Unsupervised classification of environmental marine microbes using a Raman spectra-based deep learning framework

Fengyun LÜ; Yanmei ZHANG; Hongtao LIANG; Luyang SUN

doi:10.1007/s00343-025-5087-z

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Unsupervised classification of environmental marine microbes using a Raman spectra-based deep learning framework

Biology | Updated：2026-05-07

- Unsupervised classification of environmental marine microbes using a Raman spectra-based deep learning framework
- Unsupervised classification of environmental marine microbes using a Raman spectra-based deep learning framework
- 海洋湖沼学报(英文) 2026年44卷第2期页码：728-742
- Affiliations：
  
  1.School of Information Science and Technology, Qingdao University of Science and Technology, Qingdao 266100, China
  2.Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao New Energy Shandong Laboratory, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
  3.College of Life Science, University of Chinese Academy of Sciences, Beijing 101408, China
- Author bio：
  
  lht@qust.edu.cn
  sunly@qibebt.ac.cn
- Funds：
  
  the National Key Research and Development Program of China(2022YFF0713102);the Key Technology Research and Development Program of Shandong Province(2024KJHZ033);the National Natural Science Foundation of China(32200448)
- DOI：10.1007/s00343-025-5087-z
  中图分类号：
- 收稿：2025-03-24，
  
  录用：2025-04-22，
  
  网络首发：2025-05-28，
  
  纸质出版：2026-03-01
- Accepted：
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Fengyun LÜ, Yanmei ZHANG, Hongtao LIANG, 等. Unsupervised classification of environmental marine microbes using a Raman spectra-based deep learning framework[J]. 海洋湖沼学报(英文), 2026,44(2):728-742.

LÜ Fengyun,ZHANG Yanmei,LIANG Hongtao,et al.Unsupervised classification of environmental marine microbes using a Raman spectra-based deep learning framework[J].Journal of Oceanology and Limnology,2026,44(02):728-742.
Fengyun LÜ, Yanmei ZHANG, Hongtao LIANG, 等. Unsupervised classification of environmental marine microbes using a Raman spectra-based deep learning framework[J]. 海洋湖沼学报(英文), 2026,44(2):728-742. DOI： 10.1007/s00343-025-5087-z.

LÜ Fengyun,ZHANG Yanmei,LIANG Hongtao,et al.Unsupervised classification of environmental marine microbes using a Raman spectra-based deep learning framework[J].Journal of Oceanology and Limnology,2026,44(02):728-742. DOI： 10.1007/s00343-025-5087-z.

摘要

Abstract

The development of microfluidic-based Raman devices has enabled the acquisition of thousands of single-cell Raman spectra from complex microbial populations

offering new avenues for characterizing environmental bacteria. We proposed and validated the convolutional deep embedded clustering (CDEC) model

a clustering framework designed for the unsupervised classification of marine microbial Raman spectra. A four-stage analytical framework was employed to systematically assess the performance of the CDEC model

with increasing dataset complexity ranging from mock communities of pure bacterial cultures to natural microbial populations isolated from seawater. The CDEC algorithm consistently distinguished bacterial species across all stages

achieving an average accuracy of 97.27%

and surpassed the baseline methods in performance. In natural microbial communities

the model resolved eight distinct clusters with unique Raman spectral markers

revealing underlying metabolic heterogeneity. These results highlight the scalability and utility of the CDEC model for studying marine microbial diversity and characterizing microbial composition and metabolic traits at single-cell resolution.

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references

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