Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
Nat Commun. 2023 Aug 8;14(1):4780. doi: 10.1038/s41467-023-40372-0.
A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.
理解与健康和疾病相关的微生物组特征是一项具有挑战性的任务，需要超越描述性的群落水平分析，深入研究微生物相互作用网络。本研究使用合成肠道细菌群落，旨在研究单个成员在群落组装中的作用，确定潜在的关键物种，并在不同环境中测试它们的影响。单种缺失实验表明，细菌菌株关系不仅在鼠肠道的不同区域，而且在几种标准培养基中都有很大差异。体外环境依赖性关键功能涉及的机制包括对多糖的专性获取以及细菌素的产生。此外，通过影响群落组成、代谢景观和炎症反应，拟杆菌 caecimuris 和 Blautia coccoides 在无菌小鼠中发挥关键作用。总之，本研究强调了细菌群落生态学与生物和非生物环境之间的强烈相互依存关系。这些结果对胃肠道生态系统中普遍存在的关键物种概念提出了质疑，并强调了关键功能和细菌相互作用网络的上下文相关性。
