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Microbial Biosensor: From Design to Applications—2nd Edition
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Microbial Biosensor: From Design to Applications—2nd Edition

A special issue of Biosensors (ISSN 2079-6374). This special issue belongs to the section "Biosensor Materials".

Deadline for manuscript submissions: closed (28 February 2026) | Viewed by 19855

Special Issue Editor

Dr. Hideaki Nakamura

E-Mail Website
Guest Editor
Department of Liberal Arts, Tokyo University of Technology, Tokyo, Japan
Interests: microbial biosensor; biosensing; mediator; BOD; toxicity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The first edition of the Special Issue, entitled “Microbial Biosensor: From Design to Applications”, was successfully published in March 2025. In response to the high interest in microbial biosensors from researchers and readers, we are now launching the second Special Issue.

The time has come for us human beings to recognize that we are no longer consumers of the Earth's ecosystem, but wasters. In order to live together with other living organisms on this planet, we need to change our lives. The Sustainable Development Goals (SDGs) were set and adopted as the “2030 Agenda” by the United Nations in 2015. Unfortunately, there are many difficulties in achieving this goal.

We must not give up on these goals; we must all do what we can, transcending national and regional boundaries. As Special Issue editors, although the actions we can take may be limited, we hope to break barriers and contribute to the development of science and technology and the preservation of the global environment.

Microbial biosensors, consisting of microbial cell(s) as analyte sensors and a transducer as an electrical signal converter, have been studied and developed for environmental, agricultural, food, and biomedical applications. These microbial biosensors have been supported by studying a variety of principles and device designs.

In the second Special Issue, we welcome submissions of research papers and critical reviews focusing on the following topics:

Design:

  • Novel designs of chip/cell/array for microbial biosensors;
  • Novel designs of self-powered devices for microbial biosensors;
  • Novel designs of online, on-site, or remote monitoring;
  • Novel designs for microbial immobilization;
  • Novel designs for single-microbial-cell biosensors

Application:

  • Application to environmental water or wastewater monitoring;
  • Application to estimate soil environment or bioremediation;
  • Application to agriculture, aquafarming, or aquaponics;
  • Micro/nanotechnology and novel materials applied to microbial biosensors;
  • Novel instrumentation systems for microbial biosensors.

Others:

  • New solutions applied in microbial biosensors;
  • Interdisciplinary study leading to microbial biosensor development

Dr. Hideaki Nakamura
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biosensors is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial biosensor
  • whole-cell biosensor
  • cell-based biosensor
  • microbial fuel cell
  • BOD
  • toxicity
  • immobilization
  • mediator
  • electron transfer
  • monitoring
  • environmental medicine

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Published Papers (8 papers)

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Research

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20 pages, 4646 KB  
Article
Portable Dual-Mode Biosensor for Quantitative Determination of Salmonella in Lateral Flow Assays Using Machine Learning and Smartphone-Assisted Operation
by Jully Blackshare, Brianna Corman, Bartek Rajwa, J. Paul Robinson and Euiwon Bae
Biosensors 2026, 16(1), 57; https://doi.org/10.3390/bios16010057 - 13 Jan 2026
Cited by 1 | Viewed by 986
Abstract
Foodborne pathogens remain a major global concern, demanding rapid, accessible, and determination technologies. Conventional methods, such as culture assays and polymerase chain reaction, offer high accuracy but are time-consuming for on-site testing. This study presents a portable, smartphone-assisted dual-mode biosensor that combines colorimetric [...] Read more.
Foodborne pathogens remain a major global concern, demanding rapid, accessible, and determination technologies. Conventional methods, such as culture assays and polymerase chain reaction, offer high accuracy but are time-consuming for on-site testing. This study presents a portable, smartphone-assisted dual-mode biosensor that combines colorimetric and photothermal speckle imaging for improved sensitivity in lateral flow assays (LFAs). The prototype device, built using low-cost components ($500), uses a Raspberry Pi for illumination control, image acquisition, and machine learning-based signal analysis. Colorimetric features were derived from normalized RGB intensities, while photothermal responses were obtained from speckle fluctuation metrics during periodic plasmonic heating. Multivariate linear regression, with and without LASSO regularization, was used to predict Salmonella concentrations. The comparison revealed that regularization did not significantly improve predictive accuracy indicating that the unregularized linear model is sufficient and that the extracted features are robust without complex penalization. The fused model achieved the best performance (R2 = 0.91) and consistently predicted concentrations down to a limit of detection (LOD) of 104 CFU/mL, which is one order of magnitude improvement of visual and benchtop measurements from previous work. Blind testing confirmed robustness but also revealed difficulty distinguishing between negative and 103 CFU/mL samples. This work demonstrates a low-cost, field-deployable biosensing platform capable of quantitative pathogen detection, establishing a foundation for the future deployment of smartphone-assisted, machine learning-enabled diagnostic tools for broader monitoring applications. Full article
(This article belongs to the Special Issue Microbial Biosensor: From Design to Applications—2nd Edition)
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16 pages, 1136 KB  
Article
Development of Metabolite-Responsive Transcription Factor Systems as Modular Platforms for Gene Expression Control
by Haekang Ji, Jiwon Lee, Kyeongseok Song, Yangwon Jeon, Geupil Jang and Youngdae Yoon
Biosensors 2025, 15(12), 820; https://doi.org/10.3390/bios15120820 - 18 Dec 2025
Cited by 1 | Viewed by 890
Abstract
Traditional inducible systems typically induce the simultaneous expression of all genes controlled by similar promoters, thereby limiting their use. In this study, we used two metabolite-inducible systems, MarR from the Escherichia coli mar operon and TtgR from the Pseudomonas putida ttg operon, to [...] Read more.
Traditional inducible systems typically induce the simultaneous expression of all genes controlled by similar promoters, thereby limiting their use. In this study, we used two metabolite-inducible systems, MarR from the Escherichia coli mar operon and TtgR from the Pseudomonas putida ttg operon, to assess their use as gene regulation platforms beyond reporter assays. Ligand-dependent transcription was validated using eGFP. The reporter was replaced with two flavonoid O-methyltransferases (OMTs), ROMT-9 and SOMT-2, under transcription factor (TF)-specific promoters. In E. coli, both systems enabled in using HPLC. TF-based expression did not impact enzyme activity. Induction with salicylic acid (MarR) produced stronger gains than that with 4′-hydroxyflavanone (TtgR), although the overall fold-changes in product levels were regulated by basal (leaky) expression. Thus, although transcriptional control was robust, enzymatic regulation was less stringent, highlighting the necessity for genetic engineering of components, including TFs, promoters, transcription factor binding sites, and ribosome binding sites, to reduce leakiness and expand the dynamic range. Overall, these orthogonal and modular TF-based systems offer a framework for independent and inducible control of multiple genes, with potential applications in biosensing, metabolic engineering, and programmable pathway design. Full article
(This article belongs to the Special Issue Microbial Biosensor: From Design to Applications—2nd Edition)
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23 pages, 8446 KB  
Article
Bacterial lux-Biosensors for Detecting Specific Cell Responses to Membrane Damage
by Vladimir A. Plyuta, Evgeny Y. Gnuchikh, Anastasiia A. Gorbunova, Veronika D. Udovichenko, Kristina A. Sinyakova, Daria E. Sidorova, Olga A. Koksharova, Sergey V. Bazhenov and Olga E. Melkina
Biosensors 2025, 15(12), 780; https://doi.org/10.3390/bios15120780 - 26 Nov 2025
Viewed by 1144
Abstract
Whole-cell biosensors represent one of the tools used for assessing the effects of various agents on living cells. Here we have constructed and tested whole-cell lux-biosensors to detect membrane damage in both Gram-negative and Gram-positive bacteria using the stress-inducible promoter of the [...] Read more.
Whole-cell biosensors represent one of the tools used for assessing the effects of various agents on living cells. Here we have constructed and tested whole-cell lux-biosensors to detect membrane damage in both Gram-negative and Gram-positive bacteria using the stress-inducible promoter of the pspA gene from Escherichia coli and Bacillus subtilis fused to the lux genes from Photorhabdus luminescens. These biosensors increase their luminescence in response to treatment with a number of known membrane-damaging compounds, such as ethanol, Triton X-100, polymyxin B, dimethylsulfoxide (DMSO) and melittin. E. coli- and B. subtilis-based biosensors demonstrated differences in response to the action of the same membrane-damaging agent. Thus, ethanol and polymyxin B specifically induced the pspA promoter in both lux-biosensors, but the induction amplitude was higher in the E. coli. Triton X-100 and melittin specifically induced the pspA promoter exclusively in B. subtilis cells, while DMSO induced it only in E. coli cells. This indicates a difference in the stress response of the Psp system to membrane-damaging agents in E. coli and B. subtilis cells. Thus, we demonstrated the functionality and efficiency of the constructed lux-biosensors and, using them, showed that some of the tested compounds are able to specifically activate Psp stress response systems in case of membrane damage. Full article
(This article belongs to the Special Issue Microbial Biosensor: From Design to Applications—2nd Edition)
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24 pages, 2773 KB  
Article
Highly Sensitive SOI-TFET Gas Sensor Utilizing Tailored Conducting Polymers for Selective Molecular Detection and Microbial Biosensing Integration
by Mohammad K. Anvarifard and Zeinab Ramezani
Biosensors 2025, 15(8), 525; https://doi.org/10.3390/bios15080525 - 11 Aug 2025
Cited by 3 | Viewed by 1363
Abstract
We present a highly sensitive and selective gas sensor based on an advanced silicon-on-insulator tunnel field-effect transistor (SOI-TFET) architecture, enhanced through the integration of customized conducting polymers. In this design, traditional metal gates are replaced with distinct functional polymers—PPP-TOS/AcCN, PP-TOS/AcCN, PP-FE(CN)63− [...] Read more.
We present a highly sensitive and selective gas sensor based on an advanced silicon-on-insulator tunnel field-effect transistor (SOI-TFET) architecture, enhanced through the integration of customized conducting polymers. In this design, traditional metal gates are replaced with distinct functional polymers—PPP-TOS/AcCN, PP-TOS/AcCN, PP-FE(CN)63−/H2O, PPP-TCNQ-TOS/AcCN, and PPP-ClO4/AcCN—which enable precise molecular recognition and discrimination of various target gases. To further enhance sensitivity, the device employs an oppositely doped source region, significantly improving gate control and promoting stronger band-to-band tunneling. This structural modification amplifies sensing signals and improves noise immunity, allowing reliable detection at trace concentrations. Additionally, optimization of the subthreshold swing contributes to faster switching and response times. Thermal stability is addressed by embedding a P-type buffer layer within the buried oxide, which increases thermal conductivity and reduces lattice temperature, further stabilizing device performance. Experimental results demonstrate that the proposed sensor outperforms conventional SOI-TFET designs, exhibiting superior sensitivity and selectivity toward analytes such as methanol, chloroform, isopropanol, and hexane. Beyond gas sensing, the unique polymer-functionalized gate design enables integration of microbial biosensing capabilities, making the platform highly versatile for biochemical detection. This work offers a promising pathway toward ultra-sensitive, low-power sensing technologies for environmental monitoring, industrial safety, and medical diagnostics. Full article
(This article belongs to the Special Issue Microbial Biosensor: From Design to Applications—2nd Edition)
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Review

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28 pages, 1138 KB  
Review
Yeast Biosensors for the Safety of Fermented Beverages
by Sílvia Afonso, Ivo Oliveira and Alice Vilela
Biosensors 2026, 16(1), 64; https://doi.org/10.3390/bios16010064 - 16 Jan 2026
Cited by 1 | Viewed by 1973
Abstract
Yeast biosensors represent a promising biotechnological innovation for ensuring the safety and quality of fermented beverages such as beer, wine, and kombucha. These biosensors employ genetically engineered yeast strains to detect specific contaminants, spoilage organisms, or hazardous compounds during fermentation or the final [...] Read more.
Yeast biosensors represent a promising biotechnological innovation for ensuring the safety and quality of fermented beverages such as beer, wine, and kombucha. These biosensors employ genetically engineered yeast strains to detect specific contaminants, spoilage organisms, or hazardous compounds during fermentation or the final product. By integrating synthetic biology tools, researchers have developed yeast strains that can sense and respond to the presence of heavy metals (e.g., lead or arsenic), mycotoxins, ethanol levels, or unwanted microbial metabolites. When a target compound is detected, the biosensor yeast activates a reporter system, such as fluorescence, color change, or electrical signal, providing a rapid, visible, and cost-effective means of monitoring safety parameters. These biosensors offer several advantages: they can operate in real time, are relatively low-cost compared to conventional chemical analysis methods, and can be integrated directly into the fermentation system. Furthermore, as Saccharomyces cerevisiae is generally recognized as safe (GRAS), its use as a sensing platform aligns well with existing practices in beverage production. Yeast biosensors are being investigated for the early detection of contamination by spoilage microbes, such as Brettanomyces and lactic acid bacteria. These contaminants can alter the flavor profile and shorten the product’s shelf life. By providing timely feedback, these biosensor systems allow producers to intervene early, thereby reducing waste and enhancing consumer safety. In this work, we review the development and application of yeast-based biosensors as potential safeguards in fermented beverage production, with the overarching goal of contributing to the manufacture of safer and higher-quality products. Nevertheless, despite their substantial conceptual promise and encouraging experimental results, yeast biosensors remain confined mainly to laboratory-scale studies. A clear gap persists between their demonstrated potential and widespread industrial implementation, underscoring the need for further research focused on robustness, scalability, and regulatory integration. Full article
(This article belongs to the Special Issue Microbial Biosensor: From Design to Applications—2nd Edition)
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24 pages, 2834 KB  
Review
Biosensors for Detection of Labile Heme in Biological Samples
by Krysta Dobill, Delphine Lechardeur and Jasmina Vidic
Biosensors 2026, 16(1), 4; https://doi.org/10.3390/bios16010004 - 19 Dec 2025
Viewed by 2289
Abstract
Heme, a protoporphyrin IX iron complex, functions as an essential prosthetic group in hemoglobin and myoglobin, mediating oxygen storage and transport. Additionally, heme serves as a critical cofactor in various enzymes such as cytochrome c, enabling electron transfer within the mitochondrial respiratory chain. [...] Read more.
Heme, a protoporphyrin IX iron complex, functions as an essential prosthetic group in hemoglobin and myoglobin, mediating oxygen storage and transport. Additionally, heme serves as a critical cofactor in various enzymes such as cytochrome c, enabling electron transfer within the mitochondrial respiratory chain. Unlike protein-bound heme, free or labile heme exhibits cytotoxic, pro-oxidant, and pro-inflammatory properties. Elevated levels of free heme are associated with various pathophysiological conditions, including hemolytic disorders such as sickle cell disease, malaria, and sepsis. In this review, we introduce the physiological roles of heme and its involvement in human health and disease. We also examine the mechanisms of heme sensing and regulation in bacterial cells. A variety of analytical methods have been developed to detect and quantify heme, enabling differentiation between protein-bound and free forms. These tools are discussed in the context of their applications in studying cellular heme regulation and their use in monitoring pathological conditions in humans. In particular, we describe examples of biosensors employing bacterial heme sensor proteins as recognition elements. Full article
(This article belongs to the Special Issue Microbial Biosensor: From Design to Applications—2nd Edition)
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38 pages, 3752 KB  
Review
Recent Advances in Metal–Organic Framework-Based Nanozymes for Intelligent Microbial Biosensing: A Comprehensive Review of Biomedical and Environmental Applications
by Alemayehu Kidanemariam and Sungbo Cho
Biosensors 2025, 15(7), 437; https://doi.org/10.3390/bios15070437 - 7 Jul 2025
Cited by 18 | Viewed by 5776
Abstract
Metal–organic framework (MOF)-based nanozymes represent a groundbreaking frontier in advanced microbial biosensing, offering unparalleled catalytic precision and structural tunability to mimic natural enzymes with superior stability and specificity. By engineering the structural features and forming composites, MOFs are precisely tailored to amplify nanozymatic [...] Read more.
Metal–organic framework (MOF)-based nanozymes represent a groundbreaking frontier in advanced microbial biosensing, offering unparalleled catalytic precision and structural tunability to mimic natural enzymes with superior stability and specificity. By engineering the structural features and forming composites, MOFs are precisely tailored to amplify nanozymatic activity, enabling the highly sensitive, rapid, and cost-effective detection of a broad spectrum of microbial pathogens critical to biomedical diagnostics and environmental monitoring. These advanced biosensors surpass traditional enzyme systems in robustness and reusability, integrating seamlessly with smart diagnostic platforms for real-time, on-site microbial identification. This review highlights cutting-edge developments in MOF nanozyme design, composite engineering, and signal transduction integration while addressing pivotal challenges such as biocompatibility, complex matrix interference, and scalable manufacturing. Looking ahead, the convergence of multifunctional MOF nanozymes with portable technologies and optimized in vivo performance will drive transformative breakthroughs in early disease detection, antimicrobial resistance surveillance, and environmental pathogen control, establishing a new paradigm in next-generation smart biosensing. Full article
(This article belongs to the Special Issue Microbial Biosensor: From Design to Applications—2nd Edition)
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54 pages, 21736 KB  
Review
Whole Cells of Microorganisms—A Powerful Bioanalytical Tool for Measuring Integral Parameters of Pollution: A Review
by Maxim Cheliukanov, George Gurkin, Roman Perchikov, Anastasia Medvedeva, Tatyana Lavrova, Tatyana Belousova, Aleksandra Titova, Yulia Plekhanova, Sergei Tarasov, Anna Kharkova, Vyacheslav Arlyapov, Philippe Mandin, Hideaki Nakamura and Anatoly Reshetilov
Biosensors 2025, 15(5), 290; https://doi.org/10.3390/bios15050290 - 4 May 2025
Cited by 17 | Viewed by 4678
Abstract
Microbial biosensors are bioanalytical devices that can measure the toxicity of pollutants or detect specific substances. This is the greatest advantage of microbial biosensors which use whole cells of microorganisms as powerful tools for measuring integral parameters of environmental pollution. This review explores [...] Read more.
Microbial biosensors are bioanalytical devices that can measure the toxicity of pollutants or detect specific substances. This is the greatest advantage of microbial biosensors which use whole cells of microorganisms as powerful tools for measuring integral parameters of environmental pollution. This review explores the core principles of microbial biosensors including biofuel devices, emphasizing their capacity to evaluate biochemical oxygen demand (BOD), toxicity, heavy metals, surfactants, phenols, pesticides, inorganic pollutants, and microbiological contamination. However, practical challenges, such as sensitivity to environmental factors like pH, salinity, and the presence of competing substances, continue to hinder their broader application and long-term stability. The performance of these biosensors is closely tied to both technological advancement and the scientific understanding of biological systems, which influence data interpretation and device optimization. The review further examines cutting-edge developments, including the integration of electroactive biofilms with nanomaterials, molecular biology techniques, and artificial intelligence, all of which significantly enhance biosensor functionality and analytical accuracy. Commercial implementations and improvement strategies are also discussed, providing a comprehensive overview of the state-of-the-art in this field. Overall, this work consolidates recent progress and identifies both the potential and limitations of microbial biosensors, offering valuable insights into their future development for environmental monitoring. Full article
(This article belongs to the Special Issue Microbial Biosensor: From Design to Applications—2nd Edition)
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