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Übergewicht ist einer der wichtigsten Risikofaktoren für kardiovaskuläre und metabolische
Erkrankungen. Vor allem eine vermehrte Akkumulation von viszeralem Fettgewebe (VAT) im
Vergleich zu subkutanem Fettgewebe (SAT) wird als Hauptursache für Adipositas-assoziierte
Erkrankungen vermutet. In der vorliegenden Arbeit wurden ungerichtete metabolische
Analysen (Metabolomics) verwendet, um metabolische Stoffwechselwege und kleinste
Moleküle zu identifizieren, die mit einer Akkumulation von VAT oder SAT assoziiert sind.
Die Studienpopulation bestand aus 491 Proband:innen ohne metabolische Erkrankungen (192
Männer, 299 Frauen), die im Rahmen einer großen populationsbasierten Studie aus dem
Nordosten Deutschlands intensiv untersucht wurden. Mit Hilfe linearer Regressionsmodelle
wurden die Assoziationen zwischen der mittels MRT quantifizierten Menge der
Fettkompartimente VAT und SAT und dem Metabolom im Plasma und Urin untersucht. Die
Metabolite wurden dabei durch massenspektrometrische Verfahren quantifiziert. Insgesamt
zeigte sich, dass VAT mehr Assoziationen zum Metabolom des Plasmas (54 Metabolite) und
Urins (101 Metabolite) aufwies als SAT (20 Plasmametabolite; 29 Urinmetabolite). Letzteres
metabolische Profil wurde fast vollständig von den zu VAT assoziierten Signaturen überlagert.
Geschlechtsspezifische Unterschiede ließen sich nur bei einem geringen Anteil der
untersuchten Assoziationen identifizieren. Signifikante Assoziationen ließen sich vor allem mit
Fettsäure-Abkömmlingen und Zwischenprodukten aus dem Metabolismus von
verzweigtkettigen Aminosäuren beobachten. Außerdem waren Metabolite signifikant
assoziiert, die einen veränderten Kohlenhydrat- und Kortisol-Metabolismus anzeigen. Darüber
hinaus ließen sich Assoziationen mit Markern aus dem Darm-Mikrobiom abbilden, die
vermutlich einen ungünstigen Lebensstil widerspiegeln. Zudem konnte eine neuartige positive
Assoziation zwischen VAT und den im Plasma gemessenen Gehalt des pharmakologischen
Wirkstoffes Piperin nachgewiesen werden. Alles in allem lassen sich Hinweise bezüglich der
Entwicklung von Adipositas-bezogenen Krankheiten liefern. Die vorliegende Studie stellt somit
die Gesundheit des Metaboloms bei „gesunden“ Personen in Frage und bietet die Möglichkeit,
die Entstehung von Adipositas auf molekularer Ebene zu verstehen. Es sind jedoch
weiterführende Untersuchungen notwendig, um diejenigen Menschen zu identifizieren,
deren Metabolom Auffälligkeiten zeigten und so bereits frühzeitig der Entstehung von
Krankheiten entgegenwirken zu können.
Metabolites are intermediates or end products of biochemical processes involved in both health and disease. Here, we take advantage of the well-characterized Cooperative Health Research in South Tyrol (CHRIS) study to perform an exome-wide association study (ExWAS) on absolute concentrations of 175 metabolites in 3294 individuals. To increase power, we imputed the identified variants into an additional 2211 genotyped individuals of CHRIS. In the resulting dataset of 5505 individuals, we identified 85 single-variant genetic associations, of which 39 have not been reported previously. Fifteen associations emerged at ten variants with >5-fold enrichment in CHRIS compared to non-Finnish Europeans reported in the gnomAD database. For example, the CHRIS-enriched ETFDH stop gain variant p.Trp286Ter (rs1235904433-hexanoylcarnitine) and the MCCC2 stop lost variant p.Ter564GlnextTer3 (rs751970792-carnitine) have been found in patients with glutaric acidemia type II and 3-methylcrotonylglycinuria, respectively, but the loci have not been associated with the respective metabolites in a genome-wide association study (GWAS) previously. We further identified three gene-trait associations, where multiple rare variants contribute to the signal. These results not only provide further evidence for previously described associations, but also describe novel genes and mechanisms for diseases and disease-related traits.
Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments have become increasingly popular because of the wide range of metabolites that can be analyzed and the possibility to measure novel compounds. LC-MS instrumentation and analysis conditions can differ substantially among laboratories and experiments, thus resulting in non-standardized datasets demanding customized annotation workflows. We present an ecosystem of R packages, centered around the MetaboCoreUtils, MetaboAnnotation and CompoundDb packages that together provide a modular infrastructure for the annotation of untargeted metabolomics data. Initial annotation can be performed based on MS1 properties such as m/z and retention times, followed by an MS2-based annotation in which experimental fragment spectra are compared against a reference library. Such reference databases can be created and managed with the CompoundDb package. The ecosystem supports data from a variety of formats, including, but not limited to, MSP, MGF, mzML, mzXML, netCDF as well as MassBank text files and SQL databases. Through its highly customizable functionality, the presented infrastructure allows to build reproducible annotation workflows tailored for and adapted to most untargeted LC-MS-based datasets. All core functionality, which supports base R data types, is exported, also facilitating its re-use in other R packages. Finally, all packages are thoroughly unit-tested and documented and are available on GitHub and through Bioconductor.
We are currently facing an antimicrobial resistance crisis, which means that a lot of bacterial pathogens have developed resistance to common antibiotics. Hence, novel and innovative solutions are urgently needed to combat resistant human pathogens. A new source of antimicrobial compounds could be bacterial volatiles. Volatiles are ubiquitous produced, chemically divers and playing essential roles in intra- and interspecies interactions like communication and antimicrobial defense. In the last years, an increasing number of studies showed bioactivities of bacterial volatiles, including antibacterial, antifungal and anti-oomycete activities, indicating bacterial volatiles as an exciting source for novel antimicrobial compounds. In this review we introduce the chemical diversity of bacterial volatiles, their antimicrobial activities and methods for testing this activity. Concluding, we discuss the possibility of using antimicrobial volatiles to antagonize the antimicrobial resistance crisis.
Periodontitis is one of the most prevalent oral diseases worldwide and is caused by multifactorial interactions between host and oral bacteria. Altered cellular metabolism of host and microbes releases a number of intermediary end products known as metabolites. There is an increasing interest in identifying metabolites from oral fluids such as saliva to widen the understanding of the complex pathogenesis of periodontitis. It is believed that some metabolites might serve as indicators toward early detection and screening of periodontitis and perhaps even for monitoring its prognosis in the future. Because contemporary periodontal screening methods are deficient, there is an urgent need for novel approaches in periodontal screening procedures. To this end, we associated oral parameters (clinical attachment level, periodontal probing depth, supragingival plaque, supragingival calculus, number of missing teeth, and removable denture) with a large set of salivary metabolites (n = 284) obtained by mass spectrometry among a subsample (n = 909) of nondiabetic participants from the Study of Health in Pomerania (SHIP-Trend-0). Linear regression analyses were performed in age-stratified groups and adjusted for potential confounders. A multifaceted image of associated metabolites (n = 107) was revealed with considerable differences according to age groups. In the young (20 to 39 y) and middle-aged (40 to 59 y) groups, metabolites were predominantly associated with periodontal variables, whereas among the older subjects (≥60 y), tooth loss was strongly associated with metabolite levels. Metabolites associated with periodontal variables were clearly linked to tissue destruction, host defense mechanisms, and bacterial metabolism. Across all age groups, the bacterial metabolite phenylacetate was significantly associated with periodontal variables. Our results revealed alterations of the salivary metabolome in association with age and oral health status. Among our comprehensive panel of metabolites, periodontitis was significantly associated with the bacterial metabolite phenylacetate, a promising substance for further biomarker research.
An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum
(2021)
Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo – an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF.
Swine are regarded as promising biomedical models, but the dynamics of theirgastrointestinal microbiome have been much less investigated than that of humans or mice. The aimof this study was to establish an integrated multi-omics protocol to investigate the fecal microbiomeof healthy swine. To this end, a preparation and analysis protocol including integrated samplepreparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integrationlinked microbiome composition with function, and metabolic activity with protein inventories, i.e.,16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites.16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated byPrevotellaceae,Lactobacillaceae,Lachnospiraceae,RuminococcaceaeandClostridiaceae.Similar microbiomecompositions in feces and colon, but not ileum samples, were observed, showing that feces can serveas minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition,e.g., temporal decreased abundance ofLactobacillaceaeandStreptococcaceaeduring the experiment,were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed arather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associatedmetaproteome functions, pointing towards functional redundancy among microbiome constituents.In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomyand functionality of the intestinal microbiome of swine.
Abstract
Metabolomics studies now approach large sample sizes and the health characterization of the study population often include complete blood count (CBC) results. Upon careful interpretation the CBC aids diagnosis and provides insight into the health status of the patient within a clinical setting. Uncovering metabolic signatures associated with parameters of the CBC in apparently healthy individuals may facilitate interpretation of metabolomics studies in general and related to diseases. For this purpose 879 subjects from the population‐based Study of Health in Pomerania (SHIP)‐TREND were included. Using metabolomics data resulting from mass‐spectrometry based measurements in plasma samples associations of specific CBC parameters with metabolites were determined by linear regression models. In total, 118 metabolites significantly associated with at least one of the CBC parameters. Strongest associations were observed with metabolites of heme degradation and energy production/consumption. Inverse association seen with mean corpuscular volume and mean corpuscular haemoglobin comprised metabolites potentially related to kidney function. The presently identified metabolic signatures are likely derived from the general function and formation/elimination of blood cells. The wealth of associated metabolites strongly argues to consider CBC in the interpretation of metabolomics studies, in particular if mutual effects on those parameters by the disease of interest are known.
Metabolomics is the scientific study of metabolites of an organism, cell, or tissue. Metabolomics makes use of different analytical approaches. In this thesis, an analytical platform consisting of proton nuclear magnetic resonance spectroscopy (1H-NMR), gas chromatography-mass spectrometry (GC-MS, EI/quadrupol) and liquid chromatography-mass spectrometry (LC-MS, ESI/TOF) was used for metabolite analysis. Due to the high physicochemical diversity of metabolites, the usage of different analytics is profitable. Focusing on metabolome analysis of microorganisms, the development of viable protocols was prerequisite. To ensure metabolome samples of best possible quality, particularly the sampling procedure has to be optimized for each microorganism to be analyzed individually. In microbial metabolomics, the energy charge value is a commonly used parameter to assure high sample quality (Atkinson 1968). The pathogenic bacterium Staphylococcus aureus and the biotechnical relevant bacterium Bacillus subtilis were main target of research. The sampling protocol development “A protocol for the investigation of the intracellular Staphylococcus aureus metabolome” (Meyer et al. 2010) and “Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis”s (Meyer et al. 2013) confirmed the need for development and verification of viable protocols. It was observed, that minor differences in the sampling procedure can cause major differences in sample quality. Using the validated analytical platform and the optimized protocols, we were able to investigate the metabolome of S. aureus and B. subtilis under different conditions. Investigations of the pathogenic bacterium S. aureus are of major interest due to its increasing resistance to antibiotics. Methicillin (multi)-resistant S. aureus (MRSA) strains are responsible for several difficult-to-treat infections. The cell wall of bacteria is the target of an array of antibiotics, like the beta-lactam antibiotics. Our study “A metabolomic view of Staphylococcus aureus and Its Ser/Thr kinase and phosphatase deletion mutants: Involvement in cell wall biosynthesis” (Liebeke et al. 2010) revealed the influence of the serine-threonine kinase on cell wall biosynthesis of S. aureus. LC-MS based metabolome data uncovered prevalent wall teichoic acid precursors in the serine-threonine kinase deletion mutant (ΔpknB), and predominantly peptidoglycan precursors in the phosphatase deletion mutant (Δstp), compared to the S. aureus wild type strain 8325. This uncovered a so far undescribed importance of the serine-threonine kinase on the cell wall metabolism and provides new insights into its regulation. The nasopharynx and the human skin are often the ecological niche of S. aureus. Furthermore, S. aureus exists outside its host, for example on catheters. Depending on its niche, S. aureus is exposed to several stress factors and limitation conditions, such as carbon source limitation and starvation. To cope with the latter, a number of regulatory cellular processes take place. In “Life and death of proteins: a case study of glucose-starved Staphylococcus aureus” (Michalik et al. 2012) protein degradation during glucose starvation was monitored. An intriguing observation was that proteins involved in branch chain amino acid biosynthesis and purine nucleotide biosynthesis were distinctly down-regulated in the clpP mutant. This lead to the assumption of a stronger repression of CodY-dependent genes in the clpP mutant. Intracellular metabolome data revealed higher GTP concentrations in the clpP mutant. This may explain the higher CodY activity and thereby stronger repression of CodY-dependent genes in the clpP mutant. Since different S. aureus strains are known to colonize different niches, global carbon source (glucose, glucose 6-phosphate, glycerol, lactate, lactose and a mixture of all) and carbon source limitation dependent exo-metabolome analyses were performed using three different S. aureus strains (HG001: laboratory strain, EN493: human endocarditis isolate and RF122: bovine mastitis strain). The most apparent observation was that RF122 can utilize lactose best, while EN493 and HG001 are better at utilizing glucose-6-phosphate compared to the bovine RF122 strain. Bacillus subtilis is an extensively studied Gram-positive and non-pathogenic bacterium. In the functional genomics approach “System-wide temporal proteomics profiling in glucose-starved Bacillus subtilis” (Otto et al. 2010) growth phase dependent changes in the proteome, transcriptome and extracellular metabolome were monitored. By mass spectrometric analysis of five different cellular subfractions, ~ 52% of the predicted proteins could be identified. To confirm and complete the proteomic data transcriptome and extracellular metabolome analyses were performed. The extracellular metabolome data ensured that cells were glucose-starved and revealed growth phase dependent metabolic footprints. In “A time resolved metabolomics study: The influence of different carbon sources during growth and starvation of Bacillus subtilis” ((Meyer et al. 2013) submitted) four different compounded cultivation media were investigated as only glucose, glucose and malate, glucose and fumarate and glucose and citrate as carbon source. It could be shown, that B. subtilis is able to maintain an intracellular metabolite homeostasis independent of the available carbon source. On the other hand, in the exo-metabolome, carbon source as well as growth phase dependent differences were detected. Furthermore, in this study the influence of ATP and GTP on the activation of the alternative RNA polymerase sigma factor B (σB) was discussed. The concentration of ATP and GTP decreased for all conditions, as cells entered the stationary growth phase. While cell growth on solely glucose and during growth on glucose and additional malate, the ATP and GTP concentrations increased slightly when the consumption of the second carbon source was initiated. Only under these conditions, a considerable σB activity increase during the transition from exponential to stationary growth phase was observed. Furthermore, the developed sampling protocol for metabolome analysis of B. subtilis enabled us to be part of a “multi omics” system biological approach to study the physiological adjustment of B. subtilis to cope with osmotic stress under chemostat conditions.