Diet strongly shapes the gut microbiome [1]. Diets rich in fibre and plant-food sources promote bacteria that produce short-chain fatty acids (SCFAs), which support gut barrier integrity and reduce inflammation [1]. In contrast, diets high in saturated fat and low in fibre can encourage pro-inflammatory or opportunistic microbes, altering microbial metabolism in ways that may harm health [1]. Controlled feeding trials allow direct comparisons of microbiome responses to different dietary patterns and help reveal mechanisms linking diet quality to microbial changes.
This study compared gut microbial diversity and species-level composition in response to a Healthy Australian Diet (HAD) versus a Typical Australian Diet (TAD) in a randomised, crossover-controlled feeding trial. Thirty-four healthy adults consumed each diet for two weeks, separated by a washout period, with all food provided. The HAD aligned with Australian Dietary Guidelines[2], while the TAD was based on national intake data[3]. Stool samples were collected at baseline and after each diet (four visits per participant) and analysed by shotgun metagenomic sequencing. Alpha diversity was measured using Shannon and Simpson indices. Species present in ≥20% of samples were retained; relative abundances were arcsin-square root transformed. Linear mixed-effects models adjusted for diet, period, age, and sex, with participant ID as a random effect. False discovery rate (FDR) correction was applied (q < 0.05).
Of 136 collected samples, three were excluded due to sequencing failure or contamination, leaving 133 for analysis. Alpha diversity was significantly higher after TAD compared with HAD. Within-diet changes (baseline to post-diet) showed 10 significant species shifts after FDR correction: six in HAD (five decreased, including Ruminococcus torques and Coprococcus comes, and one increased: unidentified Firmicutes species GGB9758_SGB15368) and four in TAD (three increased, including Lawsonibacter asaccharolyticus and Phocaeicola massiliensis, and one decreased). Between-diet comparisons found 13 species differing significantly, including Alistipes putredinis and Flavonifractor plautii, both higher in TAD.
While greater diversity is often considered beneficial, enrichment of taxa following the TAD such as Ruminococcus torques, a mucin‑degrading species linked to gut barrier thinning and inflammatory bowel disease [4], may indicate shifts towards less favourable microbiome states. Flavonifractor plautii, although capable of SCFA production and flavonoid degradation, has been associated in recent Indian colorectal cancer cohorts with the loss of protective flavonoids[5], suggesting context‑dependent effects.
The TAD increased microbial diversity but favoured taxa previously linked to adverse health outcomes, possibly reflecting a reduced intake of diverse, fibre‑rich substrates. The HAD reduced several opportunistic species, supporting the concept that diet quality, not microbial diversity alone, may be critical in determining health‑promoting gut microbiome. Future analyses should consider metagenomic data to investigate potential functional changes along with metabolites.