Table_1_Host Preference of Beneficial Commensals in a Microbially-Diverse Environment.xlsx

Gut bacteria are often described by the neutral term commensals. However, the more we learn about their interactions with hosts, the more apparent it becomes that gut commensals often contribute positively to host physiology and fitness. Whether hosts can prefer beneficial bacteria, and how they do so, is not clear. This is of particular interest in the case of the bacterivore C. elegans, which depends on bacteria as food source, but also as gut colonizers that contribute to its physiology, from development to immunity. It is further unclear to what extent worms living in their microbially-diverse habitats can sense and distinguish between beneficial bacteria, food, and pathogens. Focusing on Enterobacteriaceae and members of closely related families, we isolated gut bacteria from worms raised in compost microcosms, as well as bacteria from the respective environments and evaluated their contributions to host development. Most isolates, from worms or from the surrounding environment, promoted faster development compared to the non-colonizing E. coli food strain. Pantoea strains further showed differential contributions of gut isolates versus an environmental isolate. Characterizing bacterial ability to hinder pathogenic colonization with Pseudomonas aeruginosa, supported the trend of Pantoea gut commensals being beneficial, in contrast to the environmental strain. Interestingly, worms were attracted to the beneficial Pantoea strains, preferring them over non-beneficial bacteria, including the environmental Pantoea strain. While our understanding of the mechanisms underlying these host-microbe interactions are still rudimentary, the results suggest that hosts can sense and prefer beneficial commensals.

肠道细菌通常以中性术语“共生菌（commensals）”进行指代。然而，随着对其与宿主互作机制研究的不断深入，肠道共生菌对宿主生理与适合度产生积极贡献的结论愈发清晰。宿主是否能够偏好有益菌，以及其偏好的具体机制，目前仍不明确。这一点在食细菌性生物秀丽隐杆线虫（C. elegans）身上尤为值得关注：这类线虫既以细菌为食物来源，同时也依赖肠道定殖的细菌调控自身从发育到免疫的各项生理过程。此外，在微生物多样性丰富的自然栖息地中生存的线虫，能在多大程度上感知并区分有益菌、食物菌与病原菌，这一问题同样尚未厘清。本研究聚焦肠杆菌科（Enterobacteriaceae）及其近缘类群成员，从堆肥微宇宙培养的线虫体内分离得到肠道细菌，同时采集对应环境中的细菌样本，并评估这些细菌对宿主发育的影响。相较于无法定殖肠道的大肠杆菌（E. coli）食物菌株，绝大多数从线虫体内或周边环境分离得到的菌株均能加速宿主发育。泛菌属（Pantoea）菌株则进一步体现出：肠道分离株与环境分离株对宿主的调控作用存在显著差异。通过表征细菌阻碍铜绿假单胞菌（Pseudomonas aeruginosa）定殖的能力，我们验证了泛菌属肠道共生菌具有益生性的结论，而环境来源的泛菌菌株则无此效果。值得注意的是，线虫会被有益的泛菌菌株吸引，相较于包括环境来源泛菌菌株在内的非有益菌株，它们更偏好此类有益菌。尽管我们对这类宿主-微生物互作背后的分子机制仍知之甚少，但研究结果表明，宿主能够感知并偏好有益共生菌。