Tracking trash to treasure: in situ monitoring of single microbial cell oil biosynthesis from waste cooking oil using Raman spectroscopy and imaging

Jiro Karlo, Victor Carrasco-Navarro, Arto Koistinen and Surya Pratap Singh

RSC Adv., 2024, 14, 33323
DOI: 10.1039/D4RA05187D

Simultaneous Raman and infrared spectroscopy: a novel combination for studying bacterial infections at the single cell level

Cassio Lima, Shwan Ahmed, Yun Xu, Howbeer Muhamadali, Christopher Parry, Rachel J. McGalliard, Enitan D. Carrol and Royston Goodacre

Chem. Sci., 2022, 13, 8171
DOI: 10.1039/D2SC02493D

Multi-element stable isotope Raman microspectroscopy of bacterial carotenoids unravels rare signal shift patterns and single-cell phenotypic heterogeneity

Julian Weng, Kara Müller, Oleksii Morgaienko, Martin Elsner and Natalia P. Ivleva

Analyst, 2023, 148, 128
DOI: 10.1039/D2AN01603F

Surface-enhanced Raman spectroscopy combined with stable isotope probing to assess the metabolic activity of Escherichia coli cells in chicken carcass wash water

Heera Jayan, Da-Wen Sun, Hongbin Pu and Qingyi Wei

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2022, 280, 121549
DOI: 10.1016/j.saa.2022.121549

Raman stable isotope probing (SIP): A novel bio-analytical tool

Jiro Karlo, Rishikesh Pandey and Surya Pratap Singh

TrAC Trends in Analytical Chemistry, 2025, 193, 118475
DOI: 10.1016/j.trac.2025.118475

Application of infrared spectroscopy to study carbon-deuterium kinetics and isotopic spectral shifts at the single-cell level

Sahand Shams, Shwan Ahmed, Daniel Smaje, Thanyaporn Tengsuttiwat, Cassio Lima, Royston Goodacre and Howbeer Muhamadali

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2025, 327, 125374
DOI: 10.1016/j.saa.2024.125374

Application of Rapid Evaporative Ionization Mass Spectrometry (REIMS) to Identify Antimicrobial Resistance in Uropathogenic Escherichia coli (UPEC) Isolates via Deuterium Isotope Probing

Sahand Shams, Sara Sadia Chowdhury, Joel Doherty, Shwan Ahmed, Dakshat Trivedi, Yun Xu, Joscelyn Sarsby, Claire E Eyers, Adam Burke, Royston Goodacre and Howbeer Muhamadali

Anal. Chem., 2025, 97, 18444
DOI: 10.1021/acs.analchem.5c00667

Analyzing macromolecular composition of E. Coli O157:H7 using Raman-stable isotope probing

Heera Jayan, Hongbin Pu and Da-Wen Sun

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2022, 276, 121217
DOI: 10.1016/j.saa.2022.121217

Optical photothermal infrared spectroscopy: A novel solution for rapid identification of antimicrobial resistance at the single-cell level via deuterium isotope labeling

Sahand Shams, Cassio Lima, Yun Xu, Shwan Ahmed, Royston Goodacre and Howbeer Muhamadali

Front. Microbiol., 2023, 14
DOI: 10.3389/fmicb.2023.1077106

Metabolic models of human gut microbiota: Advances and challenges

Daniel Rios Garza, Didier Gonze, Haris Zafeiropoulos, Bin Liu and Karoline Faust

Cell Systems, 2023, 14, 109
DOI: 10.1016/j.cels.2022.11.002

Surface-Enhanced Raman Scattering Nanosensing and Imaging in Neuroscience

Ryma Boudries, Hannah Williams, Soraya Paquereau--Gaboreau, Saba Bashir, Maryam Hojjat Jodaylami, Malama Chisanga, Louis-Éric Trudeau and Jean-Francois Masson

ACS Nano, 2024, 18, 22620
DOI: 10.1021/acsnano.4c05200

Raman-Activated, Interactive Sorting of Isotope-Labeled Bacteria

Sepehr Razi, Nicolae Tarcea, Thomas Henkel, Ramya Ravikumar, Aikaterini Pistiki, Annette Wagenhaus, Sophie Girnus, Martin Taubert, Kirsten Küsel, Petra Rösch and Jürgen Popp

Sensors, 2024, 24, 4503
DOI: 10.3390/s24144503

Mapping endocrine networks by stable isotope tracing

Ruth Andrew and Roland H. Stimson

Current Opinion in Endocrine and Metabolic Research, 2022, 26, 100381
DOI: 10.1016/j.coemr.2022.100381

Monitoring of microbial proteome dynamics using Raman stable isotope probing

Jiro Karlo, Ashish Kumar Dhillon, Soumik Siddhanta and Surya Pratap Singh

Journal of Biophotonics, 2023, 16
DOI: 10.1002/jbio.202200341

Sensing and hyperspectral imaging of the newly synthesized carotenoids in single-cell micro-factories

Jiro Karlo, Nilesh Kumar Dewangan, Anaya Atul Phatak and Surya Pratap Singh

Sensors and Actuators B: Chemical, 2026, 451, 139367
DOI: 10.1016/j.snb.2025.139367

Environmental microbial bioprospecting enabled by a Raman fingerprinting and functional sorting on a microfluidic static droplet array

Guoxia Zheng, Yanwen Liu, Huicheng Chen, Ling Lu, Lin Wang, Tingting Jia and Yunhua Wang

Analytica Chimica Acta, 2026, 1400, 345319
DOI: 10.1016/j.aca.2026.345319

Reverse stable isotope labelling with Raman spectroscopy for microbial proteomics

Jiro Karlo, Ashish Kumar Dhillon, Soumik Siddhanta and Surya Pratap Singh

Journal of Biophotonics, 2024, 17
DOI: 10.1002/jbio.202300341

Metabolite microextraction on surface-enhanced Raman scattering nanofibres and D2O probing accelerate antibiotic susceptibility testing

Malama Chisanga, Claudèle Lemay-St-Denis, Xinran Wei, Yuzhang Liang, Mengdi Lu, Wei Peng, Joelle N. Pelletier and Jean-Francois Masson

npj Biosensing, 2025, 2
DOI: 10.1038/s44328-025-00039-w

Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes

Wannes Nauwynck, Karoline Faust and Nico Boon

FEMS Microbiology Reviews, 2025, 49
DOI: 10.1093/femsre/fuaf032

Investigating Salmonella biofilm responses to antibiotic treatment using optical photothermal infrared spectroscopy

Daniel Smaje, Xiaojun Zhu, Jay C. D. Hinton, Rasmita Raval, Royston Goodacre and Howbeer Muhamadali

Commun Biol, 2026, 9
DOI: 10.1038/s42003-026-09655-2

Raman Microspectroscopy to Trace the Incorporation of Deuterium from Labeled (Micro)Plastics into Microbial Cells

Kara Müller, Martin Elsner, Anna E. Leung, Hanna Wacklin-Knecht, Jürgen Allgaier, Maria Heiling and Natalia P. Ivleva

Anal. Chem., 2025, 97, 4440
DOI: 10.1021/acs.analchem.4c05827

Visualization of de novo synthesized nascent purine and pyrimidine using carbon isotope imaging and spectral tracing (CIIST) in single microbial cell

Jiro Karlo, Tejas Ajit Mhaiskar, Hrishikesh Ravindra Karande and S.P. Singh

Analytica Chimica Acta, 2026, 1384, 344986
DOI: 10.1016/j.aca.2025.344986