Spatial metabolomics of in situ host–microbe interactions at the micrometre scale

[1]  N. Dubilier,et al.  Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels , 2019, Nature Microbiology.

[2]  N. Dubilier,et al.  Spatial metabolomics of in situ, host-microbe interactions (practical guide for combining MALDI-MSI and FISH microscopy on the same section) v1 , 2019, protocols.io.

[3]  Bernhard Spengler,et al.  Spatial metabolomics of in situ, host-microbe interactions (practical guide for combining MALDI-MSI and FISH microscopy on the same section) v1 , 2019, protocols.io.

[4]  Theodore Alexandrov,et al.  METASPACE: A community-populated knowledge base of spatial metabolomes in health and disease , 2019, bioRxiv.

[5]  N. Dubilier,et al.  Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated , 2019, The ISME Journal.

[6]  J. Carlson,et al.  Microbiome interactions shape host fitness , 2018, Proceedings of the National Academy of Sciences.

[7]  Harald R. Gruber-Vodicka,et al.  Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria) , 2018, The ISME Journal.

[8]  E. Shank.  Considering the Lives of Microbes in Microbial Communities , 2018, mSystems.

[9]  A E Brunetti,et al.  An integrative omics perspective for the analysis of chemical signals in ecological interactions. , 2018, Chemical Society reviews.

[10]  A. M. Caraballo-Rodríguez,et al.  Chemical signaling involved in plant-microbe interactions. , 2018, Chemical Society reviews.

[11]  D. Newman,et al.  Hopanoid lipids: from membranes to plant–bacteria interactions , 2018, Nature Reviews Microbiology.

[12]  David S. Wishart,et al.  HMDB 4.0: the human metabolome database for 2018 , 2017, Nucleic Acids Res..

[13]  Guo-Cheng Yuan,et al.  Economic and biophysical limits to seaweed farming for climate change mitigation , 2022, Nature Plants.

[14]  A. Katsarou,et al.  Reporting for specific materials, systems and methods , 2018 .

[15]  F. Jourdan,et al.  MetaNetter 2: A Cytoscape plugin for ab initio network analysis and metabolite feature classification , 2017, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[16]  Morgan R Alexander,et al.  The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power , 2017, Nature Methods.

[17]  G. Borisy,et al.  Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice , 2017, Proceedings of the National Academy of Sciences.

[18]  B. Spengler,et al.  Chemical and topographical 3D surface profiling using atmospheric pressure LDI and MALDI MS imaging , 2017 .

[19]  Bernhard Spengler,et al.  Autofocusing MALDI mass spectrometry imaging of tissue sections and 3D chemical topography of nonflat surfaces , 2017, Nature Methods.

[20]  Nico Verbeeck,et al.  Connecting imaging mass spectrometry and magnetic resonance imaging-based anatomical atlases for automated anatomical interpretation and differential analysis. , 2017, Biochimica et biophysica acta. Proteins and proteomics.

[21]  C. Tropini,et al.  The Gut Microbiome: Connecting Spatial Organization to Function. , 2017, Cell host & microbe.

[22]  Katherine E. Zink,et al.  Calling all hosts: Bacterial communication in situ. , 2017, Chem.

[23]  Mark R Viant,et al.  How close are we to complete annotation of metabolomes? , 2017, Current opinion in chemical biology.

[24]  Kevin W. Eliceiri,et al.  ImageJ2: ImageJ for the next generation of scientific image data , 2017, BMC Bioinformatics.

[25]  B. Spengler,et al.  AP-MALDI MSI of lipids in mouse brain tissue sections , 2017 .

[26]  Eike E. Peters,et al.  Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges , 2017, Proceedings of the National Academy of Sciences.

[27]  Sage J. B. Dunham,et al.  Mass Spectrometry Imaging of Complex Microbial Communities , 2016, Accounts of chemical research.

[28]  R. Amann,et al.  Direct‐geneFISH: a simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms , 2017, Environmental microbiology.

[29]  Bernhard Spengler,et al.  Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution , 2016, Nature Methods.

[30]  Michael Becker,et al.  FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry , 2016, Nature Methods.

[31]  John M. Asara,et al.  A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source , 2017, Metabolomics.

[32]  Forest Rohwer,et al.  Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen , 2016, mSystems.

[33]  N. Dubilier,et al.  A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria. , 2016, Environmental microbiology reports.

[34]  Kristian Fog Nielsen,et al.  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.

[35]  A. Svatoš,et al.  Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH , 2015, The ISME Journal.

[36]  Olga Vitek,et al.  Probabilistic Segmentation of Mass Spectrometry (MS) Images Helps Select Important Ions and Characterize Confidence in the Resulting Segments* , 2016, Molecular & Cellular Proteomics.

[37]  Christoph Steinbeck,et al.  ChEBI in 2016: Improved services and an expanding collection of metabolites , 2015, Nucleic Acids Res..

[38]  P. Dorrestein,et al.  Molecular and chemical dialogues in bacteria-protozoa interactions , 2015, Scientific Reports.

[39]  Martin Ackermann,et al.  A functional perspective on phenotypic heterogeneity in microorganisms , 2015, Nature Reviews Microbiology.

[40]  S. Duperron,et al.  Relative abundances of methane- and sulfur-oxidizing symbionts in gills of the deep-sea hydrothermal vent mussel Bathymodiolus azoricus under pressure , 2015 .

[41]  M. Hatamoto,et al.  In situ DNA-hybridization chain reaction (HCR): a facilitated in situ HCR system for the detection of environmental microorganisms. , 2015, Environmental microbiology.

[42]  K. Dreisewerd,et al.  Mass spectrometry imaging with laser-induced postionization , 2015, Science.

[43]  Olga Vitek,et al.  Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments , 2015, Bioinform..

[44]  Richard M. Caprioli,et al.  Tissue protein imaging at 1 μm laser spot diameter for high spatial resolution and high imaging speed using transmission geometry MALDI TOF MS , 2015, Analytical and Bioanalytical Chemistry.

[45]  R. Hatzenpichler,et al.  Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs. , 2015, International journal of systematic and evolutionary microbiology.

[46]  R. Knight,et al.  Finding the missing links among metabolites, microbes, and the host. , 2014, Immunity.

[47]  Gonzalo Giribet,et al.  Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography , 2014, PloS one.

[48]  C. Cruaud,et al.  The contrasted evolutionary fates of deep-sea chemosynthetic mussels (Bivalvia, Bathymodiolinae)a , 2013, Ecology and evolution.

[49]  Jenan J Kharbush,et al.  Composite Bacterial Hopanoids and Their Microbial Producers across Oxygen Gradients in the Water Column of the California Current , 2013, Applied and Environmental Microbiology.

[50]  Andreas Bartels,et al.  Testing for presence of known and unknown molecules in imaging mass spectrometry , 2013, Bioinform..

[51]  O. Geiger,et al.  Phosphatidylcholine biosynthesis and function in bacteria. , 2013, Biochimica et biophysica acta.

[52]  Christoph Steinbeck,et al.  MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data , 2012, Nucleic Acids Res..

[53]  S. V. Nyholm,et al.  Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses , 2012, Nature Reviews Microbiology.

[54]  Anders Folkesson,et al.  Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective , 2012, Nature Reviews Microbiology.

[55]  Ajay Limaye,et al.  Drishti: a volume exploration and presentation tool , 2012, Optics & Photonics - Optical Engineering + Applications.

[56]  Q. Hu,et al.  Phospholipid:Diacylglycerol Acyltransferase Is a Multifunctional Enzyme Involved in Membrane Lipid Turnover and Degradation While Synthesizing Triacylglycerol in the Unicellular Green Microalga Chlamydomonas reinhardtii[C][W] , 2012, Plant Cell.

[57]  Josephine Bunch,et al.  Inclusive sharing of mass spectrometry imaging data requires a converter for all. , 2012, Journal of proteomics.

[58]  Richard J A Goodwin,et al.  Sample preparation for mass spectrometry imaging: small mistakes can lead to big consequences. , 2012, Journal of proteomics.

[59]  Natalie I. Tasman,et al.  A Cross-platform Toolkit for Mass Spectrometry and Proteomics , 2012, Nature Biotechnology.

[60]  N. Dubilier,et al.  Symbiont–host relationships in chemosynthetic mussels: A comprehensive lipid biomarker study , 2012 .

[61]  J. McGrath,et al.  The Genes and Enzymes of Phosphonate Metabolism by Bacteria, and Their Distribution in the Marine Environment , 2011, Front. Microbio..

[62]  A. Heddi,et al.  Antimicrobial Peptides Keep Insect Endosymbionts Under Control , 2011, Science.

[63]  R. Amann,et al.  Hydrogen is an energy source for hydrothermal vent symbioses , 2011, Nature.

[64]  P. Dorrestein,et al.  Imaging mass spectrometry in microbiology , 2011, Nature Reviews Microbiology.

[65]  Pieter C Dorrestein,et al.  Microbial metabolic exchange--the chemotype-to-phenotype link. , 2011, Nature chemical biology.

[66]  Bernd Schneider,et al.  Symbiotic Streptomycetes provide antibiotic combination prophylaxis for wasp offspring. , 2010, Nature chemical biology.

[67]  E. Delong,et al.  Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. , 2010, Environmental microbiology.

[68]  Michael Wagner,et al.  Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility , 2009, Applied and Environmental Microbiology.

[69]  V. Orphan,et al.  Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia , 2009, Science.

[70]  Rudolf Amann,et al.  A single-cell view on the ecophysiology of anaerobic phototrophic bacteria , 2008, Proceedings of the National Academy of Sciences.

[71]  N. Dubilier,et al.  Symbiotic diversity in marine animals: the art of harnessing chemosynthesis , 2008, Nature Reviews Microbiology.

[72]  P. Dorrestein,et al.  Visualizing the spatial distribution of secondary metabolites produced by marine cyanobacteria and sponges via MALDI-TOF imaging. , 2008, Molecular bioSystems.

[73]  P. Dorrestein,et al.  Biosynthetic origin of natural products isolated from marine microorganism–invertebrate assemblages , 2008, Proceedings of the National Academy of Sciences.

[74]  Nigel W. Hardy,et al.  Proposed minimum reporting standards for chemical analysis , 2007, Metabolomics.

[75]  N. Dubilier,et al.  A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern Mid-Atlantic Ridge. , 2006, Environmental microbiology.

[76]  B. Finlay,et al.  Anti-Immunology: Evasion of the Host Immune System by Bacterial and Viral Pathogens , 2006, Cell.

[77]  R. Abagyan,et al.  METLIN: A Metabolite Mass Spectral Database , 2005, Therapeutic drug monitoring.

[78]  S. Goffredi,et al.  Methane‐based symbiosis in a mussel, Bathymodiolus platifrons, from cold seeps in Sagami Bay, Japan , 2005 .

[79]  R. Amann,et al.  Dual Symbiosis in a Bathymodiolus sp. Mussel from a Methane Seep on the Gabon Continental Margin (Southeast Atlantic): 16S rRNA Phylogeny and Distribution of the Symbionts in Gills , 2005, Applied and Environmental Microbiology.

[80]  P. Dixon.  VEGAN, a package of R functions for community ecology , 2003 .

[81]  Graham R. Stewart,et al.  Tuberculosis: a problem with persistence , 2003, Nature Reviews Microbiology.

[82]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[83]  A. Steinbüchel,et al.  Triacylglycerols in prokaryotic microorganisms , 2002, Applied Microbiology and Biotechnology.

[84]  Bernhard Spengler,et al.  Scanning microprobe matrix-assisted laser desorption ionization (SMALDI) mass spectrometry: Instrumentation for sub-micrometer resolved LDI and MALDI surface analysis , 2002, Journal of the American Society for Mass Spectrometry.

[85]  Rudolf Amann,et al.  Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria , 2002, Applied and Environmental Microbiology.

[86]  R. Caprioli,et al.  Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. , 1997, Analytical chemistry.

[87]  R. Amann,et al.  Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. , 1993, Cytometry.

[88]  R. Amann,et al.  Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations , 1990, Applied and environmental microbiology.