Literature DB >> 32888037

Droplet Microfluidics for Microbial Biotechnology.

Sundar Hengoju1,2, Miguel Tovar1, DeDe Kwun Wai Man1, Stefanie Buchheim1,2, Miriam A Rosenbaum3,4.   

Abstract

Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.
© 2020. Springer Nature Switzerland AG.

Entities:  

Keywords:  Antibiotic screening; Cultivation of rare microbes; Droplet microfluidics; Enzyme screening; Fluorescence-activated cell sorting; Ultrahigh-throughput microbial cultivation

Mesh:

Year:  2022        PMID: 32888037     DOI: 10.1007/10_2020_140

Source DB:  PubMed          Journal:  Adv Biochem Eng Biotechnol        ISSN: 0724-6145            Impact factor:   2.768


  105 in total

1.  Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

Authors:  Allon M Klein; Linas Mazutis; Ilke Akartuna; Naren Tallapragada; Adrian Veres; Victor Li; Leonid Peshkin; David A Weitz; Marc W Kirschner
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

2.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Authors:  Evan Z Macosko; Anindita Basu; Rahul Satija; James Nemesh; Karthik Shekhar; Melissa Goldman; Itay Tirosh; Allison R Bialas; Nolan Kamitaki; Emily M Martersteck; John J Trombetta; David A Weitz; Joshua R Sanes; Alex K Shalek; Aviv Regev; Steven A McCarroll
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

3.  Single-cell barcoding and sequencing using droplet microfluidics.

Authors:  Rapolas Zilionis; Juozas Nainys; Adrian Veres; Virginia Savova; David Zemmour; Allon M Klein; Linas Mazutis
Journal:  Nat Protoc       Date:  2016-12-08       Impact factor: 13.491

4.  Evolution of enzyme catalysts caged in biomimetic gel-shell beads.

Authors:  Martin Fischlechner; Yolanda Schaerli; Mark F Mohamed; Santosh Patil; Chris Abell; Florian Hollfelder
Journal:  Nat Chem       Date:  2014-07-20       Impact factor: 24.427

5.  Single-cell deep phenotyping of IgG-secreting cells for high-resolution immune monitoring.

Authors:  Klaus Eyer; Raphaël C L Doineau; Carlos E Castrillon; Luis Briseño-Roa; Vera Menrath; Guillaume Mottet; Patrick England; Alexei Godina; Elodie Brient-Litzler; Clément Nizak; Allan Jensen; Andrew D Griffiths; Jérôme Bibette; Pierre Bruhns; Jean Baudry
Journal:  Nat Biotechnol       Date:  2017-09-11       Impact factor: 54.908

6.  Single-cell analysis and sorting using droplet-based microfluidics.

Authors:  Linas Mazutis; John Gilbert; W Lloyd Ung; David A Weitz; Andrew D Griffiths; John A Heyman
Journal:  Nat Protoc       Date:  2013-04-04       Impact factor: 13.491

7.  Phasing of single DNA molecules by massively parallel barcoding.

Authors:  Erik Borgström; David Redin; Sverker Lundin; Emelie Berglund; Anders F Andersson; Afshin Ahmadian
Journal:  Nat Commun       Date:  2015-06-09       Impact factor: 14.919

8.  Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

Authors:  Freeman Lan; Benjamin Demaree; Noorsher Ahmed; Adam R Abate
Journal:  Nat Biotechnol       Date:  2017-05-29       Impact factor: 54.908

9.  Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.

Authors:  Grace X Y Zheng; Billy T Lau; Michael Schnall-Levin; Mirna Jarosz; John M Bell; Christopher M Hindson; Sofia Kyriazopoulou-Panagiotopoulou; Donald A Masquelier; Landon Merrill; Jessica M Terry; Patrice A Mudivarti; Paul W Wyatt; Rajiv Bharadwaj; Anthony J Makarewicz; Yuan Li; Phillip Belgrader; Andrew D Price; Adam J Lowe; Patrick Marks; Gerard M Vurens; Paul Hardenbol; Luz Montesclaros; Melissa Luo; Lawrence Greenfield; Alexander Wong; David E Birch; Steven W Short; Keith P Bjornson; Pranav Patel; Erik S Hopmans; Christina Wood; Sukhvinder Kaur; Glenn K Lockwood; David Stafford; Joshua P Delaney; Indira Wu; Heather S Ordonez; Susan M Grimes; Stephanie Greer; Josephine Y Lee; Kamila Belhocine; Kristina M Giorda; William H Heaton; Geoffrey P McDermott; Zachary W Bent; Francesca Meschi; Nikola O Kondov; Ryan Wilson; Jorge A Bernate; Shawn Gauby; Alex Kindwall; Clara Bermejo; Adrian N Fehr; Adrian Chan; Serge Saxonov; Kevin D Ness; Benjamin J Hindson; Hanlee P Ji
Journal:  Nat Biotechnol       Date:  2016-02-01       Impact factor: 54.908

10.  Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.

Authors:  Assaf Rotem; Oren Ram; Noam Shoresh; Ralph A Sperling; Alon Goren; David A Weitz; Bradley E Bernstein
Journal:  Nat Biotechnol       Date:  2015-10-12       Impact factor: 54.908

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  4 in total

Review 1.  Microfluidics for Biotechnology: Bridging Gaps to Foster Microfluidic Applications.

Authors:  Vera Ortseifen; Martina Viefhues; Lutz Wobbe; Alexander Grünberger
Journal:  Front Bioeng Biotechnol       Date:  2020-11-13

2.  Microdroplet-based system for culturing of environmental microorganisms using FNAP-sort.

Authors:  Kanako Saito; Yuri Ota; Dieter M Tourlousse; Satoko Matsukura; Hirotsugu Fujitani; Masamune Morita; Satoshi Tsuneda; Naohiro Noda
Journal:  Sci Rep       Date:  2021-05-04       Impact factor: 4.379

3.  Antimicrobial resistance: progress and challenges in antibiotic discovery and anti-infective therapy.

Authors:  Tino Krell; Miguel A Matilla
Journal:  Microb Biotechnol       Date:  2021-10-05       Impact factor: 5.813

Review 4.  Calibrating spatiotemporal models of microbial communities to microscopy data: A review.

Authors:  Aaron Yip; Julien Smith-Roberge; Sara Haghayegh Khorasani; Marc G Aucoin; Brian P Ingalls
Journal:  PLoS Comput Biol       Date:  2022-10-13       Impact factor: 4.779

  4 in total

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