Three country cohort

The goal of the DIABIMMUNE three country cohort is to study the hygiene hypothesis: DIABIMMUNE researchers are seeking to find biological mechanisms that may explain the increased incidence of autoimmune diseases and allergies in modern western societies compared to developing countries.

We recruited families from three countries that have substantial differences of incidence of type 1 diabetes (T1D) and allergies: Finland, which has the highest incidence of T1D globally; Estonia, where the rate of autoimmune disease is increasing rapidly as its society is modernizing; and Russia, where T1D and allergies are still rare compared to Finland and Estonia.

Early infancy (roughly the first six months of life) is consider to be important for the maturation of the immune system, or "immune education". Therefore, we have followed newborn infant from each country from birth until the age of three. Seventy-four infants from each country were selected on the basis of similar HLA risk (predisposition to T1D) and matching gender. For each infant, three years of monthly stool samples, laboratory assays, and questionnaires regarding breastfeeding, diet, allergies, infections, family history, use of drugs and clinical examinations were collected. In accordance with the recruitment criteria for the DIABIMMUNE cohort, all subjects had increased HLA-conferred susceptibility to autoimmunity.

In order to study the gut microbiome of these infants, we sequenced a total of 1584 stool samples using 16S rRNA amplicon sequencing and 785 stool samples using whole-genome shotgun sequencing. You can download various data generated in this project using the Resource pages. In file names, this cohort is referred as karelia (Russian samples are collected in Russian Karelia) in comparison to other cohorts, such as the T1D cohort. We also provide analysis script in R programming language to replicate the metadata association analysis conducted in the accompanying research article.

For information about our findings, read Broad news story about this study.


Vatanen T, Kostic A, d’Hennezel E, et al. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in HumansCell. Online April 28, 2016. DOI: 10.1016/j.cell.2016.04.007


The NCBI BioProject ID for these data is PRJNA290380

Resource Pages 5

  • 16S sequence data

    16S rRNA gene amplicon sequence data can be downloaded using the data table below. The data are paired-end sequences of V4 region of the gene generated using...

  • Metagenomic sequence data

    The whole genome shotgun (WGS) sequencing data can be downloaded using the data table below.

    Taxonomic profiles generated using MetaPhlAn 2.2 can be...

  • Subject metadata

    Subject metadata can be downloaded using the buttons below.

    Download RData

  • Functional data

    Below is a list of HUMAnN2.0 gene family output data. See HUMAnN 2.0 manual for detailed information about the content of these files.

  • Metadata association analysis

    This page gives a detailed description of the microbiota vs. metadata association analyses we have conducted in the three country cohort. For selected highlights see...