University of Chinese Academy of Sciences, Beijing, 100049, China.
Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
Microbiome. 2024 May 24;12(1):96. doi: 10.1186/s40168-024-01809-w.
The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates.
To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range.
As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.
真核-细菌共生系统在各种生理、发育和进化过程中起着重要作用。然而，我们目前的理解在很大程度上仅限于多细胞真核生物，而没有充分考虑到包括纤毛虫在内的各种单细胞原生生物。
为了研究与单细胞生物相关的细菌特征，我们收集了涵盖整个纤毛门的 246 个纤毛虫样本，并进行了基于单细胞的宏基因组测序。这一努力获得了迄今为止与单细胞原生生物相关的最广泛的细菌集合。从这个数据集，我们确定了 883 种能够与纤毛虫共存的细菌，揭示了 116 种新型细菌共生体以及 7 种新型古菌共生体的基因组。突出纤毛虫与其共生体之间的密切关系，我们的研究表明，超过 90%的纤毛虫与细菌共存，单个宿主同时与多种细菌共生，导致观察到七种不同的细菌共生模式。我们对共生机制的探索揭示了宿主消化对共生体细胞内多样性的影响。此外，我们还发现细菌中存在真核样蛋白是其抵抗宿主消化的潜在因素，从而扩大了它们的潜在宿主范围。
作为首次对纤毛虫原生生物与细菌共生关系的大规模分析，本研究为未来真核-细菌共生研究提供了有价值的资源。视频摘要。
