Recent advances in microfluidic devices for single-cell cultivation: methods and applications

Dian Anggraini, Nobutoshi Ota, Yigang Shen, Tao Tang, Yo Tanaka, Yoichiroh Hosokawa, Ming Li and Yaxiaer Yalikun

Lab Chip, 2022, 22, 1438
DOI: 10.1039/D1LC01030A

Are bacteria claustrophobic? The problem of micrometric spatial confinement for the culturing of micro-organisms

Céline Molinaro, Violette Da Cunha, Aurore Gorlas, François Iv, Laurent Gallais, Ryan Catchpole, Patrick Forterre and Guillaume Baffou

RSC Adv., 2021, 11, 12500
DOI: 10.1039/D1RA00184A

Microfluidic approaches in microbial ecology

Giovanni Stefano Ugolini, Miaoxiao Wang, Eleonora Secchi, Roberto Pioli, Martin Ackermann and Roman Stocker

Lab Chip, 2024, 24, 1394
DOI: 10.1039/D3LC00784G

Evaluation of intercellular communication between breast cancer cells and adipose-derived stem cells via passive diffusion in a two-layer microfluidic device

Sharif M. Rahman, Joshua M. Campbell, Rachael N. Coates, Katie M. Render, C. Ethan Byrne, Elizabeth C. Martin and Adam T. Melvin

Lab Chip, 2020, 20, 2009
DOI: 10.1039/D0LC00142B

Microfluidic flow-through reactor and 3D Raman imaging forin situassessment of mineral reactivity in porous and fractured porous media

Jenna Poonoosamy, Cyprien Soulaine, Alina Burmeister, Guido Deissmann, Dirk Bosbach and Sophie Roman

Lab Chip, 2020, 20, 2562
DOI: 10.1039/D0LC00360C

Insights into constructing a stable and efficient microbial consortium system

Yinshan Lin, Haohong Lin, Jingyuan Liu, Fengxue Xin, Minjiao Chen, Weiliang Dong, Xiujuan Qian and Min Jiang

Chinese Journal of Chemical Engineering, 2024, 76, 95
DOI: 10.1016/j.cjche.2024.08.003

Microfluidics for Biotechnology: Bridging Gaps to Foster Microfluidic Applications

Vera Ortseifen, Martina Viefhues, Lutz Wobbe and Alexander Grünberger

Front. Bioeng. Biotechnol., 2020, 8
DOI: 10.3389/fbioe.2020.589074

Microbioreactors for nutrient‐controlled microbial cultures: Bridging the gap between bioprocess development and industrial use

Kartik Totlani, Rinke J. van Tatenhove‐Pel, Michiel T. Kreutzer, Walter M. van Gulik and Volkert van Steijn

Biotechnology Journal, 2023, 18
DOI: 10.1002/biot.202200549

Harnessing microfluidic technology for bacterial single-cell analysis in mammals

Xiaoting Guo, Qiuxia Shen, Ziyu Chen, Ziyi He and Xianghua Yan

TrAC Trends in Analytical Chemistry, 2023, 166, 117168
DOI: 10.1016/j.trac.2023.117168

Are endophytes essential partners for plants and what are the prospects for metal phytoremediation?

Alexis Durand, Pierre Leglize and Emile Benizri

Plant Soil, 2021, 460, 1
DOI: 10.1007/s11104-020-04820-w

Genetically Encoded Photosensitizers as Light-Triggered Antimicrobial Agents

Fabienne Hilgers, Nora Lisa Bitzenhofer, Yannic Ackermann, Alina Burmeister, Alexander Grünberger, Karl-Erich Jaeger and Thomas Drepper

IJMS, 2019, 20, 4608
DOI: 10.3390/ijms20184608

Microfluidic and mathematical modeling of aquatic microbial communities

Fangchen Liu, Andrea Giometto and Mingming Wu

Anal Bioanal Chem, 2021, 413, 2331
DOI: 10.1007/s00216-020-03085-7

Recent advances of integrated microfluidic suspension cell culture system

Yi Jing Kerk, Aysha Jameel, Xin‐Hui Xing and Chong Zhang

Engineering Biology, 2021, 5, 81
DOI: 10.1049/enb2.12015

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Xiangyu Zhu, Kun Wang, Huicong Yan, Congcong Liu, Xiaoying Zhu and Baoliang Chen

Environ. Sci. Technol., 2022, 56, 711
DOI: 10.1021/acs.est.1c03899

Development and application of a cultivation platform for mammalian suspension cell lines with single‐cell resolution

Julian Schmitz, Sarah Täuber, Christoph Westerwalbesloh, Eric von Lieres, Thomas Noll and Alexander Grünberger

Biotech & Bioengineering, 2021, 118, 992
DOI: 10.1002/bit.27627

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

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

Mar Life Sci Technol, 2021, 3, 169
DOI: 10.1007/s42995-020-00082-8

Harnessing microbial division of labor for biomanufacturing: a review of laboratory and formal modeling approaches

Fatima Ceballos Rodriguez-Conde, Sophie Zhu and Duygu Dikicioglu

Critical Reviews in Biotechnology, 2025, 45, 1249
DOI: 10.1080/07388551.2025.2455607

Synthetic microbial consortia for small molecule production

Elvira Sgobba and Volker F Wendisch

Current Opinion in Biotechnology, 2020, 62, 72
DOI: 10.1016/j.copbio.2019.09.011

Phenotypic variation in spatially structured microbial communities: ecological origins and consequences

Glen G D’Souza

Current Opinion in Biotechnology, 2020, 62, 220
DOI: 10.1016/j.copbio.2019.12.013

Microfluidics for adaptation of microorganisms to stress: design and application

Ahmed E. Zoheir, Camilla Stolle and Kersten S. Rabe

Appl Microbiol Biotechnol, 2024, 108
DOI: 10.1007/s00253-024-13011-x

The engineering of spatially linked microbial consortia – potential and perspectives

Sami Ben Said, Robin Tecon, Benedict Borer and Dani Or

Current Opinion in Biotechnology, 2020, 62, 137
DOI: 10.1016/j.copbio.2019.09.015

New dynamic microreactor system to mimic biofilm formation and test anti-biofilm activity of nanoparticles

Natalia Bourguignon, Vivek Kamat, Maximiliano Perez, Kalai Mathee, Betiana Lerner and Shekhar Bhansali

Appl Microbiol Biotechnol, 2022, 106, 2729
DOI: 10.1007/s00253-022-11855-9

A Co-culture of Staphylococcus epidermidis and Staphylococcus aureus in a Monodisperse Droplet to Investigate Microbial Interaction at Defined Microenvironment

So-Yeon Jung, Kyung Han Kim, Jae Seong Kim, Bo-Hyeon Hwang and Chang-Soo Lee

Korean J. Chem. Eng., 2025, 42, 2355
DOI: 10.1007/s11814-025-00476-3

Engineering artificial microbial consortia for personalized gut microbiome modulation and disease treatment

Timoth Mkilima

Ann NY Acad Sci, 2025, 1548, 29
DOI: 10.1111/nyas.15352

Digital models in biotechnology: Towards multi-scale integration and implementation

Fabian S.F. Hartmann, Isuru A. Udugama, Gerd M. Seibold, Hirokazu Sugiyama and Krist V. Gernaey

Biotechnology Advances, 2022, 60, 108015
DOI: 10.1016/j.biotechadv.2022.108015

Fluorescence-Based Online Monitoring Enables Differentiation in Co-Cultures of Untagged Streptomyces Species and Trichoderma reesei

Gesa Brauneck, Mareke Sophie Heykena, Dorothea M. Schütterle, Marcel Mann, Ivan Schlembach, Miriam A. Rosenbaum and Jorgen Barsett Magnus

Appl Biochem Biotechnol, 2025, 197, 7276
DOI: 10.1007/s12010-025-05378-y

Microfluidic approaches for synthetic gene circuits’ construction and analysis

Fengyu Zhang, Yanhong Sun and Chunxiong Luo

Quant. Biol., 2021, 9, 47
DOI: 10.15302/J-QB-021-0235

Optogenetic Tools for Control of Public Goods in Saccharomyces cerevisiae

Neydis Moreno Morales, Michael T. Patel, Cameron J. Stewart, Kieran Sweeney, Megan N. McClean and Michael Lorenz

mSphere, 2021, 6
DOI: 10.1128/mSphere.00581-21

Dynamic Co-Cultivation Process of Corynebacterium glutamicum Strains for the Fermentative Production of Riboflavin

Fernando Pérez-García, Arthur Burgardt, Dina R. Kallman, Volker F. Wendisch and Nadav Bar

Fermentation, 2021, 7, 11
DOI: 10.3390/fermentation7010011

Emerging single-cell microfluidic technology for microbiology

Yanqing Song, Jianan Yin, Wei E. Huang, Bei Li and Huabing Yin

TrAC Trends in Analytical Chemistry, 2024, 170, 117444
DOI: 10.1016/j.trac.2023.117444

Toward the Enhancement of Microalgal Metabolite Production through Microalgae–Bacteria Consortia

Lina Maria González-González and Luz E. de-Bashan

Biology, 2021, 10, 282
DOI: 10.3390/biology10040282

Investigating the dynamics of microbial consortia in spatially structured environments

Sonali Gupta, Tyler D. Ross, Marcella M. Gomez, Job L. Grant, Philip A. Romero and Ophelia S. Venturelli

Nat Commun, 2020, 11
DOI: 10.1038/s41467-020-16200-0

Optochemical Control of Bacterial Gene Expression: Novel Photocaged Compounds for Different Promoter Systems

Fabian Hogenkamp, Fabienne Hilgers, Nora Lisa Bitzenhofer, Vera Ophoven, Mona Haase, Claus Bier, Dennis Binder, Karl‐Erich Jaeger, Thomas Drepper and Jörg Pietruszka

ChemBioChem, 2022, 23
DOI: 10.1002/cbic.202100467

Gradient Functionalization of Various Quaternized Polyethylenimines on Microfluidic Chips for the Rapid Appraisal of Antibacterial Potencies

Wei Tong, Xin Yao, Shun Duan, Bingran Yu, Xiaokang Ding, Xuejia Ding and Fu-Jian Xu

Langmuir, 2020, 36, 354
DOI: 10.1021/acs.langmuir.9b02747

Single-Cell Technologies to Understand the Mechanisms of Cellular Adaptation in Chemostats

Naia Risager Wright, Nanna Petersen Rønnest and Nikolaus Sonnenschein

Front. Bioeng. Biotechnol., 2020, 8
DOI: 10.3389/fbioe.2020.579841

Insights into constructing a stable and efficient microbial consortium

Chunmeng Xu and Huimin Yu

Chinese Journal of Chemical Engineering, 2021, 30, 112
DOI: 10.1016/j.cjche.2020.12.012

Masks As a New Hotspot for Antibiotic Resistance Gene Spread: Reveal the Contribution of Atmospheric Pollutants and Potential Risks

Yanjie Wang, Qi Wang, Guodong Zhang, Yutong Li, He Guo, Jian Zhou, Tiecheng Wang, Hanzhong Jia and Lingyan Zhu

Environ. Sci. Technol., 2024, 58, 16100
DOI: 10.1021/acs.est.4c03399

Noninvasive tool for optical online monitoring of individual biomass concentrations in a defined coculture

Bertram Geinitz, Lars Rehmann, Jochen Büchs and Lars Regestein

Biotech & Bioengineering, 2020, 117, 999
DOI: 10.1002/bit.27256

Simultaneous Discovery of Positive and Negative Interactions Among Rhizosphere Bacteria Using Microwell Recovery Arrays

Niloy Barua, Ashlee M. Herken, Kyle R. Stern, Sean Reese, Roger L. Powers, Jennifer L. Morrell-Falvey, Thomas G. Platt and Ryan R. Hansen

Front. Microbiol., 2021, 11
DOI: 10.3389/fmicb.2020.601788

Studying root–environment interactions in structured microdevices

Christian-Frederic Kaiser, Alessia Perilli, Guido Grossmann, Yasmine Meroz and Ivan Reyna-Llorens

Journal of Experimental Botany, 2023, 74, 3851
DOI: 10.1093/jxb/erad122

High-Throughput and Continuous Chaotic Bioprinting of Spatially Controlled Bacterial Microcosms

Carlos Fernando Ceballos-González, Edna Johana Bolívar-Monsalve, Diego Alonso Quevedo-Moreno, Li Lu Lam-Aguilar, Karen Ixchel Borrayo-Montaño, Juan F. Yee-de León, Yu Shrike Zhang, Mario Moisés Alvarez and Grissel Trujillo-de Santiago

ACS Biomater. Sci. Eng., 2021, 7, 2408
DOI: 10.1021/acsbiomaterials.0c01646

A screening platform in Escherichia coli for modified antimicrobial peptide by combining surface display and co-culture

Yanli Xu and Oscar P. Kuipers

Microbiological Research, 2026, 307, 128484
DOI: 10.1016/j.micres.2026.128484

Synthetic soil microcosms as emerging model systems to study the rhizosphere

Andrew Mair, Daniel Patko, Yangminghao Liu, Ilonka Engelhardt and Lionel X. Dupuy

Plant Soil, 2025, 514, 1597
DOI: 10.1007/s11104-025-07495-3

Unraveling antimicrobial resistance using metabolomics

Maik Kok, Loes Maton, Marielle van der Peet, Thomas Hankemeier and J. G. Coen van Hasselt

Drug Discovery Today, 2022, 27, 1774
DOI: 10.1016/j.drudis.2022.03.015

Recent Advances in Bioethanol Production from Rice Straw: Strategies, New Concepts, and Challenges

Andhika Cahaya Titisan Sukma, Budiyono Budiyono and Ahmad Ni’matullah Al-Baarri

Int J Environ Res, 2025, 19
DOI: 10.1007/s41742-024-00681-8

Metabolic Profiling of Rhizobacteria Serratia plymuthica and Bacillus subtilis Revealed Intra- and Interspecific Differences and Elicitation of Plipastatins and Short Peptides Due to Co-cultivation

Riya C. Menezes, Birgit Piechulla, Dörte Warber, Aleš Svatoš and Marco Kai

Front. Microbiol., 2021, 12
DOI: 10.3389/fmicb.2021.685224

Subsurface Life on Earth as a Key to Unlock Extraterrestrial Mysteries

Emeline Vidal, Melody R. Lindsay, James A. Bradley, Magdalena R. Osburn and S. Emil Ruff

Microbial Biotechnology, 2025, 18
DOI: 10.1111/1751-7915.70286

(Optochemical) Control of Synthetic Microbial Coculture Interactions on a Microcolony Level

Alina Burmeister, Qiratt Akhtar, Lina Hollmann, Niklas Tenhaef, Fabienne Hilgers, Fabian Hogenkamp, Sascha Sokolowsky, Jan Marienhagen, Stephan Noack, Dietrich Kohlheyer and Alexander Grünberger

ACS Synth. Biol., 2021, 10, 1308
DOI: 10.1021/acssynbio.0c00382

Artificial Microbial Arenas: Materials for Observing and Manipulating Microbial Consortia

Lothar Wondraczek, Georg Pohnert, Felix H. Schacher, Angela Köhler, Michael Gottschaldt, Ulrich S. Schubert, Kirsten Küsel and Axel A. Brakhage

Advanced Materials, 2019, 31
DOI: 10.1002/adma.201900284

A microfluidic experiment and pore scale modelling diagnostics for assessing mineral precipitation and dissolution in confined spaces

Jenna Poonoosamy, Christoph Westerwalbesloh, Guido Deissmann, Mohamed Mahrous, Enzo Curti, Sergey V. Churakov, Martina Klinkenberg, Dietrich Kohlheyer, Eric von Lieres, Dirk Bosbach and Nikolaos I. Prasianakis

Chemical Geology, 2019, 528, 119264
DOI: 10.1016/j.chemgeo.2019.07.039

Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes

Ivan Schlembach, Alexander Grünberger, Miriam A. Rosenbaum and Lars Regestein

Trends in Biotechnology, 2021, 39, 1093
DOI: 10.1016/j.tibtech.2021.01.006

Microsensor in Microbioreactors: Full Bioprocess Characterization in a Novel Capillary-Wave Microbioreactor

Kevin Viebrock, Dominik Rabl, Sven Meinen, Paul Wunder, Jan-Angelus Meyer, Lasse Jannis Frey, Detlev Rasch, Andreas Dietzel, Torsten Mayr and Rainer Krull

Biosensors, 2022, 12, 512
DOI: 10.3390/bios12070512

Microfluidic cultivation and analysis tools for interaction studies of microbial co-cultures

Alina Burmeister and Alexander Grünberger

Current Opinion in Biotechnology, 2020, 62, 106
DOI: 10.1016/j.copbio.2019.09.001

Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing

Rahul Vijay Kapoore, Gloria Padmaperuma, Supattra Maneein and Seetharaman Vaidyanathan

Critical Reviews in Biotechnology, 2022, 42, 46
DOI: 10.1080/07388551.2021.1921691

Photo-Regulation of Enzyme Activity: The Inactivation of a Carboligase with Genetically Encoded Photosensitizer Fusion Tags

Tim Gerlach, Jendrik Schain, Simone Söltl, Morten M. C. H. van Schie, Fabienne Hilgers, Nora L. Bitzenhofer, Thomas Drepper and Dörte Rother

Front. Catal., 2022, 2
DOI: 10.3389/fctls.2022.835919

Metabolic engineering advances and prospects for amino acid production

Volker F. Wendisch

Metabolic Engineering, 2020, 58, 17
DOI: 10.1016/j.ymben.2019.03.008

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

Gabriela Kapinusova, Marco A. Lopez Marin and Ondrej Uhlik

Front. Microbiol., 2023, 14
DOI: 10.3389/fmicb.2023.1089630

Analyzing Microbial Population Heterogeneity—Expanding the Toolbox of Microfluidic Single-Cell Cultivations

Markus Leygeber, Dorina Lindemann, Christian Carsten Sachs, Eugen Kaganovitch, Wolfgang Wiechert, Katharina Nöh and Dietrich Kohlheyer

Journal of Molecular Biology, 2019, 431, 4569
DOI: 10.1016/j.jmb.2019.04.025

Microfluidics at the interface of bacteria and fresh produce

Mohsen Ranjbaran and Mohit S. Verma

Trends in Food Science & Technology, 2022, 128, 102
DOI: 10.1016/j.tifs.2022.07.014

Microfluidic Dielectrophoretic Method Enables On-Demand Spatial Arrangement of Bacteria-Encapsulated Agarose Gel Microparticles

Jing Dai, Can Huang, Han Zhang, Ryan Samuel, Yuwen Li, Arul Jayaraman, Paul de Figueiredo and Arum Han

Anal. Chem., 2022, 94, 13197
DOI: 10.1021/acs.analchem.2c02724

Analysis of protein secretion in Bacillus subtilis by combining a secretion stress biosensor strain with an in vivo split GFP assay

Patrick Lenz, Patrick J. Bakkes, Carolin Müller, Marzena Malek, Roland Freudl, Marco Oldiges, Thomas Drepper, Karl-Erich Jaeger and Andreas Knapp

Microb Cell Fact, 2023, 22
DOI: 10.1186/s12934-023-02199-8

Design and Modeling of a Microfluidic Coral Polyps Culture Chip with Concentration and Temperature Gradients

Shizheng Zhou, Edgar S. Fu, Bingbing Chen and Hong Yan

Micromachines, 2022, 13, 832
DOI: 10.3390/mi13060832

Photo-addressable microwell devices for rapid functional screening and isolation of pathogen inhibitors from bacterial strain libraries

Niloy Barua, Ashlee M. Herken, Natalie Melendez-Velador, Thomas G. Platt and Ryan R. Hansen

Biomicrofluidics, 2024, 18
DOI: 10.1063/5.0188270

Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages

J. Andres Martinez, Matheo Delvenne, Lucas Henrion, Fabian Moreno, Samuel Telek, Christian Dusny, Frank Delvigne and Sunil Laxman

PLoS Comput Biol, 2022, 18, e1010674
DOI: 10.1371/journal.pcbi.1010674

Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion

Hsieh-Fu Tsai, Daniel Carlson, Anzhelika Koldaeva, Simone Pigolotti and Amy Shen

Micromachines, 2022, 13, 576
DOI: 10.3390/mi13040576

Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel

A. Monmeyran, W. Benyoussef, P. Thomen, N. Dahmane, A. Baliarda, M. Jules, S. Aymerich and N. Henry

npj Biofilms Microbiomes, 2021, 7
DOI: 10.1038/s41522-021-00233-4

Multiscale micro-/nanofluidic devices incorporating self-assembled particle membranes for bioanalysis: A review

Jongwan Lee, Jaeseok Lee and Minseok Kim

TrAC Trends in Analytical Chemistry, 2023, 160, 116940
DOI: 10.1016/j.trac.2023.116940

Recent Progress in the Development of Droplet-based Microfluidic Technologies for Phenotypic Screening using Cell-cell Interactions

Seungjin Kim, Jo Hyun Moon and Gyoo Yeol Jung

Biotechnol Bioproc E, 2023, 28, 929
DOI: 10.1007/s12257-022-0081-1

High‐Resolution Patterned Delivery of Chemical Signals From 3D‐Printed Picoliter Droplet Networks

Jorin Riexinger, Thomas Caganek, Xingzao Wang, Yutong Yin, Khoa Chung, Linna Zhou, Hagan Bayley and Ravinash Krishna Kumar

Advanced Materials, 2025, 37
DOI: 10.1002/adma.202412292

Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis

Keitaro Kasahara, Markus Leygeber, Johannes Seiffarth, Karina Ruzaeva, Thomas Drepper, Katharina Nöh and Dietrich Kohlheyer

Front. Microbiol., 2023, 14
DOI: 10.3389/fmicb.2023.1198170

Zooming in to acquire micro-reaction: Application of microfluidics on soil microbiome

Xiongkun Zhang, Shan Wu, Xiaojie Sun, Monika Mortimer, Yichao Wu, Ming Zhang, Qiaoyun Huang and Peng Cai

Soil Ecol. Lett., 2022, 4, 213
DOI: 10.1007/s42832-021-0073-7

Microbial synthesis of the plant natural product precursor p-coumaric acid with Corynebacterium glutamicum

Mario Mutz, Dominic Kösters, Benedikt Wynands, Nick Wierckx and Jan Marienhagen

Microb Cell Fact, 2023, 22
DOI: 10.1186/s12934-023-02222-y

A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures

Andreas Ulmer, Stefan Veit, Florian Erdemann, Andreas Freund, Maren Loesch, Attila Teleki, Ahmad A. Zeidan and Ralf Takors

Bioengineering, 2023, 10, 103
DOI: 10.3390/bioengineering10010103

Bacterial Behavior in Confined Spaces

Hang Du, Weili Xu, Zhizhou Zhang and Xiaojun Han

Front. Cell Dev. Biol., 2021, 9
DOI: 10.3389/fcell.2021.629820

Microfluidic single-cell analysis in biotechnology: from monitoring towards understanding

Christian Dusny and Alexander Grünberger

Current Opinion in Biotechnology, 2020, 63, 26
DOI: 10.1016/j.copbio.2019.11.001

In Situ and Individual-Based Analysis of the Influence of Polystyrene Microplastics on Escherichia coli Conjugative Gene Transfer at the Single-Cell Level

Li Liu, Qiang-hong Zhang and Rui-tong Li

Environ. Sci. Technol., 2023, 57, 15936
DOI: 10.1021/acs.est.3c05476

Droplet-Based Microfluidics in Single-Bacterium Analysis: Advancements in Cultivation, Detection, and Application

Haiyan Ma, Yuewen Zhang, Ren Shen and Yanwei Jia

Biosensors, 2025, 15, 535
DOI: 10.3390/bios15080535