Investigating host-microbiome interactions by droplet based microfluidics
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RESEARCH
Open Access
Investigating host-microbiome interactions by droplet based microfluidics Alexandra S. Tauzin1, Mariana Rangel Pereira2,3, Liisa D. Van Vliet2,4, Pierre-Yves Colin2, Elisabeth Laville1, Jeremy Esque1, Sandrine Laguerre1, Bernard Henrissat5,6,7, Nicolas Terrapon5,6, Vincent Lombard5,6, Marion Leclerc8, Joël Doré8,9, Florian Hollfelder2* and Gabrielle Potocki-Veronese1*
Abstract Background: 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. Results: 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. Conclusion: 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. Keywords: Functional metagenomics, Droplet microfluidics, Human gut microbiota, Human glycans, Beta-N-acetylgalactosaminidase
* Correspondence: [email protected]; [email protected] 2 Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK 1 TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400 Toulouse, France Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the o
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