**Background:** Traditional methods for assessing dietary intake—24-hour recall, food frequency questionnaires, and food diaries—rely on self-reporting and are subject to biases including poor memory, motivation, and cultural misinterpretation. There is growing interest in developing objective biomarkers of food intake using metabolomic and metagenomic approaches. The gut microbiota (GM) is modulated by diet and can be sampled non-invasively via feces, making it a candidate for dietary biomarker development. This narrative review summarizes evidence on associations between GM composition and dietary intake, and evaluates the potential of fecal bacteria as biomarkers of food/nutrient consumption and dietary adherence.
**Methods:** This is a narrative review synthesizing published literature on gut microbiota associations with dietary patterns (Mediterranean, plant-based, Western), macronutrients (carbohydrates/fiber, fats, proteins), micronutrients (vitamins and minerals), and bioactive compounds/probiotics. The review also covers GM associations with obesity, weight loss response, type 2 diabetes mellitus (T2DM), cardiovascular disease, intestinal diseases/colorectal cancer, and mental health conditions.
**Key Results:** The review reports that the Mediterranean diet is associated with GM composed of 77.31% ± 2.88 Firmicutes, 15.86% ± 0.28 Bacteroidetes, 3.13% ± 0.65 Actinobacteria, 1.78% ± 1.22 Verrucomicrobia, and <1% Proteobacteria in high-adherence adults. Plant-based diets are associated with higher Prevotella species and, in a comparative study of children, African children (vegetable-based diet) had 57.7% Bacteroidetes versus 22.4% in Italian children (Western-like diet), while Italian children had 63.7% Firmicutes versus 27.3% in African children. The Western diet/high-fat diet is associated with reduced Actinobacteria, increased Proteobacteria, and dominance of Bacteroidia, Clostridia, Bacilli, and Erysipelotrichi classes (90% of GM). High saturated fat intake increases the Firmicutes:Bacteroidetes ratio (73%:21%). Low-carbohydrate diets reduce Firmicutes (mean abundance 5.53), Verrucomicrobia (mean abundance 0.51), and increase Bacteroidetes (mean abundance 5.29). Vitamin E deficiency is associated with 61% Firmicutes, 36% Bacteroidetes, 0.5% Verrucomicrobia, and 1.3% Proteobacteria. The PREDICT 1 trial (Personalized Responses to Dietary Composition Trial 1) used metagenomic sequencing (average 8.8 ± 2.2 gigabases/sample) and identified microbial species linked to cardiometabolic biomarkers, obesity, postprandial responses, and dietary patterns. Specific bacterial associations with disease include: reduced Akkermansia muciniphila in obesity; reduced Bifidobacterium, Bacteroides, Faecalibacterium, Akkermansia, and Roseburia in T2DM; increased Collinsella, Roseburia, and Eubacterium in cardiovascular disease; reduced Faecalibacterium prausnitzii in IBD; and reduced Dialister and Coprococcus in poor mental health.
**Clinical Implications:** The review suggests that fecal microbiota composition could serve as a non-invasive, objective biomarker for dietary intake assessment, potentially replacing or complementing subjective self-report methods. Specific microbial signatures associated with dietary patterns could be used to monitor adherence to nutritional interventions. The authors note that 3 days of dietary intervention can induce changes in bacterial composition. However, they acknowledge that robust, validated nutritional intake biomarkers remain scarce, and that heterogeneity between individuals (sex, age, genetics, lifestyle) and methodological variability across studies are practical limitations. The authors conclude that metagenomic approaches represent a promising tool for personalized nutrition strategies through GM modulation.