ArticlePloS one2017
Preservation of three-dimensional spatial structure in the gut microbiome.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- The Relation between Red Meat and Whole-Grain Intake and the Colonic Mucosal Barrier: A Cross-Sectional Study.Nutrients · 2020Trial
- Rapid Cold Fixation of Mouse Colon (Col'RFix) Enables High-Resolution Mass Spectrometry Imaging.Analytical chemistry · 2026Article
- In situ visualization of Clostridioides difficile phenotypic heterogeneity and single-cell morphology during gut infection.Nature communications · 2026Article
- The food matrix as a confounder in diet‒microbiome studies: methodological challenges and research gaps.Gut microbes reports · 2026Review
- Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage.Nature biotechnology · 2026Article
- Foundational kelp species reveal links between host traits, the environment and the associated microbial community.Royal Society open science · 2025Article
- Colonizing bacteria around aggregated lymphoid tissue of the rat ascending colon change diurnally and affect the host local transcriptome.Cell and tissue research · 2025Article
- Improved Visualization of Oral Microbial Consortia.Journal of dental research · 2024Article
- Optimized Protocol for Intestinal Swiss Rolls and Immunofluorescent Staining of Paraffin Embedded Tissue.Journal of visualized experiments : JoVE · 2024Article
- Reinforcement of the intestinal mucosal barrier via mucus-penetrating PEGylated bacteria.Nature biomedical engineering · 2024Article
- Differential Colonization and Mucus Ultrastructure Visualization in Bovine Ileal and Rectal Organoid-Derived Monolayers Exposed to EnterohemorrhagicInternational journal of molecular sciences · 2024Article
- Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs.Science advances · 2024Article
- Impact of mucus modulation byInternational journal of pharmaceutics: X · 2023Article
- Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing.Genome research · 2023Article
- Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila.The Journal of experimental medicine · 2023Article
- Variation in spatial organization of the gut microbiota along the longitudinal and transverse axes of the intestines.Archives of microbiology · 2022Article
- Vocal fold mucus layer: Comparison of histological protocols for visualization in mice.Laryngoscope investigative otolaryngology · 2022Article
- Recent progress in analyzing the spatial structure of the human microbiome: distinguishing biogeography and architecture in the oral and gut communities.Current opinion in endocrine and metabolic research · 2021Article
- Ultrasound mediated delivery of quantum dots from a proof of concept capsule endoscope to the gastrointestinal wall.Scientific reports · 2021Article
- Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms.NPJ biofilms and microbiomes · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this study, we evaluated preparation methods for mouse gut with the goal of preserving micron-scale spatial structure while performing fluorescence imaging assays. Our evaluation of embedding methods showed that commonly used media such as Tissue-Tek Optimal Cutting Temperature (OCT) compound, paraffin, and polyester waxes resulted in redistribution of luminal contents. By contrast, a hydrophilic methacrylate resin, Technovit H8100, preserved three-dimensional organization. Our mouse intestinal preparation protocol optimized using the Technovit H8100 embedding method was compatible with microbial fluorescence in situ hybridization (FISH) and other labeling techniques, including immunostaining and staining with both wheat germ agglutinin (WGA) and 4', 6-diamidino-2-phenylindole (DAPI). Mucus could be visualized whether the sample was fixed with paraformaldehyde (PFA) or with Carnoy's fixative. The protocol optimized in this study enabled simultaneous visualization of micron-scale spatial patterns formed by microbial cells in the mouse intestines along with biogeographical landmarks such as host-derived mucus and food particles.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.