Mononuclear phagocytes are a heterogeneous population of leukocytes essential for immune homeostasis that develop tissue-specific functions due to unique transcriptional programs driven by local microenvironmental cues. Single cell RNA sequencing (scRNA-seq) of colonic myeloid cells from specific pathogen free (SPF) and germ-free (GF) C57BL/6 mice revealed extensive heterogeneity of both colon macrophages (MPs) and dendritic cells (DCs). Modeling of developmental pathways combined with inference of gene regulatory networks indicate two major trajectories from common CCR2⁺ precursors resulting in colon MP populations with unique transcription factors and downstream target genes. Compared to SPF mice, GF mice had decreased numbers of total colon MPs, as well as selective proportional decreases of two major CD11c⁺CD206^intCD121b⁺ and CD11c⁻CD206^hiCD121b⁻ colon MP populations, whereas DC numbers and proportions were not different. Importantly, these two major colon MP populations were clearly distinct from other colon MP populations regarding their gene expression profile, localization within the lamina propria (LP) and ability to phagocytose macromolecules from the blood. These data uncover the diversity of intestinal myeloid cell populations at the molecular level and highlight the importance of microbiota on the unique developmental as well as anatomical and functional fates of colon MPs.

单核吞噬细胞是一种对免疫稳态至关重要的异质白细胞群，由于局部微环境线索驱动的独特转录程序而产生组织特异性功能。对来自特定病原体 (SPF) 和无菌 (GF) C57BL/6 小鼠的结肠骨髓细胞进行单细胞 RNA 测序 (scRNA-seq)，揭示了结肠巨噬细胞 (MP) 和树突状细胞 (DC) 的广泛异质性。发育途径的建模与基因调控网络的推断相结合，表明来自常见 CCR2 ⁺前体的两条主要轨迹，导致结肠 MP 群体具有独特的转录因子和下游靶基因。与SPF小鼠相比，GF小鼠的结肠MP总数减少，并且两个主要CD11c ⁺ CD206 ^int CD121b ⁺和CD11c ^- CD206 ^hi CD121b ^-结肠MP群体选择性比例减少，而DC数量和比例没有不同。重要的是，这两个主要的结肠​​ MP 群体在基因表达谱、固有层 (LP) 内的定位以及吞噬血液中大分子的能力方面与其他结肠 MP 群体明显不同。这些数据在分子水平上揭示了肠道骨髓细胞群的多样性，并强调了微生物群对结肠 MP 的独特发育以及解剖和功能命运的重要性。