Cornfield with glowing DNA strands and electronic probe.

Decoding Aflatoxin: How New Tech Can Spot Dangerous Fungi Faster

Reese Marlowe monogram
Reese Marlowe in Science & Nature November 2026 • 4 min read.

"Cutting-edge RNA sequencing and e-probes are changing how we detect aflatoxin-producing Aspergillus flavus, safeguarding our food supply"


Imagine biting into your favorite snack, unaware that it's been contaminated by a potent toxin produced by a sneaky fungus. That's the reality for many crops, including maize, peanuts, and spices, which can be infected by Aspergillus flavus. This fungus produces aflatoxins, a group of toxic compounds, with aflatoxin B₁ being particularly nasty due to its carcinogenic properties. Keeping our food safe from these toxins is a major challenge for food biosecurity.

Traditional methods for detecting aflatoxins, like chromatography and immunoassays, have their limitations, especially when it comes to speed and cost. Aflatoxin regulations are strict worldwide, making it crucial to have rapid and accurate testing methods to prevent contaminated products from reaching consumers. This is where innovative technology comes in.

Now, researchers are exploring a new approach: using RNA sequencing and electronic probes (EDNAtran) to quickly detect the presence of aflatoxin-producing Aspergillus flavus strains. This method focuses on identifying specific gene activity related to aflatoxin production, offering a faster and potentially cheaper way to screen crops for contamination.

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The Global Aflatoxin Burden

Aflatoxins are food contaminants associated with human and animal health risks, and they enter exposure pathways through contaminated food and feed. A 2026 narrative review examines global exposure levels, exposure routes, health effects, and modern detection technologies. Rapid and reliable analysis remains important because conventional methods can require complex preparation, lengthy analysis times, and multiple handling stages.

Unlocking the Power of EDNAtran: A New Tool for Aflatoxin Detection

Cornfield with glowing DNA strands and electronic probe.

E-probe Diagnostic for Nucleic acid Analysis (EDNA) has been around for a while, originally designed to spot plant pathogens by digging through metagenomic databases. Now, with a few upgrades, EDNA can do much more. EDNA transcriptomics (EDNAtran) can detect very specific gene targets in transcriptomic databases. Think of it like a super-powered search engine specifically designed to find signs of trouble in a plant's genetic material. Scientists can develop e-probes to target specific pathogenicity factors, which are transcripts related to that function.

The core idea is simple: create electronic probes (e-probes) that target genes that ramp up their activity during aflatoxin production. By tracking these specific genes, scientists can quickly determine if the fungus is actively producing the toxin. In this study, scientists designed e-probes from genes that were highly active during aflatoxin production in A. flavus. They then used EDNAtran to see if these e-probes could detect gene transcripts related to aflatoxin production in corn samples.

Here's a breakdown of how EDNAtran works:
  • E-probe Design: Create unique e-probes that match specific gene sequences involved in aflatoxin production.
  • RNA Sequencing: Extract RNA from the sample and sequence it to identify active genes.
  • EDNAtran Analysis: Use EDNAtran to search the RNA sequence data for the presence of the e-probes.
  • Detection: If the e-probes are found, it indicates that the aflatoxin-related genes are active, suggesting the presence of aflatoxin-producing fungi.
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From Fungal Screening to Advanced Biosensing

Research on aflatoxin control spans both biological inhibition and improved detection. In fermented maize slurry, toxigenic Aspergillus flavus and A. parasiticus were isolated after ammonium hydroxide screening, with reported aflatoxin levels of 877 and 797 ng g-1, respectively. A 2025 review describes the field's progression from classical detection methods toward advanced biosensing techniques for aflatoxins produced by Aspergillus species.

Validation Is Still the Hurdle

Transcriptomic screening approaches remain promising but incompletely validated for determining whether aflatoxin production is active. The EDNAtran study calls for multiple blind samples, while related work says further validation should include more toxigenic strains sequenced in metatranscriptomes. These limitations matter because regulatory expectations are based on keeping contamination within permissible levels established by national guidelines.

Comparing Aflatoxin M1 Tests

A comparative guide examines Aflatoxin M1 determination in raw milk using an HPLC-FL method alongside commercial ELISA kits. The cited application used raw milk samples from various regions of Greece. The same guide also points to a 2024 review of the advantages and limitations of mycotoxin detection techniques in food and feed.

The results were promising. EDNAtran successfully detected gene transcripts related to aflatoxin production in corn samples known to be contaminated with aflatoxin. This was a clear signal that the method works. In contrast, when the e-probes were used on samples where aflatoxin was not produced, the results were significantly different. This confirms that EDNAtran can accurately distinguish between samples with and without aflatoxin production.

A Safer Future for Our Food Supply

EDNAtran offers a new, rapid, and potentially cost-effective way to screen crops for aflatoxin contamination. By focusing on gene activity, this method can quickly identify the presence of aflatoxin-producing fungi, helping to prevent contaminated food from reaching consumers. As sequencing technology continues to advance and become more affordable, EDNAtran could become a standard tool for ensuring food safety worldwide. Imagine a world where we can quickly and accurately detect these toxins, protecting our health and securing our food supply for everyone.

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Why Method Choice Matters

Thin-layer chromatography remains an accepted reference method for detecting aflatoxins. However, quantitative analysis has in most cases shifted to high-performance liquid chromatography and ultra-performance liquid chromatography. The transition reflects the central role of quantitative measurement when assessing aflatoxin contamination across food matrices.

Technology Across the Supply Chain

Aflatoxin has remained a decades-old food-safety problem despite long-standing efforts to control it. The cited review argues that artificial intelligence and biotechnology could improve control throughout the food supply chain. Its emphasis is on technologies that address aflatoxin risks across crops and multiple stages of production and distribution.

A One Health Challenge

Aflatoxin contamination is presented as an agri-food systems problem rather than only a laboratory detection problem. A 2025 review concludes that reducing risk requires integrated, multi-sectoral interventions anchored in a One Health approach. The stated goals include reducing aflatoxin risks, promoting food security, and protecting human and environmental health globally.

Trust in Food-Safety Data

A 2026 Foods case study proposes a blockchain-based dual-track mechanism for trusted circulation of food-safety detection data and batch-level risk control. The study focuses specifically on an aflatoxin B1 case and is identified as Foods 2026, volume 15, article 3055. Its approach connects laboratory detection records with batch-level food-safety management.

AF36 and AF70 tested in broth and ground corn

PopulationAspergillus flavus AF36 and AF70 strains grown on PDB and ground corn[1]
Sample sizefour RNA sequencing samples[1]
Settinglaboratory; strains grown on PDB and ground corn[1]
ComparisonAF70 growing on PDB, and AF36 on corn and PDB[1]
Main outcomeEDNAtran discriminated between transcriptomic datasets with abundant and low aflatoxin production[1]
Effect size231 e-probes had hits creating High-Quality Matches in AF70-corn transcriptome datasets[1]
p-valuelower than 0.05[1]
FundingOklahoma Agricultural Research Station (project number OKL 02859), Department of Entomology and Plant Pathology, Oklahoma State University, and U.S. Department of Agriculture, Agricultural Research Service (Appropriated Project #8044-22000-040-00D)[1]
Times cited21[1]

What the probe signal can and cannot tell us

The probe design may extend to toxigenic strains with similar SNP patterns in the toxin-gene cluster, but this does not establish equal detection across all such strains.[2]

Where the evidence is still narrow

  • Only one replicate was used for each of the four sequencing samples, limiting how well the results capture variation between repeated samples.[1]
  • The authors called for blind-sample testing to determine whether the protocol can indicate active toxin production reliably.[2]
  • The study did not generate genome-wide probes for AF36 because that strain’s genome sequence was unavailable to the researchers.[2]

What remains unresolved about EDNAtran

  • Would the probe signal remain dependable when samples are analyzed blind and their toxin-production status is not known in advance?[2]
  • How well would the approach perform with a broader range of toxigenic strains represented in mixed-community transcriptomes?[2]

Sources

  1. Inferring the presence of aflatoxin-producing Aspergillus flavus strains using RNA sequencing and electronic probes as a transcriptomic screening tool (Public Library of Science (PLoS), 2018)
  2. Inferring the presence of aflatoxin-producing Aspergillus flavus strains using RNA sequencing and electronic probes as a transcriptomic screening tool (Europe PMC, 2018)

About this Article -

Written with AI assistance from published research, and reviewed by the Mystum team. See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.1371/journal.pone.0198575, Alternate LINK

Title: Inferring The Presence Of Aflatoxin-Producing Aspergillus Flavus Strains Using Rna Sequencing And Electronic Probes As A Transcriptomic Screening Tool

Subject: Multidisciplinary

Journal: PLOS ONE

Publisher: Public Library of Science (PLoS)

Authors: Andres S. Espindola, William Schneider, Kitty F. Cardwell, Yisel Carrillo, Peter R. Hoyt, Stephen M. Marek, Hassan A. Melouk, Carla D. Garzon

Published: 2018-10-16

Everything You Need To Know

1

What are aflatoxins and why are they a concern?

Aflatoxins are a group of toxic compounds produced by the fungus Aspergillus flavus, with aflatoxin B₁ being particularly dangerous due to its carcinogenic properties. These toxins contaminate various crops like maize, peanuts, and spices. Exposure to aflatoxins poses a significant health risk, emphasizing the importance of detecting and preventing their presence in the food supply.

2

What is Aspergillus flavus and why is it important?

Aspergillus flavus is a fungus that produces aflatoxins, which are toxic compounds that can contaminate crops. Its significance lies in its ability to cause severe health issues. Identifying the presence of Aspergillus flavus is crucial for food safety because it directly indicates the potential for aflatoxin contamination, necessitating rapid and accurate testing methods to prevent contaminated products from reaching consumers. It's a key concern for food biosecurity.

3

What is EDNAtran and why is it significant?

EDNAtran is a new diagnostic tool that utilizes electronic probes (e-probes) to detect specific gene activity related to aflatoxin production in Aspergillus flavus. The process involves designing e-probes that target genes active during aflatoxin production, sequencing RNA from a sample, and using EDNAtran to analyze the RNA sequence data. The presence of e-probes indicates the activity of aflatoxin-related genes, signifying the presence of aflatoxin-producing fungi. This technology is significant as it offers a faster, more efficient, and potentially cost-effective method for screening crops, thereby enhancing food safety.

4

What are e-probes and how are they used?

E-probes are electronic probes designed to match specific gene sequences involved in aflatoxin production in the fungus Aspergillus flavus. They act like molecular search engines, targeting genes that become active when aflatoxins are being produced. These e-probes are crucial for EDNAtran technology, which uses them to identify and detect the presence of the fungus and its toxins. Using these probes, scientists can quickly determine if the fungus is actively producing the toxin, enabling rapid detection of contamination.

5

What is RNA sequencing and why is it used in this context?

RNA sequencing is a process used in conjunction with EDNAtran to identify active genes within a sample, such as crops. This method extracts RNA, sequences it, and analyzes the data to find specific gene activity. The significance of RNA sequencing lies in its ability to provide a detailed snapshot of gene expression, allowing scientists to detect the presence of aflatoxin-producing fungi by identifying the activity of genes involved in aflatoxin production. This provides a method to detect contamination.

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