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

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

Microbial communities play crucial roles in shaping natural ecosystems, impacting human well-being, and driving advancements in industrial biotechnology. However, associating specific metabolic functions with bacteria proves challenging due to the vast diversity of microorganisms within these communities. In the past decades stable isotope probing (SIP) approaches, coupled with vibrational spectroscopy, have emerged as a novel method for revealing microbial metabolic roles and interactions in complex communities. In this study, we employed various combinations of heavy stable isotopes (D, 13C, 15N, and 18O), to evaluate all possible isotopic spectral shifts in the mid-IR region using Fourier-Transform Infrared (FT-IR) and Optical Photothermal Infrared (O-PTIR) spectroscopy, at both community and single-cell levels. Additionally, we conducted a time-course study to explore the kinetics of CD vibration in Escherichia coli bacteria, allowing time-based sampling and assessment of isotopic labeling kinetics. The FT-IR and O-PTIR, along with the second derivative spectra of E. coli cells cultured in minimal medium supplemented with various combinations of heavy isotopes exhibited notable similarities. Several spectral shifts in primary vibrational peaks were observed due to the incorporation of heavy isotopes into various biomolecules. Remarkably, the incorporation of deuterium into amide groups, resulting in the formation of nitrogen-deuterium bonds, caused a shift in amide A and B into the silent region, overlapping with CD signature peaks. The incorporation of 18O into the ester group of lipids and the carbonyl group of proteins resulted in a notable shift to the lower wavenumber region. Additionally, the second derivative of FT-IR spectral data highlighted the integration of 18O into α-helix and β-sheet structures. Furthermore, the spectra, second derivative, and PC-DFA scores and loadings plot of FT-IR data collectively illustrated the practicality of monitoring 13C and D incorporation into E. coli bacterial cells within the first 30-min incubation period. The findings of this study suggest that FT-IR and O-PTIR can serve as efficient tools for monitoring the incorporation of heavy isotopes into bacteria at both the population and single-cell levels. Additionally, the SIP approach allowed us to assign two new deuterium-associated vibrational peaks to their corresponding functional groups, which to the best of our knowledge have not been reported previously.

Probing Mineral-Organic Interfaces in Soils and Sediments Using Optical Photothermal Infrared Microscopy

Interactions among microbes, minerals, and organic matter are key controls on carbon, nutrient, and contaminant dynamics in soils and sediments. However, probing these interactions at relevant scales and through time remains an analytical challenge due to both their complex nature and the need for tools permitting nondestructive and real-time analysis at sufficient spatial resolution. Here, we demonstrate the ability and provide analytical recommendations for the submicron-scale characterization of complex mineral-organic microstructures using optical photothermal infrared (O-PTIR) microscopy. Compared to conventional infrared techniques, O-PTIR spectra collected at submicron resolution of environmentally relevant mineral and organic reference compounds demonstrated similar spectral quality and sensitivity. O-PTIR detection sensitivity was greatest for highly crystalline minerals and potentially for low molecular weight organic compounds. Due to photothermal effects, O-PTIR was more sensitive toward organics than minerals compared to conventional IR approaches, even when organics were mineral-bound. Moreover, O-PTIR resolved mineral-bound and unbound organics in a complex mixture at submicron (<500 nm) resolution. Finally, we provide best practices for artifact-free analysis of organic and mineral samples by determining the appropriate laser power using damage thresholds. Our results highlight the potential of O-PTIR microscopy for nondestructive and time-resolved analysis of dynamic microbe-mineral-organic matter interactions in soils and sediments.

INSPIRE: Single-beam probed complementary vibrational bioimaging

Molecular spectroscopy provides intrinsic contrast for in situ chemical imaging, linking the physiochemical properties of biomolecules to the functions of living systems. While stimulated Raman imaging has found successes in deciphering biological machinery, many vibrational modes are Raman inactive or weak, limiting the broader impact of the technique. It can potentially be mitigated by the spectral complementarity from infrared (IR) spectroscopy. However, the vastly different optical windows make it challenging to develop such a platform. Here, we introduce in situ pump-probe IR and Raman excitation (INSPIRE) microscopy, a nascent cross-modality spectroscopic imaging approach by encoding the ultrafast Raman and the IR photothermal relaxation into a single probe beam for simultaneous detection. INSPIRE inherits the merits of complementary modalities and demonstrates high-content molecular imaging of chemicals, cells, tissues, and organisms. Furthermore, INSPIRE applies to label-free and molecular tag imaging, offering possibilities for optical sensing and imaging in biomedicine and materials science.

A Multimodal Spectroscopic Approach Combining Mid-infrared and Near-infrared for Discriminating Gram-positive and Gram-negative Bacteria

The rapid and accurate identification of pathogenic bacteria is crucial for combating the growing threat of antibiotic resistance, nosocomial infections, and food safety concerns. This study presents a novel and comprehensive comparison of two vibrational spectroscopic techniques - attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and a low-cost miniature near-infrared (NIR) spectrometer - for distinguishing Gram-positive and Gram-negative bacterial samples grown using the same stock media solution. This is the first report of NIR spectroscopy being applied to differentiate Gram-positive and Gram-negative bacteria, as well as the first direct comparison of ATR-FTIR and NIR for the combined multimodal analysis of clinical bacterial isolates. Using a data set of five Gram-positive and seven Gram-negative species and recording spectra in triplicate, the study employed advanced data fusion and multivariate analysis techniques to classify the spectra and facilitate NIR band assignment. 2D correlation analysis revealed strong positive correlations between key spectral markers identified in both modalities. Partial least-squares- and support vector machine discriminant analysis models were validated using a methodology based on 100 repeated random sampling of calibration and test sets. Models demonstrated that both the standalone ATR-FTIR and the combined ATR-FTIR/NIR approach achieved exceptional classification accuracy (>98%) in differentiating the two bacterial groups. Differences observed in the spectra were attributed to the distinct cell wall compositions of Gram-Positive and Gram-negative bacteria. Notably, the low-cost NIR technique also showed promising performance, with classification accuracy values above 90%. The findings highlight the potential of these rapid, noninvasive, and cost-effective vibrational spectroscopic techniques, particularly the NIR method, for point-of-care applications in clinical microbiology and food safety monitoring. The combination of ATR-FTIR and NIR data further enhances the robustness and reliability of bacterial identification, paving the way for broader adoption of these advanced analytical tools in various healthcare and food safety settings.

Photonic and electrochemical biosensors for near-patient tests-a critical comparison

Research into diagnostic biosensors is a vibrant field that combines scientific challenge with translational opportunities; innovation in healthcare is of great societal interest and is an essential element of future healthcare provision. Photonic and electrochemical biosensors are the dominant modalities, both scientifically and commercially, yet the two scientific communities largely remain separated and siloed. It seems astute to better understand what the two fields can learn from one another so as to progress the key scientific, translational, and commercial challenges. Here, we provide an analysis of the fundamental operational characteristics of photonic and electrochemical biosensors using a classification based on energy transfer; in photonics, this separates refractive index sensors from fluorescence and vibrational spectroscopy, while in electrochemistry, it distinguishes Faradaic from non-Faradaic processes. This classification allows us to understand some of the key performance characteristics, such as the susceptibility to fouling and dependence on the clinical matrix that is being analyzed. We discuss the use of labels and the ultimate performance limits, and some of the unique advantages of photonics, such as multicolor operation and fingerprinting, and critically evaluate the requirements for translation of these technologies for clinical use. We trust that this critical review will inform future research in biosensors and support both scientific and commercial developments.

Cisplatin-Induced Metabolic Responses Measured with Raman Spectroscopy in Cancer Cells, Spheroids, and Canine-Derived Organoids

Ex vivo assessment of drug response with conventional cell viability assays remains the standard practice for guiding initial therapeutic choices. However, such ensemble approaches fail to capture heterogeneities in treatment response and cannot identify early markers of response. Here, we leverage Raman spectroscopy (RS) as an accurate, low-cost, extraction-free, and label-free approach to track metabolic changes in cancer cells, spheroids, and organoids in response to cisplatin treatment. We identified 12 statistically significant metabolites in cells and 19 metabolites in spheroids and organoids as a function of depth. We show that the cisplatin treatment of 4T1 cells and spheroids results in a shift in metabolite levels; metabolites including nucleic acids such as DNA, 783 cm-1 with p = 0.00021 for cells; p = 0.02173 for spheroids, major amino acids such as threonine, 1338 cm-1 with p = 0.00045 for cells; p = 0.01022 for spheroids, proteins such as amide III, 1248 cm-1 with p = 0.00606 for cells; p = 0.00511 for spheroids serve as early predictors of response. Our RS findings were also applicable to canine-derived organoids, showing spatial variations in metabolic changes as a function of organoid depth in response to cisplatin. Further, the metabolic pathways such as tricarboxylic acid (TCA)/citric acid cycle and glyoxylate and dicarboxylate metabolism that drive drug response showed significant differences based on organoid depth, replicating the heterogeneous treatment response seen in solid tumors where there is a difference from the periphery to the tumor core. Our study showcases the versatility of RS as a predictive tool for treatment response applicable from cells to organotypic cultures, that has the potential to decrease animal burden and readout time for preclinical drug efficacy.

A tutorial on optical photothermal infrared (O-PTIR) microscopy

This tutorial reviews the rapidly growing field of optical photothermal infrared (O-PTIR) spectroscopy and chemical imaging. O-PTIR is an infrared super-resolution measurement technique where a shorter wavelength visible probe is used to measure and map infrared (IR) absorption with spatial resolution up to 30× better than conventional techniques such as Fourier transform infrared and direct IR laser imaging systems. This article reviews key limitations of conventional IR instruments, the O-PTIR technology breakthroughs, and their origins that have overcome the prior limitations. This article also discusses recent developments in expanding multi-modal O-PTIR approaches that enable complementary Raman spectroscopy and fluorescence microscopy imaging, including wide-field O-PTIR imaging with fluorescence-based detection of IR absorption. Various practical subjects are covered, including sample preparation techniques, optimal measurement configurations, use of IR tags/labels and techniques for data analysis, and visualization. Key O-PTIR applications are reviewed in many areas, including biological and biomedical sciences, environmental and microplastics research, (bio)pharmaceuticals, materials science, cultural heritage, forensics, photonics, and failure analysis.

Rapid Classification and Differentiation of Sepsis-Related Pathogens Using FT-IR Spectroscopy

Sepsis is a life-threatening condition arising from a dysregulated host immune response to infection, leading to a substantial global health burden. The accurate identification of bacterial pathogens in sepsis is essential for guiding effective antimicrobial therapy and optimising patient outcomes. Traditional culture-based bacterial typing methods present inherent limitations, necessitating the exploration of alternative diagnostic approaches. This study reports the successful application of Fourier-transform infrared (FT-IR) spectroscopy in combination with chemometrics as a potent tool for the classification and discrimination of microbial species and strains, primarily sourced from individuals with invasive infections. These samples were obtained from various children with suspected sepsis infections with bacteria and fungi originating at different sites. We conducted a comprehensive analysis utilising 212 isolates from 14 distinct genera, comprising 202 bacterial and 10 fungal isolates. With the spectral analysis taking several weeks, we present the incorporation of quality control samples to mitigate potential variations that may arise between different sample plates, especially when dealing with a large sample size. The results demonstrated a remarkable consistency in clustering patterns among 14 genera when subjected to principal component analysis (PCA). Particularly, Candida, a fungal genus, was distinctly recovered away from bacterial samples. Principal component discriminant function analysis (PC-DFA) allowed for distinct discrimination between different bacterial groups, particularly Gram-negative and Gram-positive bacteria. Clear differentiation was also observed between coagulase-negative staphylococci (CNS) and Staphylococcus aureus isolates, while methicillin-resistant S. aureus (MRSA) was also separated from methicillin-susceptible S. aureus (MSSA) isolates. Furthermore, highly accurate discrimination was achieved between Enterococcus and vancomycin-resistant enterococci isolates with 98.4% accuracy using partial least squares-discriminant analysis. The study also demonstrates the specificity of FT-IR, as it effectively discriminates between individual isolates of Streptococcus and Candida at their respective species levels. The findings of this study establish a strong groundwork for the broader implementation of FT-IR and chemometrics in clinical and microbiological applications. The potential of these techniques for enhanced microbial classification holds significant promise in the diagnosis and management of invasive bacterial infections, thereby contributing to improved patient outcomes.

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

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.

Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea

Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.

Rapid discrimination of Lentilactobacillus parabuchneri biofilms via in situ infrared spectroscopy

Microbial contamination in food industry is a source of foodborne illnesses and biofilm-related diseases. In particular, biogenic amines (BAs) accumulated in fermented foods via lactic acid bacterial activity exert toxic effects on human health. Among these, biofilms of histamine-producer Lentilactobacillus parabuchneri strains adherent at food processing equipment surfaces can cause food spoilage and poisoning. Understanding the chain of contamination is closely related to elucidating molecular mechanisms of biofilm formation. In the present study, an innovative approach using integrated chemical sensing technologies is demonstrated to fundamentally understand the temporal behavior of biofilms at the molecular level by combining mid-infrared (MIR) spectroscopy and fluorescence sensing strategies. Using these concepts, the biofilm forming capacity of six cheese-isolated L. parabuchneri strains (IPLA 11151, 11150, 11129, 11125, 11122 and 11117) was examined. The cut-off values for the biofilm production ability of each strain were quantified using crystal violet (CV) assays. Real-time infrared attenuated total reflection spectroscopy (IR-ATR) combined with fluorescence quenching oxygen sensing provides insight into distinct molecular mechanisms for each strain. IR spectra showed significant changes in characteristic bands of amides, lactate, nucleic acids, and extracellular polymeric substances (i.e., lipopolysaccharides, phospholipids, phosphodiester, peptidoglycan, etc.), which are major contributors to biofilm maturation involved in the initial adhesion processes. Chemometric methods including principal component analysis and partial least square-discriminant analysis facilitated the rapid determination and classification of cheese isolated L. parabuchneri strains unambiguously differentiating the IR signatures based on their ability to produce biofilm. All biofilms were morphologically characterized by confocal laser scanning microscopy on relevant industrial equipment surfaces. In summary, this innovative approach combining MIR spectroscopy with luminescence sensing enables real-time insight into the molecular composition and formation of L. parabuchneri biofilms.

Dual-signal and one-step monitoring of Staphylococcus aureus in milk using hybridization chain reaction based fluorescent sensor

Food-borne pathogens in dairy products that was contaminated from raw ingredients or improper food handling can cause a major threaten to human health. Here, to construct the pathogens detection, a dual-signal readout fluorescent switching sensor was designed for one-step determination of Staphylococcus aureus (S. aureus), which was a marker of food contamination. Graphene oxide (GO) was used as a fluorescence quencher, while fluorophore-labeled hairpin DNA was used as a donor, resulting in fluorescence resonance energy transfer (FRET) from the fluorophore to GO (signal off). Enzyme-free hybridization chain reaction could generate remarkable signal amplification, which avoided the nonspecific desorption caused by any enzymatic proteins in GO surface. With the strong binding ability of aptamer to S. aureus, a long bifluorescent molecules-labeled double-stranded DNA product was formed, bringing in dual-signal readout responses (signal on). Consequently, a reliable, sensitive and selective sensor was obtained for one-step quantification of S. aureus concentration from 10 to 108 CFU/mL with a detection limit of 1 CFU/mL. Furthermore, satisfactory stability, reproducibility, specificity and good recovery efficiency in milk samples revealed that the proposed sensor could be served as a prospective tool for food safety analysis.

Monitoring Phenotype Heterogeneity at the Single-Cell Level within Bacillus Populations Producing Poly-3-hydroxybutyrate by Label-Free Super-resolution Infrared Imaging

Phenotypic heterogeneity is commonly found among bacterial cells within microbial populations due to intrinsic factors as well as equipping the organisms to respond to external perturbations. The emergence of phenotypic heterogeneity in bacterial populations, particularly in the context of using these bacteria as microbial cell factories, is a major concern for industrial bioprocessing applications. This is due to the potential impact on overall productivity by allowing the growth of subpopulations consisting of inefficient producer cells. Monitoring the spread of phenotypes across bacterial cells within the same population at the single-cell level is key to the development of robust, high-yield bioprocesses. Here, we discuss the novel development of optical photothermal infrared (O-PTIR) spectroscopy to probe phenotypic heterogeneity within Bacillus strains by monitoring the production of the bioplastic poly-3-hydroxybutyrate (PHB) at the single-cell level. Measurements obtained on single-point and in imaging mode show significant variability in the PHB content within bacterial cells, ranging from whether or not a cell produces PHB to variations in the intragranular biochemistry of PHB within bacterial cells. Our results show the ability of O-PTIR spectroscopy to probe PHB production at the single-cell level in a rapid, label-free, and semiquantitative manner. These findings highlight the potential of O-PTIR spectroscopy in single-cell microbial metabolomics as a whole-organism fingerprinting tool that can be used to monitor the dynamic of bacterial populations as well as for understanding their mechanisms for dealing with environmental stress, which is crucial for metabolic engineering research.

Combined analytical approach empowers precise spectroscopic interpretation of subcellular components of pancreatic cancer cells

The lack of specific and sensitive early diagnostic options for pancreatic cancer (PC) results in patients being largely diagnosed with late-stage disease, thus inoperable and burdened with high mortality. Molecular spectroscopic methodologies, such as Raman or infrared spectroscopies, show promise in becoming a leader in screening for early-stage cancer diseases, including PC. However, should such technology be introduced, the identification of differentiating spectral features between various cancer types is required. This would not be possible without the precise extraction of spectra without the contamination by necrosis, inflammation, desmoplasia, or extracellular fluids such as mucous that surround tumor cells. Moreover, an efficient methodology for their interpretation has not been well defined. In this study, we compared different methods of spectral analysis to find the best for investigating the biomolecular composition of PC cells cytoplasm and nuclei separately. Sixteen PC tissue samples of main PC subtypes (ductal adenocarcinoma, intraductal papillary mucinous carcinoma, and ampulla of Vater carcinoma) were collected with Raman hyperspectral mapping, resulting in 191,355 Raman spectra and analyzed with comparative methodologies, specifically, hierarchical cluster analysis, non-negative matrix factorization, T-distributed stochastic neighbor embedding, principal components analysis (PCA), and convolutional neural networks (CNN). As a result, we propose an innovative approach to spectra classification by CNN, combined with PCA for molecular characterization. The CNN-based spectra classification achieved over 98% successful validation rate. Subsequent analyses of spectral features revealed differences among PC subtypes and between the cytoplasm and nuclei of their cells. Our study establishes an optimal methodology for cancer tissue spectral data classification and interpretation that allows precise and cognitive studies of cancer cells and their subcellular components, without mixing the results with cancer-surrounding tissue. As a proof of concept, we describe findings that add to the spectroscopic understanding of PC.

Fractionation of bacteria by electrophoresis as pre-separation method before MALDI-MS detection

The present study attempted to apply the capillary electrophoresis technique for the fractionation and separation of S. Staphylococcus hominis and Escherichia coli bacteria isolated from urine samples and the detection of migrated fraction with spectrometric method. This involved the selection of suitable conditions for separation as well as the identification of pathogens. The result of the research was the separation of Gram-negative and Gram-positive bacteria, as well as their subsequent identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using two different approaches (culture of fractions on an agar plate and direct analysis of the collected fractions). The preliminary results provide a solid basis for further research on the use of electromigration techniques with LDI detection to identify pathogens such as bacteria and viruses in biological samples.

Unlocking the secrets of the microbiome: exploring the dynamic microbial interplay with humans through metabolomics and their manipulation for synthetic biology applications

Metabolomics is a powerful research discovery tool with the potential to measure hundreds to low thousands of metabolites. In this review, we discuss the application of GC-MS and LC-MS in discovery-based metabolomics research, we define metabolomics workflows and we highlight considerations that need to be addressed in order to generate robust and reproducible data. We stress that metabolomics is now routinely applied across the biological sciences to study microbiomes from relatively simple microbial systems to their complex interactions within consortia in the host and the environment and highlight this in a range of biological species and mammalian systems including humans. However, challenges do still exist that need to be overcome to maximise the potential for metabolomics to help us understanding biological systems. To demonstrate the potential of the approach we discuss the application of metabolomics in two broad research areas: (1) synthetic biology to increase the production of high-value fine chemicals and reduction in secondary by-products and (2) gut microbial interaction with the human host. While burgeoning in importance, the latter is still in its infancy and will benefit from the development of tools to detangle host-gut-microbial interactions and their impact on human health and diseases.

Plasmonic nanorod probes' journey inside plant cells for in vivo SERS sensing and multimodal imaging

Nanoparticle-based platforms are gaining strong interest in plant biology and bioenergy research to monitor and control biological processes in whole plants. However, in vivo monitoring of biomolecules using nanoparticles inside plant cells remains challenging due to the impenetrability of the plant cell wall to nanoparticles beyond the exclusion limits (5-20 nm). To overcome this physical barrier, we have designed unique bimetallic silver-coated gold nanorods (AuNR@Ag) capable of entering plant cells, while conserving key plasmonic properties in the near-infrared (NIR). To demonstrate cellular internalization and tracking of the nanorods inside plant tissue, we used a comprehensive multimodal imaging approach that included transmission electron microscopy (TEM), confocal fluorescence microscopy, two-photon luminescence (TPL), X-ray fluorescence microscopy (XRF), and photoacoustics imaging (PAI). We successfully acquired SERS signals of nanorods in vivo inside plant cells of tobacco leaves. On the same leaf samples, we applied orthogonal imaging methods, TPL and PAI techniques for in vivo imaging of the nanorods. This study first demonstrates the intracellular internalization of AuNR@Ag inside whole plant systems for in vivo SERS analysis in tobacco cells. This work demonstrates the potential of this nanoplatform as a new nanotool for intracellular in vivo biosensing for plant biology.

Host Response Biomarkers for Sepsis in the Emergency Room

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2023. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2023 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .

Plant and microbial sciences as key drivers in the development of metabolomics research

This year marks the 25th anniversary of the coinage of the term metabolome [S. G. Oliver et al., Trends Biotech. 16, 373-378 (1998)]. As the field rapidly advances, it is important to take stock of the progress which has been made to best inform the disciplines future. While a medical-centric perspective on metabolomics has recently been published [M. Giera et al., Cell Metab. 34, 21-34 (2022)], this largely ignores the pioneering contributions made by the plant and microbial science communities. In this perspective, we provide a contemporary overview of all fields in which metabolomics is employed with particular emphasis on both methodological and application breakthroughs made in plant and microbial sciences that have shaped this evolving research discipline from the very early days of its establishment. This will not cover all types of metabolomics assays currently employed but will focus mainly on those utilizing mass spectrometry-based measurements since they are currently by far the most prominent. Having established the historical context of metabolomics, we will address the key challenges currently facing metabolomics and offer potential approaches by which these can be faced. Most salient among these is the fact that the vast majority of mass features are as yet not annotated with high confidence; what we may refer to as definitive identification. We discuss the potential of both standard compound libraries and artificial intelligence technologies to address this challenge and the use of natural variance-based approaches such as genome-wide association studies in attempt to assign specific functions to the myriad of structurally similar and complex specialized metabolites. We conclude by stating our contention that as these challenges are epic and that they will need far greater cooperative efforts from biologists, chemists, and computer scientists with an interest in all kingdoms of life than have been made to date. Ultimately, a better linkage of metabolome and genome data will likely also be needed particularly considering the Earth BioGenome Project.

Fourier Transform Infrared (FTIR) Spectroscopic Study of Biofilms Formed by the Rhizobacterium Azospirillum baldaniorum Sp245: Aspects of Methodology and Matrix Composition

Biofilms represent the main mode of existence of bacteria and play very significant roles in many industrial, medical and agricultural fields. Analysis of biofilms is a challenging task owing to their sophisticated composition, heterogeneity and variability. In this study, biofilms formed by the rhizobacterium Azospirillum baldaniorum (strain Sp245), isolated biofilm matrix and its macrocomponents have for the first time been studied in detail, using Fourier transform infrared (FTIR) spectroscopy, with a special emphasis on the methodology. The accompanying novel data of comparative chemical analyses of the biofilm matrix, its fractions and lipopolysaccharide isolated from the outer membrane of the cells of this strain, as well as their electrophoretic analyses (SDS-PAGE) have been found to be in good agreement with the FTIR spectroscopic results.

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

The rise and extensive spread of antimicrobial resistance (AMR) has become a growing concern, and a threat to the environment and human health globally. The majority of current AMR identification methods used in clinical setting are based on traditional microbiology culture-dependent techniques which are time-consuming or expensive to be implemented, thus appropriate antibiotic stewardship is provided retrospectively which means the first line of treatment is to hope that a broad-spectrum antibiotic works. Hence, culture-independent and single-cell technologies are needed to allow for rapid detection and identification of antimicrobial-resistant bacteria and to support a more targeted and effective antibiotic therapy preventing further development and spread of AMR. In this study, for the first time, a non-destructive phenotyping method of optical photothermal infrared (O-PTIR) spectroscopy, coupled with deuterium isotope probing (DIP) and multivariate statistical analysis was employed as a metabolic fingerprinting approach to detect AMR in Uropathogenic Escherichia coli (UPEC) at both single-cell and population levels. Principal component-discriminant function analysis (PC-DFA) of FT-IR and O-PTIR spectral data showed clear clustering patterns as a result of distinctive spectral shifts (C-D signature peaks) originating from deuterium incorporation into bacterial cells, allowing for rapid detection and classification of sensitive and resistant isolates at the single-cell level. Furthermore, the single-frequency images obtained using the C-D signature peak at 2,163 cm-1 clearly displayed the reduced ability of the trimethoprim-sensitive strain for incorporating deuterium when exposed to this antibiotic, compared to the untreated condition. Hence, the results of this study indicated that O-PTIR can be employed as an efficient tool for the rapid detection of AMR at the single-cell level.

High-Throughput Antimicrobial Susceptibility Testing of Escherichia coli by Wide-Field Mid-Infrared Photothermal Imaging of Protein Synthesis

Antimicrobial resistance poses great threats to global health and economics. Current gold-standard antimicrobial susceptibility testing (AST) requires extensive culture time (36-72 h) to determine susceptibility. There is an urgent need for rapid AST methods to slow down antimicrobial resistance. Here, we present a rapid AST method based on wide-field mid-infrared photothermal imaging of protein synthesis from ¹³C-glucose in Escherichia coli. Our wide-field approach achieved metabolic imaging for hundreds of bacteria at the single-cell resolution within seconds. The perturbed microbial protein synthesis can be probed within 1 h after antibiotic treatment in E. coli cells. The susceptibility of antibiotics with various mechanisms of action has been probed through monitoring protein synthesis, which promises great potential of the proposed platform toward clinical translation.

Domain-level Identification of Single Prokaryotic Cells by Optical Photothermal Infrared Spectroscopy

Infrared spectroscopy is used for the chemical characterization of prokaryotes. However, its application has been limited to cell aggregates and lipid extracts because of the relatively low spatial resolution of diffraction. We herein report optical photothermal infrared (O-PTIR) spectroscopy of prokaryotes for a domain-level diagnosis at the single-cell level. The technique provided infrared spectra of individual bacterial as well as archaeal cells, and the resulting aliphatic CH3/CH2 intensity ratios showed domain-specific signatures, which may reflect distinctive cellular lipid compositions; however, there was interference by other cellular components. These results suggest the potential of O-PTIR for a domain-level diagnosis of single prokaryotic cells in natural environments.

Optical photothermal infrared spectroscopy with simultaneously acquired Raman spectroscopy for two-dimensional microplastic identification

In recent years, vibrational spectroscopic techniques based on Fourier transform infrared (FTIR) or Raman microspectroscopy have been suggested to fulfill the unmet need for microplastic particle detection and identification. Inter-system comparison of spectra from reference polymers enables assessing the reproducibility between instruments and advantages of emerging quantum cascade laser-based optical photothermal infrared (O-PTIR) spectroscopy. In our work, IR and Raman spectra of nine plastics, namely polyethylene, polypropylene, polyvinyl chloride, polyethylene terephthalate, polycarbonate, polystyrene, silicone, polylactide acid and polymethylmethacrylate were simultaneously acquired using an O-PTIR microscope in non-contact, reflection mode. Comprehensive band assignments were presented. We determined the agreement of O-PTIR with standalone attenuated total reflection FTIR and Raman spectrometers based on the hit quality index (HQI) and introduced a two-dimensional identification (2D-HQI) approach using both Raman- and IR-HQIs. Finally, microplastic particles were prepared as test samples from known materials by wet grinding, O-PTIR data were collected and subjected to the 2D-HQI identification approach. We concluded that this framework offers improved material identification of microplastic particles in environmental, nutritious and biological matrices.