Protocol for bacterial typing using Fourier transform infrared spectroscopy

Huayan Yang; Haimei Shi; Bin Feng; Li Wang; Liangqiang Chen; Avelino Alvarez-Ordóñez; Li Zhang; Hao Shen; Jianhua Zhu; Shouning Yang; Chuanfan Ding; Miguel Prietod; Fan Yang; Shaoning Yu

doi:10.1016/j.xpro.2023.102223

Protocol for bacterial typing using Fourier transform infrared spectroscopy

STAR Protoc. 2023 Apr 15;4(2):102223. doi: 10.1016/j.xpro.2023.102223. Online ahead of print.

Authors

Huayan Yang¹, Haimei Shi¹, Bin Feng¹, Li Wang², Liangqiang Chen², Avelino Alvarez-Ordóñez³, Li Zhang⁴, Hao Shen¹, Jianhua Zhu⁵, Shouning Yang⁶, Chuanfan Ding⁶, Miguel Prietod⁷, Fan Yang⁸, Shaoning Yu⁹

Affiliations

¹ Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China; Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
² Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
³ Institute of Food Science and Technology, University of León, 24071 León, Spain.
⁴ Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.
⁵ Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China.
⁶ Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
⁷ Institute of Food Science and Technology, University of León, 24071 León, Spain. Electronic address: miguel.prieto@unileon.es.
⁸ Kweichow Moutai Group, Renhuai, Guizhou 564501, China. Electronic address: yangfanmt@189.cn.
⁹ Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China; Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China. Electronic address: yushaoning@nbu.edu.cn.

Abstract

The Fourier transform infrared (FT-IR) signals obtained from bacterial samples are specific and reproducible, making FT-IR an efficient tool for bacterial typing at a subspecies level. However, the typing accuracy could be affected by many factors, including sample preparation and spectral acquisition. Here, we present a unified protocol for bacterial typing based on FT-IR spectroscopy. We describe sample preparation from bacterial culture and FT-IR spectrum collection. We then detail FT-IR spectrum preprocessing and multivariate analysis of spectral data for bacterial typing.

Keywords: Bioinformatics; Biophysics; Cell Biology; Cell culture; Health Sciences; Microbiology.