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利用微滴微流控培养揭示肠道细菌对膳食碳水化合物代谢的个体间差异。

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture.

作者信息

Villa Max M, Bloom Rachael J, Silverman Justin D, Durand Heather K, Jiang Sharon, Wu Anchi, Dallow Eric P, Huang Shuqiang, You Lingchong, David Lawrence A

机构信息

Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA.

Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA.

出版信息

mSystems. 2020 Jun 30;5(3):e00864-19. doi: 10.1128/mSystems.00864-19.

Abstract

Culture and screening of gut bacteria enable testing of microbial function and therapeutic potential. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput DNA sequencing to develop a platform for separating and assaying growth of microbiota members in picoliter droplets (MicDrop). MicDrop enabled us to cultivate 2.8 times more bacterial taxa than typical batch culture methods. We then used MicDrop to test whether individuals possess similar abundances of carbohydrate-degrading gut bacteria, using an approach which had previously not been possible due to throughput limitations of traditional bacterial culture techniques. Single MicDrop experiments allowed us to characterize carbohydrate utilization among dozens of gut bacterial taxa from distinct human stool samples. Our aggregate data across nine healthy stool donors revealed that all of the individuals harbored gut bacterial species capable of degrading common dietary polysaccharides. However, the levels of richness and abundance of polysaccharide-degrading species relative to monosaccharide-consuming taxa differed by up to 2.6-fold and 24.7-fold, respectively. Additionally, our unique dataset suggested that gut bacterial taxa may be broadly categorized by whether they can grow on single or multiple polysaccharides, and we found that this lifestyle trait is correlated with how broadly bacterial taxa can be found across individuals. This demonstration shows that it is feasible to measure the function of hundreds of bacterial taxa across multiple fecal samples from different people, which should in turn enable future efforts to design microbiota-directed therapies and yield new insights into microbiota ecology and evolution. Bacterial culture and assay are components of basic microbiological research, drug development, and diagnostic screening. However, community diversity can make it challenging to comprehensively perform experiments involving individual microbiota members. Here, we present a new microfluidic culture platform that makes it feasible to measure the growth and function of microbiota constituents in a single set of experiments. As a proof of concept, we demonstrate how the platform can be used to measure how hundreds of gut bacterial taxa drawn from different people metabolize dietary carbohydrates. Going forward, we expect this microfluidic technique to be adaptable to a range of other microbial assay needs.

摘要

肠道细菌的培养和筛选能够对微生物功能及治疗潜力进行测试。然而,人类肠道微生物群落(微生物群)的多样性阻碍了对单个细菌类群的全面实验研究。在此,我们结合了微滴微流控技术和高通量DNA测序的进展,开发了一个用于在皮升微滴中分离和测定微生物群成员生长情况的平台(MicDrop)。与典型的分批培养方法相比,MicDrop使我们能够培养出多2.8倍的细菌类群。然后,我们使用MicDrop来测试个体是否拥有相似丰度的可降解碳水化合物的肠道细菌,采用的方法是一种由于传统细菌培养技术的通量限制而此前无法实现的方法。单个MicDrop实验使我们能够表征来自不同人类粪便样本的数十种肠道细菌类群的碳水化合物利用情况。我们对9名健康粪便捐赠者的汇总数据显示,所有个体都含有能够降解常见膳食多糖的肠道细菌物种。然而,相对于消耗单糖的类群,多糖降解物种的丰富度和丰度水平分别相差高达2.6倍和24.7倍。此外,我们独特的数据集表明,肠道细菌类群可以根据它们是否能够在单一或多种多糖上生长进行大致分类,并且我们发现这种生活方式特征与细菌类群在个体中的分布广度相关。这一示范表明,测量来自不同人的多个粪便样本中数百种细菌类群的功能是可行的,这反过来应该能够推动未来设计针对微生物群的疗法的努力,并为微生物群生态学和进化带来新的见解。细菌培养和测定是基础微生物学研究、药物开发和诊断筛查的组成部分。然而,群落多样性可能使全面开展涉及单个微生物群成员的实验具有挑战性。在此,我们展示了一个新的微流控培养平台,该平台使在一组实验中测量微生物群成分的生长和功能成为可能。作为概念验证,我们展示了该平台如何用于测量从不同人身上获取的数百种肠道细菌类群如何代谢膳食碳水化合物。展望未来,我们预计这种微流控技术能够适应一系列其他微生物测定需求。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/363b/7329328/161e5d0bf80a/mSystems.00864-19-f0001.jpg

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