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Food / Diets / Nutrients is one of the main factors that influence gut microbiota (GM) composition, accounting for 57% of the structural variation in the mouse gut microbiome (69), throughout the life course. In turn, microbiota mediate the interplay between habitual diet and various processes of a host organism, including cognitive performance.
In this context, gut microbiota may interact with dietary factors by:
These interactions highlight the significant role of gut microbiota in maintaining overall health and cognitive function (22, 23, 24, 25, 26, 27, 28, 29, 43, 50, 51, 52, 53, 58, 59, 60).
The change of the gut microbiota due to Food / Diets / Nutrients is very sensitive to things like the host's gender, what they eat, their daily routines, and how often they eat (54, 55, 56, 57).
Nutrients, whether derived from the host diet or from endogenous host sources, are critically important in shaping the structure of host-associated microbial communities (67, 68).
The composition and function of the gut microbiota are intimately tied to nutrient acquisition strategies and metabolism, with significant implications for host health. Both dietary and host-intrinsic factors influence community structure and the basic modes of bacterial energy metabolism (1). The gut microbiota engages in a physiological dialogue with humans, forming a bidirectional relationship with the micronutrients, macronutrients, and phytochemicals consumed by the host. Notably, the composition of the gut microbiota can differ from one individual to another and is highly susceptible to dietary changes. Consequently, several recent studies have investigated the application of personalized nutrition in relation to intestinal microflora (11, 14).
Long-term diet has a greater influence than the Short-term diet (17, 18).
The highly fermented diet steadily increased microbiota diversity and decreased inflammatory markers. Fermented foods can thus counteract the reduced microbiome diversity and increased inflammation pervasive in industrial society (20). Among the Food Groups analyzed, grain and fruit fibers showed the strongest correlation with microbial composition (21).
The high-fat / high-fructose diet caused shifts in the host gut microbiota in Syrian hamsters. These dietary-induced alterations in gut microbial composition were linked to changes in the production of secondary metabolites, which contributed to the development of metabolic syndrome in the host (30). Meat consumption alters the human and mouse gut microbiome (31). It has been shown in mice that switching to a high-fat , high-sugar “Western” diet from a low-fat, plant-based, polysaccharide-rich diet can alter the microbiota within a day (66).
A ten-day clinical trial with nine participants reported that the composition and function of the gut microbiota were rapidly changed when Carbohydrates were eliminated from the diet (33), even though the exclusion of all carbohydrates is unsustainable and unlikely to be beneficial to human health. In our recent 6-month randomized controlled-feeding trial study, we showed that a high-fat, low-carbohydrate diet was associated with unfavorable changes in gut microbiota, fecal microbial metabolites, and plasma pro-inflammatory factors in healthy young adults (32).
Diet is known to drive gut microbiota variation, yet the precise mechanisms by which specific dietary components modulate the microbiome and by which the microbiome produces byproducts and secondary metabolites from dietary components are not well understood. Unfortunately, there are no clear standards for collecting dietary data or designing a dietary microbiome study (36).
Direct effects of diet on gut microbiota are likely observable within days. In contrast, the duration of an intervention required to observe microbiome-mediated effects on host phenotype or biomarkers may be much longer, either weeks or months, depending on the outcome (36).
Finally, recent studies show that diet and gut microbiota interactions vary across individuals (36). A 2019 study tracked diets and stool samples over 17 days, finding that even nutritionally similar foods (e.g., different leafy greens) elicited different microbiome responses across participants. Identical foods like Soylent shakes caused daily microbiota shifts unique to each person, with only rare shared patterns—and some in opposite directions (38).
In a daily sampling study in 34 healthy human participants, diet, as assessed using multiple 24-h food recalls, accounted for 44% of the variation in microbiome composition, with another third of the variation explained by factors such as gender, BMI and age (38).
The effect of raw potatoes on the gut microbiome is markedly different from that of cooked ones (37).
Other diets that have also been associated with changes in gut microbiota compositions include the Mediterranean diet and vegetarian diet (41, 42).
The contribution of Food / Diets / Nutrients to modulating the microbiota and its crucial role in orchestrating the host–microbiota crosstalk is evident from the beginning of life, when human milk oligosaccharides (HMOs) participate in the maturation of the microbiota in early infancy, followed by increased bacterial richness associated with the introduction of solid foods, and concludes with decreased richness observed in frail aging populations in longstay care, probably due to reduced food diversity (47, 48, 49).
In an human study, switching from a high-fat/low-fiber diet to a low-fat/high-fiber diet caused notable changes in gut microbiota within 24 hours. Interestingly, diet is also correlated with enterotype, as individuals on a high-fat diet have a Bacteroides-dominant enterotype. In contrast, a high-carbohydrate diet is associated with the Prevotella-dominant enterotype (61). Some of the microbiota members most responsive to diet include the Clostridium Cluster IV and Clostridium Cluster XIVa (62).
The intestinal tract is rich in carbon and nitrogen sources; however, limited access to oxygen restricts energy-generating reactions to fermentation. In contrast, increased availability of electron acceptors during episodes of intestinal inflammation results in phylum-level changes in gut microbiota composition. This suggests that bacterial energy metabolism is a key driver of gut microbiota function (1).
Food / Diets / Nutrients can directly interact with microorganisms to promote or inhibit their growth, and the capability to extract energy from specific dietary constituents bestows a direct competitive advantage to selected members of the gut microbial community, rendering them more capable of proliferating at the expense of less-adept members (43).
Diet is the most powerful and immediate modulator of the gut microbiota.
Epidemiological studies around the world show that diet influences gut-microbiome profiles even more so than do people’s genes, says Christine Spencer, director of informatics at the Parker Institute for Cancer Immunotherapy in San Francisco, California (7).
The importance of nutrition for metabolic health seems undisputed. A universal dietary approach is ineffective due to individual differences in genetics, metabolism, and lifestyle (3, 4, 5, 6).
Food / Diets / Nutrients is the greatest modulator of the Immune System-Gut Microbiota Crosstalk (8, 9). Dietary changes in mice can also lead to significant changes in bacterial metabolism, especially small chain fatty acids and amino acids, in as little as one week, and can lead to large changes after only one day (66, 70).
Early-life consumption of cafeteria diet and sugary drinks can have long-lasting adverse effects on metabolic function. Rats of unhealthy diet-fed (cafeteria diet and sugary drinks) presented higher glucose, total cholesterol, and Creatinine serum levels than the CD (a standard Chow diet with ad libitum access to water) rats (14).
Several diseases tend to primarily inflict those living a Westernised lifestyle and consuming a Western diet, which is characterized by low fruit and vegetable intake and high consumption of animal-derived protein (meat and processed meat), saturated fats, refined grains, sugar, salt, alcohol, and corn-derived fructose (40). Dietary constituents might also disrupt protective functions of the intestinal barrier in ways that could affect the host–microbiome interface and prompt dysbiosis, contributing to inflammatory processes and conferring downstream implications on the host (43). Some members of the microbiota, including lactic-acid producing bacteria, Candida and Penicillium fungi and Plant viruses (33), can be foodborne and therefore passively transferred and introduced into the indigenous gut microbial ecosystem by the Food / Diets / Nutrients (43).
Meat consumption promotes the growth of bacteria that exacerbate mouse models of inflammatory bowel disease and decreases the levels of bacteria that metabolize fiber (33).
For example, the shift from plant-based to animal-based diets increase bile-tolerant microbes and decrease the abundance of Firmicutes that help to metabolize plant polysaccharides (33).
In vitro data suggest that indoxyl sulfate, a protein-bound uremic toxin, may induce vascular dysfunction and thrombosis (63). Microbial metabolites, especially those derived from dietary nutrients, can generate paracrine and endocrine effects that can also lead to an increased susceptibility to heart failure (64). The bacterial L-methionine biosynthesis is linked to lower fruit intake, unfavorable metabolic profile, higher risk of cardiovascular disease and was significantly associated with the presence of plaque (P=0.001) and maximum stenosis (P=0.001) (65).
Food / Diets / Nutrients and prebiotics can profoundly influence existing commensal gut microbes and those administered for therapeutic intent. Numerous dietary intervention studies are currently under way (34), ranging from a somewhat simple intervention of adding one cup of canned beans per day to existing diets (NCT02843425 ) to extended (or longerterm) dietary interventions, where meals are prepared for (and shipped to) participants NCT03950635 - Fiber-rich diet vs (Standard) Ketogenic diet & Melanoma (cutaneous) (35).
The microbial molecules and downstream Signal transduction pathways that activate food digestion remain unexplored (10).
The main input to microbial carbohydrate fermentation is dietary fiber and to branched-chain fatty acids and aromatic metabolites is Dietary proteins / Protein (nutrient). Circulating host lactate , 3-Hydroxybutyrate / beta-Hydroxybutyric acid (BHB), and urea (but not glucose or amino acids ) feed the gut microbiota. We found systematic differences in nutrient use: most genera in the phylum Firmicutes prefer Dietary proteins / Protein (nutrient), Bacteroides dietary fiber, and Akkermansia circulating host lactate. Such preferences correlate with microbiome composition changes in response to dietary modifications. Thus, Food / Diets / Nutrients shapes the microbiome by promoting the growth of bacteria that preferentially use the ingested nutrients (12).
The primary substance that feeds “beneficial” gut microbes is “microbiota-accessible carbohydrates” (15), and in the absence of these, protein and fat will deteriorate our gut health (16).
Some of the earliest microbial colonizers readily ferment select oligosaccharides, influencing the ongoing establishment of the microbiome (39).
Both fat content and fiber content have profound impacts on microbiota composition in mice (13).
Omnivore and vegan, but not synthetic enteral nutrition (EEN), diets altered fecal amino acid levels by supporting the growth of Firmicutes capable of amino acid metabolism. The impact of diet, particularly fiber, on the human microbiome influences broad classes of metabolites that may modify health. The effect on the plasma Metabonome / Metabolome, in contrast, were modest (19).
The gut microbiota offers new chances for personalized nutrition. The human gut microbiota changes with the environment. Diet plays a key role in this change. Eating patterns and gut microbiota differ among people affecting physiological responses (44, 45, 46).
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see also:
Alzheimer's disease (AD) & Gut microbiota
Branched-Chain Amino Acids (BCAAs)
Cardiovascular diseases (CVD) & Gut microbiota
Circadian Clock / Circadian rhythm & Gut microbiota
Composition & Gut microbiota
Dietary Fibers (DF) & Adiposity / Obesity
Dysbiosis & Food / Diets / Nutrients
Dysbiosis & Metabolic Syndrome (MetS)
Energy source
Gut microbiota & Malnutrition / Poor nutrition / Malnutrition
Gut microbiota & Race / Ethnicity
Gut microbiota & Neurodegeneration / Neurodegenerative Diseases (NDDs)
Gut microbiota & Osteosarcopenia
Human microbiota / Human microbiome
Manipulation / Modulation of Gut microbiota
Neurodegeneration / Neurodegenerative Diseases (NDDs)
Nutrition
Personalized nutrition
Resistant starch (RS)