Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science have recently emerged as new tools for studying common complex human diseases. We report in this study notable differences in gut microbiome in adult patients with obesity and diabetes in Egypt. The experimental design was based on comparisons of four study groups: (1) Controls (C) with a normal body mass index, without obesity or diabetes, (2) Obese adults (O) without diabetes, (3) adults with diabetes (D) who are not obese, and (4) Adults who are both obese and diabetic (OD). In a total study sample of 60 participants, we sequenced the 16S ribosomal RNA (rRNA) gene using the Illumina MiSeq platform. Alpha diversity analysis revealed greater diversity in bacterial communities of (D) than controls. Phylum-level analysis identified a trend for overrepresentation of Bacteroidetes (p < 0.07) in (O) and (D) than controls. The ratio of Firmicutes/Bacteroidetes (F/B) displayed a remarkable increase in (OD) than controls. At genus level, Faecalibacterium (p < 0.05) and Akkermansia (p < 0.001) distinguished (O) from controls, while Fusobacterium (p < 0.001) and Bacteroides (p < 0.001) was significantly more abundant in (OD) compared with D. Surprisingly, isoquinoline, quinone and ubiquinone alkaloid biosynthesis were overrepresented in controls compared with other three study groups. Presumably, the latter observation might potentially suggest an antihyperglycemic activity of the gut microbiota. In conclusion, the health state of the adults in our study defined the composition of the gut microbiota. Moreover, obesity and diabetes were associated with remarkably enriched populations of Firmicutes and Bacteroidetes. The abundance of Fusobacterium is worth further research and exploration as a candidate biomarker for prediabetes especially in obese individuals. The potential antihyperglycemic activity of the gut microbiota is also noteworthy for future studies in other world populations.
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