Gut microbiota beta-diversity and genus-level differential abundance in GCK-MODY and HNF1A-MODY: A pilot study

Abstract

Objective

To investigate differences in gut microbiota (GM) beta-diversity and genus-level differential abundance between individuals with glucokinase-maturity-onset diabetes of the young (GCK-MODY) and hepatocyte nuclear factor 1-alpha (HNF1A-MODY).

To investigate differences in gut microbiota (GM) beta-diversity and genus-level differential abundance between individuals with glucokinase-maturity-onset diabetes of the young (GCK-MODY) and hepatocyte nuclear factor 1-alpha (HNF1A-MODY).

Methods

This observational study included 33 individuals with genetically confirmed MODY caused by pathogenic or likely pathogenic variants in the GCK (n = 16) and HNF1A (n = 17) genes, classified according to the American College of Medical Genetics and Genomics guidelines. Participants had a mean age of 38.3 ± 14.7 years. Blood samples were collected for genetic analysis, and fecal samples were obtained using a swab-based stool collection kit for DNA extraction and 16S rRNA gene sequencing. GM beta-diversity was assessed using Bray–Curtis, Jaccard, unweighted UniFrac, and weighted UniFrac distance metrics. Differential abundance analyses at the genus level were performed using LinDA, limma-voom, and MaAsLin2. Statistical analyses were conducted in R version 4.2.1, with P < 0.05 considered statistically significant. The study received ethical approval from HUCFF/UFRJ (CAAE 04232512.4.0000.5257), IPPMG/UFRJ (Approval No. 6.126.045), and IOC/FIOCRUZ (CAAE 44726720.4.0000.5248).

This observational study included 33 individuals with genetically confirmed MODY caused by pathogenic or likely pathogenic variants in the GCK (n = 16) and HNF1A (n = 17) genes, classified according to the American College of Medical Genetics and Genomics guidelines. Participants had a mean age of 38.3 ± 14.7 years. Blood samples were collected for genetic analysis, and fecal samples were obtained using a swab-based stool collection kit for DNA extraction and 16S rRNA gene sequencing. GM beta-diversity was assessed using Bray–Curtis, Jaccard, unweighted UniFrac, and weighted UniFrac distance metrics. Differential abundance analyses at the genus level were performed using LinDA, limma-voom, and MaAsLin2. Statistical analyses were conducted in R version 4.2.1, with P < 0.05 considered statistically significant. The study received ethical approval from HUCFF/UFRJ (CAAE 04232512.4.0000.5257), IPPMG/UFRJ (Approval No. 6.126.045), and IOC/FIOCRUZ (CAAE 44726720.4.0000.5248).

Results

No significant differences in beta-diversity were observed between groups. Weighted UniFrac analysis suggested differences in GM community structure between GCK-MODY and HNF1A-MODY individuals (PERMANOVA, R² = 0.078, P = 0.014), although statistical significance was not maintained after multiple-testing correction (adjusted P = 0.072). Differential abundance analyses did not identify any genera that remained significant after false discovery rate correction. However, Enterorhabdus, Anaerotruncus, and Collinsella consistently showed higher abundance in HNF1A-MODY across analytical approaches. The strongest association was observed for an uncultured genus identified by MaAsLin2 (P = 0.0004; FDR-adjusted P = 0.071). These taxa have been implicated in metabolic and inflammatory processes including glucose and lipid metabolism.

No significant differences in beta-diversity were observed between groups. Weighted UniFrac analysis suggested differences in GM community structure between GCK-MODY and HNF1A-MODY individuals (PERMANOVA, R² = 0.078, P = 0.014), although statistical significance was not maintained after multiple-testing correction (adjusted P = 0.072). Differential abundance analyses did not identify any genera that remained significant after false discovery rate correction. However, Enterorhabdus, Anaerotruncus, and Collinsella consistently showed higher abundance in HNF1A-MODY across analytical approaches. The strongest association was observed for an uncultured genus identified by MaAsLin2 (P = 0.0004; FDR-adjusted P = 0.071). These taxa have been implicated in metabolic and inflammatory processes including glucose and lipid metabolism.

Conclusion

Although no genera remained significantly different after multiple-testing correction, weighted UniFrac analysis and consistent abundance patterns across multiple analytical methods suggest potential differences in GM composition between GCK-MODY and HNF1A-MODY individuals. These preliminary findings support further investigation to better characterize GM profiles associated with distinct MODY subtypes.

Although no genera remained significantly different after multiple-testing correction, weighted UniFrac analysis and consistent abundance patterns across multiple analytical methods suggest potential differences in GM composition between GCK-MODY and HNF1A-MODY individuals. These preliminary findings support further investigation to better characterize GM profiles associated with distinct MODY subtypes.