The gastrointestinal tract is a multi-organ system crucial for efficient nutrient uptake and barrier immunity. Advances in genomics and a surge in gastrointestinal diseases^1,2 has fuelled efforts to catalogue cells constituting gastrointestinal tissues in health and disease³. Here we present systematic integration of 25 single-cell RNA sequencing datasets spanning the entire healthy gastrointestinal tract in development and in adulthood. We uniformly processed 385 samples from 189 healthy controls using a newly developed automated quality control approach (scAutoQC), leading to a healthy reference atlas with approximately 1.1 million cells and 136 fine-grained cell states. We anchor 12 gastrointestinal disease datasets spanning gastrointestinal cancers, coeliac disease, ulcerative colitis and Crohn’s disease to this reference. Utilizing this 1.6 million cell resource (gutcellatlas.org), we discover epithelial cell metaplasia originating from stem cells in intestinal inflammatory diseases with transcriptional similarity to cells found in pyloric and Brunner’s glands. Although previously linked to mucosal healing⁴, we now implicate pyloric gland metaplastic cells in inflammation through recruitment of immune cells including T cells and neutrophils. Overall, we describe inflammation-induced changes in stem cells that alter mucosal tissue architecture and promote further inflammation, a concept applicable to other tissues and diseases.

胃肠道是一个多器官系统，对于有效吸收营养和屏障免疫至关重要。基因组学的进步和胃肠道疾病的激增^1,2 推动了对构成健康和疾病中胃肠道组织的细胞进行分类的努力³。在这里，我们系统整合了 25 个单细胞 RNA 测序数据集，涵盖发育中和成年期的整个健康胃肠道。我们使用新开发的自动化质量控制方法 （scAutoQC） 统一处理了来自 189 个健康对照的 385 个样品，从而产生了具有大约 110 万个细胞和 136 个细粒细胞状态的健康参考图谱。我们将涵盖胃肠道癌症、乳糜泻、溃疡性结肠炎和克罗恩病的 12 个胃肠道疾病数据集锚定在此参考中。利用这 160 万个细胞资源 （gutcellatlas.org），我们发现了肠道炎症性疾病中起源于干细胞的上皮细胞化生，与幽门和 Brunner 腺中的细胞具有转录相似性。虽然以前与粘膜愈合有关⁴，但现在我们通过募集免疫细胞（包括 T 细胞和中性粒细胞）将幽门腺化生细胞与炎症有关。总体而言，我们描述了炎症诱导的干细胞变化，这些变化会改变粘膜组织结构并促进进一步的炎症，这一概念适用于其他组织和疾病。