Key Points
- Researchers developed an innovative method combining adaptive Raman spectral acquisition (ACRA-SNR) and a Raman Shifted Window transformer (Ra-ST) AI model to classify lactic acid bacteria (LAB) colonies with high speed and 98.2% accuracy.
- The ACRA-SNR technique addresses the challenge of colony-level spatial heterogeneity by selectively capturing high-quality spectral data, ensuring more consistent and reliable classification results.
- The Ra-ST model outperformed existing deep learning models like ResNet and RaT, showed strong generalization to new strains, and demonstrated potential for broader use in detecting various functional bacteria beyond LAB.
A recent study explored a new technique that combines adaptive Raman spectral acquisition and an artificial intelligence (AI) model to enable rapid and accurate classification of lactic acid bacteria (LAB) colonies. This study, which was published in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, proposed an adaptive colony Raman acquisition method based on the signal-to-noise ratio (ACRA-SNR), which, when integrated with Raman Shifted Window (Swin) transformer (Ra-ST), improved the classification of LAB colonies (1). This study shows how Raman spectroscopy and AI are being combined in unique ways to improve microbial analysis and innovate industrial biotechnology.
What are LAB?
Lactic acid bacteria, or LAB, are microorganisms used in the fermented food industry (2). Their role in this industry is to ferment carbohydrates to produce lactic acid, which helps create several food products (2). LABs can improve the flavor of fermented foods and reduce harmful substances, but they can also be used as probiotics (2). Because of the benefits that they offer, LAB are important in several industries, which makes their efficient and accurate identification necessary.
The issue is that traditional methods struggle with colony-level variability and are time-intensive (1). In their study, the researchers show how the new ACRA-SNR and Ra-ST pipeline addresses these bottlenecks by delivering in situ classification with improved speed and accuracy (1).
What are some of the challenges in microbial colony analysis?
In microbial colony analysis, one of the main challenges is the spatial heterogeneity within colonies. The problem with this variability is that it can directly impact the spectral data and reduce classification reliability (1). The ACRA-SNR technique is designed to resolve this issue by adaptively acquiring Raman signals based on the signal-to-noise ratio. This approach ensures that only high-quality spectral data are collected, thus enhancing the consistency and representativeness of the spectra used for identification (1).
What did the Ra-ST model do to improve accuracy?
Building on the robust data provided by ACRA-SNR, the team implemented the Ra-ST model, which is a neural network (NN) architecture that leverages hierarchical layers and a shifted window-based self-attention mechanism (1). When applied to a data set comprising fourteen LAB strains, the Ra-ST model achieved an impressive classification accuracy of 98.2% (1).
Then, the researchers tested the model’s generalization capability. To do so, the researchers used LAB strains that belonged to the same species included in the original dataset but were sourced from entirely different environments (1). The researchers found that the Ra-ST model still achieved identification accuracy exceeding 70% (1).
Comparative analysis with other state-of-the-art deep learning architectures, including ResNet and Raman Transformer (RaT) models, further underscored the superiority of the Ra-ST model in both classification accuracy and predictive performance.
What was notable about the Ra-ST model?
A notable aspect of the Ra-ST model is its nuanced attention distribution across Raman spectral bands. The model showed a denser and broader focus on biologically relevant peaks, particularly at 784 cm⁻¹, 1104 cm⁻¹, 1096 cm⁻¹, 1340 cm⁻¹, 1452 cm⁻¹, and 1660 cm⁻¹, than either the RaT or ResNet models (1).
The integration of ACRA-SNR and Ra-ST presents a scalable solution for real-time, high-accuracy bacterial identification in industrial settings. The method holds particular promise for sectors reliant on fermentation and microbial quality control, where misclassification can lead to costly delays or product failures (1).
Moreover, the researchers suggest that this framework is not limited to LAB alone. This experimental model can be extended to the multi-class rapid detection tasks of other functional bacteria (1). By addressing the dual challenges of spectral noise and microbial heterogeneity at the colony level, and coupling this with an advanced transformer model, the research sets a new benchmark for the rapid and accurate classification of bacteria (1).
References
- Wang, Y.; Xu, L.; Shang, L.; et al. Deep Learning-assisted Raman Spectroscopy for Rapid Lactic Acid Bacteria Identification at the Colony Level. Spectrochimica Acta Part A: Mol. Biomol. Spectrosc. 2026, 344 Part 1, 126662. DOI: 10.1016/j.saa.2025.126662
- Wang, Y.; Wu, J.; Lv, M.; et al. Metabolism Characteristics of Lactic Acid Bacteria and the Expanding Applications in Food Industry. Front. Bioeng. Biotechnol. 2021, 9, 612285. DOI: 10.3389/fbioe.2021.612285
