MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria

Schümann, Peter; Maier, Τ.

doi:10.1016/bs.mim.2014.06.002

Cited by 69 publications

(44 citation statements)

References 102 publications

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“…Analyses included cell morphology by microscopy, enzymatic testing, cellular fatty acids, diaminopimelic acid, automated ribotyping and mass spectrometry analysis using a MALDI-biotyper (Bruker). Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) sample preparation was performed according to protocol 3 as described by Schumann and Maier 47 . Ribotyping was carried out using the automated Riboprinter microbial characterization system (Dupont, Qualicon).…”

Section: Methodsmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

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Section: Methodsmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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“…Using a sterile toothpick, bacterial colonies that grew on nutrient agar were applied as a thin film onto a MALDI ground-steel target plate (Bruker Daltonics, Billerica, MA). Over each bacterial smear, 1 µL of 70% LC-MS grade formic acid (Optima, Fisher Chemical) was added and allowed to evaporate, followed by the addition and subsequent evaporation of 1 µL of 10 mg/mL α-cyano-hydroxycinnamic acid (recrystallized from the 98% pure Sigma-Aldrich) solubilized in 50% acetonitrile, 2.5% trifluoroacetic acid and 47.5% water (39). All solvents were HPLC or MS grade.…”

Section: Maldi-tof Ms Sample Preparationmentioning

confidence: 99%

Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

Clark

Costa

Sanchez

et al. 2017

Preprint

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For decades, researchers have lacked the ability to rapidly correlate microbial identity with bacterial metabolism. Since specialized metabolites are critical to bacterial function and survival in the environment, we designed a data acquisition and bioinformatics technique (IDBac) that utilizes in situ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze protein and specialized metabolite spectra of single bacterial colonies from agar plates. We demonstrated the power of our approach by discriminating between two Bacillus subtilis colonies in under 30 minutes, which differ by a single genomic mutation, solely on the basis of their differential ability to produce cyclic peptide antibiotics surfactin and plipastatin. Next, we employed our IDBac technique to detect subtle intra-species differences in the production of metal scavenging acyl-desferrioxamines in a group of eight freshwater Micromonospora isolates that share >99% sequence similarity in the 16S rRNA gene. Finally, we employed our method to simultaneously extract protein and specialized metabolite MS profiles from unidentified species of Lake Michigan sponge-associated bacteria cultivated on an agar plate. In just 3 hours, we created hierarchical protein MS groupings of 11 environmental isolates (10 MS replicates each, for a total of 110 samples) that accurately mirrored phylogenetic groupings. We further distinguished isolates within these groupings, which share nearly identical 16S rRNA gene sequence identity, based on inter- and intra-species differences in specialized metabolite production. To our knowledge, IDBac is the first attempt to couple in situ MS analyses of protein content and specialized metabolite production to allow the distinction of closely related bacterial colonies.SignificanceMass spectrometry is a powerful technique that has been used to identify bacteria via protein content, and to assess bacterial function in an environment via analysis of specialized metabolites. However, until now these analyses have operated independently, and this has resulted in the inability to rapidly connect bacterial phylogenetic identity with patterns of specialized metabolism. To bridge this gap, we designed a MALDI-TOF mass spectrometry data acquisition and bioinformatics pipeline (IDBac) to discriminate both intact protein and specialized metabolite spectra directly from bacterial cells grown on agar. To our knowledge, this is the first technique that organizes bacteria into highly similar phylogenetic groups and allows for comparison of metabolic differences of hundreds of isolates in just a few hours.

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“…These results also demonstrate a serious potential of this method for clinical application, as well as for early detection of these bacteria. MALDI-TOF MS as a tool for classifi cation and identifi cation of bacteria has been systematically used for about ten years (150), and its use as an alternative to conventional methods for identification of food pathogens was described by Schumann and Maier (151). It was also shown that this method can be used as a very effi cient tool for the identifi cation of high-risk toxin-producing E. coli strains (152).…”

Section: Maldi-tof Mass Spectrometrymentioning

confidence: 99%

Foodomics and Food Safety: Where We Are

Andjelković

Gajdošik

Gašo-Sokač

et al. 2017

Food Technol. Biotechnol.

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SummaryThe power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identifi cation, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special att ention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is infl uenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affi nity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affi nity-based methods, are the cross-reactivity between similar molecules and the infl uence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identifi cation and quantifi cation, and for corresponding modeling.

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MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria

Cited by 69 publications

References 102 publications

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

Foodomics and Food Safety: Where We Are

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