Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes. Kanno et al.

In the natural environments, there are various phylogenetic groups of Bacteria and Archaea including unknown microorganisms. Non-destructive, single-cell level species discrimination will contribute to single-cell genomics, ecophysiological analysis at the single-cell level, and isolation. Using single-cell Raman spectra of six microorganisms (three bacteria and three archaea) and machine learning, we tested whether it is possible to identify microbial species at the single-cell level, and succeeded in classifying them with high accuracy. The datasets are raw single-cell Raman spectra acquired from microbial cells suspended in phosphate buffer solution (PBS). Contents: 1) Single-cell Raman spectra of 6 prokaryotic species Escherichia coli JCM 20135 Bacillus subtilis JCM 1465T Thermus thermophilus JCM 10941T Thermococcus kodakarensisJCM 12380T Sulfolobus acidocaldarius JCM 8929T Nitrososphaera viennensis JCM 19564T 2) Raman spectra of PBS (10 times/file) 3) Neon standard The numerical part of the file name is related to the numerical part of the folder name that contains the Raman spectra of the microorganisms. # Column 1 in the file is only a reference for the Raman shift. Do not use it. # Please follow the method described in the paper to remove cosmic rays, subtract PBS spectrum, use neon standards to integrate data from different days, make baseline corrections, and normalize the data.

在自然环境中，存在涵盖未知微生物在内的各类细菌与古菌系统发育类群。
无损的单细胞水平物种鉴定将对单细胞基因组学、单细胞水平生理生态分析以及菌株分离工作具有重要推动作用。
本研究采用6种微生物（3种细菌、3种古菌）的单细胞拉曼光谱（single-cell Raman spectra）结合机器学习方法，验证了单细胞水平鉴定微生物物种的可行性，并成功实现了高精度分类。
本数据集为悬浮于磷酸缓冲液（Phosphate Buffer Solution，PBS）中的微生物细胞所采集的原始单细胞拉曼光谱。数据集内容如下：
1) 6种原核生物的单细胞拉曼光谱：大肠杆菌JCM 20135、枯草芽孢杆菌JCM 1465^T、嗜热栖热菌JCM 10941^T、柯达热球菌JCM 12380^T、酸热硫化叶菌JCM 8929^T、维也纳亚硝化球菌JCM 19564^T；
2) 磷酸缓冲液（PBS）的拉曼光谱（每份文件含10次测量结果）；
3) 氖气标准光谱。
文件名中的数字部分与存储微生物拉曼光谱的文件夹名称中的数字部分相对应。
# 文件中的第1列仅为拉曼位移参考，请勿使用。
# 请遵循论文中描述的方法去除宇宙射线、扣除PBS光谱、使用氖气标准品整合不同日期的数据集、进行基线校正与数据归一化。