Ethnic differences in gut microbiota composition and functional capacity persist over six years in the HELIUS multi-ethnic longitudinal cohort
Background: Ethnic minority groups in Western Europe carry a disproportionate cardiometabolic disease burden not fully explained by conventional risk factors, and their gut microbiomes differ markedly from those of European-origin populations. Whether these differences persist over time has not been examined prospectively. Results: We followed 1,903 participants from six ethnic groups in the HELIUS cohort over 6 years, using faecal 16S rRNA sequencing across all groups and shotgun metagenomics in a matched Dutch and South-Asian Surinamese subset (N = 238 per group). The extent of microbiota compositional change over time differed between ethnic groups: Moroccan participants showed the largest change, while the Dutch and South-Asian Surinamese participants were most stable. Diabetes mellitus and medication use at baseline were associated with greater compositional drift. However, ethnic differences in composition were largely preserved across all six groups (16S: ethnicity R2 0.044 to 0.037; all 15 pairwise contrasts significant at follow-up) and in the shotgun subset (R2 0.047 to 0.037). At the species level, 61 of 78 ethnicity-associated species remained differentially abundant at follow-up. Alistipes putredinis, the species converging most strongly, was absent at baseline in 43% of South-Asian Surinamese participants, and the convergence was consistent with acquisition of this species by this group. At strain level, within-person strain sharing declined with follow-up duration but was similar between ethnic groups. Within hosts, 90% of A. putredinis populations were retained as the same or a closely related lineage, and within the retained subset, microdiversity increased in both groups. Ethnic differences in functional profiles persisted to a similar extent as those in composition, with limited convergence in fibre-degrading enzyme families (GH5_37, GH26). The total antibiotic resistance gene (ARG) burden in the gut microbiome declined similarly in both groups over time. Dutch participants showed higher baseline ARG diversity that converged toward South-Asian Surinamese levels, while class-level differences were predominantly stable. Conclusions: Six years of follow-up in a shared urban environment narrowed ethnic differences in the gut microbiome only modestly; assuming exponential decline, the observed change corresponds to a half-life of roughly two decades.