Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota. Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired. By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships.

中文翻译：

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通过基于液滴的微流体研究宿主-微生物组相互作用

尽管微生物群和宿主之间的粘膜界面在肠道稳态中很重要，但人们对细菌肠道定植的机制知之甚少，其中涉及寻找上皮细胞产生的聚糖。理解潜在分子机制的进展缓慢很大程度上是由于缺乏有效的发现工具，特别是那些针对微生物群中未培养部分的工具。在这里，我们介绍了一种基于液滴微流控的超高通量宏基因组方法来筛选 fosmid 文库。1 小时内即可覆盖数千个细菌基因组，且底物不足 10 微克。该方法应用于筛选粘膜微生物群的 β-N-乙酰氨基半乳糖苷酶活性，可以鉴定参与人神经节苷脂和乳寡糖（肠道粘蛋白聚糖的结构同源物）降解的途径。这些途径的流行与炎症性肠病有关，可能是拟杆菌属水平基因转移的结果。这些途径代表了研究炎症性肠病（粘膜屏障完整性受损）背景下微生物群与宿主相互作用的新靶点。通过在微流体液滴内划分实验，与传统方法相比，该方法将筛选过程加速并小型化几个数量级，以从宏基因组库中捕获整个代谢途径。该方法与所有类型的（宏）基因组文库兼容，并采用市售流式细胞仪代替定制的分选系统来检测细胞内或细胞外酶活性。这种多功能且通用的工作流程将加速功能宏基因组学和全生物组学研究中的实验探索活动，以进一步破译宿主与微生物群的关系。