Metagenomic shotgun sequencing and metabolomic profiling identify specific human gut microbiota associated with diabetic retinopathy in patients with type 2 diabetes

Abstract

BackgroundDiabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM) and is one of the leading causes of blindness among DM patients. However, the molecular mechanism involving DR remains unclear.MethodsA case–control study with age-, sex-, and duration-matched diabetic patients and controls was conducted, which included 15 type 2 DM (T2DM) patients with DR and 15 T2DM patients without DR. Shotgun sequencing and non-targeted metabolomic profiling analyses of fecal samples were performed, and comprehensive bioinformatics analyses were conducted.ResultsUsing metagenomic analyses, we identified 293,460 unique genes in the non-DR group, while that in the DR group was 283,235, and the number of overlapping genes was 1,237,914. Regarding phylum levels, Actinobacteria decreased but Bacteroidetes increased in the DR group when compared with those in the control group. Regarding genus levels, Bifidobacterium and Lactobacillus decreased. Cellular processes, environmental information processes, and metabolism-related pathways were found at higher levels in the gut microbiome of DR patients. Using metabolomic analyses, we found 116 differentially expressed metabolites with a positive ion model and 168 differentially expressed metabolites with a negative ion model between the two groups. Kyoto Encyclopedia of Genes and Genomes annotation revealed six pathways with different levels between DR and diabetic controls, namely, cellular processes, environmental information processing, genetic information processing, human diseases, organismal systems and metabolism. Moreover, lysine biosynthesis and lysine degradation were enriched using a positive model, but histidine metabolism and β-alanine metabolism were enriched using a negative model.ConclusionsTogether, the metagenomic profiles of DR patients indicated different gut microbiota compositions and characteristic fecal metabolic phenotypes in DR patients. Our findings of microbial pathways therefore provided potential etiological and therapeutic targets for DR patients.

A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions

“…Shotgun metagenomic (SM) data enable high resolution in estimation of taxon abundance from phylum (Sunagawa et al, 2013 ), to strain level (Scholz et al, 2016 ) within the original sample. In addition to taxonomic profiling, shotgun sequencing data is used for studying the functional potential of the human microbiome (Li et al, 2022 ). In the analysis of SM data, the sequencing depth serves as a crucial factor for understanding how it might affect the results.…”

Sex-Related Effects of Gut Microbiota in Metabolic Syndrome-Related Diabetic Retinopathy

“…Recently, a cross-sectional study carried out in Japanese individuals has shown that the composition and functional profiles for GM in T2D patients were significantly different from those in the healthy group [ 74 ]. Moreover, the habitual dietary intake, especially sucrose intake, was more strongly associated with these differences, suggesting that reducing sucrose intake might help prevent the onset of T2D through prevention of gut dysbiosis [ 75 ].…”

“…In addition, at the genus level, Bifidobacterium and Lactobacillus decreased in faecal samples. Cellular, environmental and metabolism-related pathways were found to be at higher levels in the GM in T2D-DR patients [ 74 ].…”

WAWASAN BIOINFORMATIKA NEXT GENERATION SEQUENCING DALAM SAMPEL METAGENOMIK MIKOBIOMA USUS: Review

“…Metode shotgun metagenomik telah digunakan untuk analisis diversitas metabolisme (L. Li et al, 2022;Sarah R Carrino-Kyke et al, 2013), investigasi outbreak patogen, deteksi biomarker (Anders B Dohlman et al, 2022), dan analisis mikrobiom usus (Salamon et al, 2021). Alur kerja analisis metagenomik shotgun secara umum ditampilkan pada gambar 3.…”