Metformin, a biguanide agent, is the first-line treatment for type 2 diabetes mellitus due to its glucose-lowering effect. Despite its wide application in the treatment of multiple health conditions, the glycemic response to metformin is highly variable, emphasizing the need for reliable biomarkers. We chose the RNA-Seq-based comparative transcriptomics approach to evaluate the systemic effect of metformin and highlight potential predictive biomarkers of metformin response in drug-naïve volunteers with type 2 diabetes in vivo. The longitudinal blood-derived transcriptome analysis revealed metformin-induced differential expression of novel and previously described genes involved in cholesterol homeostasis (SLC46A1 and LRP1), cancer development (CYP1B1, STAB1, CCR2, TMEM176B), and immune responses (CD14, CD163) after administration of metformin for three months. We demonstrate for the first time a transcriptome-based molecular discrimination between metformin responders (delta HbA1c ≥ 1% or 12.6 mmol/mol) and non-responders (delta HbA1c < 1% or 12.6 mmol/mol), that is determined by expression levels of 56 genes, explaining 13.9% of the variance in the therapeutic efficacy of the drug. Moreover, we found a significant upregulation of IRS2 gene (log₂FC 0.89) in responders compared to non-responders before the use of metformin. Finally, we provide evidence for the mitochondrial respiratory complex I as one of the factors related to the high variability of the therapeutic response to metformin in patients with type 2 diabetes mellitus.

The gut microbiome plays a pivotal role in the modulation of host responses during viral infections, and recent studies have underscored its significance in the context of coronavirus disease 2019 (COVID-19). We aimed to investigate the dynamics and compositional changes in the gut microbiome of COVID-19 patients, addressing both the acute phase and the recovery process, with a particular focus on the emergence of post-COVID-19 conditions. Involving 146 COVID-19 patients and 110 healthy controls, this study employed a shotgun metagenomics approach for cross-sectional and longitudinal analyses with one- and three-month follow-ups. We observed a decline in taxonomic diversity among hospitalized COVID-19 patients compared to healthy controls, while a subsequent increase in alpha diversity was shown during the recovery process. A notable contribution of Enterococcus faecium was identified in the acute phase of the infection, accompanied by an increasing abundance of butyrate-producing bacteria (e.g., Roseburia, Lachnospiraceae_unclassified) during the recovery period. We highlighted a protective role of the Prevotella genus in the long-term recovery process and suggested a potential significance of population-specificity in the early gut microbiome markers of post-acute COVID-19 syndrome. Our study represents distinctive gut microbiome signatures in COVID-19, with potential diagnostic and prognostic implications, pinpointing potential modulators of the disease progression.

The gut microbiome composition is intricately linked to the host’s health status, yet the mechanisms underlying its interaction with the host are not fully understood. MicroRNAs (miRNAs), facilitating intercellular communication, are found in bodily fluids, including the intestinal content, where they may affect the microbiome. However, their role in type 2 diabetes (T2D)-associated microbiome and treatment implications are not explored. Our study investigated how host miRNAs may influence gut microbiome changes related to metformin treatment in a T2D mouse model. Analyzing fecal and gut mucosal samples via small RNA sequencing, we correlated results with microbiome sequencing data, identifying miRNA-microbiome correlations, bacterial targets, and proteins targeted in these bacteria. Significant differences in miRNA expression based on diet and intestinal location were noted, with minor effects from metformin treatment in the proximal small intestine of non-diabetic male mice. Key fecal miRNAs targeting bacteria included mmu-miR-5119, mmu-miR-5126, mmu-miR-6538, and mmu-miR-2137, primarily affecting Oscillospiraceae_NOV, Lachnospiraceae_NOV, and Bacteroides. Our analysis of targeted proteins revealed diverse biological and molecular effects. Further research into miRNA-bacteria interactions could lead to new strategies for manipulating the gut microbiome in T2D and beyond.