沈锡辉、张磊等《Microbiome》2022年

论文题目：Exploring AI-2-mediated interspecies communications within rumen microbial communities

论文作者：Xiaozhen Liu, Qinmeng Liu, Sihuai Sun, Hengxi Sun, Yao Wang, Xihui Shen, Lei Zhang

论文摘要：Background:The rumen is an ecosystem with a complex microbial microflora in which microbes initiate biofilm formation by attaching to plant surfaces for plant degradation and are capable of converting feed to nutrients and energy via microbial processes. Quorum sensing (QS) is a cell-to-cell communication mechanism that allows microbes to synchronize the expression of multiple genes in the group to perform social behaviors such as chemotaxis and biofilm formation using self-synthesized QS signaling molecules. Whereas QS has been extensively studied in model microorganisms under pure culture conditions, QS mechanisms are poorly understood in complex bacterial communities, such as the rumen microflora, in which cell-to-cell communication may be common.

Results: Here, we analyzed 981 rumens bacterial and archaeal genomes from the Joint Genome Institute (JGI) and GenBank databases and identified 15 types of known QS signaling molecule-related genes. The analysis of the prevalence and abundance of genes involved in QS showed that 767 microbial genomes appeared to possess QS-related genes, including 680 bacterial genomes containing autoinducer-2 (AI-2) synthase- or receptor-encoding genes.Prevotella,Butyivibrio,Ruminococcus,Oribacterium,Selenomonas, andTreponema, known abundant bacterial genera in the rumen, possessed the greatest numbers of AI-2-related genes; these genes were highly expressed within the metatranscriptome dataset, suggesting that intra- and interspecies communication mediated by AI-2 among rumen microbes was universal in the rumen. The QS processes mediated by the dCache_1-containing AI-2 receptors (CahRs) with various functional modules may be essential for degrading plants, digesting food, and providing energy and nutrients to the host. Additionally, a universal natural network based on QS revealed how rumen microbes coordinate social behaviors via the AI-2-mediated QS system, most of which may potentially function via AI-2 binding to the extracellular sensor dCache_1 domain to activate corresponding receptors involved in different signal transduction pathways, such as methyl-accepting chemotaxis proteins, histidine kinases, serine phosphatases, c-di-GMP synthases and phosphodiesterases, and serine/threonine kinases in the rumen.

Conclusions: The exploration of AI-2-related genes, especially CahR-type AI-2 receptors, greatly increased our insight into AI-2 as a potentially “universal” signal mediating social behaviors and will help us better understand microbial communication networks and the function of QS in plant-microbe interactions in complex microecosystems.

反刍动物的瘤胃是一个天然发酵体系，依赖其中存在的大量不同种类的厌氧微生物联合作用对木质纤维素进行降解和利用。目前对瘤胃微生物菌群的种间交流及协同作用机制知之甚少。群体感应(QS)是细菌种内和种间细胞间交流的普遍机制，通过感知菌群密度变化协调细菌的群体行为。本研究对数据库中已有的瘤胃细菌完整基因组信息进行分析，发现QS合成酶基因存在于绝大多数瘤胃细菌中，尤其是介导细菌种间交流的通用QS分子AI-2的合成酶基因存在于一半以上瘤胃细菌中，而AI-2受体编码基因存在于超过1/3以上瘤胃细菌中，且尚有大量潜在AI-2受体编码基因有待进一步发掘。宏转录组分析发现瘤胃优势菌群中AI-2合成酶和受体基因均能高水平表达，表明AI-2介导的种间交流在瘤胃微生态系统中广泛发生。挖掘的AI-2受体类型包括甲基化趋化受体、组氨酸激酶、c-di-GMP合成与水解酶、丝氨酸磷酸酶、丝氨酸/苏氨酸蛋白激酶等跨膜信号转导蛋白，表明AI-2信号可以调控瘤胃菌群的各种重要生理功能和群体行为。基于以上发现，我们进一步构建了AI-2介导的瘤胃微生物种间交流网络。本研究极大促进了对瘤胃微生态系统微生物种间交流机制的认识，也为研究其他生境微生物群落成员之间的交流与协作机制提供重要参考。

文章链接：https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01367-z