Fourier transform infrared and Raman spectroscopies for the rapid detection, enumeration, and growth interaction of the bacteria Staphylococcus aureus and Lactococcus lactis ssp. cremoris in milk

Targeted Bioimaging of Microencapsulated Recombinant LAB Vector Expressing Fluorescent Reporter Protein: A Non-invasive Approach for Microbial Tracking

Lactococcus lactis (L. lactis), the first genetically modified Generally Recognized As Safe (GRAS) category Lactic Acid producing Bacteria (LAB), is best known for its generalized health-promoting benefits and ability to express heterologous proteins. However, achieving the optimal probiotic effects requires a selective approach that would allow us to study in vivo microbial biodistribution, fate, and immunological consequences. Although the chemical conjugation of fluorophores and chromophores represent the standard procedure to tag microbial cells for various downstream applications, it requires a high-throughput synthesis scheme, which is often time-consuming and expensive. On the contrary, the genetic manipulation of LAB vector, either chromosomally or extra-chromosomally, to express bioluminescent or fluorescent reporter proteins has greatly enhanced our ability to monitor bacterial transit through a complex gut environment. However, with faster passage and quick washing out from the gut due to rhythmic contractions of the digestive tract, real-time tracking of LAB vectors, particularly non-commensal ones, remains problematic. To get a deeper insight into the biodistribution of non-commensal probiotic bacteria in vivo, we bioengineered L. lactis to express fluorescence reporter proteins, mCherry (bright red monomeric fluorescent protein) and mEGFP (monomeric enhanced green fluorescent protein), followed by microencapsulation with a mucoadhesive and biodegradable polymer, chitosan. We show that coating of recombinant Lactococcus lactis (rL. lactis) with chitosan polymer, cross-linked with tripolyphosphate (TPP), retains their ability to express the reporter proteins stably without altering the specificity and sensitivity of fluorescence detection in vitro and in vivo. Further, we provide evidence of enhanced intragastric stability by chitosan-TPP (CS) coating of rL. lactis cells, allowing us to study the spatiotemporal distribution for an extended time in the gut of two unrelated hosts, avian and murine. The present scheme involving genetic modification and chitosan encapsulation of non-commensal LAB vector demonstrates great promise as a non-invasive and intensive tool for active live tracking of gut microbes.

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.

Surface-enhanced Raman spectroscopy for the characterization of bacterial pellets of Staphylococcus aureus infected by bacteriophage

Drug-resistant pathogenic bacteria are a major cause of infectious diseases in the world and they have become a major threat through the reduced efficacy of developed antibiotics. This issue can be addressed by using bacteriophages, which can kill lethal bacteria and prevent them from causing infections. Surface-enhanced Raman spectroscopy (SERS) is a promising technique for studying the degradation of infectious bacteria by the interaction of bacteriophages to break the vicious cycle of drug-resistant bacteria and help to develop chemotherapy-independent remedial strategies. The phage (viruses)-sensitive Staphylococcus aureus (S. aureus) bacteria are exposed to bacteriophages (Siphoviridae family) in the time frame from 0 min (control) to 50 minutes with intervals of 5 minutes and characterized by SERS using silver nanoparticles as SERS substrate. This allows us to explore the effects of the bacteriophages against lethal bacteria (S. aureus) at different time intervals. The differentiating SERS bands are observed at 575 (C-C skeletal mode), 620 (phenylalanine), 649 (tyrosine, guanine (ring breathing)), 657 (guanine (COO deformation)), 728-735 (adenine, glycosidic ring mode), 796 (tyrosine (C-N stretching)), 957 (C-N stretching (amide lipopolysaccharides)), 1096 (PO2 (nucleic acid)), 1113 (phenylalanine), 1249 (CH2 of amide III, N-H bending and C-O stretching (amide III)), 1273 (CH2, N-H, C-N, amide III), 1331 (C-N stretching mode of adenine), 1373 (in nucleic acids (ring breathing modes of the DNA/RNA bases)) and 1454 cm-1 (CH2 deformation of saturated lipids), indicating the degradation of bacteria and replication of bacteriophages. Multivariate data analysis was performed by employing principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) to study the biochemical differences in the S. aureus bacteria infected by the bacteriophage. The SERS spectral data sets were successfully differentiated by PLS-DA with 94.47% sensitivity, 98.61% specificity, 94.44% precision, 98.88% accuracy and 81.06% area under the curve (AUC), which shows that at 50 min interval S. aureus bacteria is degraded by the replicating bacteriophages.

Simultaneous Raman and Infrared Spectroscopy of Stable Isotope Labelled Escherichia coli

We report the use of a novel technology based on optical photothermal infrared (O-PTIR) spectroscopy for obtaining simultaneous infrared and Raman spectra from the same location of the sample allowing us to study bacterial metabolism by monitoring the incorporation of 13C- and 15N-labeled compounds. Infrared data obtained from bulk populations and single cells via O-PTIR spectroscopy were compared to conventional Fourier transform infrared (FTIR) spectroscopy in order to evaluate the reproducibility of the results achieved by all three approaches. Raman spectra acquired were concomitant with infrared data from bulk populations as well as infrared spectra collected from single cells, and were subjected to principal component analysis in order to evaluate any specific separation resulting from the isotopic incorporation. Similar clustering patterns were observed in infrared data acquired from single cells via O-PTIR spectroscopy as well as from bulk populations via FTIR and O-PTIR spectroscopies, indicating full incorporation of heavy isotopes by the bacteria. Satisfactory discrimination between unlabeled (viz. 12C14N), 13C14N- and 13C15N-labeled bacteria was also obtained using Raman spectra from bulk populations. In this report, we also discuss the limitations of O-PTIR technology to acquire Raman data from single bacterial cells (with typical dimensions of 1 × 2 µm) as well as spectral artifacts induced by thermal damage when analyzing very small amounts of biomass (a bacterium tipically weighs ~ 1 pg).

A Multivariate Approach to Study the Bacterial Diversity Associated to the Wooden Shelves Used for Aging Traditional Sicilian Cheeses

The present study was carried to correlate the microbial diversity of the biofilms developed on the wooden boards used for aging traditional Sicilian cheeses with cheese typology. To this end, the microbial diversity of the shelves in contact with the cheeses PDO Pecorino Siciliano, PDO Piacentinu Ennese, and TAP Caciocavallo Palermitano, during ripening, was evaluated by a multivariate statistical approach. The shelf biofilms of this study were previously analyzed for their microbial composition, but no correlation between biodiversity and cheese type was investigated. Canonical discriminant analysis confirmed a cheese typology effect on the microbial loads of the wooden shelves investigated. Regarding the plate count data, the centroids of different cheeses were statistically distant from one another. This analysis also showed a good graphic separation of data regarding bacterial order operational taxonomy units (OTUs). Thus, the microbiological differences imputed to the cheese typologies were not affected by the environmental conditions of the facilities. Furthermore, wooden shelf lactic acid bacteria (LAB) were investigated for their ability to inhibit the main dairy pathogens. Although inhibitors were mainly enterococci, P. pentosaceus WS287 and W. paramesenteroides WS581 showed the highest inhibition activity, indicating their possible application to control the undesired bacteria in situ.

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

Sepsis is a life-threatening clinical condition responsible for approximately 11 million deaths worldwide. Rapid and accurate identification of pathogenic bacteria and its antimicrobial susceptibility play a critical role in reducing the morbidity and mortality rates related to sepsis. Raman and infrared spectroscopies have great potential to be used as diagnostic tools for rapid and culture-free detection of bacterial infections. Despite numerous reports using both methods to analyse bacterial samples, there is to date no study collecting both Raman and infrared signatures from clinical samples simultaneously due to instrument incompatibilities. Here, we report for the first time the use of an emerging technology that provides infrared signatures via optical photothermal infrared (O-PTIR) spectroscopy and Raman spectra simultaneously. We use this approach to analyse 12 bacterial clinical isolates including six isolates of Gram-negative and six Gram-positive bacteria commonly associated with bloodstream infection in humans. To benchmark the single cell spectra obtained by O-PTIR spectroscopy, infrared signatures were also collected from bulk samples via both FTIR and O-PTIR spectroscopies. Our findings showed significant similarity and high reproducibility in the infrared signatures obtained by all three approaches, including similar discrimination patterns when subjected to clustering algorithms. Principal component analysis (PCA) showed that O-PTIR and Raman data acquired simultaneously from bulk bacterial isolates displayed different clustering patterns due to the ability of both methods to probe metabolites produced by bacteria. By contrast, signatures of microbial pigments were identified in Raman spectra, providing complementary and orthogonal information compared to infrared, which may be advantageous as it has been demonstrated that certain pigments play an important role in bacterial virulence. We found that infrared spectroscopy showed higher sensitivity than Raman for the analysis of individual cells. Despite the different patterns obtained by using Raman and infrared spectral data as input for clustering algorithms, our findings showed high data reproducibility in both approaches as the biological replicates from each bacterial strain clustered together. Overall, we show that Raman and infrared spectroscopy offer both advantages and disadvantages and, therefore, having both techniques combined in one single technology is a powerful tool with promising applications in clinical microbiology.

O-PTIR was used for simultaneous collection of infrared and Raman spectra from clinical pathogens associated with bloodstream infections.

Application of Optical Quality Control Technologies in the Dairy Industry: An Overview

Sustainable development of the agricultural industry, in particular, the production of milk and feed for farm animals, requires accurate, fast, and non-invasive diagnostic tools. Currently, there is a rapid development of a number of analytical methods and approaches that meet these requirements. Infrared spectrometry in the near and mid-IR range is especially widespread. Progress has been made not only in the physical methods of carrying out measurements, but significant advances have also been achieved in the development of mathematical processing of the received signals. This review is devoted to the comparison of modern methods and devices used to control the quality of milk and feed for farm animals.

Imaging Isotopically Labeled Bacteria at the Single-Cell Level Using High-Resolution Optical Infrared Photothermal Spectroscopy

We report that the cellular uptake of stable isotope-labeled compounds by bacteria can be probed at the single-cell level using infrared spectroscopy, and this monitors the chemical vibrations affected by the incorporation of "heavy" atoms by cells and thus can be used to understand microbial systems. This presents a significant advancement as most studies have focused on evaluating communities of cells due to the poor spatial resolution achieved by classical infrared microspectrometers, and to date, there is no study evaluating the incorporation of labeled compounds by bacteria at single-cell levels using infrared spectroscopy. The development of new technologies and instrumentations that provide information on the metabolic activity of a single bacterium is critical as this will allow for a better understanding of the interactions between microorganisms as well as the function of individual members and their interactions in different microbial communities. Thus, the present study demonstrates the ability of a novel far-field infrared imaging technique, optical photothermal infrared (O-PTIR) spectroscopy, as a tool to monitor the uptake of ¹³C-glucose and ¹⁵N-ammonium chloride by Escherichia coli bacteria at single-cell levels using spectral signatures recorded via single-point and imaging modes. An additional novelty is that imaging was achieved using six vibrational bands in the amide I and II regions, which were analyzed with chemometrics by employing partial least squares-discriminant analysis to predict ¹³C/¹²C and ¹⁵N/¹⁴N simultaneously.

M13 phage-based nanoprobe for SERS detection and inactivation of Staphylococcus aureus

Rapid and sensitive diagnosis of bacterial infections at early stage is of great significance for food safety monitoring as well as clinical treatment. Herein, we construct a surface-enhanced Raman scattering (SERS) nanoprobe based on M13 phages for the selective detection and inactivation of Staphylococcus aureus (S. aureus). M13 phage with specific S. aureus-binding heptapeptide displayed on the N-terminal of pIII protein is selected from phage display peptide library. The S. aureus-specific SERS probe is thus constructed by in situ growth of gold nanoparticles (AuNPs) on M13 phage surface, followed by modification with 5,5-dithiobis-(2-nitrobenzoic acid) (DTNB) as SERS active molecule. Upon the addition of this SERS probe, M13 phage selectively binds with S. aureus to induce anchoring of AuNPs on S. aureus surface, and the SERS probe-labeled S. aureus cells are collected by centrifugation for SERS detection. For the quantification of S. aureus, a linear range of 10-10⁶ cfu mL^-1 is achieved in aqueous medium. It is further demonstrated by spiking recovery in soft drinks. Furthermore, this SERS probe exhibits bactericidal capabilities towards S. aureus, which shows promising potential to serve as a multifunctional platform for simultaneous detection and inactivation of S. aureus.

Investigation of the Applicability of Raman Spectroscopy as Online Process Control during Consumer Milk Production

Online detection of product defects using fast spectroscopic measurements is beneficial for producers in the dairy industry since it allows readjustment of product characteristics or redirection of product streams during production. Raman spectroscopy has great potential for such application due to the fast and simple measurement. Its suitability as online sensor for process control was investigated at typical control points in consumer milk production being raw milk storage, standardization, and heat treatment. Additionally, the appropriateness of Raman spectroscopy to act as indicator for product application parameters was investigated using the example of barista foam. To assess the suitability of a pure online system, the merit of Raman spectra was evaluated by a principal component analysis (PCA). Thereby, proteolytic spoilage due to the presence of extracellular enzymes of Pseudomonas sp. was detected and samples based on the applied heat treatment (extended shelf life (ESL) and ultra-high temperature (UHT)) could be separated. A correlation of the content of free fatty acids and foam stability with spectra of the respective milk samples was found, allowing a prediction of the technofunctional quality criterion “Barista” suitability of a UHT milk. The results underlined the suitability of Raman spectroscopy for the detection of deviations from a defined product standard of consumer milk.

Applications of Raman spectroscopic techniques for quality and safety evaluation of milk: A review of recent developments

Milk is a complete nutrient source for humans. The quality and safety of milk are critical for both producers and consumers, thereby the dairy industry requires rapid and nondestructive methods to ensure milk quality and safety. However, conventional methods are time-consuming and laborious, and require complicated preparation procedures. Therefore, the exploration of new milk analytical methods is essential. This current review introduces the principles of Raman spectroscopy and presents recent advances since 2012 of Raman spectroscopic techniques mainly involving surface-enhanced Raman spectroscopy (SERS), fourier-transform (FT) Raman spectroscopy, near-infrared (NIR) Raman spectroscopy, and micro-Raman spectroscopy for milk analysis including milk compositions, microorganisms and antibiotic residues in milk, as well as milk adulterants. Additionally, some challenges and future outlooks are proposed. The current review shows that Raman spectroscopic techniques have the promising potential for providing rapid and nondestructive detection of milk parameters. However, the application of Raman spectroscopy on milk analysis is not common yet since some limitations of Raman spectroscopy need to be overcome before making it a routine tool for the dairy industry.

Use of Fourier transform infrared spectroscopy for monitoring the shelf life of ham slices packed with probiotic supplemented edible films after treatment with high pressure processing

The aim of the present study was to investigate the potential use of Fourier transform infrared (FTIR) spectroscopy to quantify biochemical changes occurring in ham slices packed with probiotic supplemented edible films and treated with High Pressure Processing (HPP), in monitoring spoilage. Details regarding the data collection and experimental procedure were presented by Pavli et al. (2017). A series of Partial Least Squares (PLS) models were developed to correlate spectral data from FTIR analysis with ham spoilage during storage under vacuum at different temperatures (4, 8 and 12°C). FTIR spectra were collected from the surface of the ham samples in parallel with microbiological analysis of total viable counts (TVC) and lactic acid bacteria (LAB). Qualitative interpretation of spectral data was based on a sensory evaluation, using a hedonic scale, classifying the samples in three quality classes, fresh, semi-fresh and spoiled. The scope of the modeling approach was to discriminate the ham slices in their respective quality class and additionally to predict the microbial population directly from spectral data. The results obtained demonstrated that the processing of the samples affected the performance of classification in the sensory classes, with better results observed in the case of for ham slices packed with probiotic supplemented (PS) edible films and of control samples without HPP. The performance of PLS regression models on providing quantitative estimations of microbial counts were based on specific figures of merit (bias factor, accuracy factor, root mean square error, percentage of prediction error). Bias and accuracy factors were close to unity for both microbial groups tested for samples without HPP, whereas for HPP treated samples the values of these indices ranged from 0.963 to 1.332, depending on the case and indice. The results of this study demonstrated for the first time that although FTIR can be used reliably for the rapid assessment of sliced ham, additional processes such as HPP can affect its performance.

Dielectric Sphere Clusters as a Model to Understand Infrared Spectroscopic Imaging Data Recorded from Complex Samples

Understanding the infrared (IR) spectral response of materials as a function of their morphology is not only of fundamental importance but also of contemporary practical need in the analysis of biological and synthetic materials. While significant work has recently been reported in understanding the spectra of particles with well-defined geometries, we report here on samples that consist of collections of particles. First, we theoretically model the importance of multiple scattering effects and computationally predict the impact of local particles' environment on the recorded IR spectra. Both monodisperse and polydisperse particles are considered in clusters with various degrees of packing. We show that recorded spectra are highly dependent on the cluster morphology and size of particles but the origin of this dependence is largely due to the scattering that depends on morphology and not absorbance that largely depends on the volume of material. The effect of polydispersity is to reduce the fine scattering features in the spectrum, resulting in a closer resemblance to bulk spectra. Fourier transform-IR (FT-IR) spectra of clusters of electromagnetically coupled poly(methyl methacrylate) (PMMA) spheres with wavelength-scale diameters were recorded and compared to simulated results. Measured spectra agreed well with those predicted. Of note, when PMMA spheres occupy a volume greater than 18% of the focal volume, the recorded IR spectrum becomes almost independent of the cluster's morphological changes. This threshold, where absorbance starts to dominate the signal, exactly matches the percolation threshold for hard spheres and quantifies the transition between the single particle and bulk behavior. Our finding enables an understanding of the spectral response of structured samples and points to appropriate models for recovering accurate chemical information from in IR microspectroscopy data.

Optical Biosensing of Bacteria and Bacterial Communities

Bacterial sensing is important for understanding the numerous roles bacteria play in nature and in technology, understanding and managing bacterial populations, detecting pathogenic bacterial infections, and preventing the outbreak of illness. Current analytical challenges in bacterial sensing center on the dilemma of rapidly acquiring quantitative information about bacteria with high detection efficiency, sensitivity, and specificity, while operating within a reasonable budget and optimizing the use of ancillary tools, such as multivariate statistics. This review starts from a general description of bacterial sensing methods and challenges, and then focuses on bacterial characterization using optical methods including Raman spectroscopy and imaging, infrared spectroscopy, fluorescence spectroscopy and imaging, and plasmonics, including both extended and localized surface plasmon resonance spectroscopy. The advantages and drawbacks of each method in relation to the others are discussed, as are their applications. A particularly promising direction in bacterial sensing lies in combining multiple approaches to achieve multiplex analysis, and examples where this has been achieved are highlighted.

Quantitative detection of codeine in human plasma using surface-enhanced Raman scattering via adaptation of the isotopic labelling principle

In this study surface-enhanced Raman scattering (SERS) combined with the isotopic labelling (IL) principle has been used for the quantification of codeine spiked into both water and human plasma.

Quantitative detection of isotopically enrichedE. colicells by SERS

It is clear that investigating how bacterial cells work by analysing their functional roles in microbial communities is very important in environmental, clinical and industrial microbiology. The benefits of linking genes to their respective functions include the reliable identification of the causative agents of various diseases, which would permit appropriate and timely treatment in healthcare systems. In industrial and municipal wastewater treatment and management, such knowledge may allow for the manipulation of microbial communities, such as through bioaugmentation, in order to improve the efficiency and effectiveness of bioremediation processes. Stable isotope probing coupled with identification techniques has emerged to be a potentially reliable tool for the discrimination, identification and characterization of bacteria at community and single cell levels, knowledge which can be utilized to link microbially mediated bioprocesses to phylogeny. Development of the surface-enhanced Raman scattering (SERS) technique offers an exciting alternative to the Raman and Fourier-transform infrared spectroscopic techniques in understanding the metabolic processes of microorganismsin situ. SERS employing Ag and Au nanoparticles can significantly enhance the Raman signal, making it an exciting candidate for the analysis of the cellular components of microorganisms. In this study,Escherichia colicells were cultivated in minimal medium containing different ratios of¹²C/¹³C glucose and/or¹⁴N/¹⁵N ammonium chloride as the only carbon and nitrogen sources respectively, with the overall final concentrations of these substrates being constant. After growth, theE. colicells were analyzed with SERS employing anin situsynthesis of Ag nanoparticles. This novel investigation of the SERS spectral data with multivariate chemometrics demonstrated clear clusters which could be correlated to the SERS spectral shifts of biomolecules from cells grown and hence labelled with¹³C and¹⁵N atoms. These shifts reflect the isotopic content of the bacteria and quantification of the isotope levels could be established using chemometrics based on partial least squares regression.

Microfluidic cantilever detects bacteria and measures their susceptibility to antibiotics in small confined volumes

In the fight against drug-resistant bacteria, accurate and high-throughput detection is essential. Here, a bimaterial microcantilever with an embedded microfluidic channel with internal surfaces chemically or physically functionalized with receptors selectively captures the bacteria passing through the channel. Bacterial adsorption inside the cantilever results in changes in the resonance frequency (mass) and cantilever deflection (adsorption stress). The excitation of trapped bacteria using infrared radiation (IR) causes the cantilever to deflect in proportion to the infrared absorption of the bacteria, providing a nanomechanical infrared spectrum for selective identification. We demonstrate the in situ detection and discrimination of Listeria monocytogenes at a concentration of single cell per μl. Trapped Escherichia coli in the microchannel shows a distinct nanomechanical response when exposed to antibiotics. This approach, which combines enrichment with three different modes of detection, can serve as a platform for the development of a portable, high-throughput device for use in the real-time detection of bacteria and their response to antibiotics.

Analysis of bacteria and their response to antibiotics in real time is challenging. Here the authors report a microcantilever based system that can detect and discriminate between bacteria species and, due to the ability to discriminate between alive and dead samples, measure response to antibiotics.

Single-cell level methods for studying the effect of antibiotics on bacteria during infection

Considerable evidence about phenotypic heterogeneity among bacteria during infection has accumulated during recent years. This heterogeneity has to be considered if the mechanisms of infection and antibiotic action are to be understood, so we need to implement existing and find novel methods to monitor the effects of antibiotics on bacteria at the single-cell level. This review provides an overview of methods by which this aim can be achieved. Fluorescence label-based methods and Raman scattering as a label-free approach are discussed in particular detail. Other label-free methods that can provide single-cell level information, such as impedance spectroscopy and surface plasmon resonance, are briefly summarized. The advantages and disadvantages of these different methods are discussed in light of a challenging in vivo environment.

Novel application of heuristic optimisation enables the creation and thorough evaluation of robust support vector machine ensembles for machine learning applications

Today's researchers have access to an unprecedented range of powerful machine learning tools with which to build models for classifying samples according to their metabolomic profile (e.g. separating diseased samples from healthy controls). However, such powerful tools need to be used with caution and the diagnostic performance of models produced by them should be rigorously evaluated if their output is to be believed. This involves considerable processing time, and has hitherto required expert knowledge in machine learning. By adopting a constrained nonlinear simplex optimisation for the tuning of support vector machines (SVMs) we have reduced SVM training times more than tenfold compared to a traditional grid search, allowing us to implement a high performance R package that makes it possible for a typical bench scientist to produce powerful SVM ensemble classifiers within a reasonable timescale, with automated bootstrapped training and rigorous permutation testing. This puts a state-of-the-art open source multivariate classification pipeline into the hands of every metabolomics researcher, allowing them to build robust classification models with realistic performance metrics.

Chicken, beams, and Campylobacter: rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry

Campylobacter species are one of the main causes of food poisoning worldwide. Despite the availability of established culturing and molecular techniques, due to the fastidious nature of these microorganisms, simultaneous detection and species differentiation still remains challenging. This study focused on the differentiation of eleven Campylobacter strains from six species, using Fourier transform infrared (FT-IR) and Raman spectroscopies, together with matrix-assisted laser desorption ionisation-time of flight-mass spectrometry (MALDI-TOF-MS), as physicochemical approaches for generating biochemical fingerprints. Cluster analysis of data from each of the three analytical approaches provided clear differentiation of each Campylobacter species, which was generally in agreement with a phylogenetic tree based on 16S rRNA gene sequences. Notably, although C. fetus subspecies fetus and venerealis are phylogenetically very closely related, using FT-IR and MALDI-TOF-MS data these subspecies were readily differentiated based on differences in the lipid (2920 and 2851 cm(-1)) and fingerprint regions (1500-500 cm(-1)) of the FT-IR spectra, and the 500-2000 m/z region of the MALDI-TOF-MS data. A finding that was further investigated with targeted lipidomics using liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that such metabolomics approaches combined with molecular biology techniques may provide critical information and knowledge related to the risk factors, virulence, and understanding of the distribution and transmission routes associated with different strains of foodborne Campylobacter spp.

Applications of Infrared and Raman Spectroscopies to Probiotic Investigation

In this review, we overview the most important contributions of vibrational spectroscopy based techniques in the study of probiotics and lactic acid bacteria. First, we briefly introduce the fundamentals of these techniques, together with the main multivariate analytical tools used for spectral interpretation. Then, four main groups of applications are reported: (a) bacterial taxonomy (Subsection 4.1); (b) bacterial preservation (Subsection 4.2); (c) monitoring processes involving lactic acid bacteria and probiotics (Subsection 4.3); (d) imaging-based applications (Subsection 4.4). A final conclusion, underlying the potentialities of these techniques, is presented.

Combining Raman and FT-IR spectroscopy with quantitative isotopic labeling for differentiation of E. coli cells at community and single cell levels

There is no doubt that the contribution of microbially mediated bioprocesses toward maintenance of life on earth is vital. However, understanding these microbes in situ is currently a bottleneck, as most methods require culturing these microorganisms to suitable biomass levels so that their phenotype can be measured. The development of new culture-independent strategies such as stable isotope probing (SIP) coupled with molecular biology has been a breakthrough toward linking gene to function, while circumventing in vitro culturing. In this study, for the first time we have combined Raman spectroscopy and Fourier transform infrared (FT-IR) spectroscopy, as metabolic fingerprinting approaches, with SIP to demonstrate the quantitative labeling and differentiation of Escherichia coli cells. E. coli cells were grown in minimal medium with fixed final concentrations of carbon and nitrogen supply, but with different ratios and combinations of (13)C/(12)C glucose and (15)N/(14)N ammonium chloride, as the sole carbon and nitrogen sources, respectively. The cells were collected at stationary phase and examined by Raman and FT-IR spectroscopies. The multivariate analysis investigation of FT-IR and Raman data illustrated unique clustering patterns resulting from specific spectral shifts upon the incorporation of different isotopes, which were directly correlated with the ratio of the isotopically labeled content of the medium. Multivariate analysis results of single-cell Raman spectra followed the same trend, exhibiting a separation between E. coli cells labeled with different isotopes and multiple isotope levels of C and N.

Thiophene acetylenes and furanosesquiterpenes from Xanthopappus subacaulis and their antibacterial activities

In a search for naturally occurring antibacterial compounds in medicinal plants, six hitherto unknown thiophene acetylenes, named 10,11-threo-xanthopappin D, 10,11-erythro-xanthopappin D, 10,11-cis-xanthopappin B, 5-(but-4-chloro-3-hydroxy-1-ynyl)-2-(Z)-pent-3-ene-1-ynylthiophene, 5-(but-4-chloro-3-hydroxy-1-ynyl)-2-(E)-pent-3-ene-1-ynylthiophene, 5-(but-3,4-dihydroxy-1-ynyl)-2-(Z)-pent-3-ene-1-ynylthiophene and two furanosesquiterpenes, as well as fifteen known compounds, were isolated from Xanthopappus subacaulis, which has been used as a traditional Tibetan medicine in China. A biosynthetic pathway to thiophene acetylenes was proposed and, the isolated compounds were tested for their antibacterial activity against five bacteria. Within the series of thiophene acetylenes tested, 10,11-threo-xanthopappin D with a threo configuration exhibited strong activity against Bacillus subtilis, with a minimum inhibitory concentration (MIC) of 7.25μg/mL, whereas 10,11-erythro-xanthopappin D with erythro configuration possessed broad-spectrum antibacterial activity against Escherichia coli, Bacillus cereus, Staphylococcus aureus and Erwinia carotovora, with MICs of 12.5, 15.5, 7.25 and 7.25μg/mL, respectively. Meanwhile, the compounds 10,11-cis-xanthopappin B, xanthopappin B, 5-(but-4-chloro-3-hydroxy-1-ynyl)-2-(Z)-pent-3-ene-1-ynylthiophene and 5-(but-4-chloro-3-hydroxy-1-ynyl)-2-(E)-pent-3-ene-1-ynylthiophene substituted with a Cl atom at C-14 showed moderate inhibitory activity against E. coli, B. cereus, S. aureus, E. carotovora and B. subtilis, with MICs ranging from 31.25 to 62.5μg/mL. The structures of these compounds were elucidated through the comprehensive analysis of spectroscopic data, including UV, IR, MS and NMR.

Raman spectroscopy in the analysis of food and pharmaceutical nanomaterials

Raman scattering is an inelastic phenomenon. Although its cross section is very small, recent advances in electronics, lasers, optics, and nanotechnology have made Raman spectroscopy suitable in many areas of application. The present article reviews the applications of Raman spectroscopy in food and drug analysis and inspection, including those associated with nanomaterials. Brief overviews of basic Raman scattering theory, instrumentation, and statistical data analysis are also given. With the advent of Raman enhancement mechanisms and the progress being made in metal nanomaterials and nanoscale metal surfaces fabrications, surface enhanced Raman scattering spectroscopy has become an extra sensitive method, which is applicable not only for analysis of foods and drugs, but also for intracellular and intercellular imaging. A Raman spectrometer coupled with a fiber optics probe has great potential in applications such as monitoring and quality control in industrial food processing, food safety in agricultural plant production, and convenient inspection of pharmaceutical products, even through different types of packing. A challenge for the routine application of surface enhanced Raman scattering for quantitative analysis is reproducibility. Success in this area can be approached with each or a combination of the following methods: (1) fabrication of nanostructurally regular and uniform substrates; (2) application of statistic data analysis; and (3) isotopic dilution.

Evaluation of the effects of ultraviolet light on bacterial contaminants inoculated into whole milk and colostrum, and on colostrum immunoglobulin G

Raw milk and colostrum can harbor dangerous microorganisms that can pose serious health risks for animals and humans. According to the USDA, more than 58% of calves in the United States are fed unpasteurized milk. The aim of this study was to evaluate the effect of UV light on reduction of bacteria in milk and colostrum, and on colostrum IgG. A pilot-scale UV light continuous (UVC) flow-through unit (45 J/cm(2)) was used to treat milk and colostrum. Colostrum and sterile whole milk were inoculated with Listeria innocua, Mycobacterium smegmatis, Salmonella serovar Typhimurium, Escherichia coli, Staphylococcus aureus, Streptococcus agalactiae, and Acinetobacter baumannii before being treated with UVC. During UVC treatment, samples were collected at 5 time points and bacteria were enumerated using selective media. The effect of UVC on IgG was evaluated using raw colostrum from a nearby dairy farm without the addition of bacteria. For each colostrum batch, samples were collected at several different time points and IgG was measured using ELISA. The UVC treatment of milk resulted in a significant final count (log cfu/mL) reduction of Listeria monocytogenes (3.2 ± 0.3 log cfu/mL reduction), Salmonella spp. (3.7 ± 0.2 log cfu/mL reduction), Escherichia coli (2.8 ± 0.2 log cfu/mL reduction), Staph. aureus (3.4 ± 0.3 log cfu/mL reduction), Streptococcus spp. (3.4 ± 0.4 log cfu/mL reduction), and A. baumannii (2.8 ± 0.2 log cfu/mL reduction). The UVC treatment of milk did not result in a significant final count (log cfu/mL) reduction for M. smegmatis (1.8 ± 0.5 log cfu/mL reduction). The UVC treatment of colostrum was significantly associated with a final reduction of bacterial count (log cfu/mL) of Listeria spp. (1.4 ± 0.3 log cfu/mL reduction), Salmonella spp. (1.0 ± 0.2 log cfu/mL reduction), and Acinetobacter spp. (1.1 ± 0.3 log cfu/mL reduction), but not of E. coli (0.5 ± 0.3 log cfu/mL reduction), Strep. agalactiae (0.8 ± 0.2 log cfu/mL reduction), and Staph. aureus (0.4 ± 0.2 log cfu/mL reduction). The UVC treatment of colostrum significantly decreased the IgG concentration, with an observed final mean IgG reduction of approximately 50%. Development of new methods to reduce bacterial contaminants in colostrum must take into consideration the barriers imposed by its opacity and organic components, and account for the incidental damage to IgG caused by manipulating colostrum.

Biomarker discovery and applications for foods and beverages: proteomics to nanoproteomics

Foods and beverages have been at the heart of our society for centuries, sustaining humankind - health, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated high-throughput sensitive technologies means that foods are being analyzed at various levels. For example and in particular, high-throughput omics approaches are being applied to develop suitable biomarkers for foods and beverages and their applications in addressing quality, technology, authenticity, and safety issues. Proteomics are one of those technologies that are increasingly being utilized to profile expressed proteins in different foods and beverages. Acquired knowledge and protein information have now been translated to address safety of foods and beverages. Very recently, the power of proteomic technology has been integrated with another highly sensitive and miniaturized technology called nanotechnology, yielding a new term nanoproteomics. Nanoproteomics offer a real-time multiplexed analysis performed in a miniaturized assay, with low-sample consumption and high sensitivity. To name a few, nanomaterials - quantum dots, gold nanoparticles, carbon nanotubes, and nanowires - have demonstrated potential to overcome the challenges of sensitivity faced by proteomics for biomarker detection, discovery, and application. In this review, we will discuss the importance of biomarker discovery and applications for foods and beverages, the contribution of proteomic technology in this process, and a shift towards nanoproteomics to suitably address associated issues. This article is part of a Special Issue entitled: Translational plant proteomics.

Production of organic acids by probiotic lactobacilli can be used to reduce pathogen load in poultry

Probiotic Lactobacillus can be used to reduce the colonization of pathogenic bacteria in food animals, and therefore reduce the risk of foodborne illness to consumers. As a model system, we examined the mechanism of protection conferred by Lactobacillus species to inhibit C. jejuni growth in vitro and reduce colonization in broiler chickens. Possible mechanisms for the reduction of pathogens by lactobacilli include: 1) stimulation of adaptive immunity; 2) alteration of the cecal microbiome; and, 3) production of inhibitory metabolites, such as organic acids. The Lactobacillus species produced lactic acid at concentrations sufficient to kill C. jejuni in vitro. We determined that lactic acid produced by Lactobacillus disrupted the membrane of C. jejuni, as judged by biophotonics. The spectral features obtained using Fourier-transform infrared (FT-IR) and Raman spectroscopy techniques were used to accurately predict bacterial viability and differentiate C. jejuni samples according to lactic acid treatment. FT-IR spectral features of C. jejuni and Lactobacillus grown in co-culture revealed that the metabolism was dominated by Lactobacillus prior to the killing of C. jejuni. Based on our results, the development of future competitive exclusion strategies should include the evaluation of organic acid production.

Fate of enterotoxigenicStaphylococcus aureusand staphylococcal enterotoxins in Feta and Galotyri cheeses

In this study the fate of enterotoxigenicStaphylococcus aureusand staphylococcal enterotoxins in Feta and Galotyri cheeses were studied. Initially, the enterotoxigenic abilities of fourStaph. aureusLHA, LHB, LHC and LHD strains isolated from raw ovine milk were examined in both BHI broth and ovine milk. In BHI broth, theStaph. aureusLHA, LHB, LHC and LHD strains were found toxigenic at 37 °C producing the staphylococcal enterotoxins (SEs) serotypes SEA, SEB, SEC and SED, respectively, whereas in ovine milk at 37 °C,Staph. aureusLHD was found to produce only SED, while no SE production was observed for the other examined strains. Thus, the fate of onlyStaph. aureusLHD and SED were examined in Feta and Galotyri cheeses. The cheeses were made from raw ovine toxic milk with preformed SED or raw ovine milk contaminated with high (ca 6 log cfu/ml) and low inocula (ca 3 log cfu/ml) ofStaph. aureusLHD. Results showed that the pathogen was eliminated at slower rate in Galotyri cheese than in Feta cheese, for the high (5 d vs. 16 d) or the low (1 d vs. 12 d) inoculum trials. In both cheeses produced from the toxic milk, SED was detected during manufacturing and storage. SED was also detected in the curd (2 h), whenStaph. aureusLHD populations had reached ca 7 log cfu/g, and up to the end of storage for the high inoculum trials of both cheeses. No SED was observed for the low inoculum trials of either cheese.

Antibacterial activity of the plant-derived compounds 23-methyl-6-O-desmethylauricepyrone and (Z,Z)-5-(trideca-4,7-dienyl)resorcinol and their synergy with antibiotics against methicillin-susceptible and -resistant Staphylococcus aureus

The present study investigated the antibacterial activity of two plant-derived compounds, 23-methyl-6-O-desmethylauricepyrone (1) and (Z,Z)-5-(trideca-4,7-dienyl)resorcinol (2), and their synergistic effects with erythromycin and gentamicin against methicillin-susceptible (MSSA) and gentamicin- and methicillin-resistant Staphylococcus aureus (MRSA). Studies of the individual antibacterial activity of each plant-derived compound and synergy experiments were carried out, by the microdilution test in agar and by the checkerboard method, respectively. Compound 1 showed minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 2 and 8 μg/mL, respectively, against both strains of S. aureus, while compound 2 exhibited anti-MSSA and anti-MRSA activity with MICs and MBCs of 4 and 8 and 2 and 8 μg/mL, respectively. Time-kill curves showed that, while compound 1 produced complete killing of both strains at 24 h from the beginning of the experiment, 2 produced the same effect in the first hour. Combinations of 1 with erythromycin or gentamicin showed a notable synergism against MSSA, which enabled the antibiotic concentration to decrease by up to 300 or 260 times, respectively. When the aminoglycoside was placed together with compound 2, only an additive effect was observed. The assayed compounds did not produce erythrocyte hemolysis or genotoxicity and they did not affect macrophage viability at the effective or higher concentrations. These results suggest that both compounds could be considered as promising antibacterial agents while compound 1 could be used in combinatory therapies with erythromycin and gentamicin.