One cell at a time: droplet-based microbial cultivation, screening and sequencing

Hu, Beiyu; Xu, Peng; Ma, Liang; Chen, Dongwei; Wang, Jian; Dai, Xin; Huang, Li; Du, Wei

doi:10.1007/s42995-020-00082-8

Cited by 34 publications

(26 citation statements)

References 134 publications

(186 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For each of the up-mentioned droplet manipulation methods, there are numerous technical solutions to meet the demand in different application scenarios. As those solutions have been elaborated in previously published review articles, they will not be introduced again in this review ( Kaminski et al, 2016 ; Matula et al, 2020 ; Hu et al, 2021 ).…”

Section: Key Microfluidic Technologies For the Microbiomementioning

confidence: 99%

“…The original intention of microfluidics is to rescale conventional biology and chemistry laboratories onto a square centimeter-level chip for higher throughput and lower cost. It has emerged as a fascinating technology in diverse biological research areas due to its perfect size matching effect with biological samples ( Sackmann et al, 2014 ; Scheler et al, 2019 ; Hu et al, 2021 ). In recent years, microfluidics has demonstrated great potential for revolutionizing the microbiome research, and it is believed that its universal application will promote our understanding of the microbiome ( Ballard et al, 2018 ; Zhang et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Emerging microfluidic technologies for microbiome research

Wen

et al. 2022

Front. Microbiol.

View full text Add to dashboard Cite

The importance of the microbiome is increasingly prominent. For example, the human microbiome has been proven to be strongly associated with health conditions, while the environmental microbiome is recognized to have a profound influence on agriculture and even the global climate. Furthermore, the microbiome can serve as a fascinating reservoir of genes that encode tremendously valuable compounds for industrial and medical applications. In the past decades, various technologies have been developed to better understand and exploit the microbiome. In particular, microfluidics has demonstrated its strength and prominence in the microbiome research. By taking advantage of microfluidic technologies, inherited shortcomings of traditional methods such as low throughput, labor-consuming, and high-cost are being compensated or bypassed. In this review, we will summarize a broad spectrum of microfluidic technologies that have addressed various needs in the field of microbiome research, as well as the achievements that were enabled by the microfluidics (or technological advances). Finally, how microfluidics overcomes the limitations of conventional methods by technology integration will also be discussed.

show abstract

Section: Key Microfluidic Technologies For the Microbiomementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Emerging microfluidic technologies for microbiome research

Wen

et al. 2022

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…These microsystems are not only limited to the isolation and cultivation of "unculturable" species. The advent of miniaturizing culturing techniques has been an inspiration for many applications we can now achieve with the control, precision, and resolution needed to identify targets of study (Hu et al, 2021). In biotechnology industries, drug and enzymatic metabolite screening is typically associated with low-throughput, high-cost methods (Boedicker et al, 2008).…”

Section: Applications Of Microbial-based Microsystems and Perceived Challengesmentioning

confidence: 99%

Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments

Davidson

Niepa

2022

Front. Microbiol.

View full text Add to dashboard Cite

With recent advances in microfabrication technologies, the miniaturization of traditional culturing techniques has provided ideal methods for interrogating microbial communities in a confined and finely controlled environment. Micro-technologies offer high-throughput screening and analysis, reduced experimental time and resources, and have low footprint. More importantly, they provide access to culturing microbes in situ in their natural environments and similarly, offer optical access to real-time dynamics under a microscope. Utilizing micro-technologies for the discovery, isolation and cultivation of “unculturable” species will propel many fields forward; drug discovery, point-of-care diagnostics, and fundamental studies in microbial community behaviors rely on the exploration of novel metabolic pathways. However, micro-technologies are still largely proof-of-concept, and scalability and commercialization of micro-technologies will require increased accessibility to expensive equipment and resources, as well as simpler designs for usability. Here, we discuss three different miniaturized culturing practices; including microarrays, micromachined devices, and microfluidics; advancements to the field, and perceived challenges.

show abstract

“…The extraordinary sensitivity of one nucleic acid molecule per 1 µl reaction volume 3 , combined with high specificity, accuracy and fast readout offered by RT-PCR assays have propelled a broad range of biological and diagnostic applications 2,[4][5][6][7] . However, a comprehensive characterization of heterogeneous biological samples [8][9][10] , such as tumors, microorganisms, or viruses, requires isolation of each individual member in a population so as to study it separately. As a result, numerous efforts have focused on developing single-cell RT-PCR (scRT-PCR) approaches using microtiter plates [11][12][13][14] , microfluidics [15][16][17][18][19][20][21][22][23][24][25][26][27][28] and other reaction formats [29][30][31] .…”

Section: Introductionmentioning

confidence: 99%

RNA cytometry of single-cells using semi-permeable microcapsules

Leonaviciene

Mažutis

2022

Preprint

View full text Add to dashboard Cite

Analytical tools for gene expression profiling of individual cells are critical for studying complex biological systems. However, the techniques enabling rapid measurements of gene expression on thousands of single-cells are lacking. Here, we report a high-throughput RNA cytometry for digital profiling of single-cells isolated in liquid droplets enveloped by a thin semi-permeable membrane (microcapsules). Due to selective permeability of the membrane, the desirable enzymes and reagents can be loaded, or replaced, in the microcapsule at any given step by simply changing the reaction buffer in which the microcapsules are dispersed. Therefore, complex molecular biology workflows can be readily adapted to conduct nucleic acid analysis on encapsulated mammalian cells, bacteria, or other biological species. The microcapsules support sequential multi-step enzymatic reactions, and remain intact under different biochemical conditions, freezing, thawing and thermocycling. Combining microcapsules with conventional FACS provides a high-throughput approach for conducting RNA cytometry of individual cells based on their digital gene expression signature.

show abstract

One cell at a time: droplet-based microbial cultivation, screening and sequencing

Cited by 34 publications

References 134 publications

Emerging microfluidic technologies for microbiome research

Emerging microfluidic technologies for microbiome research

Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments

RNA cytometry of single-cells using semi-permeable microcapsules

Contact Info

Product

Resources

About