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液滴微流控技术在微生物研究中的应用

李政毅,  彭显

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李政毅, 彭显. 液滴微流控技术在微生物研究中的应用[J]. 四川大学学报（医学版）, 2023, 54(3): 673-678. doi: 10.12182/20230560303
引用本文: 李政毅, 彭显. 液滴微流控技术在微生物研究中的应用[J]. 四川大学学报（医学版）, 2023, 54(3): 673-678. doi: 10.12182/20230560303
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LI Zheng-yi, PENG Xian. Application of Droplet-Based Microfluidics in Microbial Research[J]. JOURNAL OF SICHUAN UNIVERSITY (MEDICAL SCIENCES), 2023, 54(3): 673-678. doi: 10.12182/20230560303
Citation: LI Zheng-yi, PENG Xian. Application of Droplet-Based Microfluidics in Microbial Research[J]. JOURNAL OF SICHUAN UNIVERSITY (MEDICAL SCIENCES), 2023, 54(3): 673-678. doi: 10.12182/20230560303
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液滴微流控技术在微生物研究中的应用

doi: 10.12182/20230560303

  • 口腔疾病研究国家重点实验室 四川大学华西口腔医院 （成都 610041）

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    通讯作者:

    E-mail：pengx@scu.edu.cn

Application of Droplet-Based Microfluidics in Microbial Research

  • State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China

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    摘要
  • 摘要: 液滴微流控技术是在精确的控制下在微小通道中产生和操控高度均一的纳升至皮升级液滴的技术。在生物学研究方面，可以用单个液滴封装一小群甚至单个细胞，并作为单独的生化反应容器，适用于高通量与高分辨率的生化分析。在微生物研究领域，从培养和鉴定微生物到研究微生物群落的时空动态；从对微生物的精准定量到系统性地研究微生物相互作用；从分离稀有和不可培养的微生物到开发工程菌株，液滴微流控技术都在其中起到了重要的推动作用，有望成为微生物学研究中探索微生物单细胞水平的基本工具。本文简要介绍了液滴微流控的技术基础并对其在微生物研究中的最新应用进行了介绍和讨论，旨在为微生物领域的相关研究起到参考意义。
    Abstract: Droplet-based microfluidics is a technology that generates and manipulates highly uniform droplets, ranging from picoliter to nanoliter droplets, in microchannels under precise control. In biological research, each droplet can be used to encapsulate a small group of cells or even a single cell, and then serve as an individual container for biochemical reaction, which is well suited for high-throughput and high-resolution biochemical analysis. In the field of microbial research, from cultivation and identification of microbes to the investigation of the spatiotemporal dynamics of microbial communities, from precise quantitation of microbiota to systematic study of microbial interactions, and from the isolation of rare and unculturable microbes to the development of genetically engineered strains, droplet microfluidic technology has played an important promotional role in all these aspects. Droplet microfluidics shows potential for becoming a basic tool for exploring single-cell microbes in microbiological research. In this review, we gave a brief overview of the technical basis of droplet microfluidics. Then, we presented its latest applications in microbial research and had some discussions, aiming to provide a reference for relevant research on microorganisms.
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    • 参考文献(66)
  • [1] LOK C. Mining the microbial dark matter. Nature,2015,522(7556): 270–273. doi: 10.1038/522270a
    [2] WHITESIDES G M. The origins and the future of microfluidics. Nature,2006,442(7101): 368–373. doi: 10.1038/nature05058
    [3] HUYS G R B, RAES J. Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes. Curr Opin Microbiol,2018,44: 1–8. doi: 10.1016/j.mib.2018.05.002
    [4] CARNES E C, LOPEZ D M, DONEGAN N P, et al. Confinement-induced quorum sensing of individual Staphylococcus aureus bacteria. Nat Chem Biol,2010,6(1): 41–45. doi: 10.1038/nchembio.264
    [5] HENGOJU S, TOVAR M, MAN D K W, et al. Droplet microfluidics for microbial biotechnology. Adv Biochem Eng Biotechnol,2020,179: 129–157. doi: 10.1007/10_2020_140
    [6] BOWMAN E K, ALPER H S. Microdroplet-assisted screening of biomolecule production for metabolic engineering applications. Trends Biotechnol,2020,38(7): 701–714. doi: 10.1016/j.tibtech.2019.11.002
    [7] SOHRABI S, MORAVEJI M K. Droplet microfluidics: fundamentals and its advanced applications. RSC Adv,2020,10(46): 27560–27574. doi: 10.1039/d0ra04566g
    [8] JIAN X, GUO X, WANG J, et al. Microbial microdroplet culture system (MMC): an integrated platform for automated, high-throughput microbial cultivation and adaptive evolution. Biotechnol Bioeng,2020,117(6): 1724–1737. doi: 10.1002/bit.27327
    [9] LAN F, DEMAREE B, AHMED N, et al. Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat Biotechnol,2017,35(7): 640–646. doi: 10.1038/nbt.3880
    [10] CHURSKI K, KAMINSKI T S, JAKIELA S, et al. Rapid screening of antibiotic toxicity in an automated microdroplet system. Lab Chip,2012,12(9): 1629–1637. doi: 10.1039/c2lc21284f
    [11] SHANG L, CHENG Y, ZHAO Y. Emerging droplet microfluidics. Chem Rev,2017,117(12): 7964–8040. doi: 10.1021/acs.chemrev.6b00848
    [12] XI H D, ZHENG H, GUO W, et al. Active droplet sorting in microfluidics: a review. Lab Chip,2017,17(5): 751–771. doi: 10.1039/c6lc01435f
    [13] KAMINSKI T S, SCHELER O, GARSTECKI P. Droplet microfluidics for microbiology: techniques, applications and challenges. Lab Chip,2016,16(12): 2168–2187. doi: 10.1039/c6lc00367b
    [14] ZHENG W, ZHAO S, YIN Y, et al. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science,2022,376(6597): eabm1483. doi: 10.1126/science.abm1483
    [15] MARTIN K, HENKEL T, BAIER V, et al. Generation of larger numbers of separated microbial populations by cultivation in segmented-flow microdevices. Lab Chip,2003,3(3): 202–207. doi: 10.1039/b301258c
    [16] BOEDICKER J, VINCENT M, ISMAGILOV R. Supporting information for mMicrofluidic confinement of single cells of bacteria in small volumes initiates high-density behavior of quorum sensing and growth and reveals its variability. Angew Chem Int Ed Engl,2009,48(32): 5908–5911. doi: 10.1002/anie.200901550
    [17] LIU H, XU X, PENG K, et al. Microdroplet enabled cultivation of single yeast cells correlates with bulk growth and reveals subpopulation phenomena. Biotechnol Bioeng,2021,118(2): 647–658. doi: 10.1002/bit.27591
    [18] WU H, CHEN X, GAO X, et al. High-throughput generation of durable droplet arrays for single-cell encapsulation, culture, and monitoring. Anal Chem,2018,90(7): 4303–4309. doi: 10.1021/acs.analchem.8b00048
    [19] VILLA M M, BLOOM R J, SILVERMAN J D, et al. Interindividual variation in dietary carbohydrate metabolism by gut bacteria revealed with droplet microfluidic culture. mSystems,2020,5(3): e00864–19. doi: 10.1128/mSystems
    [20] JIANG C Y, DONG L, ZHAO J K, et al. High-throughput single-cell cultivation on microfluidic streak plates. Appl Environ Microbiol,2016,82(7): 2210–2218. doi: 10.1128/AEM
    [21] ZHOU N, SUN Y T, CHEN D W, et al. Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis. Microbiol Open,2019,8(3): e00654. doi: 10.1002/mbo3.654
    [22] CHEN D, LIU S J, DU W. Chemotactic screening of imidazolinone-degrading bacteria by microfluidic SlipChip. J Hazard Mater,2019,366: 512–519. doi: 10.1016/j.jhazmat
    [23] HU B, XU B, YUN J, et al. High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the Southwest Indian Ridge. Lab Chip,2020,20(2): 363–372. doi: 10.1039/c9lc00761j
    [24] HE Z, WU H, YAN X, et al. Recent advances in droplet microfluidics for microbiology. Chinese Chem Lett,2022,33(4): 1729–1742. doi: 10.1016/j.cclet.2021.08.059
    [25] LIU W, KIM H J, LUCCHETTA E M, et al. Isolation, incubation, and parallel functional testing and identification by FISH of rare microbial single-copy cells from multi-species mixtures using the combination of chemistrode and stochastic confinement. Lab Chip,2009,9(15): 2153–2162. doi: 10.1039/b904958d
    [26] HSIEH K, ZEC H C, CHEN L, et al. Simple and precise counting of viable bacteria by resazurin-amplified picoarray detection. Anal Chem,2018,90(15): 9449–9456. doi: 10.1021/acs.analchem.8b02096
    [27] HE Y, WANG X, MA B, et al. Ramanome technology platform for label-free screening and sorting of microbial cell factories at single-cell resolution. Biotechnol Adv,2019,37(6): 107388. doi: 10.1016/j.biotechadv.2019.04.010
    [28] XU T, GONG Y, SU X, et al. Phenome–genome profiling of single bacterial cell by Raman-activated gravity-driven encapsulation and sequencing. Small,2020,16(30): 2001172. doi: 10.1002/smll.202001172
    [29] WANG X, XIN Y, REN L, et al. Positive dielectrophoresis-based Raman-activated droplet sorting for culture-free and label-free screening of enzyme function in vivo. Sci Adv,2020,6(32): eabb3521. doi: 10.1126/sciadv.abb3521
    [30] OU Y, CAO S, ZHANG J, et al. Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology. Trends Analyt Chem,2021,143: 116333. doi: 10.1016/j.trac.2021.116333
    [31] BARLOW J T, BOGATYREV S R, ISMAGILOV R F. A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities. Nat Commun,2020,11(1): 1–13. doi: 10.1038/s41467-020-16224-6
    [32] MANZARI C, ORANGER A, FOSSO B, et al. Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels. Microb Genom,2020,6(10): mgen000417. doi: 10.1099/mgen.0.000417
    [33] DONG G, MENG F, ZHANG Y, et al. Development and evaluation of a droplet digital PCR assay for the detection of fowl adenovirus serotypes 4 and 10 in attenuated vaccines. J Virol Methods,2019,265: 59–65. doi: 10.1016/j.jviromet.2018.09.005
    [34] XU L, QU H, ALONSO D G, et al. Portable integrated digital PCR system for the point-of-care quantification of BK virus from urine samples. Biosens Bioelectron,2021,175: 112908. doi: 10.1016/j.bios.2020.112908
    [35] JIANG Y, MANZ A, WU W. Fully automatic integrated continuous-flow digital PCR device for absolute DNA quantification. Anal Chim Acta,2020,1125: 50–56. doi: 10.1016/j.aca.2020.05.044
    [36] YU Z, LYU W, YU M, et al. Self-partitioning SlipChip for slip-induced droplet formation and human papillomavirus viral load quantification with digital LAMP. Biosens Bioelectron,2020,155: 112107. doi: 10.1016/j.bios.2020.112107
    [37] YU F, YAN L, WANG N, et al. Quantitative detection and viral load analysis of SARS-CoV-2 in infected patients. Clin Infect Dis,2020,71(15): 793–798. doi: 10.1093/cid/ciaa345
    [38] CHEN L, YADAV V, ZHANG C, et al. Elliptical pipette generated large microdroplets for POC visual ddPCR quantification of low viral load. Anal Chem,2021,93(16): 6456–6462. doi: 10.1021/acs.analchem.1c00192
    [39] SHETH R U, LI M, JIANG W, et al. Spatial metagenomic characterization of microbial biogeography in the gut. Nat Biotechnol,2019,37(8): 877–883. doi: 10.1038/s41587-019-0183-2
    [40] SHI X, SHAO C, LUO C, et al. Microfluidics-based enrichment and whole-genome amplification enable strain-level resolution for airway metagenomics. mSystems,2019,4(4): e00198-19. doi: 10.1128/mSystems.00198-19
    [41] PARK J, KERNER A, BURNS M A, et al. Microdroplet-enabled highly parallel co-cultivation of microbial communities. PLoS One,2011,6(2): e17019. doi: 10.1371/journal.pone.0017019
    [42] TAN J Y, WANG S, DICK G J, et al. Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’. Integr Biol,2020,12(11): 263–274. doi: 10.1093/intbio/zyaa021
    [43] JAROSZ D F, BROWN J C, WALKER G A, et al. Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformation of metabolism. Cell,2014,158(5): 1083–1093. doi: 10.1016/j.cell.2014.07.025
    [44] LAM T, MAIENSCHEIN-CLINE M, EDDINGTON D T, et al. Multiplex gene transfer by genetic transformation between isolated S. pneumoniae cells confined in microfluidic droplets. Integr Biol,2020,11(12): 415–424. doi: 10.1093/intbio/zyz036
    [45] LAM T, BRENNAN M D, MORRISON D A, et al. Femtoliter droplet confinement of Streptococcus pneumoniae: bacterial genetic transformation by cell-cell interaction in droplets. Lab Chip,2019,19(4): 682–692. doi: 10.1039/c8lc01367e
    [46] HSU R H, CLARK R L, TAN J W, et al. Microbial interaction network inference in microfluidic droplets. Cell Syst,2019,9(3): 229–42.e4. doi: 10.1016/j.cels.2019.06.008
    [47] SALESKI T E, KERNER A R, CHUNG M T, et al. Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries. Metab Eng,2019,54: 232–243. doi: 10.1016/j.ymben.2019.04.007
    [48] TEREKHOV S S, SMIRNOV I V, MALAKHOVA M V, et al. Ultrahigh-throughput functional profiling of microbiota communities. Proc Natl Acad Sci U S A,2018,115(38): 9551–9556. doi: 10.1073/pnas.1811250115
    [49] ZHANG K, QIN S, WU S, et al. Microfluidic systems for rapid antibiotic susceptibility tests (ASTs) at the single-cell level. Chem Sci,2020,11(25): 6352–6361. doi: 10.1039/d0sc01353f
    [50] HASSAN S U, ZHANG X. Microfluidics as an emerging platform for tackling antimicrobial resistance (AMR): a review. Curr Anal Chem,2020,16(1): 41–51. doi: 10.2174/1573411015666181224145845
    [51] BOEDICKER J Q, LI L, KLINE T R, et al. Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics. Lab Chip,2008,8(8): 1265–1272. doi: 10.1039/b804911d
    [52] KAUSHIK A M, HSIEH K, CHEN L, et al. Accelerating bacterial growth detection and antimicrobial susceptibility assessment in integrated picoliter droplet platform. Biosens Bioelectron,2017,97: 260–266. doi: 10.1016/j.bios.2017.06.006
    [53] POSTEK W, GARGULINSKI P, SCHELER O, et al. Microfluidic screening of antibiotic susceptibility at a single-cell level shows the inoculum effect of cefotaxime on E. coli. Lab Chip,2018,18(23): 3668–3677. doi: 10.1039/c8lc00916c
    [54] KANG W, SARKAR S, LIN Z S, et al. Ultrafast parallelized microfluidic platform for antimicrobial susceptibility testing of Gram positive and negative bacteria. Anal Chem,2019,91(9): 6242–6249. doi: 10.1021/acs.analchem.9b00939
    [55] MASHAGHI S, Van OIJEN A M. Droplet microfluidics for kinetic studies of viral fusion. Biomicrofluidics,2016,10(2): 024102. doi: 10.1063/1.4943126
    [56] YUCHA R W, HOBBS K S, HANHAUSER E, et al. High-throughput characterization of HIV-1 reservoir reactivation using a single-cell-in-droplet PCR assay. eBioMedicine,2017,20: 217–229. doi: 10.1016/j.ebiom.2017.05.006
    [57] HERNANDEZ-VALDES J A, AAN De STEGGE M, HERMANS J, et al. Enhancement of amino acid production and secretion by Lactococcus lactis using a droplet-based biosensing and selection system. Metab Eng Commun,2020,11: e00133. doi: 10.1016/j.mec.2020.e00133
    [58] MAHLER L, NIEHS S P, MARTIN K, et al. Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities. eLife,2021,10: e64774. doi: 10.7554/eLife.64774
    [59] GUO L, ZENG W, XU S, et al. Fluorescence-activated droplet sorting for enhanced pyruvic acid accumulation by Candida glabrata. Bioresour Technol,2020,318: 124258. doi: 10.1016/j.biortech.2020.124258
    [60] SCHIRMER M, WINK K, OHLA S, et al. Conversion efficiencies of a few living microbial cells detected at a high throughput by droplet-based ESI-MS. Anal Chem,2020,92(15): 10700–10708. doi: 10.1021/acs.analchem.0c01839
    [61] MA F, GUO T, ZHANG Y, et al. An ultrahigh-throughput screening platform based on flow cytometric droplet sorting for mining novel enzymes from metagenomic libraries. Environ Microbiol,2021,23(2): 996–1008. doi: 10.1111/1462-2920.15257
    [62] TAUZIN A S, PEREIRA M R, Van VLIET L D, et al. Investigating host-microbiome interactions by droplet based microfluidics. Microbiome,2020,8(1): 1–20. doi: 10.1186/s40168-020-00911-z
    [63] XU P, MODAVI C, DEMAREE B, et al. Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery. Nucleic Acids Res,2020,48(8): e48. doi: 10.1093/nar/gkaa131
    [64] NING R, FAN J, KONG L, et al. Recent developments of droplets-based microfluidics for bacterial analysis. Chinese Chem Lett,2022,33(5): 2243–2252. doi: 10.1016/j.cclet.2021.08.096
    [65] VALLEJO D, NIKOOMANZAR A, PAEGEL B M, et al. Fluorescence-activated droplet sorting for single-cell directed evolution. ACS Synth Biol,2019,8(6): 1430–1440. doi: 10.1021/acssynbio.9b00103
    [66] ZUREK P J, HOURS R, SCHELL U, et al. Growth amplification in ultrahigh-throughput microdroplet screening increases sensitivity of clonal enzyme assays and minimizes phenotypic variation. Lab Chip,2021,21(1): 163–173. doi: 10.1039/d0lc00830c
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出版历程
  • 收稿日期:  2022-06-16
  • 修回日期:  2023-04-23
  • 网络出版日期:  2023-05-20
  • 刊出日期:  2023-05-20

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