Background
The role of the gut microbiota in health is increasingly appreciated and reported to be influenced by dietary intake. However, current assessment methods overlook microbiota-specific metabolism, hampering our understanding. Advances in genetic sequencing have revealed microbiota-host metabolic interactions, but sample collection and study design remain challenging, limiting data integration. Improvements in dietary assessment methods are essential for microbiota-focused precision interventions to optimize health. Therefore, researchers in this systematic review aimed to identify foods and ingredients that influence human gut microbiota composition, highlighting current gaps in the field.
About the study
This review systematically searched PubMed for systematic reviews of diet-gut microbiome associations in healthy individuals and patients with gastrointestinal (GI) diseases. Original studies (n = 106) were distinguished from reference lists of systematic reviews (n = 38) and narrative reviews. Data were extracted, including study design, dietary assessment, and analytical methods.
Results and discussion
‘Healthy’, ‘plant-based’, and Mediterranean diets were associated with higher abundance of Bacteroidetes and Firmicutes, whereas Western diets were associated with lower abundance of microbiota. Vegan/vegetarian diets were associated with an increase in Prevotella and a decrease in Clostridium. Changes in total energy intake were associated with changes in the abundance of Bacteroidetes and Firmicutes and an increase in microbial diversity. However, the methods used to classify dietary patterns varied, affecting the results.
Fiber-rich diets were generally associated with increases in microbial diversity and beneficial bacteria such as Bifidobacteria and Lactobacilli. Resistant starch intake affected bacterial proliferation, with significant effects on Eubacteria and Ruminococci. Prebiotic fiber also showed a positive association with microbial diversity and abundance, while a low FODMAP (an abbreviation for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet affected microbiota composition in patients with irritable bowel syndrome.
Higher protein intake was associated with fewer beneficial bacteria, while studies on dietary gluten intake have yielded inconsistent conclusions. Limited studies have explored the effects of individual amino acids on the microbiota, with some reporting specific associations, such as a decrease in the Firmicutes:Bacteroidetes ratio after L-glutamine supplementation.
Higher intakes of total fat and saturated fatty acids were consistently associated with reduced microbiome richness and diversity, as well as unfavorable microbial community characteristics. Studies have shown that unsaturated fats have mixed effects on the microbiome, but generally have less detrimental effects than saturated fats.
Vitamin B6 has been found to be essential for certain microbial enzyme activities, while vitamin B12 intake has been associated with microbiome diversity and short-chain fatty acid (SCFA) production. Calcium and phosphorus intake increased Clostridium and fecal SCFAs. Gut microbes are also involved in the synthesis of vitamins B12, B6, and folate, with Bifidobacteria utilizing resistant starch to produce folate.
Polyphenols, including those found in foods such as tea and fruit, have been associated with increases in beneficial bacteria such as Bifidobacteria and Lactobacilli, as well as butyrate-producing bacteria, improving gut integrity. Polyphenols also inhibit the growth of pathogenic bacteria such as Clostridium and Salmonella. In addition, natural food chemicals associated with food intolerances, such as salicylates and amines, have been found to be associated with the gut microbiome and microbial metabolites, suggesting a possible role in gastrointestinal disease.
Emulsifiers such as carboxymethylcellulose and polysorbate-80 can cause dysbiosis, while maltodextrin can alter the microbiome, including Firmicutes, Bacteroidetes, Lactobacillus, and Bifidobacterium. Other additives, such as monosodium glutamate and carrageenan, have varying effects. Some additives, such as dishwashing liquids and some sweeteners, increase pathogenic bacteria while decreasing beneficial bacteria. Preservatives, such as nisin, have shown beneficial effects by inhibiting harmful bacteria. Overall, food additives have varying effects on the gut microbiota, with some producing dysbiosis effects and others producing beneficial effects.
Studies have found that nuts have prebiotic effects, especially walnut consumption, which increases Roseburia and Clostridium. Alcoholic beverages, such as red wine, can also affect microbiome composition. Fermented foods, including dairy products such as yogurt and buttermilk, are associated with increased bacterial diversity and an increase in beneficial microorganisms, such as Lactobacillus and Bifidobacterium. Overall, these foods have the potential to positively influence gut microbiome composition.
Additionally, dietary factors associated with the microbiota were categorized as (1) “degradable, evaluable,” (2) “digestible, evaluable,” (3) “degradable, evaluable alone,” or (4) “degradable, not evaluable, or not evaluable,” based on digestibility and evaluability in standard food composition databases.
Although this review comprehensively evaluated the associations between diet and the microbiota, inconsistencies in reporting microbial sequencing methods hampered comparability between studies, limiting data synthesis.