Low dimensional ecology of microbiomes: niche dimensionality drives microbial community structure

Niche dimensionality is a foundational concept in niche theory that links environmental complexity to community structure. Although niche theory is often applied to microbiomes, most models assume high-dimensional coexistence, rendering niche dimensionality effectively irrelevant to community organization. Yet, direct estimates of niche dimensionality of microbiomes have been lacking. Here, we introduce a joint species distribution modeling framework to infer niche dimensionality from relative abundance data. Applied to paired 16S rRNA and metabolomics datasets, inferred niche dimensionality closely tracked the complexity of the metabolic environment, validating our abundance-only approach. Across nearly 400 human gut microbiome studies, lower dimensionality was associated with stronger inter-species competition and reduced biodiversity, consistent with the macroecological niche dimensionality hypothesis. Consumer–resource simulations reproduced these empirical relationships, revealing that low dimensionality and its ecological consequences arise naturally from species-intrinsic metabolic tradeoffs and extrinsic environmental tradeoffs, with the latter exerting the dominant effect. Together, these results establish niche dimensionality as an empirically measurable and unifying driver of microbial community structure.