Enterosignatures define common bacterial guilds in the human gut microbiome

The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures.Temporal analysis implies that the Bacteroides-associated ES is corein the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.

Automated summary

The composition of the human gut microbiome is usually in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states that are detrimental to host health. We have identified five generalizable enterosignatures dominated by different types of bacteria, which can be used to characterize the gut microbiome in health and disease. This model allows for the detection of gradual shifts in community structures and can reliably identify atypical gut microbiomes associated with adverse host health conditions and the presence of pathobionts.