The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown^1,2,3. Classical pathogens often invade host tissues and modulate immune responses through interactions with human extracellular and secreted proteins (the ‘exoproteome’). Commensal microorganisms may also facilitate niche colonization and shape host biology by engaging host exoproteins; however, direct exoproteome–microbiota interactions remain largely unexplored. Here we developed and validated a novel technology, BASEHIT, that enables proteome-scale assessment of human exoproteome–microbiome interactions. Using BASEHIT, we interrogated more than 1.7 million potential interactions between 519 human-associated bacterial strains from diverse phylogenies and tissues of origin and 3,324 human exoproteins. The resulting interactome revealed an extensive network of transkingdom connectivity consisting of thousands of previously undescribed host–microorganism interactions involving 383 strains and 651 host proteins. Specific binding patterns within this network implied underlying biological logic; for example, conspecific strains exhibited shared exoprotein-binding patterns, and individual tissue isolates uniquely bound tissue-specific exoproteins. Furthermore, we observed dozens of unique and often strain-specific interactions with potential roles in niche colonization, tissue remodelling and immunomodulation, and found that strains with differing host interaction profiles had divergent interactions with host cells in vitro and effects on the host immune system in vivo. Overall, these studies expose a previously unexplored landscape of molecular-level host–microbiota interactions that may underlie causal effects of indigenous microorganisms on human health and disease.

与人类密切相关的无数微生物对生理学有不同的影响，但这些影响的分子基础仍然大多未知^1,2,3。经典病原体经常侵入宿主组织并通过与人类细胞外和分泌蛋白（“外蛋白质组”）的相互作用来调节免疫反应。共生微生物还可以通过与宿主外蛋白结合来促进生态位定植并塑造宿主生物学。然而，直接的外蛋白质组-微生物群相互作用在很大程度上仍未被探索。在这里，我们开发并验证了一项新技术 BASEHIT，它能够对人类外蛋白质组-微生物组相互作用进行蛋白质组规模评估。使用 BASEHIT，我们询问了来自不同系统发育和起源组织的 519 种人类相关细菌菌株与 3,324 种人类外蛋白之间超过 170 万种潜在的相互作用。由此产生的相互作用组揭示了一个广泛的跨界连接网络，由数千个先前未描述的宿主-微生物相互作用组成，涉及 383 个菌株和 651 个宿主蛋白。该网络内的特定结合模式暗示了潜在的生物逻辑；例如，同种菌株表现出共享的外蛋白结合模式，而各个组织分离物则独特地结合组织特异性外蛋白。此外，我们观察到了数十种独特且通常是菌株特异性的相互作用，在生态位定植、组织重塑和免疫调节中具有潜在作用，并发现具有不同宿主相互作用谱的菌株在体外与宿主细胞具有不同的相互作用，并对宿主免疫系统产生不同的影响。体内。总体而言，这些研究揭示了先前未探索的分子水平宿主-微生物群相互作用的景观，这可能是本土微生物对人类健康和疾病的因果影响的基础。