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Preservation of three-dimensional spatial structure in the gut microbiome
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 labeling patterns of the samples fixed with paraformaldehyde (PFA) and Carnoy’s fixative were comparable. 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.
Enterohemorrhagic Escherichia coli (EHEC) is a critical public health concern due to its role in severe gastrointestinal illnesses in humans, including hemorrhagic colitis and the life-threatening hemolytic uremic syndrome. While highly pathogenic to humans, cattle, the main reservoir for EHEC, often remain asymptomatic carriers, complicating efforts to control its spread. Our study introduces a novel method to investigate EHEC using organoid-derived monolayers from adult bovine ileum and rectum. These polarized epithelial monolayers were exposed to EHEC for four hours, allowing us to perform comparative analyses between the ileal and rectal tissues. Our findings mirrored in vivo observations, showing a higher colonization rate in the rectum compared with the ileum (44.0% vs. 16.5%, p < 0.05). Both tissues exhibited an inflammatory response with increased expression levels of TNF-a (p < 0.05) and a more pronounced increase of IL-8 in the rectum (p < 0.01). Additionally, the impact of EHEC on the mucus barrier varied across these gastrointestinal regions. Innovative visualization techniques helped us study the ultrastructure of mucus, revealing a net-like mucin glycoprotein organization. While further cellular differentiation could enhance model accuracy, our research significantly deepens understanding of EHEC pathogenesis in cattle and informs strategies for the preventative measures and therapeutic interventions.
Human respiratory mucus lining the airway epithelium forms a challenging barrier to inhalation therapeutics. Therefore, structural elucidation of hydrated mucus is essential for an efficient drug delivery development. The structure of mucus has been primarily investigated by conventional electron microscopy techniques, which operate under vacuum conditions and require sample preparation steps that might alter the structure of mucus. In this study we investigated the impact of dehydration on mucus and analyzed the structure of mucus in its hydrated state. Cryo–scanning electron microscopy (Cryo–SEM) analysis of mucus showed, that during the process of sublimation, non-porous structure of mucus is transformed into a porous network. Similarly, images acquired by environmental scanning electron microscopy (ESEM), revealed a non-porous structure of hydrated mucus, while further observation of the structure of mucus at decreasing pressure demonstrated the strong influence of dehydration on mucus structure. We could successfully visualize the structural organization of the major gel forming mucin MUC5B in its hydrated state by employing stimulated emission depletion (STED) microscopy, which allowed resolving the nano–scale patterns of mucin macromolecules within the essentially pore–free mucus structure. The general structural organization of mucus components was addressed by confocal laser scanning microscopy (CLSM), which revealed the heterogeneous and composite structure of mucus. These results provide a novel view on the native structure of mucus and will affect drug delivery development.
The Colonic Mucosal Barrier (CMB) is the site of interaction between the human body and the colonic microbiota. The mucus is the outer part of the CMB and is considered as the front-line defense of the colon. It separates the host epithelial lining from the colonic content, and it has previously been linked to health and diseases. In this study, we assessed the relationship between red meat and whole-grain intake and (1) the thickness of the colonic mucus (2) the expression of the predominant mucin gene in the human colon (MUC2). Patients referred to colonoscopy at the University Hospital of Southern Denmark- Sonderjylland were enrolled between June 2017 and December 2018, and lifestyle data was collected in a cross-sectional study design. Colonic biopsies, blood, urine, and fecal samples were collected. The colonic mucus and bacteria were visualized by immunostaining and fluorescence in situ hybridization techniques. We found a thinner mucus was associated with high red meat intake. Similarly, the results suggested a thinner mucus was associated with high whole-grain intake, albeit to a lesser extent than red meat. This is the first study assessing the association between red meat and whole-grain intake and the colonic mucus in humans. This study is approved by the Danish Ethics Committee (S-20160124) and the Danish Data Protecting Agency (2008-58-035). A study protocol was registered at clinical trials.gov under NCT04235348.
Significance
Spatial structure is postulated to have a powerful influence on establishing and sustaining the signaling and metabolic exchanges that define relationships among members of the gut microbiota and host. However, information about gut community spatial structure is limited. Simultaneous imaging of components of a 15-member model human gut bacterial community over a range of spatial scales in gnotobiotic mice revealed that the colon is better conceptualized as an incompletely mixed bioreactor, rather than having sharply stratified luminal and mucosal compartments. Identifying host and microbial factors that constrain the ability of community members to establish sizeable single or oligotaxon agglomerations should yield new insights about how “micro”-scale mixing defines community function.
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