bioRxiv2025
BackgroundEmerging evidence highlights the complex interplay between gut microbiota and type 2 diabetes mellitus (T2D); however, the temporal trajectory of microbial community succession and the concomitant shifts in associated metabolic pathways across the disease lifecycle remain poorly characterized. In this study, we conducted a multi-dimensional analysis of gut microbiota composition and functional pathways in rats, spanning the continuum from health, through the T2D pathological state, to post-intervention recovery phases. ResultsHealthy aged rats exhibited significantly greater gut microbial diversity compared to both younger healthy cohorts and T2D rats. In the absence of intervention, progressive T2D development led to a sustained decline in microbial diversity that persisted until death. Notably, {beta}-tocotrienol ({beta}-T3), metformin hydrochloride (MET) and healthy dietary interventions not only improved fasting blood glucose (FPG) levels in T2D mice but also restored their gut microbial diversity and metabolic functions. At the phylum level, the ratio of p Bacteroidota to p Firmicutes exhibited an age-dependent increase in healthy rats but displayed a progressive decline in T2D rats. Notably, species-specific expansions were observed across both healthy and pathological states. For example, s Bacteroides_acidifaciens (B. acidifaciens) showed a significant expansion in early T2D stage disease, while s Anaerostipes_hadrus became the dominant species in advanced-stage T2D. Among intervention groups, s Phascolarctobacterium_faecium was enriched in the {beta}-tocotrienol ({beta}-T3) group; the abundance of s Escherichia_coli (E. coli) increased dramatically in the deceased rats. Gut metabolites also exhibited distinct characteristics across different physiological stages. In young rats, the metabolite profile was characterized by lower abundances of most metabolites, which stabilized with age accompanied by upregulation of select molecules in older rats. Notably, during T2D progression, the metabolite profile displayed a largely opposite pattern compared to healthy controls. Importantly, dietary interventions including healthy food, {beta}-T3, MET partially restored metabolic homeostasis in T2D rats. Further analysis revealed that key differential metabolites across groups were enriched in bile acids (BAs), amino acids, benzene and its substituted derivatives, and organic acids with their derivatives. Specifically, amino acid metabolism was more active in healthy rats, whereas BA and benzene derivative metabolism were upregulated in T2D. Key microbial species driving these shifts included s Lactobacillus_johnsonii, s Lactobacillus_reuteri, and B. acidifaciens, which exhibited positive correlations with BAs and select amino acids. The B. acidifaciens could be a biomarker of T2D and glycoursodeoxycholic acid, sohyodeoxycholic acid, beta-muricholic acid and allocholic acid were the key BAs to regulate glycometabolism of the host. ConclusionsDuring the T2D stage, both gut microbiota composition and metabolic profiles exhibited distinct characteristics compared to those of healthy age-matched older rats. Notably, {beta}-T3 and MET interventions not only facilitated the recovery of gut microbial diversity and metabolite levels in T2D mice but also promoted the proliferation of specific dominant species, each intervention favoring distinct taxa. In this context, B. acidifaciens emerged as a dominant bacterial species in T2D, exerting regulatory effects on glycometabolism through BA and amino acid metabolic pathways. Collectively, these findings advance our understanding of T2D pathophysiology and highlight the potential of probiotic-based therapies for its management. ImportanceThe T2D is a kind of chronic disease and the gut microbiota shows a continuously slow succession from some microbial populations to other ones in the disease progress. Uncovering the rule of change in gut bacteria from healthy rats to T2D ones and the recovering capacity of gut microbiota through interventions of healthy food, {beta}-T3 and antidiabetic drug are beneficial to understand the real regulation mechanism of gut bacteria in T2D progress. Then the results lay the foundation of developing probiotics and researching new metabolic therapeutic target of gut microorganisms. In addition, to research the metabolic regulation mechanism of gut bacteria, using multi-omics including microbiomics and metabonomics is an effective way.