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The Future of Personalized Nutrition: Trends Shaping 2025 – Microbiome Testing

Personalized nutrition, driven by advancements in microbiome testing, is transforming healthcare by offering tailored dietary recommendations based on an individual's gut microbiota, genetics, and lifestyle. By 2025, enhanced testing methods and integration with molecular biotechnology will enable more precise dietary interventions, but challenges like privacy concerns and access disparities must be addressed.

AUTHOR: Ira Renko, MSc, Master in Molecular biotechnology

Introduction

Personalized nutrition has taken centre stage in modern healthcare, offering a tailored approach to dietary recommendations based on an individual’s unique biological, genetic, and lifestyle factors. Among these, the gut microbiome is proving to be a game changer. The human microbiome – a collection of trillions of microorganisms living in the digestive tract – plays an essential role in metabolism, immune function, and disease progression1,2. Through its interaction with endocrine, humoral, immunological, metabolic, and neural pathways, it influences overall health3,4.

As we move towards 2025, the evolution of microbiome testing is rapidly increasing, dramatically influencing the field of personalised nutrition. The application of gut microbiome modulators has become more and more represented.  Moreover, new methods for treating serious gastrointestinal conditions have been implemented. The integration of nutrition, pharmacology, and molecular biotechnology is set to launch a new era of personalised dietary interventions, potentially transforming healthcare.

What we know about gut microbiome

Microbiome testing has gained significant attraction in the last decade, with growing evidence linking the composition of gut bacteria to various health conditions, such as obesity, diabetes, inflammatory bowel disease, and even mental health disorders2,5-7. Currently, most microbiome tests use next-generation sequencing (NGS) technologies, which identify microbial DNA from stool samples. These tests analyse the relative abundance of bacterial species and provide insights into the balance of beneficial versus harmful bacteria8. What we know is that gut microbiome typically consists of 6 phyla Actinomycetota (past Actinobateria), Pseudomonadota (past Proteobacteria), Fusobacteriota (past Fusobateria), and Verrucomicrobiota (past Verrucomicrobia), Bacillota (past Firmicutes) and Bacteroidota (past Bacteroidetes)9. However, it is challenging to establish a definitive definition of a “normal” microbiota.

Understanding the factors that shape gut microbiome composition is essential for developing strategies to support a healthy, diverse microbiota, which plays a key role in overall well-being and protection against various health conditions10,11. Although early life stages and the host’s genetic traits strongly impact the gut microbiota, it remains adaptable and can be shaped by various environmental factors, particularly diet12,13. Depending on the type and quantity of food that is consumed, gut microbiome composition changes. Dietary components directly affect the abundance of various microbial species in the gut, which in turn produce essential metabolites and signals that regulate the host’s overall health. For example, a plant-based diet increases the abundance of Lactobacillus and Bifidobacterium, while a carnivore diet increases Bacteroides level14,15. What is more, metabolites produced by one species are used as a substrate for others and some are used by the human organism. Some of them can’t even be synthesised by the human body itself. Table 1. presents the main secondary metabolites that are produced by the gut microbiome. As it is clear from Table 1., some of the gut bacteria produce essential metabolites, while the others are unwanted, for example, methane16-18.

TABLE 1. Secondary metabolites

Name of the metaboliteBacteria
Tryptophan derivativesLactobacillus, Bacteroides, Escherichia coli, Clostridium
Phenolic compoundsClostridium difficile, Bacteroides
Hydrogen sulfideDesulfovibrio, Bilophila wadsworthia
MethaneMethanobrevibacter smithii
Secondary aminesClostridium, Bacteroides, Escherichia coli
Short-chain fatty acidsLactobacillaceae, Ruminococcaceae and Lachnospiraceae

Regarding the bacterial enterotypes, recent studies suggest that enterotypes may be useful for predicting dietary responses. The Prevotella-to-Bacteroides ratio has been closely linked to changes in body fat, weight, BMI, total cholesterol, and hormonal responses following dietary interventions19. Moreover, a capsaicin intervention study demonstrated that butyrate levels were significantly higher in individuals with a Bacteroides-dominated enterotype after capsaicin intake20. The increase in gastrointestinal hormones, such as GLP-1, GIP, and ghrelin, was associated with a greater abundance of Bacteroides21. Similarly, Hjorth et al. observed that individuals with high Prevotella levels experienced greater weight loss on the fiber-rich New Nordic Diet compared to a lower-fiber Danish diet, while those with low Prevotella showed no changes in body weight19. However, gut microbiome modulation showed even more significant results in diseases such as irritable bowel syndrome, neuropsychiatric disorders, irritable bowel syndrome etc.5-7, 22. A study by Zhang et al. showed that the efficacy of nutritional treatment for epilepsy depends on the gut microbiota23. Other study indicates that patients with IBS have different responsiveness depending on the baseline status of specific gut microbiota after consuming a low-FODMAP diet24.

Future direction

Based on the evidence that gut microbiota can be rapidly changed with nutrition intervention, new food trends appear. For example, the change from an omnivorous diet to a vegetarian diet shows substantial changes in the intestinal microbiota in 4 days, while the variation in the consumption of the type of fats or dietary fiber is reflected in 14 days. Regarding dietary patterns, some of the new highly represented trends include keto diet, carnivore and vegan diet. Table 2 presents studies with different dietary interventions and their results25-29.

TABLE 2. Dietary interventions

As it is evident, from Table 2, shifts in nutrition lead to changes in composition, sometimes even an abundance of pathogenic bacteria.  That is in correlation with data shown in Table 1 where specific bacteria metabolise certain substrates and produce metabolites that are either useful or harmful to the human body. Taking that into account, dietary interventions could be used for treating several diseases by modulating the gut microbiome.

By 2025, the costs of microbiome testing will likely decrease due to advancements in sequencing technologies. Also, the shift from 16S rRNA gene sequencing to full metagenomic sequencing will allow for more comprehensive analyses, not just of bacterial species but also viruses, fungi, and other microorganisms that inhabit the gut. This will provide a holistic view of the gut ecosystem and lead to more precise recommendations for personalized nutrition30. Understanding the interplay between a person’s genetic makeup and their gut microbiome will allow for a more refined approach to nutrition. Personalized nutrition plans will be customized not only based on the microbiome but also on a person’s genetic predisposition to conditions like lactose intolerance, gluten sensitivity, or cardiovascular disease31. Probiotic and prebiotic supplements are already a significant part of the personalized nutrition landscape, but the future will bring more targeted approaches. For example, if a person has low levels of Bifidobacterium or Lactobacillus species, specific strains of probiotics may be recommended to restore balance32. Additionally, new types of prebiotics will be designed to selectively enhance the growth of certain microbes. As more research unveils how different fibers and compounds affect microbiota, customized prebiotics will become an integral part of personalized nutrition regimens, promoting specific health outcomes like enhanced metabolism or improved mental health33.

Challenges and ethical considerations

As microbiome testing becomes a cornerstone of personalized nutrition, several ethical and practical challenges will emerge. Privacy concerns regarding microbiome data will be paramount, as such data could potentially be used by insurance companies or employers. Additionally, while personalized nutrition promises improved health outcomes, there is a risk of widening health disparities. Access to microbiome testing and related services may be limited to those who can afford them, potentially exacerbating health inequalities34.

Despite its promise, the field still faces challenges. Standardization is one major issue; results can vary depending on the testing method or platform used. Furthermore, the interpretation of microbiome data remains a complex task, with many unknowns about what constitutes a “healthy” microbiome35. However, advancements in molecular biotechnology, combined with better clinical validation, are expected to resolve many of these limitations.

Furthermore, the science behind microbiome testing and its application in personalized nutrition is still evolving. While molecular biotechnologists and clinicians are uncovering exciting connections between the microbiome and health, the field is still in its infancy in terms of clinical applicability. It is essential that healthcare professionals, including pharmacists and dietitians, approach microbiome-based recommendations cautiously, ensuring they are supported by strong scientific evidence.

Conclusion

The future of personalized nutrition by 2025 is deeply intertwined with advancements in microbiome testing. As technologies evolve, the integration of microbiome data with genetic, pharmacological, and dietary information will enable healthcare providers to offer highly individualized nutritional advice. Molecular biotechnologists, pharmacists, and nutritionists will play pivotal roles in translating microbiome research into practical, personalized solutions that improve patient outcomes. Although challenges remain, the trends shaping microbiome testing hold immense potential to revolutionize how we approach diet, health, and disease prevention.


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