Flörl Lena, Meyer Annina, Bokulich Nicholas A
Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
Appl Environ Microbiol. 2025 May 21;91(5):e0052425. doi: 10.1128/aem.00524-25. Epub 2025 Apr 30.
Within-species diversity of microorganisms in food systems significantly shapes community function. While next-generation sequencing (NGS) methods have advanced our understanding of microbiomes at the community level, it is essential to recognize the importance of within-species variation for understanding and predicting the functional activities of these communities. This review highlights the substantial variation observed among microbial species in food systems and its implications for their functionality. We discuss a selection of key species in fermented foods and food systems, highlighting examples of strain-level variation and its influence on quality and safety. We present a comprehensive roadmap of methodologies aimed at uncovering this often overlooked underlying diversity. Technologies like long-read marker-gene or shotgun metagenome sequencing offer enhanced resolution of microbial communities and insights into the functional potential of individual strains and should be integrated with techniques such as metabolomics, metatranscriptomics, and metaproteomics to link strain-level microbial community structure to functional activities. Furthermore, the interactions between viruses and microbes that contribute to strain diversity and community stability are also critical to consider. This article highlights existing research and emphasizes the importance of incorporating within-species diversity in microbial community studies to harness their full potential, advance fundamental science, and foster innovation.
食品系统中微生物的种内多样性显著影响群落功能。虽然下一代测序（NGS）方法增进了我们对群落水平微生物组的理解，但认识到种内变异对于理解和预测这些群落的功能活动的重要性至关重要。本综述强调了在食品系统中观察到的微生物物种间的显著变异及其对功能的影响。我们讨论了发酵食品和食品系统中的一些关键物种，突出了菌株水平变异的例子及其对质量和安全的影响。我们提出了一个全面的方法路线图，旨在揭示这种常常被忽视的潜在多样性。长读长标记基因或鸟枪法宏基因组测序等技术能够提高微生物群落的分辨率，并深入了解单个菌株的功能潜力，应与代谢组学、宏转录组学和宏蛋白质组学等技术相结合，将菌株水平的微生物群落结构与功能活动联系起来。此外，病毒与微生物之间有助于菌株多样性和群落稳定性的相互作用也是需要考虑的关键因素。本文重点介绍了现有研究，并强调了在微生物群落研究中纳入种内多样性以充分发挥其潜力、推动基础科学发展和促进创新的重要性。
