Single-cell analysis of macrophage responses to gut microbiota

Macrophages serve as sentinels at the intestinal surface, responding to organismal cues to drive proinflammatory or tolerogenic responses. To date, studies of combinations of these cues do not fully capture the heterogeneity of macrophage responses. To address this gap, we performed multiplexed single-cell RNA sequencing on 74,476 human monocyte-derived macrophages following exposure to 15 bacteria, mostly commensals. We observe clusters that appeared only after macrophages exposure to bacteria and transcriptional responses within each cluster varied by species and Gram status. The proportion of each cluster also varied among exposure conditions. We validated these responses in vitro and applied machine learning to identify signatures predictive of exposure to specific bacteria. Macrophages exposed to defined combinations of organisms revealed that Fusobacterium nucleatum drives inflammatory responses, whereas Mediterraneibacter gnavus tempers them. Overall, our results show that macrophages distinguish between commensal organisms, relevant to intestinal diseases characterized by altered microbiome compositions. This sequencing dataset will be a useful resource to probe human macrophage response to a broad range of bacteria.