PMID- 37674095
OWN - NLM
STAT- Publisher
LR  - 20231005
IS  - 1750-2799 (Electronic)
IS  - 1750-2799 (Linking)
VI  - 18
IP  - 10
DP  - 2023 Oct
TI  - Visualization of metabolites and microbes at high spatial resolution using MALDI 
      mass spectrometry imaging and in situ fluorescence labeling.
PG  - 3050-3079
LID - 10.1038/s41596-023-00864-1 [doi]
AB  - Label-free molecular imaging techniques such as matrix-assisted laser desorption 
      ionization mass spectrometry imaging (MALDI-MSI) enable the direct and 
      simultaneous mapping of hundreds of different metabolites in thin sections of 
      biological tissues. However, in host-microbe interactions it remains challenging 
      to localize microbes and to assign metabolites to the host versus members of the 
      microbiome. We therefore developed a correlative imaging approach combining 
      MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to 
      identify and localize microbial cells. Here, we detail metaFISH as a robust and 
      easy method for assigning the spatial distribution of metabolites to microbiome 
      members based on imaging of nucleic acid probes, down to single-cell resolution. 
      We describe the steps required for tissue preparation, on-tissue hybridization, 
      fluorescence microscopy, data integration into a correlative image dataset, 
      matrix application and MSI data acquisition. Using metaFISH, we map hundreds of 
      metabolites and several microbial species to the micrometer scale on a single 
      tissue section. For example, intra- and extracellular bacteria, host cells and 
      their associated metabolites can be localized in animal tissues, revealing their 
      complex metabolic interactions. We explain how we identify low-abundance 
      bacterial infection sites as regions of interest for high-resolution MSI 
      analysis, guiding the user to a trade-off between metabolite signal intensities 
      and fluorescence signals. MetaFISH is suitable for a broad range of users from 
      environmental microbiologists to clinical scientists. The protocol requires ~2 
      work days.
CI  - (c) 2023. Springer Nature Limited.
FAU - Bourceau, Patric
AU  - Bourceau P
AD  - Max Planck Institute for Marine Microbiology, Bremen, Germany.
AD  - MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, 
      Germany.
FAU - Geier, Benedikt
AU  - Geier B
AUID- ORCID: 0000-0002-2942-2624
AD  - Max Planck Institute for Marine Microbiology, Bremen, Germany.
AD  - Stanford University School of Medicine, Stanford, CA, USA.
FAU - Suerdieck, Vincent
AU  - Suerdieck V
AD  - Institute of Hygiene, University of Munster, Munster, Germany.
FAU - Bien, Tanja
AU  - Bien T
AUID- ORCID: 0000-0002-6080-548X
AD  - Institute of Hygiene, University of Munster, Munster, Germany.
AD  - Bruker Daltonics GmbH & Co. KG, Bremen, Germany.
FAU - Soltwisch, Jens
AU  - Soltwisch J
AUID- ORCID: 0000-0002-0258-1561
AD  - Institute of Hygiene, University of Munster, Munster, Germany.
FAU - Dreisewerd, Klaus
AU  - Dreisewerd K
AD  - Institute of Hygiene, University of Munster, Munster, Germany.
FAU - Liebeke, Manuel
AU  - Liebeke M
AUID- ORCID: 0000-0002-2339-1409
AD  - Max Planck Institute for Marine Microbiology, Bremen, Germany. 
      mliebeke@mpi-bremen.de.
AD  - Institute of Human Nutrition and Food Sciences, University of Kiel, Kiel, 
      Germany. mliebeke@mpi-bremen.de.
LA  - eng
GR  - LT0015/2022-L/Human Frontier Science Program (HFSP)/
GR  - DR 416/12-1/Deutsche Forschungsgemeinschaft (German Research Foundation)/
GR  - O976/41/Deutsche Forschungsgemeinschaft (German Research Foundation)/
GR  - CRC TRR332 (Z1)/Deutsche Forschungsgemeinschaft (German Research Foundation)/
GR  - SO976/5-1/Deutsche Forschungsgemeinschaft (German Research Foundation)/
PT  - Journal Article
PT  - Review
DEP - 20230906
PL  - England
TA  - Nat Protoc
JT  - Nature protocols
JID - 101284307
SB  - IM
EDAT- 2023/09/07 00:41
MHDA- 2023/09/07 00:41
CRDT- 2023/09/06 23:32
PHST- 2023/01/31 00:00 [received]
PHST- 2023/05/31 00:00 [accepted]
PHST- 2023/09/07 00:41 [pubmed]
PHST- 2023/09/07 00:41 [medline]
PHST- 2023/09/06 23:32 [entrez]
AID - 10.1038/s41596-023-00864-1 [pii]
AID - 10.1038/s41596-023-00864-1 [doi]
PST - ppublish
SO  - Nat Protoc. 2023 Oct;18(10):3050-3079. doi: 10.1038/s41596-023-00864-1. Epub 2023 
      Sep 6.