Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms

Overview

Journal Molecules

Publisher MDPI

Specialty Biology

Date 2024 Mar 13

PMID 38474589

Authors

Sandra Baaba Frempong

Markus Salbreiter

Sara Mostafapour

Aikaterini Pistiki

Thomas W Bocklitz

Petra Rosch

Jurgen Popp

Affiliations

Soon will be listed here.

Abstract

Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.

Citing Articles

Lighting the Path: Raman Spectroscopy's Journey Through the Microbial Maze.

Salbreiter M, Frempong S, Even S, Wagenhaus A, Girnus S, Rosch P Molecules. 2025; 29(24).

PMID: 39770046 PMC: 11870064. DOI: 10.3390/molecules29245956.

References

Yamamoto T, Taylor J, Koseki S, Koyama K . Classification of food spoilage bacterial species and their sodium chloride, sodium acetate and glycine tolerance using chemometrics analysis and Raman spectroscopy. J Microbiol Methods. 2021; 190:106326. DOI: 10.1016/j.mimet.2021.106326. View

Klein D, Breuch R, von der Mark S, Wickleder C, Kaul P . Detection of spoilage associated bacteria using Raman-microspectroscopy combined with multivariate statistical analysis. Talanta. 2019; 196:325-328. DOI: 10.1016/j.talanta.2018.12.094. View

Liu B, Liu K, Wang N, Ta K, Liang P, Yin H . Laser tweezers Raman spectroscopy combined with deep learning to classify marine bacteria. Talanta. 2022; 244:123383. DOI: 10.1016/j.talanta.2022.123383. View

Garcia-Timermans C, Rubbens P, Kerckhof F, Buysschaert B, Khalenkow D, Waegeman W . Label-free Raman characterization of bacteria calls for standardized procedures. J Microbiol Methods. 2018; 151:69-75. DOI: 10.1016/j.mimet.2018.05.027. View

Stockel S, Meisel S, Elschner M, Melzer F, Rosch P, Popp J . Raman spectroscopic detection and identification of Burkholderia mallei and Burkholderia pseudomallei in feedstuff. Anal Bioanal Chem. 2014; 407(3):787-94. DOI: 10.1007/s00216-014-7906-5. View

Muhamadali H, Weaver D, Subaihi A, AlMasoud N, Trivedi D, Ellis D . Chicken, beams, and Campylobacter: rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry. Analyst. 2015; 141(1):111-22. DOI: 10.1039/c5an01945a. View

Kumar B N V, Kampe B, Rosch P, Popp J . Characterization of carotenoids in soil bacteria and investigation of their photodegradation by UVA radiation via resonance Raman spectroscopy. Analyst. 2015; 140(13):4584-93. DOI: 10.1039/c5an00438a. View

Ho C, Jean N, Hogan C, Blackmon L, Jeffrey S, Holodniy M . Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learning. Nat Commun. 2019; 10(1):4927. PMC: 6960993. DOI: 10.1038/s41467-019-12898-9. View

Azemtsop Matanfack G, Pistiki A, Rosch P, Popp J . Raman Stable Isotope Probing of Bacteria in Visible and Deep UV-Ranges. Life (Basel). 2021; 11(10). PMC: 8539138. DOI: 10.3390/life11101003. View

10.

Germond A, Ichimura T, Horinouchi T, Fujita H, Furusawa C, Watanabe T . Raman spectral signature reflects transcriptomic features of antibiotic resistance in . Commun Biol. 2018; 1:85. PMC: 6123714. DOI: 10.1038/s42003-018-0093-8. View

11.

Rodriguez L, Zhang Z, Wang D . Recent advances of Raman spectroscopy for the analysis of bacteria. Anal Sci Adv. 2024; 4(3-4):81-95. PMC: 10989577. DOI: 10.1002/ansa.202200066. View

12.

Jarvis R, Goodacre R . Discrimination of bacteria using surface-enhanced Raman spectroscopy. Anal Chem. 2003; 76(1):40-7. DOI: 10.1021/ac034689c. View

13.

Shokrekhodaei M, Quinones S . Review of Non-invasive Glucose Sensing Techniques: Optical, Electrical and Breath Acetone. Sensors (Basel). 2020; 20(5). PMC: 7085605. DOI: 10.3390/s20051251. View

14.

Lopez-Diez E, Winder C, Ashton L, Currie F, Goodacre R . Monitoring the mode of action of antibiotics using Raman spectroscopy: investigating subinhibitory effects of amikacin on Pseudomonas aeruginosa. Anal Chem. 2005; 77(9):2901-6. DOI: 10.1021/ac048147m. View

15.

Mikoliunaite L, Rodriguez R, Sheremet E, Kolchuzhin V, Mehner J, Ramanavicius A . The substrate matters in the Raman spectroscopy analysis of cells. Sci Rep. 2015; 5:13150. PMC: 4550836. DOI: 10.1038/srep13150. View

16.

Berry M, Kearns H, Graham D, Faulds K . Surface enhanced Raman scattering for the multiplexed detection of pathogenic microorganisms: towards point-of-use applications. Analyst. 2021; 146(20):6084-6101. PMC: 8504440. DOI: 10.1039/d1an00865j. View

17.

Butler H, Ashton L, Bird B, Cinque G, Curtis K, Dorney J . Using Raman spectroscopy to characterize biological materials. Nat Protoc. 2016; 11(4):664-87. DOI: 10.1038/nprot.2016.036. View

18.

Daniel F, Kesterson D, Lei K, Hord C, Patel A, Kaffenes A . Application of Microfluidics for Bacterial Identification. Pharmaceuticals (Basel). 2022; 15(12). PMC: 9781190. DOI: 10.3390/ph15121531. View

19.

Roelofsen E, van Leeuwen M, Wilkinson M, Degener J . Evaluation of the effects of storage in two different swab fabrics and under three different transport conditions on recovery of aerobic and anaerobic bacteria. J Clin Microbiol. 1999; 37(9):3041-3. PMC: 85450. DOI: 10.1128/JCM.37.9.3041-3043.1999. View

20.

Azemtsop Matanfack G, Ruger J, Stiebing C, Schmitt M, Popp J . Imaging the invisible-Bioorthogonal Raman probes for imaging of cells and tissues. J Biophotonics. 2020; 13(9):e202000129. DOI: 10.1002/jbio.202000129. View