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Background <p>Emerging evidence suggests a pivotal role for gut microbiota in the pathogenesis of Type 1 Diabetes (T1D). However, the compositional and functional characteristics of microbial dysbiosis in T1D remain incompletely understood. This study aimed to comprehensively characterize gut microbial alterations and associated metabolic shifts in individuals with T1D.</p> Methods <p>The present study is based on re-analysis of publicly available 16S rRNA sequencing and fecal untargeted metabolomics data from T1D patients and healthy controls generated by Yuan et al. (2022, <i>Nature Communications</i>). Microbial diversity was assessed using Chao1 and Fisher indices (alpha diversity), and Bray-Curtis-based Principal Coordinates Analysis (PCoA) (beta diversity). Taxonomic differences were examined at phylum, genus, and species levels, and differentially abundant taxa were identified via Linear Discriminant Analysis Effect Size (LEfSe). Correlation analyses were conducted to explore microbe-metabolite interactions.</p> Results <p>T1D individuals exhibited reduced alpha diversity and distinct beta diversity clustering compared to controls, indicating substantial shifts in microbial richness and community structure. Taxonomic analysis revealed an increased abundance of <i>Escherichia-Shigella</i>, <i>Veillonella atypica</i>, and <i>Erysipeloclostridium ramosum</i> in T1D, and depletion of beneficial taxa such as <i>Bifidobacterium</i>, <i>Parabacteroides distasonis</i>, <i>Alistipes putredinis</i>, and <i>Bacteroides plebeius</i>. LEfSe analysis confirmed these patterns and highlighted a T1D-specific microbial signature. Integrative correlation analysis uncovered functional dysbiosis, wherein depleted commensals were positively associated with anti-inflammatory and bioenergetic metabolites (e.g., D-gluconic acid, lactic acid, pyruvate), while T1D-enriched taxa were linked to metabolites involved in oxidative stress and immune activation.</p> Conclusion <p>Our study reveals profound structural and functional alterations in the gut microbiome of individuals with T1D. These findings support the existence of a gut microbial-metabolite axis in autoimmune diabetes and suggest that microbial biomarkers and metabolic pathways may serve as novel targets for early diagnosis and therapeutic intervention. Longitudinal studies are warranted to validate these signatures and explore microbiota-based therapies for T1D prevention and management.</p>

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Distinct gut microbiota signatures and metabolic dysregulation in individuals with type 1 diabetes: insights into a microbiome-metabolite axis

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月6日

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  • Shafiul Haque,
  • Abdulhadi I. Bima,
  • Ahmad O. Babalghith,
  • Naif A. Jalal,
  • Abdullah F. Aldairi,
  • Mohd Wahid,
  • Faraz Ahmad,
  • Farkad Bantun

摘要

Background

Emerging evidence suggests a pivotal role for gut microbiota in the pathogenesis of Type 1 Diabetes (T1D). However, the compositional and functional characteristics of microbial dysbiosis in T1D remain incompletely understood. This study aimed to comprehensively characterize gut microbial alterations and associated metabolic shifts in individuals with T1D.

Methods

The present study is based on re-analysis of publicly available 16S rRNA sequencing and fecal untargeted metabolomics data from T1D patients and healthy controls generated by Yuan et al. (2022, Nature Communications). Microbial diversity was assessed using Chao1 and Fisher indices (alpha diversity), and Bray-Curtis-based Principal Coordinates Analysis (PCoA) (beta diversity). Taxonomic differences were examined at phylum, genus, and species levels, and differentially abundant taxa were identified via Linear Discriminant Analysis Effect Size (LEfSe). Correlation analyses were conducted to explore microbe-metabolite interactions.

Results

T1D individuals exhibited reduced alpha diversity and distinct beta diversity clustering compared to controls, indicating substantial shifts in microbial richness and community structure. Taxonomic analysis revealed an increased abundance of Escherichia-Shigella, Veillonella atypica, and Erysipeloclostridium ramosum in T1D, and depletion of beneficial taxa such as Bifidobacterium, Parabacteroides distasonis, Alistipes putredinis, and Bacteroides plebeius. LEfSe analysis confirmed these patterns and highlighted a T1D-specific microbial signature. Integrative correlation analysis uncovered functional dysbiosis, wherein depleted commensals were positively associated with anti-inflammatory and bioenergetic metabolites (e.g., D-gluconic acid, lactic acid, pyruvate), while T1D-enriched taxa were linked to metabolites involved in oxidative stress and immune activation.

Conclusion

Our study reveals profound structural and functional alterations in the gut microbiome of individuals with T1D. These findings support the existence of a gut microbial-metabolite axis in autoimmune diabetes and suggest that microbial biomarkers and metabolic pathways may serve as novel targets for early diagnosis and therapeutic intervention. Longitudinal studies are warranted to validate these signatures and explore microbiota-based therapies for T1D prevention and management.