Spatial metabolomics of in situ, host-microbe interactions (MALDI imaging MS assay) (MTBLS744)

DOI: 10.1038/s41564-019-0664-6
创建时间: 2024-12-27 22:02:32

Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defence molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we present a spatial metabolomics pipeline (metaFISH) that combines fluorescence in situ hybridization (FISH) microscopy and high-resolution atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry to image host–microbe symbioses and their metabolic interactions. The metaFISH pipeline aligns and integrates metabolite and fluorescent images at the micrometre scale to provide a spatial assignment of host and symbiont metabolites on the same tissue section. To illustrate the advantages of metaFISH, we mapped the spatial metabolome of a deep-sea mussel and its intracellular symbiotic bacteria at the scale of individual epithelial host cells. Our analytical pipeline revealed metabolic adaptations of the epithelial cells to the intracellular symbionts and variation in metabolic phenotypes within a single symbiont 16S rRNA phylotype, and enabled the discovery of specialized metabolites from the host–microbe interface. metaFISH provides a culture-independent approach to link metabolic phenotypes to community members in situ and is a powerful tool for microbiologists across fields.

Geier, B., Sogin, E.M., Michellod, D. et al. Spatial metabolomics of in situ host–microbe interactions at the micrometre scale. Nat Microbiol 5, 498–510 (2020). https://doi.org/10.1038/s41564-019-0664-6

人工注释组织解剖术语列表
gill lamella, gill filament
Cite as:
Geier, B., Sogin, E.M., Michellod, D. et al. Spatial metabolomics of in situ host–microbe interactions at the micrometre scale. Nat Microbiol 5, 498–510 (2020). https://doi.org/10.1038/s41564-019-0664-6

当前项目中的样本列表

MPIBremen_Bputeoserpentis_MALDI-FISH_DHB_233x233pixel_3um_mz400-1200_240k@200

创建时间: 2024-12-27 22:02:32
空间分辨率: 3μm,   233x233
扫描: MALDI (DHB)
物种: Bathymodiolus (epithelial host cells) - normal

Note The Bathymodiolus puteoserpentis specimen used for high resolution AP-MALDI-MSI was collected during the RV Meteor M126 cruise in 2016 at the Logatchev hydrothermal vent field on the Mid-Atlantic Ridge. The specimen was retrieved with the MARUM-Quest remotely operated vehicle (ROV) at the Irina II vent site at 3038 m depth, 14°45’11.01”N and 44°58’43.98”W, and placed in an insulated container to prevent temperature changes during recovery. Gills were dissected from the mussel as soon as brought on board after ROV retrieval, submerged in precooled 2% w/v carboxymethyl cellulose gel (CMC, Mw ~ 700,000, Sigma-Aldrich Chemie GmbH) and snap-frozen in liquid N2. Samples were stored at -80 °C until use.
The CMC-embedded gills were cross-sectioned at 10 µm thickness with a cryostat (Leica CM3050 S, Leica Biosystems Nussloch GmbH) at a chamber temperature of -35 °C and object holder at -22 °C. Individual sections were thaw-mounted onto coated Polysine slides (Thermo Scientific) and subsequently frozen in the cryostat chamber. Slides with tissue sections were stored in slide containers with silica granules, to prevent air moisture condensation on the tissue upon removal from the freezer. Before AP-MALDI matrix application, the sample was warmed to room temperature under a dry atmosphere in a sealed slide container (LockMailer microscope slide jar, Sigma-Aldrich, Steinheim, Germany), filled with silica granules (Carl Roth GmbH) to avoid condensation on the cold glass slide. The sample glass slide was marked with white paint around the tissue for orientation during image acquisition as previously described[1]. Additionally, optical images of the tissue section were acquired with a digital microscope (VHX-5000 Series, Keyence, Neu-Isenburg, Germany) prior to matrix application. To apply the matrix, we used an ultrafine pneumatic sprayer system with N2 gas (SMALDIPrep, TransMIT GmbH, Giessen, Germany)[2], to deliver 100 μl of a 30 mg/ml solution of 2,5-dihydroxybenzoic acid (DHB; 98% 574 purity, Sigma-Aldrich, Steinheim, Germany) dissolved in acetone/water (1:1 v/v) containing 0.1% trifluoroacetic acid (TFA). To locate the field of view and facilitate laser focusing, a red marker was applied adjacent to the matrix-covered tissue section. Ref: [1] Kaltenpoth M, Strupat K, Svatoš A Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH. ISME J. 2016 Feb;10(2):527-31. doi: 10.1038/ismej.2015.122. PMID:26172211 [2] Kompauer M, Heiles S, Spengler B. Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution. Nat Methods. 2017 Jan;14(1):90-96. doi: 10.1038/nmeth.4071. PMID:27842060
High-resolution AP-MALDI-MSI measurements were carried out at an experimental ion source setup [1][2], coupled to a Fourier transform orbital trapping mass spectrometer (Q Exactive HF, Thermo Fisher Scientific GmbH, Bremen, Germany). The sample was rastered with 233 x 233 laser spots with a step size of 3 µm without oversampling, resulting in an imaged area of 699 x 699 µm. AP-MALDI-MSI measurements were performed in positive mode for a mass detection range of 400–1200 Da and a mass resolving power of 240,000 (at 200 m/z). After AP-MALDI-MSI, the measured sample surface was recorded using a stereomicroscope (SMZ25, Nikon, Düssedorf, Germany). Ref: [1] Kompauer M, Heiles S, Spengler B. Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution. Nat Methods. 2017 Jan;14(1):90-96. doi: 10.1038/nmeth.4071. PMID:27842060 [2] Kompauer M, Heiles S, Spengler B. Autofocusing MALDI mass spectrometry imaging of tissue sections and 3D chemical topography of nonflat surfaces. Nat Methods. 2017 Dec;14(12):1156-1158. doi:10.1038/nmeth.4433. PMID:28945703

MPIMM_039_QE_P_BP_CF_Bputeoserpentis_MALDI-FISH8_Sl14_s1_DHB_233x233_3um

创建时间: 2024-12-28 01:05:13
空间分辨率: 3μm,   233x234
扫描: MALDI (DHB)
物种: Bathymodiolus (epithelial host cells) - normal

Note

MPIMM_054_QE_P_BP_CF_Bputeoserpentis_MALDI-FISH8_Sl16_s1_DHB_233x233_3um

创建时间: 2024-12-27 22:13:22
空间分辨率: 3μm,   233x233
扫描: MALDI (DHB)
物种: Bathymodiolus (epithelial host cells) - normal

Note