An automated Raman-based platform for the sorting of live cells by functional properties

被引：204

作者：

Lee, Kang Soo ^{[1
,2
]}

Palatinszky, Marton ^{[3
]}

Pereira, Fatima C. ^{[3
]}

Nguyen, Jen ^{[1
,2
]}

Fernandez, Vicente, I ^{[1
,2
]}

Mueller, Anna J. ^{[3
]}

Menolascina, Filippo ^{[4
]}

Daims, Holger ^{[3
,5
]}

Berry, David ^{[3
]}

Wagner, Michael ^{[3
,5
]}

Stocker, Roman ^{[1
,2
]}

机构：

[1] MIT, Dept Civil & Environm Engn, Ralph M Parsons Lab Environm Sci & Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[2] Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland

[3] Univ Vienna, Ctr Microbiol & Environm Syst Sci, Div Microbial Ecol, Vienna, Austria

[4] Univ Edinburgh, Sch Engn, Inst Bioengn, Edinburgh, Midlothian, Scotland

[5] Univ Vienna, Comammox Res Platform, Vienna, Austria

来源：

NATURE MICROBIOLOGY | 2019年 / 4卷 / 06期

基金：

欧洲研究理事会; 英国工程与自然科学研究理事会; 奥地利科学基金会; 欧盟地平线“2020”;

关键词：

IN-SITU HYBRIDIZATION; SINGLE; BACTERIA; MICROBIOTA; SPECTROSCOPY; GENOMICS; PARTICLE; REVEALS; SPECTRA; FORCES;

D O I：

10.1038/s41564-019-0394-9

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 +/- 1.7%), throughput (200-500 cells h(-1); 3.3-8.3 cells min(-1)) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.

引用

页码：1035 / 1048

页数：14

共 91 条

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