Capturing bacterial metabolic exchange using thin film desorption electrospray ionization-imaging mass spectrometry

A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua

Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms.

Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms

Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.

Noninvasive Detection of Skin Cancer by Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging

We report a technique for the noninvasive detection of skin cancer by imprint desorption electrospray ionization mass spectrometry imaging (DESI-MSI) using a transfer agent that is pressed against the tissue of interest. By noninvasively pressing a tape strip against human skin, metabolites, fatty acids, and lipids on the skin surface are transferred to the tape with little spatial distortion. Running DESI-MSI on the tape strip provides chemical images of the molecules on the skin surface, which are valuable for distinguishing cancer from healthy skin. Chemical components of the tissue imprint on the tape strip and the original basal cell carcinoma (BCC) section from the mass spectra show high consistency. By comparing MS images (about 150-μm resolution) of same molecules from the tape strip and from the BCC section, we confirm that chemical patterns are successfully transferred to the tape stripe. We also used the technique to distinguish cherry angiomas from normal human skin by comparing the molecular patterns from a tape strip. These results demonstrate the potential of the imprint DESI-MSI technique for the noninvasive detection of skin cancers as well as other skin diseases before and during clinical surgery.

MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology

Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.

The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging

As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.

Rapid Profiling of Metabolic Perturbations to Antibiotics in Living Bacteria by Induced Electrospray Ionization Mass Spectrometry

Rapid monitoring of real bacterial metabolic perturbations to antibiotics may be helpful to better understand the mechanisms of action and more targeted treatment. In this study, the real metabolic responses to antibiotic treatment in living bacteria were profiled rapidly by induced electrospray ionization mass spectrometry. Significant metabolic perturbations were profiled after antibiotic treatment compared with untreated bacteria. Similar and unique metabolic responses were observed with different antibiotic treatments. Further multivariable analysis was performed to determine significant metabolites as potential biomarkers. Moreover, different metabolic disturbances were detected for serial dilutions of antibiotic treatments. Overall, combined with induced electrospray ionization mass spectrometry, the rapid and real bacterial metabolic status caused by antibiotics was monitored, suggesting the potential application of our method in mechanism exploration and clinical diagnosis.

Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads

Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera.

IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.

Rapid visualization of lipopeptides and potential bioactive groups of compounds by combining ion mobility and MALDI imaging mass spectrometry

Mass spectrometry imaging (MSI) has become a powerful method for mapping metabolite distribution in a tissue. Applied to bacterial colonies, MSI has a bright future, both for the discovery of new bioactive compounds and for a better understanding of bacterial antibiotic resistance mechanisms. Coupled with separation techniques such as ion mobility mass spectrometry (IM-MS), the identification of metabolites directly on the image is now possible and does not require additional analysis such as HPLC-MS/MS. In this article, we propose to apply a semi-targeted workflow for rapid IM-MSI data analysis focused on the search for bioactive compounds. First, chemically-related compounds showing a repetitive mass unit (i.e. lipids and lipopeptides) were targeted based on the Kendrick mass defect analysis. The detected groups of potentially bioactive compounds were then confirmed by fitting their measured ion moibilites to their measured m/z values. Using both their m/z and ion mobility values, the selected groups of compounds were identified using the available databases and finally their distribution was observed on the image. Using this workflow on a co-culture of bacteria, we were able to detect and localize bioactive compounds involved in the microbial interaction.

Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil

Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.

Assessing direct analysis in real-time mass spectrometry for the identification and serotyping of Legionella pneumophila

AIMS

The efficacy of ambient mass spectrometry to identify and serotype Legionella pneumophila was assessed. To this aim, isolated waterborne colonies were submitted to a rapid extraction method and analysed by direct analysis in real-time mass spectrometry (DART-HRMS).

METHODS AND RESULTS

The DART-HRMS profiles, coupled with partial least squares discriminant analysis (PLS-DA), were first evaluated for their ability to differentiate Legionella spp. from other bacteria. The resultant classification model achieved an accuracy of 98.1% on validation. Capitalising on these encouraging results, DART-HRMS profiling was explored as an alternative approach for the identification of L. pneumophila sg. 1, L. pneumophila sg. 2-15 and L. non-pneumophila; therefore, a different PLS-DA classifier was built. When tested on a validation set, this second classifier reached an overall accuracy of 95.93%. It identified the harmful L. pneumophila sg. 1 with an impressive specificity (100%) and slightly lower sensitivity (91.7%), and similar performances were reached in the classification of L. pneumophila sg. 2-15 and L. non-pneumophila.

CONCLUSIONS

The results of this study show the DART-HMRS method has good accuracy, and it is an effective method for Legionella serogroup profiling.

SIGNIFICANCE AND IMPACT OF THE STUDY

These preliminary findings could open a new avenue for the rapid identification and quick epidemiologic tracing of L. pneumophila, with a consequent improvement to risk assessment.

Spatial Mapping of Cellular Metabolites Using DESI Ion Mobility Mass Spectrometry

Spatial mapping of cellular metabolites, such as neurotransmitters and lipids, on the tissue, can increase our understanding of the biological functions of those molecules. Mass spectrometry imaging (MSI) techniques, such as desorption electrospray ionization (DESI), have not demonstrated the ability to perform metabolite analysis at mammalian single cell level yet. However, they can be a valuable tool to provide insight into cellular metabolism in a very small population (tens) of cells. DESI MSI, coupled with ion mobility separation, improves the peak capacity and signal-to-noise ratio of detected analytes by separating a molecule of interest from interfering isobaric species found in a complex biological matrix. Here we present a protocol for mapping cellular metabolites neurotransmitters, such as serotonin, adenosine, and glutamine directly in brain tissue samples using DESI MSI.

Antifungal potential of secondary metabolites involved in the interaction between citrus pathogens

Numerous postharvest diseases have been reported that cause substantial losses of citrus fruits worldwide. Penicillium digitatum is responsible for up to 90% of production losses, and represent a problem for worldwide economy. In order to control phytopathogens, chemical fungicides have been extensively used. Yet, the use of some artificial fungicides cause concerns about environmental risks and fungal resistance. Therefore, studies focusing on new approaches, such as the use of natural products, are getting attention. Co-culture strategy can be applied to discover new bioactive compounds and to understand microbial ecology. Mass Spectrometry Imaging (MSI) was used to screen for potential antifungal metabolites involved in the interaction between Penicillium digitatum and Penicillium citrinum. MSI revealed a chemical warfare between the fungi: two tetrapeptides, deoxycitrinadin A, citrinadin A, chrysogenamide A and tryptoquialanines are produced in the fungi confrontation zone. Antimicrobial assays confirmed the antifungal activity of the investigated metabolites. Also, tryptoquialanines inhibited sporulation of P. citrinum. The fungal metabolites reported here were never described as antimicrobials until this date, demonstrating that co-cultures involving phytopathogens that compete for the same host is a positive strategy to discover new antifungal agents. However, the use of these natural products on the environment, as a safer strategy, needs further investigation. This paper aimed to contribute to the protection of agriculture, considering health and ecological risks.

Genome-Centered Metagenomics Analysis Reveals the Symbiotic Organisms Possessing Ability to Cross-Feed with Anammox Bacteria in Anammox Consortia

Although using anammox communities for efficient wastewater treatment has attracted much attention, the pure anammox bacteria are difficult to obtain, and the potential roles of symbiotic bacteria in anammox performance are still elusive. Here, we combined long-term reactor operation, genome-centered metagenomics, community functional structure, and metabolic pathway reconstruction to reveal multiple potential cross-feedings during anammox reactor start-up according to the 37 recovered metagenome-assembled genomes (MAGs). We found Armatimonadetes and Proteobacteria could contribute the secondary metabolites molybdopterin cofactor and folate for anammox bacteria to benefit their activity and growth. Chloroflexi-affiliated bacteria encoded the function of biosynthesizing exopolysaccharides for anammox consortium aggregation, based on the partial nucleotide sugars produced by anammox bacteria. Chlorobi-affiliated bacteria had the ability to degrade extracellular proteins produced by anammox bacteria to amino acids to affect consortium aggregation. Additionally, the Chloroflexi-affiliated bacteria harbored genes for a nitrite loop and could have a dual role in anammox performance during reactor start-up. Cross-feeding in anammox community adds a different dimension for understanding microbial interactions and emphasizes the importance of symbiotic bacteria in the anammox process for wastewater treatment.

Exploration of Fungal Metabolic Interactions Using Imaging Mass Spectrometry on Nanostructured Silicon

Application of matrix-assisted laser desorption/ionization imaging mass spectrometry to microbiology and natural product research has opened the door to the exploration of microbial interactions and the consequent discovery of new natural products and their functions in the interactions. However, several drawbacks of matrix-assisted laser desorption/ionization imaging mass spectrometry have limited its application especially to complicated and uneven microbial samples. Here, we applied nanostructured silicon as a substrate for surface-assisted laser desorption/ionization mass spectrometry for microbial imaging mass spectrometry to explore fungal metabolic interactions. We chose Phellinus noxius and Aspergillus strains to evaluate the potential of microbial imaging mass spectrometry on nanostructured silicon because both fungi produce a dense mass of aerial mycelia, which is known to complicate the collection of high-quality imaging mass spectrometry data. Our simple and straightforward sample imprinting method and low background interference resulted in an efficient analysis of small metabolites from the complex microbial interaction samples.

Imaging the Unimaginable: Desorption Electrospray Ionization - Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research

Imaging mass spectrometry (IMS) has recently established itself in the field of "spatial metabolomics." Merging the sensitivity and fast screening of high-throughput mass spectrometry with spatial and temporal chemical information, IMS visualizes the production, location, and distribution of metabolites in intact biological models. Since metabolite profiling and morphological features are combined in single images, IMS offers an unmatched chemical detail on complex biological and microbiological systems. Thus, IMS-type "spatial metabolomics" emerges as a powerful and complementary approach to genomics, transcriptomics, and classical metabolomics studies. In this review, we summarize the current state-of-the-art IMS methods with a strong focus on desorption electrospray ionization (DESI)-IMS. DESI-IMS utilizes the original principle of electrospray ionization, but in this case solvent droplets are rastered and desorbed directly on the sample surface. The rapid and minimally destructive DESI-IMS chemical screening is achieved at ambient conditions and enables the accurate view of molecules in tissues at the µm-scale resolution. DESI-IMS analysis does not require complex sample preparation and allows repeated measurements on samples from different biological sources, including microorganisms, plants, and animals. Thanks to its easy workflow and versatility, DESI-IMS has successfully been applied to many different research fields, such as clinical analysis, cancer research, environmental sciences, microbiology, chemical ecology, and drug discovery. Herein we discuss the present applications of DESI-IMS in natural product research.

Quantitative SIMS Imaging of Agar-Based Microbial Communities

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

Mass spectrometry characterization of endophytic bacterium Curtobacterium sp. strain ER1/6 isolated from Citrus sinensis

The bacteria of the genus Curtobacterium are usually seen as plant pathogen, but some species have been identified as endophytes of different crops and could as such present a potential for disease control and plant growth promotion. We have therefore applied the desorption electrospray ionization mass spectrometry imaging (DESI-MSI) in the direct analysis of living Curtobacterium sp. strain ER1/6 colonies to map the surface metabolites, and electrospray ionization tandem mass spectrometry (ESI-MS/MS) for characterization of these compounds. Several colony-associated metabolites were detected. The ESI-MS/MS showed characteristic fragmentations for phospholipids including the classes of glycerophosphocholine, glycerophosphoglycerol, and glycerophosphoinositol as well as several fatty acids. Although a secure identification was not obtained, many other metabolites were also detected for this bacteria species. Principal component analysis showed that fatty acids were discriminatory for Curtobacterium sp. ER1/6 during inoculation on periwinkle wilt (PW) medium, whereas phospholipids characterize the bacterium when grown on the tryptic soy agar (TSA) medium.

Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) imaging has been used for rapid phenotyping of enzymatic activities, but is mainly limited to single-step conversions. Herein we report a label-free method for high-throughput engineering of multistep biochemical reactions based on optically guided MALDI-ToF MS analysis of bacterial colonies. The bacterial cells provide containment of multiple enzymes and access to substrates and cofactors via metabolism. Automated MALDI-ToF MS acquisition from randomly distributed colonies simplifies procedures to prepare strain libraries without liquid handling. MALDI-ToF MS profiling was utilized to screen both substrate and enzyme libraries for natural product biosynthesis. Computational algorithms were developed to process and visualize the resulting mass spectral data sets. For analogues of the peptidic antibiotic plantazolicin, multivariate analyses by t-distributed stochastic neighbor embedding were used to group similar spectra for rapid identification of nonisobaric variants. After MALDI-ToF MS screening, follow-up analyses using high-resolution MS and tandem MS were readily performed on the same sample target. Separately, relative ion intensities of rhamnolipid congeners with various lipid moieties were evaluated to engineer enzymatic specificity. The glycolipid profiles of each colony were overlaid with optical images to facilitate the recovery of desirable mutants. For both the antibiotic and rhamnolipid cases, large populations of colonies were rapidly surveyed at the molecular level, providing information-rich insights not easily obtained with traditional screening assays. Utilizing standard microbiological techniques with routine microscopy and MALDI-ToF MS instruments, this simple yet effective workflow is applicable for a wide range of screening campaigns targeting multistep enzymatic reactions.

Visualizing spatial distribution of small molecules in the rhubarb stalk (Rheum rhabarbarum) by surface-transfer mass spectrometry imaging

Laser desorption/ionization mass spectrometry imaging (LDI-MSI) with gold nanoparticle-enhanced target (AuNPET) was used for visualization of small molecules in the rhubarb stalk (Rheum rhabarbarum L.). Analysis was focused on spatial distribution of biologically active compounds which are found in rhubarb species. Detected compounds belong to a very wide range of chemical compound classes such as anthraquinone derivatives and their glucosides, stilbenes, anthocyanins, flavonoids, polyphenols, organic acids, chromenes, chromanones, chromone glycosides and vitamins. The analysis of the spatial distribution of these compounds in rhubarb stalk with the nanoparticle-rich surface of AuNPET target plate has been made without additional matrix and with minimal sample preparation steps.

Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions

Imaging mass spectrometry (IMS) allows the study of the spatial distribution of small molecules in biological samples. IMS is able to identify and quantify chemicals in situ from whole tissue sections to single cells. Both vacuum mass spectrometry (MS) and ambient MS systems have advanced considerably over the last decade; however, some limitations are still hard to surmount. Sample pretreatment, matrix or solvent choices, and instrument improvement are the key factors that determine the successful application of IMS to different samples and analytes. IMS with innovative MS analyzers, powerful MS spectrum databases, and analysis tools can efficiently dereplicate, identify, and quantify natural products. Moreover, multimodal imaging systems and multiple MS-based systems provide additional structural, chemical, and morphological information and are applied as complementary tools to explore new fields. IMS has been applied to reveal interactions between living organisms at molecular level. Recently, IMS has helped solve many previously unidentifiable relations between bacteria, fungi, plants, animals, and insects. Other significant interactions on the chemical level can also be resolved using expanding IMS techniques. WIREs Syst Biol Med 2017, 9:e1387. doi: 10.1002/wsbm.1387 For further resources related to this article, please visit the WIREs website.

Mass Spectrometry Imaging of Complex Microbial Communities

In the two decades since mass spectrometry imaging (MSI) was first applied to visualize the distribution of peptides across biological tissues and cells, the technique has become increasingly effective and reliable. MSI excels at providing complementary information to existing methods for molecular analysis—such as genomics, transcriptomics, and metabolomics—and stands apart from other chemical imaging modalities through its capability to generate information that is simultaneously multiplexed and chemically specific. Today a diverse family of MSI approaches are applied throughout the scientific community to study the distribution of proteins, peptides, and small-molecule metabolites across many biological models.

The inherent strengths of MSI make the technique valuable for studying microbial systems. Many microbes reside in surface-attached multicellular and multispecies communities, such as biofilms and motile colonies, where they work together to harness surrounding nutrients, fend off hostile organisms, and shield one another from adverse environmental conditions. These processes, as well as many others essential for microbial survival, are mediated through the production and utilization of a diverse assortment of chemicals. Although bacterial cells are generally only a few microns in diameter, the ecologies they influence can encompass entire ecosystems, and the chemical changes that they bring about can occur over time scales ranging from milliseconds to decades. Because of their incredible complexity, our understanding of and influence over microbial systems requires detailed scientific evaluations that yield both chemical and spatial information. MSI is well-positioned to fulfill these requirements. With small adaptations to existing methods, the technique can be applied to study a wide variety of chemical interactions, including those that occur inside single-species microbial communities, between cohabitating microbes, and between microbes and their hosts.

In recognition of this potential for scientific advancement, researchers have adapted MSI methodologies for the specific needs of the microbiology research community. As a result, workflows exist for imaging microbial systems with many of the common MSI ionization methods. Despite this progress, there is substantial room for improvements in instrumentation, sample preparation, and data interpretation. This Account provides a brief overview of the state of technology in microbial MSI, illuminates selected applications that demonstrate the potential of the technique, and highlights a series of development challenges that are needed to move the field forward. In the coming years, as microbial MSI becomes easier to use and more universally applicable, the technique will evolve into a fundamental tool widely applied throughout many divisions of science, medicine, and industry.

From single cells to our planet-recent advances in using mass spectrometry for spatially resolved metabolomics

Spatial information in the form of 3D digital content has been increasingly integrated into our daily lives. Metabolomic studies parallel this trend with spatial and time resolved information being acquired. Mass spectrometry imaging (MSI), which combines qualitative and quantitative molecular information with spatial information, plays a crucial role in mass spectrometry-based metabolomics. The lateral spatial resolution obtained by MSI continues to improve and allows mass spectrometers to be used as molecular microscopes-enabling the exploration of the cellular and subcellular metabolome. Towards the other end of the scale, MS is also being used to map (image) molecules on our skin, habitats, and entire ecosystems. In this article, we provide a perspective of imaging mass spectrometry for metabolomic studies from the subcellular to planetary scale.

Desorption electrospray ionization mass spectrometry imaging reveals chemical defense of Burkholderia seminalis against cacao pathogens

DESI-MSI of metabolites identified inB. seminalis.

Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography

A new approach for constant-distance mode mass spectrometry imaging (MSI) of biological samples using nanospray desorption electrospray ionization (nano-DESI) was developed by integrating a shear-force probe with the nano-DESI probe. The technical concept and basic instrumental setup, as well as the general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enabled the constant-distance imaging mode via a computer-controlled closed-feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites, including nonribosomal peptides (surfactin, plipastatin, and iturin) on the surface of living bacterial colonies, ranging in diameter from 10 to 13 mm, with height variations up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Based on this effort, constant-mode nano-DESI MSI proved to be ideally suited for imaging biological samples of complex topography in their native states.

Ambient ionization and miniature mass spectrometry system for chemical and biological analysis

Ambien ionization and miniaturization of mass spectrometers are two fields in mass spectrometry that have advanced significantly in the last decade. The integration of the techniques developed in these two fields is leading to the development of complete miniature analytical systems that can be used for on-site or point-of-care analysis by non-expert users. In this review, we report the current status of development in ambient ionization and miniature mass spectrometers, with an emphasis on those techniques with potential impact on the point-of-care (POC) diagnostics. The challenges in the future development of the integrated systems are discussed with possible solutions presented.

A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms

Matrix-assisted laser desorption/ionization imaging of biofilms cultured on agar plates is challenging because of problems related to matrix deposition onto agar. We describe a one-step, spray-based application of a 2,5-dihydroxybenzoic acid solution for direct matrix-assisted laser desorption/ionization imaging of hydrated Bacillus subtilis biofilms on agar. Using both an optimized airbrush and a home-built automatic sprayer, region-specific distributions of signaling metabolites and cannibalistic factors were visualized from B. subtilis cells cultivated on biofilm-promoting medium. The approach provides a homogeneous, relatively dry coating on hydrated samples, improving spot to spot signal repeatability compared with sieved matrix application, and is easily adapted for imaging a range of agar-based biofilms. Copyright © 2016 John Wiley & Sons, Ltd.

Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures

The ability to visualize biochemical interactions between microbial communities using MALDI MSI has provided tremendous insights into a variety of biological fields. Matrix application using a sieve proved to be incredibly useful, but it has many limitations that include uneven matrix coverage and limitation in the types of matrices that could be employed in studies. Recently, there has been a concerted effort to improve matrix application for studying agar plated microbial cultures, many of which utilized automated matrix sprayers. Here, we describe the usefulness of using a robotic sprayer for matrix application. The robotic sprayer has two-dimensional control over where matrix is applied, and a heated capillary that allows for rapid drying of the applied matrix. This method provided a significant increase in MALDI sensitivity over the sieve method, as demonstrated by FT-ICR MS analysis, facilitating the ability to gain higher lateral resolution MS images of Bacillus subtilis than previously reported. This method also allowed for the use of different matrices to be applied to the culture surfaces.

Mass spectrometry imaging for visualizing organic analytes in food

The demand for rapid chemical imaging of food products steadily increases. Mass spectrometry (MS) is featured by excellent molecular specificity of analysis and is, therefore, a very attractive method for chemical profiling. MS for food imaging has increased significantly over the past decade, aided by the emergence of various ambient ionization techniques that allow direct and rapid analysis in ambient environment. In this article, the current status of food imaging with MSI is reviewed. The described approaches include matrix-assisted laser desorption/ionization (MALDI), but emphasize desorption atmospheric pressure photoionization (DAPPI), electrospray-assisted laser desorption/ionization (ELDI), probe electrospray ionization (PESI), surface desorption atmospheric pressure chemical ionization (SDAPCI), and laser ablation flowing atmospheric pressure afterglow (LA-FAPA). The methods are compared with regard to spatial resolution; analysis speed and time; limit of detection; and technical aspects. The performance of each method is illustrated with the description of a related application. Specific requirements in food imaging are discussed.

Mass spectrometry tools and workflows for revealing microbial chemistry

Since the time Van Leeuwenhoek was able to observe microbes through a microscope, an innovation that led to the birth of the field of microbiology, we have aimed to understand how microorganisms function, interact and communicate. The exciting progress in the development of analytical technologies and workflows has demonstrated that mass spectrometry is a very powerful technique for the interrogation of microbiology at the molecular level. In this review, we aim to highlight the available and emerging tools in mass spectrometry for microbial analysis by overviewing the methods and workflow advances for taxonomic identification, microbial interaction, dereplication and drug discovery. We emphasize their potential for future development and point out unsolved problems and future directions that would aid in the analysis of the chemistry produced by microbes.

Direct Protocol for Ambient Mass Spectrometry Imaging on Agar Culture

Herein we describe a new protocol that allows direct mass spectrometry imaging (IMS) of agar cultures. A simple sample dehydration leads to a thin solid agar, which enables the direct use of spray-based ambient mass spectrometry techniques. To demonstrate its applicability, metal scavengers siderophores were imaged directly from agar culture of S. wadayamensis, and well resolved and intense images were obtained using both desorption electrospray ionization (DESI) and easy ambient sonic-spray ionization (EASI) with well-defined selective spatial distributions for the free and the metal-bound molecules, providing clues for their roles in cellular metabolism.

Metabolomics in the natural products field--a gateway to novel antibiotics

Metabolomics is a high throughput analytical technique used to globally measure low molecular weight metabolites, allowing simultaneous metabolic comparison of different biological samples and thus highlighting differentially produced compounds as potential biomarkers. Although microbes are renowned as prolific sources of antibiotics, the traditional approach for new anti-infectives discovery is time-consuming and labor-intensive. In this review, the use of NMR- or MS-based metabolomics is proposed as an efficient approach to find antimicrobials in microbial single- or co-cultures.

Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps

Secondary metabolite biosynthesis in microorganisms responds to discrete chemical and biological stimuli; however, untargeted identification of these responses presents a significant challenge. Herein we apply multiplexed stimuli to Streptomyces coelicolor and collect the resulting response metabolomes via ion mobility-mass spectrometric analysis. Self-organizing map (SOM) analytics adapted for metabolomic data demonstrate efficient characterization of the subsets of primary and secondary metabolites that respond similarly across stimuli. Over 60% of all metabolic features inventoried from responses are either not observed under control conditions or produced at greater than 2-fold increase in abundance in response to at least one of the multiplexing conditions, reflecting how metabolites encode phenotypic changes in an organism responding to multiplexed challenges. Using abundance as an additional filter, each of 16 known S. coelicolor secondary metabolites is prioritized via SOM and observed at increased levels (1.2- to 22-fold compared with unperturbed) in response to one or more challenge conditions.

Rapid evaporative ionization mass spectrometry imaging platform for direct mapping from bulk tissue and bacterial growth media

Rapid evaporative ionization mass spectrometry (REIMS) technology allows real time intraoperative tissue classification and the characterization and identification of microorganisms. In order to create spectral libraries for training the classification models, reference data need to be acquired in large quantities as classification accuracy generally improves as a function of number of training samples. In this study, we present an automated high-throughput method for collecting REIMS data from heterogeneous organic tissue. The underlying instrumentation consists of a 2D stage with an additional high-precision z-axis actuator that is equipped with an electrosurgical diathermy-based sampling probe. The approach was validated using samples of human liver with metastases and bacterial strains, cultured on solid medium, belonging to the species P. aeruginosa, B. subtilis, and S. aureus. For both sample types, spatially resolved spectral information was obtained that resulted in clearly distinguishable multivariate clustering between the healthy/cancerous liver tissues and between the bacterial species.

Imaging of plant materials using indirect desorption electrospray ionization mass spectrometry

Indirect desorption electrospray ionization mass spectrometry (DESI-MS) imaging is a method for imaging distributions of metabolites in plant materials, in particular leaves and petals. The challenge in direct imaging of such plant materials with DESI-MS is particularly the protective layer of cuticular wax present in leaves and petals. The cuticle protects the plant from drying out, but also makes it difficult for the DESI sprayer to reach the analytes of interest inside the plant material. A solution to this problem is to imprint the plant material onto a surface, thus releasing the analytes of interest from parts of their matrix while preserving the spatial information in the two dimensions. The imprint can then easily be imaged by DESI-MS. The method delivers simple and robust mass spectrometry imaging of plant material with very high success ratios.

Evaluation of imprint DESI-MS substrates for the analysis of fungal metabolites

Optimized in situ screening, characterization and imaging of fungal metabolites by imprint DESI-MS.

DESI imaging of small molecules in biological tissues

Desorption electrospray ionization (DESI) allows the direct analysis of ordinary objects or preprocessed samples under ambient conditions. Among other applications, DESI is used to identify and to record spatial distributions of small molecules in situ, sliced or imprinted biological tissue. Manipulation of the chemistry accompanying ambient analysis ionization can be used to optimize chemical analysis, including molecular imprinting. Images are obtained by continuously moving the sample relative to the DESI sprayer and the inlet of the mass spectrometer. The acquisition time depends on the size of the surface to be analyzed and on the desired resolution.

Insect-specific production of new GameXPeptides in photorhabdus luminescens TTO1, widespread natural products in entomopathogenic bacteria

Discovery of new natural products by heterologous expression reaches its limits, especially when specific building blocks are missing in the heterologous host or the production medium. Here, we describe the insect-specific production of the new GameXPeptides E-H (5-8) from Photorhabdus luminescens TTO1, which can be produced heterologously from expression of the GameXPeptide synthetase GxpS only upon supplementation of the production media with the missing building blocks, and thus must be regarded as the true natural products under natural conditions.

Direct analysis of intact proteins from Escherichia coli colonies by liquid extraction surface analysis mass spectrometry

Top-down identification of proteins by liquid extraction surface analysis (LESA) mass spectrometry has previously been reported for tissue sections and dried blood spot samples. Here, we present a modified "contact" LESA method for top-down analysis of proteins directly from living bacterial colonies grown in Petri dishes, without any sample pretreatment. It was possible to identify a number of proteins by use of collision-induced dissociation tandem mass spectrometry followed by searches of the data against an E. coli protein database. The proteins identified suggest that the method may provide insight into the bacterial response to environmental conditions. Moreover, the results show that the "contact" LESA approach results in a smaller sampling area than typical LESA, which may have implications for spatial profiling.

Visualizing life with ambient mass spectrometry

Since the development of desorption electrospray ionization (DESI), many other ionization methods for ambient and atmospheric pressure mass spectrometry have been developed. Ambient ionization mass spectrometry has now been used for a wide variety of biological applications, including plant science, microbiology, neuroscience, and cancer pathology. Multimodal integration of atmospheric ionization sources with the other biotechnologies, as well as high performance computational methods for mass spectrometry data processing is one of the major emerging area's for ambient mass spectrometry. In this opinion article, we will highlight some of the most influential technological advances of ambient mass spectrometry in recent years and their applications to the life sciences.

The re-emerging role of microbial natural products in antibiotic discovery

New classes of antibacterial compounds are urgently needed to respond to the high frequency of occurrence of resistances to all major classes of known antibiotics. Microbial natural products have been for decades one of the most successful sources of drugs to treat infectious diseases but today, the emerging unmet clinical need poses completely new challenges to the discovery of novel candidates with the desired properties to be developed as antibiotics. While natural products discovery programs have been gradually abandoned by the big pharma, smaller biotechnology companies and research organizations are taking over the lead in the discovery of novel antibacterials. Recent years have seen new approaches and technologies being developed and integrated in a multidisciplinary effort to further exploit microbial resources and their biosynthetic potential as an untapped source of novel molecules. New strategies to isolate novel species thought to be uncultivable, and synthetic biology approaches ranging from genome mining of microbial strains for cryptic biosynthetic pathways to their heterologous expression have been emerging in combination with high throughput sequencing platforms, integrated bioinformatic analysis, and on-site analytical detection and dereplication tools for novel compounds. These different innovative approaches are defining a completely new framework that is setting the bases for the future discovery of novel chemical scaffolds that should foster a renewed interest in the identification of novel classes of natural product antibiotics from the microbial world.

Emerging capabilities of mass spectrometry for natural products

Covering up to the end of 2013 A brief history of mass spectrometry in natural products research serves to identify themes which have driven progress in this area of application and in mass spectrometry itself. This account covers six decades of ionization methods, starting with traditional electron ionization and progressing through today's ambient ionization methods. Corresponding developments in mass analyzers are indicated, ranging from sector magnetic fields, through hybrid quadrupole mass filters to miniature ion traps. Current capabilities of mass spectrometry in natural products studies include direct in situ analysis, mass spectrometry imaging, and the study of biosynthetic pathways using metabolomic information. The survey concludes with a discussion of new experiments and capabilities including ion soft landing, preparative mass spectrometry, and accelerated ionic reactions in confined volumes.

Ion sources for mass spectrometric identification and imaging of molecular species

Covering: 2013 The ability to transfer molecular species to the gas phase and ionize them is central to the study of natural products and other molecular species by mass spectrometry (MS). MS-based strategies in natural products have focused on a few established ion sources, such as electron impact and electrospray ionization. However, a variety of other ion sources are either currently in use to evaluate natural products or show significant future promise. This review discusses these various ion sources in the context of other articles in this special issue, but is also applicable to other fields of analysis, including materials science. Ion sources are grouped based on the current understanding of their predominant ion formation mechanisms. This broad overview groups ion sources into the following categories: electron ionization and single photon ionization; chemical ionization-like and plasma-based; electrospray ionization; and, laser desorption-based. Laser desorption-based methods are emphasized with specific examples given for laser desorption postionization sources and their use in the analysis of intact microbial biofilms. Brief consideration is given to the choice of ion source for various sample types and analyses, including MS imaging.