Investigating host-microbiome interactions by droplet based microfluidics

Microbiome

Nicolas Terrapon¹  Vincent Lombard¹  Bernard Henrissat²  Pierre-Yves Colin³  Florian Hollfelder³  Mariana Rangel Pereira⁴  Liisa D. Van Vliet⁵  Marion Leclerc⁶  Joël Doré⁷  Alexandra S. Tauzin⁸  Jeremy Esque⁸  Elisabeth Laville⁸  Gabrielle Potocki-Veronese⁸  Sandrine Laguerre⁸ 

[1] CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France;USC 1408 AFMB, INRAE, F-13288, Marseille, France;CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France;USC 1408 AFMB, INRAE, F-13288, Marseille, France;Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia;Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK;Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK;CAPES Foundation, Ministry of Education of Brazil, 70040-020, BrasÍlia, DF, Brazil;Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK;Drop-Tech, Canterbury Court, CB4 3QU, Cambridge, UK;Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France;Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France;Metagenopolis, INRAE, F-78350, Jouy-en-Josas, France;TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France;

关键词: Functional metagenomics;    Droplet microfluidics;    Human gut microbiota;    Human glycans;    Beta-N-acetyl-galactosaminidase;   

DOI  :  10.1186/s40168-020-00911-z

来源: Springer

【 摘 要 】

BackgroundDespite 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.ResultsHere, 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.ConclusionBy 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.D5FCwMfgm6tWFFUGEYz5eaVideo Abstract

【 授权许可】

CC BY