant impact on digestive function, but susceptibility to this effect varies depending on genes. In particular, genes involved in the secretion of stress hormones (cortisol) and neurotransmitters (serotonin, dopamine) are involved in regulating digestive function.
1. Stress response and the NR3C1 gene
The NR3C1 gene encodes the cortisol receptor and determines the body’s response to stress. Mutations in this gene affect cortisol sensitivity, which determines whether a person is resilient to stress. ( ncbi.nlm.nih.gov )
Stress-sensitive type (people with NR3C1 mutations) → Excessive cortisol secretion leads to increased secretion of gastric acid, resulting in an increased risk of stomach ulcers and gastritis.
Stress-resistant type (people without NR3C1 mutations) → Gastrointestinal function tends to be stable, but because they are insensitive to stress, they tend to neglect health management.
People with this gene may benefit from mindfulness meditation and relaxation techniques for stress management.
2. Serotonin and digestive function: The influence of the HTR2A gene
Serotonin (the “happiness hormone”) is produced not only in the brain but also in the intestines, where it regulates intestinal peristalsis. The HTR2A gene encodes a serotonin receptor, and mutations in this gene affect the function of serotonin. ( sciencedirect.com )
People with HTR2A mutations have reduced serotonin function and are prone to constipation and irritable bowel syndrome (IBS).
People with normal HTR2A have normal intestinal peristalsis and smooth digestion.。
People with this genotype can promote serotonin synthesis by actively consuming fermented foods (yogurt, kimchi, natto) and foods containing tryptophan (bananas, soybeans, nuts).
10. Individually optimized supplements utilizing genetic information
① How to choose a digestive enzyme supplement
Based on the results of genetic testing, if you are deficient in certain digestive enzymes, you can choose supplements to make up for them.
People with a mutation in the LCT gene should take lactase supplements to help digest lactose.
People with a low copy number of the AMY1 gene : Use amylase supplements to promote carbohydrate digestion.
People with a mutation in the PEP1 gene → Supplementing with pepsin improves protein digestion.
② Probiotics and intestinal bacteria balance adjustment
The balance of intestinal bacteria is likely determined by genetic factors, so it is important to utilize genetic information to select the optimal probiotic. ( nature.com )
People with a high Bacteroidetes phylum have a high ability to digest carbohydrates, so they should eat foods that are rich in oligosaccharides to improve their intestinal environment.
People with a high Firmicutes phylum → Because fat absorption is high, make sure to consume dietary fiber to improve the balance of intestinal bacteria.
11. Future Improvement of Digestive Function: Application of Gene Editing Technology
In recent years, research has been conducted into improving digestive function using gene editing technology (CRISPR-Cas9).
1. Overcoming lactose intolerance through gene editing
Research is being conducted into the possibility that artificial activation of LCT gene expression may enable adults to digest lactose ( ncbi.nlm.nih.gov ) .
2. Genetic modification of intestinal bacteria
Efforts are being made to genetically modify gut bacteria so that they can break down and absorb certain nutrients more efficiently. (cell.com)
12. Utilizing genetic information to further improve digestive function
① Personalized nutrition and the use of AI
Nutritional management using genetic information can be more personalized when combined with AI technology. Currently, many companies are offering diet plan proposal services that utilize genetic testing and AI.
The benefits of AI-based nutritional analysis
Real-time nutrition adjustments : Integrates genetic data and food records to automatically suggest meal plans that optimize digestion.
Personalized supplement recommendations : Identify potential nutrient deficiencies and select the necessary supplements.
Analysis of the interaction between diet and exercise : Achieve a more effective balance between diet and exercise through a comprehensive analysis of genes and lifestyle.。
This will make it possible to develop an optimal dietary strategy based on an individual’s genetic information, rather than the conventional approach of “general health management.”
② Integration of genetic testing and intestinal flora testing
In recent years, there has been an increasing trend to integrate intestinal flora testing, which examines the balance of intestinal bacteria, with genetic testing, which aims to more accurately optimize digestive function by combining the composition of intestinal bacteria with an individual’s genetic characteristics.
Benefits of Integrated Analytics
Visualizing the relationship between genes and the intestinal environment : Analyzing how specific gene mutations affect the composition of intestinal bacteria.
Individual assessment of digestive capacity : Detailed analysis of lactose-digesting enzymes and dietary fiber digestion capacity to provide guidelines for improving your diet.
Early detection of disease risk : Predict the risk of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) and develop preventive measures.
For example, people with a high Bacteroides content in their intestines have a high ability to break down dietary fiber, while people with a high Firmicutes content have a tendency to be more prone to obesity due to their increased fat absorption. ( nature.com )
3. The relationship between genetically based diet plans and digestive function
The effectiveness of dieting varies from person to person depending on the genes involved in digestion and metabolism. By choosing a diet method that is optimized for digestive function based on genetic information, more efficient weight management becomes possible.
Representative genes and diet effects
FTO gene : People with a mutation in this gene burn fat less efficiently, so avoiding high-fat foods can improve the effectiveness of their diet.
PPARG gene : Involved in carbohydrate metabolism, and people with mutations are effective on a low-carbohydrate diet (low-carb).
ADRB2 gene : Controls basal metabolism, and people with the mutation are more effective at burning fat through high-intensity interval training (HIIT).
Using this information, dietary restrictions that are suited to individual digestive abilities can be designed, improving the success rate of dieting.
4. The cutting edge of food development using genetic information
The food industry is also making progress in developing foods with excellent digestibility by utilizing genetic information.
① Development of personalized food
Foods with digestive enzymes tailored to your genotype : Yogurt with lactase enzymes for people with lactose intolerance and foods that help digest gluten are now available.
Functional foods that optimize nutrient absorption : A supplement combining vitamin C and iron to enhance absorption has been developed for people with genetic types that result in poor iron absorption.
② Food improvement using gene editing
Development of hypoallergenic foods : Using gene editing technology (CRISPR), easy-to-digest low-gluten wheat and hypoallergenic nuts are being developed.
New fermented foods utilizing intestinal bacteria : Research is being conducted into foods containing intestinal bacteria suited to specific genotypes, and it is believed that in the future it will be possible to create fermented foods tailored to the intestinal bacteria of each individual. (cell.com)
⑤ Future medical care and digestive treatment using genetic information
Advances in genetic information are making personalized medicine (precision medicine) a reality.
① Treatment of digestive diseases through gene therapy
Gene editing for gastrointestinal diseases using CRISPR technology : Efforts are underway to modify specific genes to treat gastrointestinal diseases.
Individualized treatment for inflammatory bowel disease (IBD) : “Targeted therapy” is being developed, in which individual therapeutic drugs are selected depending on the mutation in the NOD2 gene.。
② Combining gut microbiota transplantation with genetic data
Fetal Microbial Transplantation (FMT) is attracting attention as a way to improve the balance of intestinal bacteria, and by combining it with genetic data, it will be possible to adjust the intestinal environment with greater precision.
Currently, some research institutes are developing technology to create an optimal gut microbiome transplant plan based on individual genetic information. (gut.bmj.com)
Utilizing genetic information makes it possible to individually optimize digestive function. Healthy digestive function can be maintained by genetically analyzing the function of digestive enzymes, the balance of intestinal bacteria, stress resistance, and other factors, and optimizing diet, supplements, and exercise. Utilizing the latest genetic research and AI technology, more precise nutritional management and disease prevention are becoming a reality. The development of personalized nutrition based on genetic information will likely lead to further advances in improving digestive function and maintaining health.
