Sallet Hugo, Calvo Marion, Titus Matteo, Jacquemin Nicolas, Meibom Karin Lederballe, Bernier-Latmani Rizlan
Ecole Polytechnique Federale de Lausanne (EPFL), Environmental Microbiology Laboratory, CH-1015 Lausanne.
ISME Commun. 2025 Jul 13;5(1):ycaf117. doi: 10.1093/ismeco/ycaf117. eCollection 2025 Jan.
Over the past two decades, metagenomics has greatly expanded our understanding of microbial phylogenetic and metabolic diversity. However, most microbial taxa remain uncultured, hindering research and biotechnological applications. Isolating environmental anaerobes using traditional methods is particularly cumbersome and low throughput. Here, we present a novel, high-throughput approach for the cultivation and isolation of anaerobes, which involves trapping and growing single microbes within selectively permeable hydrogel capsules followed by fluorescence-activated cell sorting to distribute compartmentalized isolates into liquid medium for further growth. We show that diverse anaerobes can grow within capsules and that slower-growing ones (e.g. methanogens) can be enriched with this platform. We also applied this approach to isolate anaerobes from soil, including strains of the sulfate-reducing bacteria and . Overall, this work introduces a robust, high-throughput alternative to traditional techniques for isolating environmental anaerobes and expands the emerging set of microfluidics-based tools for the cultivation of novel taxa.
在过去二十年中，宏基因组学极大地拓展了我们对微生物系统发育和代谢多样性的理解。然而，大多数微生物类群仍未得到培养，这阻碍了相关研究和生物技术应用。使用传统方法分离环境厌氧菌特别繁琐且通量低。在此，我们提出一种用于培养和分离厌氧菌的新型高通量方法，该方法包括将单个微生物捕获并培养在选择性渗透水凝胶胶囊中，随后通过荧光激活细胞分选将分隔的分离物分配到液体培养基中以进一步生长。我们表明，多种厌氧菌能够在胶囊内生长，并且生长较慢的菌（如产甲烷菌）可以通过该平台得到富集。我们还应用此方法从土壤中分离厌氧菌，包括硫酸盐还原菌菌株。总体而言，这项工作为分离环境厌氧菌的传统技术引入了一种强大的高通量替代方法，并扩展了基于微流控技术用于培养新型类群的新兴工具集。
