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Volume 16
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Review

Advances in Detecting Viable/Dead Foodborne Microorganisms Using Diverse Functional Nucleic Acid-Based Molecular Recognition

by
Yanger Liu
1,
Huifu Yuan
2,
Juan Zhang
1,
Xiaoyun Sun
1,
Peili Wang
1,
Pazilaiti Yiming
3,
Ailiang Chen
1,* and
Yanyang Xu
1,*
1
State Key Laboratory for Quality and Safety of Agro-Products, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
2
College of Agriculture and Forestry, Hebei North University, Zhangjiakou 075000, China
3
Xinjiang Institute of Veterinary Medicine and Feed Supervision, Urumqi 830063, China
*
Authors to whom correspondence should be addressed.
Biosensors 2026, 16(7), 364; https://doi.org/10.3390/bios16070364
Submission received: 13 May 2026 / Revised: 27 June 2026 / Accepted: 29 June 2026 / Published: 3 July 2026
(This article belongs to the Special Issue Advanced Biosensors Based on Molecular Recognition)
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Abstract

Accurately detecting viable foodborne pathogenic bacteria is essential for food safety risk assessments and public health interventions. Traditional plate counting is time-consuming and operationally cumbersome. Immunological assays are unable to distinguish viable from dead cells, whereas conventional nucleic acid amplification is often affected by residual DNA originating from dead bacteria. These limitations render conventional approaches inadequate for rapid and precise field detection. Functional nucleic acids (FNAs) offer a promising alternative for viability detection because of their high sensitivity, specificity, target diversity, and programmable integrability. This review provides a systematic overview of molecular recognition strategies and FNA-based detection technologies for identifying viable foodborne microorganisms. We categorize the biomarkers targeted by FNAs into nucleic acids, surface structures, and metabolic activities. Building on this categorization, we examine the core principles and technological evolution of primers, aptamers, DNAzymes, guide nucleic acids, and oligonucleotide probes in viability discrimination. We then outline the practical applications of these technologies across the food supply chain and discuss the remaining challenges and future directions in the field. Ultimately, this work provides a theoretical reference and practical guidance for ensuring food safety and advancing precise microbial risk management.
Keywords: FNA; viable bacteria detection; dead bacteria detection; food safety; foodborne pathogens FNA; viable bacteria detection; dead bacteria detection; food safety; foodborne pathogens

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MDPI and ACS Style

Liu, Y.; Yuan, H.; Zhang, J.; Sun, X.; Wang, P.; Yiming, P.; Chen, A.; Xu, Y. Advances in Detecting Viable/Dead Foodborne Microorganisms Using Diverse Functional Nucleic Acid-Based Molecular Recognition. Biosensors 2026, 16, 364. https://doi.org/10.3390/bios16070364

AMA Style

Liu Y, Yuan H, Zhang J, Sun X, Wang P, Yiming P, Chen A, Xu Y. Advances in Detecting Viable/Dead Foodborne Microorganisms Using Diverse Functional Nucleic Acid-Based Molecular Recognition. Biosensors. 2026; 16(7):364. https://doi.org/10.3390/bios16070364

Chicago/Turabian Style

Liu, Yanger, Huifu Yuan, Juan Zhang, Xiaoyun Sun, Peili Wang, Pazilaiti Yiming, Ailiang Chen, and Yanyang Xu. 2026. "Advances in Detecting Viable/Dead Foodborne Microorganisms Using Diverse Functional Nucleic Acid-Based Molecular Recognition" Biosensors 16, no. 7: 364. https://doi.org/10.3390/bios16070364

APA Style

Liu, Y., Yuan, H., Zhang, J., Sun, X., Wang, P., Yiming, P., Chen, A., & Xu, Y. (2026). Advances in Detecting Viable/Dead Foodborne Microorganisms Using Diverse Functional Nucleic Acid-Based Molecular Recognition. Biosensors, 16(7), 364. https://doi.org/10.3390/bios16070364

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