Raman microspectroscopy, surface-enhanced Raman scattering microspectroscopy, and stable-isotope Raman microspectroscopy for biofilm characterization

Uncovering the Molecular Composition and Architecture of the Bacillus subtilis Biofilm via Solid-State NMR Spectroscopy

The complex and dynamic compositions of biofilms, along with their sophisticated structural assembly mechanisms, endow them with exceptional capabilities to thrive in diverse conditions that are typically unfavorable for individual cells. Characterizing biofilms in their native state is significantly challenging due to their intrinsic complexities and the limited availability of noninvasive techniques. Here, we utilized solid-state nuclear magnetic resonance (NMR) spectroscopy to analyze Bacillus subtilis biofilms in-depth. Our data uncover a dynamically distinct organization within the biofilm: a dominant, hydrophilic, and mobile framework interspersed with minor, rigid cores of limited water accessibility. In these heterogeneous rigid cores, the major components are largely self-assembled. TasA fibers, the most robust elements, further provide a degree of mechanical support for the cell aggregates and some lipid vesicles. Notably, rigid cell aggregates can persist even without the major extracellular polymeric substance (EPS) polymers, although this leads to slight variations in their rigidity and water accessibility. Exopolysaccharides are exclusively present in the mobile domain, playing a pivotal role in its water retention property. Specifically, all water molecules are tightly bound within the biofilm matrix. These findings reveal a dual-layered defensive strategy within the biofilm: a diffusion barrier through limited water mobility in the mobile phase and a physical barrier posed by limited water accessibility in the rigid phase. Complementing these discoveries, our comprehensive, in situ compositional analysis is not only essential for delineating the sophisticated biofilm architecture but also reveals the presence of alternative genetic mechanisms for synthesizing exopolysaccharides beyond the known pathway.

Quantitative Real-Time Analysis of Living Materials by Stimulated Raman Scattering Microscopy

Composite materials built in part from living organisms have the potential to exhibit useful autonomous, adaptive, and self-healing behavior. The physicochemical, biological, and mechanical properties of such materials can be engineered through the genetic manipulation of their living components. Successful development of living materials will require not only new methods for design and preparation but also new analytical tools that are capable of real-time noninvasive mapping of chemical compositions. Here, we establish a strategy based on stimulated Raman scattering microscopy to monitor phosphatase-catalyzed mineralization of engineered bacterial films in situ. Real-time label-free imaging elucidates the mineralization process, quantifies both the organic and inorganic components of the material as functions of time, and reveals spatial heterogeneity at multiple scales. In addition, we correlate the mechanical performance of films with the extent of mineralization. This work introduces a promising strategy for quantitatively analyzing living materials, which should contribute to the accelerated development of such materials in the future.

Life at the borderlands: microbiomes of interfaces critical to One Health

Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.

Surface-enhanced Raman spectroscopy for characterization of supernatant samples of biofilm forming bacterial strains

Staphylococcus epidermidis is considered major cause of nosocomial infections. Its pathogenicity is mainly due to the ability to form biofilms on different surfaces, particularly indwelling medical devices. This bacterium consists of different strains consisting of non, medium and strong biofilm forming ones. Surface-enhanced Raman spectroscopy (SERS) is a powerful analytical technique that can be used to detect and analyze biochemical composition of the supernatant samples of different strains of bacteria including non, medium and strong biofilm forming bacterial strains. SERS is a powerful technique for the robust, reliable, rapid detection and discrimination of bacteria in the form of characteristic SERS spectral features which can be used for detection and classification. SERS is used to differentiate three classes of bacteria with respect to their biofilm forming ability. Silver nanoparticles (Ag NPs) are used as SERS substrate and synthesized with chemical reduction method. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) are used to discriminate SERS spectral data sets of non, medium and strong biofilm forming bacteria. PLS-DA analysis is a multivariate statistical technique that can be used to analyze data from bacterial sets.

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.

Simultaneous bond-selective deuterium-based isotopic labeling sensing with disposable ultra-miniature CARS fiber probe

Deuterium-based isotopic labeling is an important technique for tracking cellular metabolism with the Raman signals analysis of low-wavenumber (LW) C-D bonds and high-wavenumber (HW) C-H bonds. We propose and demonstrate a disposable ultra-miniature fiber probe to detect LW and HW coherent anti-Stokes Raman scattering (CARS) spectra for deuterated compounds simultaneously and bond-selectively sensing. The 10.78 µm diameter disposable fiber probe, comprised of focusing taper as fiber probe head and time-domain walk-off eliminating fiber section with designed length, realizes wide-frequency-interval dual Stokes pulse delivering and focusing. The fiber probe enables quantitative concentration determination with resolution down to 11 mM. The chemical vibration modes of LW region C-D bonds and HW region C-H bonds of the mixture samples of organic compounds and their deuterated counterparts in a simulated cell are simultaneously excited and characterized. The CARS disposable fiber probe introduces a promising handle for in vivo biochemical detection based on isotopic labeling sensing.

Monitoring of microbial proteome dynamics using Raman stable isotope probing

Abnormal protein kinetics could be a cause of several diseases associated with essential life processes. An accurate understanding of protein dynamics and turnover is essential for developing diagnostic or therapeutic tools to monitor these changes. Raman spectroscopy in combination with stable isotope probes (SIP) such as carbon-13, and deuterium has been a breakthrough in the qualitative and quantitative study of various metabolites. In this work, we are reporting the utility of Raman-SIP for monitoring dynamic changes in the proteome at the community level. We have used ¹³ C-labeled glucose as the only carbon source in the medium and verified its incorporation in the microbial biomass in a time-dependent manner. A visible redshift in the Raman spectral vibrations of major biomolecules such as nucleic acids, phenylalanine, tyrosine, amide I, and amide III were observed. Temporal changes in the intensity of these bands demonstrating the feasibility of protein turnover monitoring were also verified. Kanamycin, a protein synthesis inhibitor was used to assess the feasibility of identifying effects on protein turnover in the cells. Successful application of this work can provide an alternate/adjunct tool for monitoring proteome-level changes in an objective and nondestructive manner.

What determines accuracy of chemical identification when using microspectroscopy for the analysis of microplastics?

Fourier transform infrared (FTIR) and Raman microspectroscopy are methods applied in microplastics research to determine the chemical identity of microplastics. These techniques enable quantification of microplastic particles across various matrices. Previous work has highlighted the benefits and limitations of each method and found these to be complimentary. Within this work, metadata collected within an interlaboratory method validation study was used to determine which variables most influenced successful chemical identification of un-weathered microplastics in simulated drinking water samples using FTIR and Raman microspectroscopy. No variables tested had a strong correlation with the accuracy of chemical identification (r = ≤0.63). The variables most correlated with accuracy differed between the two methods, and include both physical characteristics of particles (color, morphology, size, polymer type), and instrumental parameters (spectral collection mode, spectral range). Based on these results, we provide technical recommendations to improve capabilities of both methods for measuring microplastics in drinking water and highlight priorities for further research. For FTIR microspectroscopy, recommendations include considering the type of particle in question to inform sample presentation and spectral collection mode for sample analysis. Instrumental parameters should be adjusted for certain particle types when using Raman microspectroscopy. For both instruments, the study highlighted the need for harmonization of spectral reference libraries among research groups, including the use of libraries containing reference materials of both weathered plastic and natural materials that are commonly found in environmental samples.

SERS-based antibiotic susceptibility testing: Towards point-of-care clinical diagnosis

Emerging antibiotic resistant bacteria constitute one of the biggest threats to public health. Surface-enhanced Raman scattering (SERS) is highly promising for detecting such bacteria and for antibiotic susceptibility testing (AST). SERS is fast, non-destructive (can probe living cells) and it is technologically flexible (readily integrated with robotics and machine learning algorithms). However, in order to integrate into efficient point-of-care (PoC) devices and to effectively replace the current culture-based methods, it needs to overcome the challenges of reliability, cost and complexity. Recently, significant progress has been made with the emergence of both new questions and new promising directions of research and technological development. This article brings together insights from several representative SERS-based AST studies and approaches oriented towards clinical PoC biosensing. It aims to serve as a reference source that can guide progress towards PoC routines for identifying antibiotic resistant pathogens. In turn, such identification would help to trace the origin of sporadic infections, in order to prevent outbreaks and to design effective medical treatment and preventive procedures.

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

Investigation of bacteria with D-carotenoids reveals unique Raman signatures, inclusive unexpected blue-shift. Simultaneous monitoring of 13C & D of carotenoids provides complementary information on cell growth and metabolic activity, respectively.

Characterization of biofilms formed on polystyrene microplastics (PS-MPs) on the shore of the Tuul River, Mongolia

Microplastic (MP) surfaces are common sites for microbial colonization and promote biofilm formation in aquatic environments, resulting in changes to the surface properties of MPs and their interaction with pollutants. Although the diversity of microbial communities adhering to MPs has been well documented in aquatic environments, surface changes in MPs due to microbial colonization are still poorly understood. In this study, we aimed to evaluate the variations in the chemical structure and components of biofilms on the surface of polystyrene microplastics (PS-MPs) collected from the shore of the Tuul River in Mongolia, using micro-Fourier transform infrared (micro-FTIR) spectroscopy. We applied a spectral subtraction approach, and the differences in spectra between peroxide-treated and untreated PS-MP particles enabled us to obtain the structural features of biofilms that developed on the plastic surface. In addition, the surface photooxidation status of the sampled PS-MPs was calculated from the subtracted spectra of peroxide-treated and pristine PS-MPs. Various functional groups of N-containing organic substances from bacterial and fungal communities were detected in the obtained biofilm spectra. Based on the spectral characteristics, biofilm spectra were classified into four groups by applying principal component analysis (PCA). A wide range of carbonyl indices (CIs: 0.00-1.40) was found in the subtracted spectra between peroxide-treated and pristine PS-MPs, revealing that different levels of surface oxidation progressed by physical influences such as solar radiation and freeze-thaw cycles. Furthermore, lignocellulose and silicate were found on the PS-MP surface as allochthonous attachments. Considering the variation in residence time of PS-MPs, they attract plant residues and mineral particles through the development of biofilms and travel together in the river environment. Given that the dynamic behavior of MPs can be greatly affected by changes in their surfaces, further studies are needed to emphasize their link to organic matter dynamics.

Compound Raman microscopy for rapid diagnosis and antimicrobial susceptibility testing of pathogenic bacteria in urine

Rapid identification and antimicrobial susceptibility testing (AST) of bacteria are key interventions to curb the spread and emergence of antimicrobial resistance. The current gold standard identification and AST methods provide comprehensive diagnostic information but often take 3 to 5 days. Here, a compound Raman microscopy (CRM), which integrates Raman spectroscopy and stimulated Raman scattering microscopy in one system, is presented and demonstrated for rapid identification and AST of pathogens in urine. We generated an extensive bacterial Raman spectral dataset and applied deep learning to identify common clinical bacterial pathogens. In addition, we employed stimulated Raman scattering microscopy to quantify bacterial metabolic activity to determine their antimicrobial susceptibility. For proof-of-concept, we demonstrated an integrated assay to diagnose urinary tract infection pathogens, S. aureus and E. coli. Notably, the CRM system has the unique ability to provide Gram-staining classification and AST results within ~3 h directly from urine samples and shows great potential for clinical applications.

A Review of Raman-Based Technologies for Bacterial Identification and Antimicrobial Susceptibility Testing

Antimicrobial resistance (AMR) is a global medical threat that seriously endangers human health. Rapid bacterial identification and antimicrobial susceptibility testing (AST) are key interventions to combat the spread and emergence of AMR. Although current clinical bacterial identification and AST provide comprehensive information, they are labor-intensive, complex, inaccurate, and slow (requiring several days, depending on the growth of pathogenic bacteria). Recently, Raman-based identification and AST technologies have played an increasingly important role in fighting AMR. This review summarizes major Raman-based techniques for bacterial identification and AST, including spontaneous Raman scattering, surface-enhanced Raman scattering (SERS), and coherent Raman scattering (CRS) imaging. Then, we discuss recent developments in rapid identification and AST methods based on Raman technology. Finally, we highlight the major challenges and potential future efforts to improve clinical outcomes through rapid bacterial identification and AST.

Environmental diagnosis with Raman Spectroscopy applied to diatoms

Freshwater quality has been changing due to the ever greater use of water resources and the contamination load resulting from human activities. Management of these systems, thus, requires constant diagnose of water quality with fast and efficient methodologies. The conventional methods adopted are, however, time-consuming, often very expensive, and require specialised expertise. Raman spectroscopy (RS) is a simple, fast and label-free technique that can be applied to environmental diagnosis using diatoms. Here, we developed a diagnostic method based on Raman spectroscopy applied to freshwater diatoms. For this, Raman spectra were recorded from diatoms of three lakes of a natural city park. The data acquired was analysed by chemometrics methods to describe the data (Partial Least Squares Regression), infer relationships in the dataset (Cluster Analysis) and produce classification models (Artificial Neural Network). The classification models developed diagnosed the lakes with excellent accuracy (89%) without requiring taxonomic information about the diatom species recorded. This study provides a proof-of-concept for the application of diatom Raman spectroscopy to diagnosing water quality, laying an important foundation for future environmental studies aiming at assessing freshwater systems, to be replicated at larger scales and to varied geographic settings.

Raman spectroscopy biochemical characterisation of bladder cancer cisplatin resistance regulated by FDFT1: a review

Bladder cancer is the fourth most common malignancy in males. It can present across the whole continuum of severity, from mild through well-differentiated disease to extremely malignant tumours with poor survival rates. As with other vital organ malignancies, proper clinical management involves accurate diagnosis and staging. Chemotherapy consisting of a cisplatin-based regimen is the mainstay in the management of muscle-invasive bladder cancers. Control via cisplatin-based chemotherapy is threatened by the development of chemoresistance. Intracellular cholesterol biosynthesis in bladder cancer cells is considered a contributory factor in determining the chemotherapy response. Farnesyl-diphosphate farnesyltransferase 1 (FDFT1), one of the main regulatory components in cholesterol biosynthesis, may play a role in determining sensitivity towards chemotherapy compounds in bladder cancer. FDFT1-associated molecular identification might serve as an alternative or appendage strategy for early prediction of potentially chemoresistant muscle-invasive bladder cancer tissues. This can be accomplished using Raman spectroscopy. Developments in the instrumentation have led to it becoming one of the most convenient forms of analysis, and there is a highly realistic chance that it will become an effective tool in the pathology lab. Chemosensitive bladder cancer tissues tend to have a higher lipid content, more protein genes and more cholesterol metabolites. These are believed to be associated with resistance towards bladder cancer chemotherapy. Herein, Raman peak assignments have been tabulated as an aid to indicating metabolic changes in bladder cancer tissues that are potentially correlated with FDFT1 expression.

Characterization of Labeled Gold Nanoparticles for Surface-Enhanced Raman Scattering

Noble metal nanoparticles (NP) such as gold (AuNPs) and silver nanoparticles (AgNPs) can produce ultrasensitive surface-enhanced Raman scattering (SERS) signals owing to their plasmonic properties. AuNPs have been widely investigated for their biocompatibility and potential to be used in clinical diagnostics and therapeutics or combined for theranostics. In this work, labeled AuNPs in suspension were characterized in terms of size dependency of their localized surface plasmon resonance (LSPR), dynamic light scattering (DLS), and SERS activity. The study was conducted using a set of four Raman labels or reporters, i.e., small molecules with large scattering cross-section and a thiol moiety for chemisorption on the AuNP, namely 4-mercaptobenzoic acid (4-MBA), 2-naphthalenethiol (2-NT), 4-acetamidothiophenol (4-AATP), and biphenyl-4-thiol (BPT), to investigate their viability for SERS tagging of spherical AuNPs of different size in the range 5 nm to 100 nm. The results showed that, when using 785 nm laser excitation, the SERS signal increases with the increasing size of AuNP up to 60 or 80 nm. The signal is highest for BPT labelled 80 nm AuNPs followed by 4-AATP labeled 60 nm AuNPs, making BPT and 4-AATP the preferred candidates for Raman labelling of spherical gold within the range of 5 nm to 100 nm in diameter.

Advanced detection and sensing strategies of Pseudomonas aeruginosa and quorum sensing biomarkers: A review

Pseudomonas aeruginosa (P. aeruginosa), a ubiquitous opportunistic pathogen, can frequently cause chronic obstructive pulmonary disease, cystic fibrosis and chronic wounds, and potentially lead to severe morbidity and mortality. Timely and adequate treatment of nosocomial infection in clinic depends on rapid detection and accurate identification of P. aeruginosa and its early-stage antibiotic susceptibility test. Traditional methods like plating culture, polymerase chain reaction, and enzyme-linked immune sorbent assays are time-consuming and require expensive equipment, limiting the rapid diagnostic application. Advanced sensing strategy capable of fast, sensitive and simple detection with low cost has therefore become highly desired in point of care testing (POCT) of nosocomial pathogens. Within this review, advanced detection and sensing strategies for P. aeruginosa cells along with associated quorum sensing (QS) molecules over the last ten years are discussed and summarized. Firstly, the principles of four commonly used sensing strategies including localized surface plasmon resonance (LSPR), surface-enhanced Raman spectroscopy (SERS), electrochemistry, and fluorescence are briefly overviewed. Then, the advancement of the above sensing techniques for P. aeruginosa cells and its QS biomarkers detection are introduced, respectively. In addition, the integration with novel compatible platforms towards clinical application is highlighted in each section. Finally, the current achievements are summarized along with proposed challenges and prospects.

Recent advances in tools to map the microbiome

Microbes thrive in diverse habitats. They often form ecological niches with rich species diversity and complex spatial structure. These communities drive biogeochemical cycles in the environment and modulate host health in the human body. Much has been learned about the makeup of human and environmental microbiota via metagenomic DNA sequencing, but information on spatial interactions between microbes and between microbes and their environment remains scarce. Here, we review recent advances in tools to map the biogeography of microbiomes. We discuss methods to spatially map microbial genes, transcripts, and metabolites. We also examine future directions for microbiome mapping technologies that will allow improved understanding of both microbiome structure and function. Finally, we reflect on the impact of these methods in Biomedical Engineering.

Water in bacterial biofilms: pores and channels, storage and transport functions

Bacterial biofilms occur in many natural and industrial environments. Besides bacteria, biofilms comprise over 70 wt% water. Water in biofilms occurs as bound- or free-water. Bound-water is adsorbed to bacterial surfaces or biofilm (matrix) structures and possesses different Infra-red and Nuclear-Magnetic-Resonance signatures than free-water. Bound-water is different from intra-cellularly confined-water or water confined within biofilm structures and bacteria are actively involved in building water-filled structures by bacterial swimmers, dispersion or lytic self-sacrifice. Water-filled structures can be transient due to blocking, resulting from bacterial growth, compression or additional matrix formation and are generally referred to as "channels and pores." Channels and pores can be distinguished based on mechanism of formation, function and dimension. Channels allow transport of nutrients, waste-products, signalling molecules and antibiotics through a biofilm provided the cargo does not adsorb to channel walls and channels have a large length/width ratio. Pores serve a storage function for nutrients and dilute waste-products or antimicrobials and thus should have a length/width ratio close to unity. The understanding provided here on the role of water in biofilms, can be employed to artificially engineer by-pass channels or additional pores in industrial and environmental biofilms to increase production yields or enhance antimicrobial penetration in infectious biofilms.

Raman spectroscopy applied to diatoms (microalgae, Bacillariophyta): Prospective use in the environmental diagnosis of freshwater ecosystems

Diatom species are good pollution bioindicators due to their large distribution, fast response to changes in environmental parameters and different tolerance ranges. These organisms are used in ecological water assessment all over the world using autoecological indices. Such assessments commonly rely on the taxonomic identification of diatom species-specific shape and frustule ornaments, from which cell counts, species richness and diversity indices can be estimated. Taxonomic identification is, however, time-consuming and requires years of expertise. Additionally, though the diatom autoecological indices are region-specific, they are often applied indiscriminately across regions. Raman spectroscopy is a simpler, fast and label-free technique that can be applied to environmental diagnosis with diatoms. However, this approach has been poorly explored. This work reviews Raman spectroscopy studies involving the structure, location and conformation of diatom cell components and their variation under different conditions. A critical appreciation of the pros and cons of its application to environmental diagnosis is also given. This knowledge provides a strong foundation for the development of environmental protocols using Raman spectroscopy in diatoms. Our work aims at stimulating further research on the application of Raman spectroscopy as a tool to assess physiological changes and water quality under a changing climate.

High-Throughput Raman Flow Cytometry and Beyond

Flow cytometry is a powerful tool with applications in diverse fields such as microbiology, immunology, virology, cancer biology, stem cell biology, and metabolic engineering. It rapidly counts and characterizes large heterogeneous populations of cells in suspension (e.g., blood cells, stem cells, cancer cells, and microorganisms) and dissociated solid tissues (e.g., lymph nodes, spleen, and solid tumors) with typical throughputs of 1,000-100,000 events per second (eps). By measuring cell size, cell granularity, and the expression of cell surface and intracellular molecules, it provides systematic insights into biological processes. Flow cytometers may also include cell sorting capabilities to enable subsequent additional analysis of the sorted sample (e.g., electron microscopy and DNA/RNA sequencing), cloning, and directed evolution. Unfortunately, traditional flow cytometry has several critical limitations as it mainly relies on fluorescent labeling for cellular phenotyping, which is an indirect measure of intracellular molecules and surface antigens. Furthermore, it often requires time-consuming preparation protocols and is incompatible with cell therapy. To overcome these difficulties, a different type of flow cytometry based on direct measurements of intracellular molecules by Raman spectroscopy, or "Raman flow cytometry" for short, has emerged. Raman flow cytometry obtains a chemical fingerprint of the cell in a nondestructive manner, allowing for single-cell metabolic phenotyping. However, its slow signal acquisition due to the weak light-molecule interaction of spontaneous Raman scattering prevents the throughput necessary to interrogate large cell populations in reasonable time frames, resulting in throughputs of about 1 eps. The remedy to this throughput limit lies in coherent Raman scattering methods such as stimulated Raman scattering (SRS) and coherent anti-Stokes Raman scattering (CARS), which offer a significantly enhanced light-sample interaction and hence enable high-throughput Raman flow cytometry, Raman imaging flow cytometry, and even Raman image-activated cell sorting (RIACS). In this Account, we outline recent advances, technical challenges, and emerging opportunities of coherent Raman flow cytometry. First, we review the principles of various types of SRS and CARS and introduce several techniques of coherent Raman flow cytometry such as CARS, multiplex CARS, Fourier-transform CARS, SRS, SRS imaging flow cytometry, and RIACS. Next, we discuss a unique set of applications enabled by coherent Raman flow cytometry, from microbiology and lipid biology to cancer detection and cell therapy. Finally, we describe future opportunities and challenges of coherent Raman flow cytometry including increasing sensitivity and throughput, integration with droplet microfluidics, utilizing machine learning techniques, or achieving in vivo flow cytometry. This Account summarizes the growing field of high-throughput Raman flow cytometry and the bright future it can bring.

Microbial Biofilms in the Food Industry-A Comprehensive Review

Biofilms, present as microorganisms and surviving on surfaces, can increase food cross-contamination, leading to changes in the food industry’s cleaning and disinfection dynamics. Biofilm is an association of microorganisms that is irreversibly linked with a surface, contained in an extracellular polymeric substance matrix, which poses a formidable challenge for food industries. To avoid biofilms from forming, and to eliminate them from reversible attachment and irreversible stages, where attached microorganisms improve surface adhesion, a strong disinfectant is required to eliminate bacterial attachments. This review paper tackles biofilm problems from all perspectives, including biofilm-forming pathogens in the food industry, disinfectant resistance of biofilm, and identification methods. As biofilms are largely responsible for food spoilage and outbreaks, they are also considered responsible for damage to food processing equipment. Hence the need to gain good knowledge about all of the factors favouring their development or growth, such as the attachment surface, food matrix components, environmental conditions, the bacterial cells involved, and electrostatic charging of surfaces. Overall, this review study shows the real threat of biofilms in the food industry due to the resistance of disinfectants and the mechanisms developed for their survival, including the intercellular signalling system, the cyclic nucleotide second messenger, and biofilm-associated proteins.

Pathogens electrogenicity as a tool for in-situ metabolic activity monitoring and drug assessment in biofilms

Concerns regarding increased antibiotic resistance arising from the emergent properties of biofilms have spurred interest in the discovery of novel antibiotic agents and techniques to directly estimate metabolic activity in biofilms. Although a number of methods have been developed to quantify biofilm formation, real-time quantitative assessment of metabolic activity in label-free biofilms remains a challenge. Production of electrical current via extracellular electron transport (EET) has recently been found in pathogens and appears to correlate with their metabolic activity. Accordingly, monitoring the production of electrical currents as an indicator of cellular metabolic activity in biofilms represents a new direction for research aiming to assess and screen the effects of antimicrobials on biofilm activity. In this article, we reviewed EET-capable pathogens and the methods to monitor biofilm activity to discuss advantages of using the capability of pathogens to produce electrical currents and effective combination of these methods. Moreover, we discussed EET mechanisms by pathogenic and environmental bacteria and open questions for the physiological roles of EET in pathogen's biofilm. The present limitations and possible future directions of in situ biofilm metabolic activity assessment for large-scale screening of antimicrobials are also discussed.

Advances in the characterization and monitoring of natural organic matter using spectroscopic approaches

Natural organic matter (NOM) is ubiquitous in environment and plays a fundamental role in the geochemical cycling of elements. It is involved in a wide range of environmental processes and can significantly affect the environmental fates of exogenous contaminants. Understanding the properties and environmental behaviors of NOM is critical to advance water treatment technologies and environmental remediation strategies. NOM is composed of characteristic light-absorbing/emitting functional groups, which are the "identification card" of NOM and susceptive to ambient physiochemical changes. These groups and their variations can be captured through optical sensing. Therefore, spectroscopic techniques are elegant tools to track the sources, features, and environmental behaviors of NOM. In this work, the most recent advances in molecular spectroscopic techniques, including UV-Vis, fluorescence, infrared, and Raman spectroscopy, for the characterization, measurement, and monitoring of NOM are reviewed, and the state-of-the-art innovations are highlighted. Furthermore, the limitations of current spectroscopic approaches for the exploration of NOM-related environmental processesand how these weaknesses/drawbacks can be addressed are explored. Finally, suggestions and directions are proposed to advance the development of spectroscopic methods in analyzing and elucidating the properties and behaviors of NOM in natural and engineered environments.

Applications of surface-enhanced Raman spectroscopy in detection fields

Surface-enhanced Raman spectroscopy (SERS) is a Raman spectroscopy technique that has been widely used in food safety, environmental monitoring, medical diagnosis and treatment and drug monitoring because of its high selectivity, sensitivity, rapidness, simplicity and specificity in identifying molecular structures. This review introduces the detection mechanism of SERS and summarizes the most recent progress concerning the use of SERS for the detection and characterization of molecules, providing references for the later research of SERS in detection fields.

Denitrifying sulfur conversion-EBPR (DS-EBPR) process for treatment of seawater-based highly saline wastewater: Evaluation on performance, kinetics and microbial community structure

DS-EBPR is an alternative to the conventional activated sludge process which face great challenge for treatment of seawater-based highly saline wastewater. This study aims to investigate the impacts of long-term (248 days) 20% and 30% seawater fractions and short-term shock of 30%, 40%, 70% and 100% seawater fractions (corresponding to 1.0, 1.4, 2.5 and 3.5% of salinity) on the DS-EBPR performance, kinetics and microbial community structure. Long-term operation with high fraction (30%) of seawater marginally decreased the sulfur conversion and phosphorus uptake, which correlated well with the microbial dynamics. Temporal salinity shock from 1.0% (30% seawater) to 3.5% (100% seawater) remarkably reduced the phosphorus release/uptake by 36-44%, which was partly due to the decrease in the abundance of functional bacteria and chlorapatite (Ca₅[PO₄]₃Cl) forming as P precipitates with 70-100% seawater addition. The formed chlorapatite contributed to approximately 8-26% of total P removal estimated by X-ray photoelectron spectroscopy analysis.

Optical nanosensors for biofilm detection in the food industry: principles, applications and challenges

Biofilms are the universal lifestyle of bacteria enclosed in extracellular polymeric substances (EPS) on the contact surfaces of food processing facilities. The EPS-encapsulated foodborne bacterial pathogens are the main food contaminant sources, posing a serious threat to human health. The microcrystalline, sophisticated and dynamic biofilms necessitate the development of conventional microscopic imaging and spectral technology. Nanosensors, which can transfer the biochemical information into optical signals, have recently emerged for biofilm optical detection with high sensitivity and high spatial resolution at nanoscale scopes. Therefore, the aim of this review is to clarify the main detection scope in biofilms and the detection principles of optical nanosensors arousing Raman enhancement, fluoresce conversion and color change. The difficulties and challenges of biofilm characterization including the secretion and variation of main biochemical components are first discussed, the details about the principles and application examples of bioassays targeting foodborne pathogens based on optical nanosensors are then summarized. Finally, the challenges and future trends in developing optical nanosensors are also highlighted. The current review indicates that optical nanosensors have taken the challenges of detecting biofilm in complex food samples, including the characterization of biofilm formation mechanism, identification of microbial metabolic activities, diagnosis of potential food pathogens and sanitation monitoring of food processing equipment. Numerous in-depth explorations and various trials have proven that the bioassays based on multifunctional optical nanosensors are promising to ensure and promote food safety and quality. However, there still remains a daunting challenge to structure reproducible, biocompatible and applicable nano-sensors for biofilm characterization, identification, and imaging.

Imaging the invisible-Bioorthogonal Raman probes for imaging of cells and tissues

A revolutionary avenue for vibrational imaging with super-multiplexing capability can be seen in the recent development of Raman-active bioortogonal tags or labels. These tags and isotopic labels represent groups of chemically inert and small modifications, which can be introduced to any biomolecule of interest and then supplied to single cells or entire organisms. Recent developments in the field of spontaneous Raman spectroscopy and stimulated Raman spectroscopy in combination with targeted imaging of biomolecules within living systems are the main focus of this review. After having introduced common strategies for bioorthogonal labeling, we present applications thereof for profiling of resistance patterns in bacterial cells, investigations of pharmaceutical drug-cell interactions in eukaryotic cells and cancer diagnosis in whole tissue samples. Ultimately, this approach proves to be a flexible and robust tool for in vivo imaging on several length scales and provides comparable information as fluorescence-based imaging without the need of bulky fluorescent tags.

A quaternary ammonium silane antimicrobial triggers bacterial membrane and biofilm destruction

To study the antimicrobial effects of quaternary ammonium silane (QAS) exposure on Streptococcus mutans and Lactobacillus acidophilus bacterial biofilms at different concentrations. Streptococcus mutans and Lactobacillus acidophilus biofilms were cultured on dentine disks, and incubated for bacterial adhesion for 3-days. Disks were treated with disinfectant (experimental QAS or control) and returned to culture for four days. Small-molecule drug discovery-suite was used to analyze QAS/Sortase-A active site. Cleavage of a synthetic fluorescent peptide substrate, was used to analyze inhibition of Sortase-A. Raman spectroscopy was performed and biofilms stained for confocal laser scanning microscopy (CLSM). Dentine disks that contained treated dual-species biofilms were examined using scanning electron microscopy (SEM). Analysis of DAPI within biofilms was performed using CLSM. Fatty acids in bacterial membranes were assessed with succinic-dehydrogenase assay along with time-kill assay. Sortase-A protein underwent conformational change due to QAS molecule during simulation, showing fluctuating alpha and beta strands. Spectroscopy revealed low carbohydrate intensities in 1% and 2% QAS. SEM images demonstrated absence of bacterial colonies after treatment. DAPI staining decreased with 1% QAS (p < 0.05). Fatty acid compositions of dual specie biofilm increased in both 1% and 2% QAS specimens (p < 0.05). Quaternary ammonium silane demonstrated to be a potent antibacterial cavity disinfectant and a plaque inhibitor and can be of potential significance in eliminating caries-forming bacteria.

Rapid detection of bacterial infection and viability assessment with high specificity and sensitivity using Raman microspectroscopy

Infectious diseases caused by bacteria still pose major diagnostic challenges in spite of the availability of various molecular approaches. Irrespective of the type of infection, rapid identification of the causative pathogen with a high degree of sensitivity and specificity is essential for initiating appropriate treatment. While existing methods like PCR possess high sensitivity, they are incapable of identifying the viability status of the pathogen and those which can, like culturing, are inherently slow. To overcome these limitations, we developed a diagnostic platform based on Raman microspectroscopy, capable of detecting biochemical signatures from a single bacterium for identification as well as viability assessment. The study also establishes a decontamination protocol for handling live pathogenic bacteria which does not affect identification and viability testing, showing applicability in the analysis of sputum samples containing pathogenic mycobacterial strains. The minimal sample processing along with multivariate analysis of spectroscopic signatures provides an interface for automatic classification, allowing the prediction of unknown samples by mapping signatures onto available datasets. Also, the novelty of the current work is the demonstration of simultaneous identification and viability assessment at a single bacterial level for pathogenic bacteria. Graphical abstract.

Next-generation physiology approaches to study microbiome function at single cell level

The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.

Detection of Antimicrobial Resistance-Related Changes in Biochemical Composition of Staphylococcus aureus by Means of Atomic Force Microscopy-Infrared Spectroscopy

The development of antimicrobial resistance (AMR) resulting from widespread antibiotic usage is occurring at an alarming pace, much faster than our understanding of the mechanisms behind resistance. Knowledge about resistance-related phenotypic and genotypic changes is critical for the development of new drugs. Here, we identify changes in the chemical composition of Staphylococcus aureus associated with the development of resistance to last resort drugs, vancomycin and daptomycin, using a novel, single cell, nanoscale technique, atomic force microscopy-infrared spectroscopy (AFM-IR), combined with chemometric analysis. We utilized paired clinical isolates, with the parent (susceptible) strain isolated prior to treatment and the daughter (resistant) strain obtained from the same patient after drug admission and clinical failure. We observed an increase in the amount of nonintracellular carbohydrates, indicating thickening or changes in the packing of the cell wall, as well as changes in the phospholipid content in relation to vancomycin resistance and daptomycin nonsusceptibility, respectively.

Quantifying Concentration Polarization - Raman Microspectroscopy for In-Situ Measurement in a Flat Sheet Cross-flow Nanofiltration Membrane Unit

In this work, the concentration polarization layer (CPL) of sulphate in a cross-flow membrane system was measured in-situ using Raman microspectroscopy (RM). The focus of this work is to introduce RM as a new tool for the study of mass transfer inside membrane channels in reverse osmosis (RO) and nanofiltration (NF) generally. Specifically, this work demonstrates how to use RM for locally resolved measurement of sulphate concentration in a cross-flow flat-sheet NF membrane flow cell with channel dimensions similar to commonly applied RO/NF spiral wound modules (channel height about 0.7 mm). Concentration polarization profiles of an aqueous magnesium sulphate solution of 10 g_sulphate·L⁻¹ were obtained at operating pressure of 10 bar and cross-flow velocities of 0.04 and 0.2 m·s⁻¹. The ability of RM to provide accurate concentration profiles is discussed thoroughly. Optical effects due to refraction present one of the main challenges of the method by substantially affecting signal intensity and depth resolution. The concentration profiles obtained in this concept study are consistent with theory and show reduced CPL thickness and membrane wall concentration with increasing cross-flow velocity. The severity of CP was quantified to reach almost double the bulk concentration at the lower velocity.

Investigation of multiple polymers in a denitrifying sulfur conversion-EBPR system: The structural dynamics and storage states

Polyhydroxyalkanoates (PHAs), polyphosphate (poly-P) and polysulfide or elemental sulfur (poly-S) are the key functionally relevant polymers involved in the recently reported Denitrifying Sulfur conversion-associated Enhanced Biological Phosphorus Removal (DS-EBPR) process. However, little is known about the structural dynamics and storage states of these polymers. In particular, investigating the poly-S generated in this process is quite a superior challenge. This study was thus aimed at simultaneously qualitative-quantitative investigating poly-S and associated poly-P and PHAs through the integrated chemical analysis and Raman micro-spectroscopy coupled with multiple microscopic methods (i.e. optical microscopy, confocal laser scanning microscopy, and differential interference contrast microscopy). The chemical analytical results displayed a stable DS-EBPR phenotype in terms of sulfur conversion, P release/uptake and the dynamics of relevant polymers. The multiple microscopic images and Raman spectrum profiles further clearly demonstrated the existence of the polymers and their dynamic changes under alternating anaerobic-anoxic conditions, consistent with the chemical analytical results. In particular, Raman analysis for the first time unraveled the co-existence of S⁰/S_n^2- species stored either intracellularly or extracellularly; and the dynamic conversions between S⁰/S_n^2- and other sulfur species suggest that there might be a universal pool of bioavailable sulfur. The results reveal the mechanisms underlying the structural dynamics and changes in storage states of the relevant polymers that are functionally relevant to the carbon/phosphorus/sulfur-cycles during different metabolic phases. These mechanisms would otherwise not be obtained only using a traditional chemical analysis-based approach.

Raman Sensing and Its Multimodal Combination with Optoacoustics and OCT for Applications in the Life Sciences

Currently, many optical modalities are being investigated, applied, and further developed for non-invasive analysis and sensing in the life sciences. To befit the complexity of the study objects and questions in this field, the combination of two or more modalities is attempted. We review our work on multimodal sensing concepts for applications ranging from non-invasive quantification of biomolecules in the living organism to supporting medical diagnosis showing the combined capabilities of Raman spectroscopy, optical coherence tomography, and optoacoustics.

Micro-Raman Spectroscopy Reveals the Presence of Octacalcium Phosphate and Whitlockite in Association with Bacteria-Free Zones Within the Mineralized Dental Biofilm

Through a correlative analytical approach encompassing backscattered electron scanning electron microscopy (BSE-SEM), energy dispersive X-ray spectroscopy (EDX), and micro-Raman spectroscopy, the composition of the mineralized biofilm around a dental implant, retrieved due to peri-implantitis, was investigated. The mineralized biofilm contains two morphologically distinct regions: (i) bacteria-containing zones (Bact+), characterized by aggregations of unmineralized and mineralized bacteria, and intermicrobial mineralization, and (ii) bacteria-free zones (Bact-), comprised mainly of randomly oriented mineral platelets. Intramicrobial mineralization, within Bact+, appears as smooth, solid mineral deposits resembling the morphologies of dental plaque bacteria. Bact- is associated with micrometer-sized Mg-rich mineral nodules. The Ca/P ratio of Bact+ is higher than Bact-. The inorganic phase of Bact+ is carbonated apatite (CHAp), while that of Bact- is predominantly octacalcium phosphate (OCP) and whitlockite (WL) inclusions. Compared with native bone, the inorganic phase of Bact+ (i.e., CHAp) exhibits higher mineral crystallinity, lower carbonate content, and lower Ca/P, C/Ca, Mg/Ca, and Mg/P ratios. The various CaPs found within the mineralized dental biofilm (CHAp, OCP, and WL) are related to the local presence/absence of bacteria. In combination with BSE-SEM and EDX, micro-Raman spectroscopy is a valuable analytical tool for nondestructive investigation of mineralized dental biofilm composition and development.

Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World

The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characterization and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals.

Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes

With the vast majority of the microbial world still considered unculturable or undiscovered, microbiologists not only require more fundamental insights concerning microbial growth requirements but also need to implement miniaturized, versatile and high-throughput technologies to upscale current microbial isolation strategies. In this respect, single-cell-based approaches are increasingly finding their way to the microbiology lab. A number of recent studies have demonstrated that analysis and separation of free microbial cells by flow-based sorting as well as physical stochastic confinement of individual cells in microenvironment compartments can facilitate the isolation of previously uncultured species and the discovery of novel microbial taxa. Still, while most of these methods give immediate access to downstream whole genome sequencing, upscaling to higher cell densities as required for metabolic readouts and preservation purposes can remain challenging. Provided that these and other technological challenges are addressed in future innovation rounds, integration of single-cell tools in commercially available benchtop instruments and service platforms is expected to trigger more targeted explorations in the microbial dark matter at a depth comparable to metagenomics.

Surface-Enhanced Raman Scattering Spectroscopy for Label-Free Analysis of P. aeruginosa Quorum Sensing

Bacterial quorum sensing systems regulate the production of an ample variety of bioactive extracellular compounds that are involved in interspecies microbial interactions and in the interplay between the microbes and their hosts. The development of new approaches for enabling chemical detection of such cellular activities is important in order to gain new insight into their function and biological significance. In recent years, surface-enhanced Raman scattering (SERS) spectroscopy has emerged as an ultrasensitive analytical tool employing rationally designed plasmonic nanostructured substrates. This review highlights recent advances of SERS spectroscopy for label-free detection and imaging of quorum sensing-regulated processes in the human opportunistic pathogen Pseudomonas aeruginosa. We also briefly describe the challenges and limitations of the technique and conclude with a summary of future prospects for the field.

Stable isotope compounds - production, detection, and application

Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.

Stable-isotope Raman microspectroscopy for the analysis of soil organic matter

We examined the potential of stable-isotope Raman microspectroscopy (SIRM) for the evaluation of differently enriched ¹³C-labeled humic acids as model substances for soil organic matter (SOM). The SOM itself can be linked to the soil water holding capacity. Therefore, artificial humic acids (HA) with known isotopic compositions were synthesized and analyzed by means of SIRM. By performing a pregraphitization, a suitable analysis method was developed to cope with the high fluorescence background. Results were verified against isotope ratio mass spectrometry (IRMS). The limit of quantification was 2.1 × 10^{-1 13}C/C _tot for the total region and 3.2 × 10^{-2 13}C/C _tot for a linear correlation up to 0.25 ¹³C/C _tot. Complementary nanoscale secondary ion mass spectrometry (NanoSIMS) analysis indicated small-scale heterogeneity within the dry sample material, even though-owing to sample topography and occurring matrix effects-obtained values deviated in magnitude from those of IRMS and SIRM. Our study shows that SIRM is well-suited for the analysis of stable isotope-labeled HA. This method requires no specific sample preparation and can provide information with a spatial resolution in the micrometer range. Graphical abstract Analysis of the isotopic composition of humic acids by Raman microspectroscopy in combination with isotope ratio mass spectrometry and nanoscale secondary ion mass spectrometry.