The microbiome at the onset of type 1 diabetes: a study from four geographically distant African and Asian countries

Objectives: Microbiome studies in type 1 diabetes (T1D) to date are limited to populations of Europe (mostly North-Eastern), with one study each from Mexico, the USA, and China. We therefore sought to characterize the gut bacteriome and virome in children after onset of T1D along with age- and place-matched control subjects from four geographically distant African and Asian countries.

Methods: Samples were collected from 73 children and adolescents shortly after T1D onset (Azerbaijan 19, Jordan 20, Nigeria 14, Sudan 20) and 104 matched control subjects of similar age and locale. The bacteriome was profiled by next-generation sequencing of 16S rDNA amplicons, whereas the virome was determined by metagenomic sequencing of RNA and DNA. Negative binomial regression was used to model associations, with adjustment for different geographic origin and for the matched structure of the study.

Results: A significant positive association with T1D was noted for the genus Escherichia (class Gammaproteobacteria, phylum Proteobacteria), whereas Eubacterium and Roseburia, two genera of class Clostridia, phylum Firmicutes, were inversely associated with T1D. No associations were noted for richness or evenness, enterotype, or components of a Dirichlet model. No prominent associations were observed for individual taxa of gut viruses.

Conclusions: Based on our results, some type of distortion of the gut bacteriome appears to be a global feature of T1D, and our findings for four distant populations add new candidates to the existing list of bacteria. It remains to be established whether the observed associations are due to the ability of some bacterial taxa to accelerate islet autoimmunity or are merely markers due to reverse causality with the pre-diabetic state promoting a change in the microbiome profile.