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Keywords = de-redundant colony selection

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12 pages, 2908 KB  
Article
An Intelligent Strategy for Colony De-Replication Using Raman Spectroscopy and Hybrid Clustering
by Xinli Li, Mingyang Liu, Jiaqi Sun and Su Wang
Fermentation 2025, 11(12), 691; https://doi.org/10.3390/fermentation11120691 - 12 Dec 2025
Viewed by 439
Abstract
Efficient de-redundant colony picking is essential to accelerating strain screening in fermentation microbiology. Conventional random picking is inefficient, exhibits high redundancy, and often misses low-abundance but valuable strains. To address this, we present a high-efficiency de-redundant selection strategy based on colony Raman spectroscopy [...] Read more.
Efficient de-redundant colony picking is essential to accelerating strain screening in fermentation microbiology. Conventional random picking is inefficient, exhibits high redundancy, and often misses low-abundance but valuable strains. To address this, we present a high-efficiency de-redundant selection strategy based on colony Raman spectroscopy and a hybrid clustering algorithm. We directly acquire colony Raman spectra and combine the complementary strengths of k-means and hierarchical clustering (HCA) to achieve both balanced global partitioning and sensitivity to low-abundance taxa. Systematic application on pure colonies and complex plate settings shows that, by picking only 12–26% of colonies, the method attains 80–100% species coverage. Relative to manual random picking and image-based feature selection, picking efficiency increased by 116.8% and 44.5%, respectively, substantially shortening the screening cycle and reducing workload. Overall, Raman-guided hybrid clustering substantially reduces redundant picking and improves detection of low-abundance strains. It provides practical support for efficient strain discovery, library construction, and process optimization. Full article
(This article belongs to the Section Fermentation Process Design)
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