DataSheet_1_A droplet-based microfluidic approach to isolating functional bacteria from gut microbiota.docx

Metabolic interactions within gut microbiota play a vital role in human health and disease. Targeting metabolically interacting bacteria could provide effective treatments; however, obtaining functional bacteria remains a significant challenge due to the complexity of gut microbiota. Here, we developed a facile droplet-based approach to isolate and enrich functional gut bacteria that could utilize metabolites from an engineered butyrate-producing bacteria (EBPB) of anti-obesity potential. This involves the high throughput formation of single-bacteria droplets, followed by culturing “droplets” on agar plates to form discrete single-cell colonies. This approach eliminates the need for sophisticated s instruments to sort droplets and thus allows the operation hosted in a traditional anaerobic chamber. In comparison to the traditional culture, the droplet-based approach obtained a community of substantially higher diversity and evenness. Using the conditioned plates containing metabolites from the EBPB supernatant, we obtained gut bacteria closely associated or interacting with the EBPB. These include anaerobic Lactobacillus and Bifidobacterium, which are often used as probiotics. The study illustrates the potential of our approach in the search for the associated bacteria within the gut microbiota and retrieving those yet-to-be cultured.

肠道菌群内的代谢互作在人类健康与疾病进程中发挥关键作用。靶向代谢互作细菌或可提供有效的干预手段，但由于肠道菌群结构复杂，获取功能性菌株仍是一项重大挑战。本研究开发了一种简便的基于微滴的方法，用于分离并富集可利用具有抗肥胖潜力的工程化产丁酸菌（EBPB）代谢产物的功能性肠道菌株。该方法先通过高通量流程制备单菌微滴，随后将微滴接种于琼脂平板上培养，形成独立的单细胞菌落。该方法无需使用复杂仪器进行微滴分选，可依托传统厌氧培养箱完成全部操作。与传统培养方法相比，基于微滴的方法获得的菌群群落具有显著更高的多样性与均匀度。通过使用含有EBPB上清液代谢产物的条件平板，我们成功分离得到与EBPB密切关联或存在代谢互作的肠道菌株，其中包括常用作益生菌的厌氧乳杆菌属与双歧杆菌属菌株。本研究证实了该方法在肠道菌群关联菌株筛选及未培养菌株复苏领域的应用潜力。