Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet–microbe interactions

TL;DR

This review explores how gut microbes contribute to type 2 diabetes and how multi-omics and diet-microbe interactions can inform new treatment strategies.

Contribution

The paper provides a comprehensive synthesis of how gut microbiome alterations mediate T2D through multiple omics layers and diet interactions.

Findings

Metagenomic studies reveal a consistent T2D-associated gut microbiome signature with reduced short-chain fatty acid producers and increased pro-inflammatory microbes.

Microbial shifts are linked to metabolic pathways affecting gut integrity, inflammation, insulin sensitivity, and β-cell function.

Strain-level analyses show that specific lineages within species carry disease-associated functions, refining microbial targets for T2D.

Abstract

Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid–producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes—including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid–related metabolism—that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and “dark matter” in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function—supporting microbiome-informed precision nutrition—and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.

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