Microbial phenomics linking the phenotype to function: The potential of Raman spectroscopy

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.

Phenotypic shifts induced by environmental pre-stressors modify antibiotic resistance in Staphylococcus aureus

Introduction

Escalating prevalence of antibiotic resistance in Staphylococcus aureus has necessitated urgent exploration into the fundamental mechanisms underlying antibiotic resistance emergence, particularly in relation to its interaction with environmental stressors. This study aimed to investigate the effects of environmental stressors prior to antibiotic exposure on the antibiotic resistance of S. aureus.

Methods

We used Raman spectroscopy and flow cytometry to measure prior stress-induced phenotypic alterations of S. aureus, and identified the association between phenotypic shifts and the antibiotic resistance.

Results

The results revealed a multifaceted relationship between stressors and the development of antibiotic resistance. The stressors effectuate distinct phenotypic diversifications and subsequently amplify these phenotypic alterations following antibiotic treatments, contingent upon the specific mode of action; these phenotypic shifts in turn promote the development of antibiotic resistance in S. aureus. This study's findings demonstrated that the presence of pre-stress conditions triggered an augmentation of resistance to vancomycin (VAN), while concurrently attenuating resistance to norfloxacin. Marked shifts in Raman peaks associated with lipids and nucleic acids demonstrated correlations with elevated survival rates following VAN treatment.

Conclusion

Consequently, these observations indicate that pre-stress conditions "prime" bacterial cells for differential responses to antibiotics and bear significant implications for formulating clinical therapeutic strategies.

Development of Polyhydroxybutyrate-Based Packaging Films and Methods to Their Ultrasonic Welding

This study developed a technical task associated with the formation of welded joints based on biodegradable polymers and their subsequent physicochemical characterization. The primary objective was to establish the effect of the welding process and modification of natural poly(3-hydroxybutyrate) (PHB) with N,N-dibutylundecenoylamide (DBUA) as a plasticizing agent on the structure and properties of PHB-based biopolymer materials as well as the process and structure of welded joints formation using ultrasonic welding technique. The weldability of biodegradable layers based on PHB and PHB/DBUA mixture was ultrasonically welded and optimized using a standard Branson press-type installation. The effect of the DBUA plasticizer and welding process on the structure of PHB-based biodegradable material was investigated using scanning electron microscopy, X-ray diffraction, FT-IR spectroscopy, differential scanning calorimetry, and thermomechanical analysis. The results confirmed that the DBUA acted as an effective plasticizer of PHB, contributing to lower crystallinity of the PHB/DBUA mixture (63%) in relation to the crystallinity degree of pure PHB film (69%). Ultrasonic welding resulted in an additional increase (approximately 8.5%) in the degree of crystallinity in the PHB/DBUA in relation to the initial PHB/DBUA mixture. The significant shift toward lower temperatures of the crystallization and melting peaks of PHB modified with DBUA were observed using DSC concerning pure PHB. The melt crystallization process of PHB was affected by welding treatment, and a shift toward higher temperature was observed compared with the unwelded PHB/DBUA sample. The butt-welded joints of biodegradable PHB/DBUA materials made using the ultrasonic method tested for tensile strength have damaged the area immediately outside the joining surface.

Demonstrating low Raman background in UV-written SiO2 waveguides

Raman spectroscopy can give a chemical 'fingerprint' from both inorganic and organic samples, and has become a viable method of measuring the chemical composition of single biological particles. In parallel, integration of waveguides and microfluidics allows for the creation of miniaturized optical sensors in lab-on-a-chip devices. The prospect of combining integrated optics and Raman spectroscopy for Raman-on-chip offers new opportunities for optical sensing. A major limitation for this is the Raman background of the waveguide. This background is very low for optical fibers but remains a challenge for planar waveguides. In this work, we demonstrate that UV-written SiO2 waveguides, designed to mimic the performance of optical fibers, offer a significantly lower background than competing waveguide materials such as Si3N4. The Raman scattering in the waveguides is measured in absolute units and compared to that of optical fibers and Si3N4 waveguides. A limited study of the sensitivity of the Raman scattering to changes in pump wavelength and in waveguide design is also conducted. It is revealed that UV-written SiO2 waveguides offer a Raman background lower than -107.4 dB relative to a 785 nm pump and -106.5 dB relative to a 660 nm pump. Furthermore, the UV-written SiO2 waveguide demonstrates a 15 dB lower Raman background than a Si3N4 waveguide and is only 8.7 - 10.3 dB higher than optical fibers. Comparison with a polystyrene bead (in free space, diameter 7 µm) reveal an achievable peak SNR of 10.4 dB, showing the potential of UV-SiO2 as a platform for a Raman-on-chip device capable of measuring single particles.

Formation and emergent dynamics of spatially organized microbial systems

Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution. These feedbacks can give rise to emergent dynamics, which need to be studied through a combination of spatio-temporal measurements and mathematical models. We highlight the initial formation of SOMS and their emergent dynamics as two open areas of investigation for future studies. These studies will benefit from the development of model systems that can mimic natural ones in terms of species composition and spatial structure.

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.

Phenotypic convergence of bacterial adaption to sub-lethal antibiotic treatment

Microorganisms can adapt quickly to changes in their environment, leading to various phenotypes. The dynamic for phenotypic plasticity caused by environmental variations has not yet been fully investigated. In this study, we analyzed the time-series of phenotypic changes in Staphylococcus cells during adaptive process to antibiotics stresses using flow cytometry and Raman spectroscopy. The nine antibiotics with four different mode of actions were treated in bacterial cells at a sub-lethal concentration to give adaptable stress. Although the growth rate initially varied depending on the type of antibiotic, most samples reached the maximum growth comparable to the control through the short-term adaptation after 24 h. The phenotypic diversity, which showed remarkable changes depending on antibiotic treatment, converged identical to the control over time. In addition, the phenotype with cellular biomolecules converted into a bacterial cell that enhance tolerance to antibiotic stress with increases in cytochrome and lipid. Our findings demonstrated that the convergence into the phenotypes that enhance antibiotic tolerance in a short period when treated with sub-lethal concentrations, and highlight the feasibility of phenotypic approaches in the advanced antibiotic treatment.

Discrimination of Stressed and Non-Stressed Food-Related Bacteria Using Raman-Microspectroscopy

As the identification of microorganisms becomes more significant in industry, so does the utilization of microspectroscopy and the development of effective chemometric models for data analysis and classification. Since only microorganisms cultivated under laboratory conditions can be identified, but they are exposed to a variety of stress factors, such as temperature differences, there is a demand for a method that can take these stress factors and the associated reactions of the bacteria into account. Therefore, bacterial stress reactions to lifetime conditions (regular treatment, 25 °C, HCl, 2-propanol, NaOH) and sampling conditions (cold sampling, desiccation, heat drying) were induced to explore the effects on Raman spectra in order to improve the chemometric models. As a result, in this study nine food-relevant bacteria were exposed to seven stress conditions in addition to routine cultivation as a control. Spectral alterations in lipids, polysaccharides, nucleic acids, and proteins were observed when compared to normal growth circumstances without stresses. Regardless of the involvement of several stress factors and storage times, a model for differentiating the analyzed microorganisms from genus down to strain level was developed. Classification of the independent training dataset at genus and species level for Escherichia coli and at strain level for the other food relevant microorganisms showed a classification rate of 97.6%.

Flow cytometric monitoring of the bacterial phenotypic diversity in aquatic ecosystems

Flow cytometry is a promising tool used to identify the phenotypic features of bacterial communities in aquatic ecosystems by measuring the physical and chemical properties of cells based on their light scattering behavior and fluorescence. Compared to molecular or culture-based approaches, flow cytometry is suitable for the online monitoring of microbial water quality because of its relatively simple sample preparation process, rapid analysis time, and high-resolution phenotypic data. Advanced statistical techniques (e.g., denoising and binning) can be utilized to successfully calculate phenotypic diversity by processing the scatter data obtained from flow cytometry. These phenotypic diversities were well correlated with taxonomic-based diversity computed using next-generation 16S RNA gene sequencing. The protocol provided in this paper should be a useful guide for a fast and reliable flow cytometric monitoring of bacterial phenotypic diversity in aquatic ecosystems.

Gold Nanomaterials as a Promising Integrated Tool for Diagnosis and Treatment of Pathogenic Infections-A Review

This review summarizes research on functionalized gold nanomaterials as pathogen detection sensors and pathogen elimination integrated tools. After presenting the challenge of current severe threat from pathogenic bacteria and the increasingly serious growth rate of drug resistance, the first section mainly introduces the conspectus of gold nanostructures from synthesis, characterization, physicochemical properties and applications of gold nanomaterials. The next section deals with gold nanomaterials-based pathogen detection sensors such as colorimetric sensors, fluorescence sensors and Surface-Enhanced Raman Scattering sensors. We then discuss strategies based on gold nanomaterials for eliminating pathogenic infections, such as the dual sterilization strategy for grafting gold nanomaterials with antibacterial substances, photothermal antibacterial and photodynamic antibacterial methods. The fourth part briefly introduces the comprehensive strategy for diagnosis and sterilization of pathogen infection based on gold nanomaterials, such as the diagnosis and treatment strategy for pathogen infection using Roman signals real-time monitoring and photothermal sterilization. A concluding section that summarizes the current status and challenges of the novel diagnosis and treatment integrated strategy for pathogenic infections, gives an outlook on potential future perspectives.

Omics-based microbiome analysis in microbial ecology: from sequences to information

Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics methods triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.

Roles of Phosphate Solubilizing Microorganisms from Managing Soil Phosphorus Deficiency to Mediating Biogeochemical P Cycle

Phosphorus (P) is a vital element in biological molecules, and one of the main limiting elements for biomass production as plant-available P represents only a small fraction of total soil P. Increasing global food demand and modern agricultural consumption of P fertilizers could lead to excessive inputs of inorganic P in intensively managed croplands, consequently rising P losses and ongoing eutrophication of surface waters. Despite phosphate solubilizing microorganisms (PSMs) are widely accepted as eco-friendly P fertilizers for increasing agricultural productivity, a comprehensive and deeper understanding of the role of PSMs in P geochemical processes for managing P deficiency has received inadequate attention. In this review, we summarize the basic P forms and their geochemical and biological cycles in soil systems, how PSMs mediate soil P biogeochemical cycles, and the metabolic and enzymatic mechanisms behind these processes. We also highlight the important roles of PSMs in the biogeochemical P cycle and provide perspectives on several environmental issues to prioritize in future PSM applications.