The authors would like to thank Dr. Kristen Earle for invaluable technique development, Amber Hann for troubleshooting help, Dr. Jen Nguyen and Deanna Pepin for critical review of the manuscript, and Dr. Hesham Soliman and the Rossi lab at the University of British Columbia for providing microscope access. The authors acknowledge support from CIHR Team Grant: Canadian Microbiome Initiative 2 (C.T.), Crohn&#39;s and Colitis Canada (to C.T. and K.M.N.), CIFAR (to C.T. and K.M.N.), Michael Smith Foundation for Health Research Scholar Award (to C.T.), the Weston Foundation: Weston Family Microbiome Initiative (to C.T.), Paul Allen Distinguished Investigator Award (to C.T.).

All animal experiments and tissue collection described in this protocol were performed in compliance with the Canadian Council on Animal Care (CCAC) guidelines and were approved by the Animal Care Committee at the University of British Columbia. Germ-free Swiss Webster mice were used. All animals were 8-10 weeks of age, both sexes were used, and all mice were co-housed with at least two mice per cage. Animals were euthanized using carbon dioxide with secondary cervical dislocation or cardiac puncture.
1. Designing an imaging experiment: considerations and sample collection
<ol>
	<li>FISH probe design
	<ol>
		<li>If an appropriate FISH probe exists, select a pre-existing published one that shows a strong signal in labeled cells compared to the background.</li>
		<li>Validate new probes in vitro to determine their efficiency of binding to fixed samples of the target bacteria and off-target binding to other bacteria.</li>
		<li>Check all 16S FISH probes to be used against 16S sequences from the target organism or against 16S rRNA sequencing from the samples to be analyzed to ensure that the expected proportion of positive matches are present, and that probes will not bind non-specifically to other microbiota members.
		<ol>
			<li>Align the FISH probes against either full-length sequences or amplicon sequence variants using a tool, such as Clustal Omega13, to evaluate the potential binding of probes and their targets.</li>
			<li>In addition to in silico testing, test the accuracy and level of FISH staining of unvalidated probes on pure cultures8,14.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
NOTE: When staining multiple community members, probes can be used combinatorially (e.g., the combination of a family-specific probe and a genus-specific probe) if the fluorophores used do not overlap in excitation and emission spectra (unless imaging on a system with the ability to perform linear unmixing). Additionally, specificity may be demonstrated by including specificity controls/scrambled probes or by competition with non-fluorescent probes.
<ol>
	<li>Sample types and tissue collection
	<ol>
		<li>Using sharp and clean tools, cut intestinal segments from gnotobiotic&#160;Swiss Webster mice for imaging. Minimize disturbing the sample as much as possible, and handle the sections by their edges to avoid affecting the imaging area. Fix the sample as soon as possible after dissection to prevent degradation. 
		&#8203;NOTE: For animal studies, intact, unflushed intestinal sections are preferred; the membrane will help keep the luminal and mucosal organization intact.</li>
		<li>Clean tools by wiping them with 70% ethanol between samples and sites. Obtain at least three biological replicates per intestinal section/biopsy location, taking care to sample consistent intestinal locations, as the mucus and intestinal architecture as well as microbiota changes significantly in different locations.</li>
	</ol>
	</li>
</ol>
2. Tissue sample fixation and infiltration
<ol>
	<li>Fixation
	<ol>
		<li>Prepare fresh methacarn in a compatible container with the following ratios: 60% absolute methanol, 30% chloroform, and 10% glacial acetic acid. Dispense each of these chemicals in a fume hood. Choose a container that can be vented by cracking open the lid. As methacarn is not compatible with polystyrene, prepare it in a polyethylene container, using glass graduated cylinders/serological pipets for the chloroform and glacial acetic acid. 
		NOTE: During mixing, fumes are produced and may cause pressure to build up inside the container. It is advisable to keep the container relatively tightly closed once removed from the fume hood if samples are not being actively added. Chloroform is toxic; do not inhale, swallow, or absorb through the skin. Methanol is toxic and highly flammable; do not inhale, swallow, or absorb through the skin. Glacial acetic acid is flammable and highly corrosive to the skin and the eyes.</li>
		<li>After dispensing, close the container, swirl to mix and then vent; repeat this until off-gassing has stopped (and pressure no longer builds up appreciably under the lid). 
		NOTE: Do not dispose of methacarn in drains; collect and dispose of as hazardous chemical waste as per institutional guidelines. Use a pencil for labeling histology cassettes, as many pen inks will come off in the methacarn solution.</li>
		<li>Place the intestinal sections in histology cassettes by delicately holding an edge of the tissue with tweezers. Close the cassette and completely submerge it in fresh methacarn solution. Ensure that the solution is not older than a few hours upon immersion of the cassettes.</li>
		<li>For clinical samples that will be collected in a clinical suite without access to a fume hood, use a polyethylene storage container with a flap cut into the lid that will permit the passage of the histology cassettes. Tape this flap shut when not passing samples to prevent the escape of toxic fumes. 
		NOTE: It is important to use masking tape to avoid the dissolution of glue onto the container-some types of tape (e.g., plastic packing tape) may not hold up well to the methacarn fumes.</li>
		<li>Fix samples for a minimum of 3 h and a maximum of two weeks. 
		NOTE: Thicker samples may require fixation times longer than 3 h.&#160;Fixation time may be chosen to enable simultaneous paraffin infiltration processing for cassettes fixed in different methacarn solutions (e.g., to simultaneously perform paraffin infiltration on groups of samples collected and fixed over two weeks).</li>
	</ol>
	</li>
	<li>Paraffin infiltration and embedding
	<ol>
		<li>Place the paraffin in a heat-resistant container and melt it in an oven at 60 &#176;C overnight. As paraffin pellets take up more space before melting, ensure that sufficient paraffin is melted to cover all the cassettes. 
		NOTE: The temperature should not be higher than 60 &#176;C as it can give rise to artifacts.</li>
		<li>Wash the tissue by pouring out the liquid in the appropriate waste receptacle and replacing it immediately with the following chemicals.
		<ol>
			<li>Incubate in absolute methanol for 30 min. Repeat once.</li>
			<li>Incubate in absolute ethanol for 20 min. Repeat once.</li>
			<li>Incubate in xylenes&#160;for 15 min. Repeat once.</li>
			<li>Exchange the washes quickly, taking care to avoid letting the cassettes dry. Ensure that each wash fully covers the cassettes in the beaker or container. 
			NOTE: Xylenes are flammable, and if inhaled, the vapors may depress the central nervous system with potential long-term neurological consequences upon exposure to high concentrations (&#62;200 ppm). Handle xylenes only within a fume hood. As xylenes are hazardous, take care to use the minimum amount necessary to cover the histological cassettes.</li>
		</ol>
		</li>
		<li>During embedding, orient the intestinal segments parallel to the length of the cassette (as opposed to upright) using tweezers to provide longitudinal, transverse sections instead of cross-sectional doughnuts to provide more potential sample area for quantitative imaging (Figure 1B).</li>
		<li>Open the cassettes slightly (~1-2 cm or 0.5 inches) to allow the paraffin to enter without losing the tissue segments. Use double gloves for this step or tweezers to prevent overheating or mild burning of fingers. Submerge and close the cassettes in the container of melted paraffin, placing the container back into the 60 &#176;C oven. Ensure that the cassettes are filled with paraffin, and no large air bubbles remain.</li>
		<li>After incubation for 2 h at 60 &#176;C, remove the container from the oven. Using forceps, carefully remove the cassettes and lay them individually on a piece of aluminum foil to cool. Store them at room temperature until ready for embedding and sectioning.</li>
		<li>Section the paraffin blocks with a microtome, sectioning deep enough into the block that luminal contents are exposed, enabling a longitudinal section of villi and/or crypts in addition to luminal contents and mucus. Take care to replace the blades as fecal material dulls the blade rapidly compared to tissue. Cut sections to 4 &#181;m of thickness for optimal sharpness of the images. Transfer the sections to regular uncoated slides.</li>
		<li>For FISH staining, stain the intestinal sections as soon as possible (i.e., within a few weeks of sectioning) to achieve a strong FISH signal. If omitting FISH staining, lectin + DAPI staining can be performed on less fresh (i.e., months-old) samples without significant loss of signal.</li>
	</ol>
	</li>
</ol>
3. Staining bacteria and host features
<ol>
	<li>Preparation
	<ol>
		<li>Heat the oven to 60 &#176;C. Pre-warm an empty Coplin jar and enough volume to cover the glass slides in the jar twice with xylenes in a glass bottle, taking care to parafilm around the lid to prevent evaporation of the xylenes. Allow the temperature of the xylenes to reach 60 &#176;C. 
		NOTE: A standard Coplin jar fits 8 slides, and the slides can be covered with roughly 50 mL of liquid (may vary between 40 and 60 mL depending on the brand). Xylene substitutes are less toxic and have been successfully used by other groups for the de-waxing step (step 3.2)8,9.</li>
		<li>If a separate oven is available, pre-warm a hybridization oven to 50 &#176;C. Otherwise, this step may be performed with the same oven used for baking the slides after step 3.2.3.</li>
		<li>Prepare the FISH hybridization solution: 20 mM Tris-HCl, pH 7.4; 0.9 M NaCl; 0.01%26&#160;- 0.1%9&#160;(w/v) sodium dodecylsulfate (SDS) in nuclease-free water. If required, add 5-50% (v/v) formamide.&#160;Pre-warm this hybridization solution at 50 &#176;C during de-paraffinization. 
		NOTE: Formamide is an amide that acts as a teratogen; handle formamide with gloves and goggles. In small doses and upon exposure to eyes, skin, or mucous membranes, it is irritating. In large amounts, formamide vapor can require medical intervention. Formamide can be stored at 100% in a -20 &#176;C freezer.</li>
	</ol>
	</li>
	<li>Preparing the slides for staining: deparaffinization
	<ol>
		<li>Place the slides in the Coplin jar, ensuring that the sections do not come in contact with other slides or the jar, and bake the slides at 60 &#176;C for 10 min.</li>
		<li>In the fume hood, fill the Coplin jar with pre-warmed xylenes from the oven, taking care not to pour directly on top of the samples and potentially dislodge the tissues. Place the Coplin jar back in the 60 &#176;C oven. Leave the bottle with the remaining xylenes in the fume hood.</li>
		<li>Pour the used xylenes into a proper waste container for disposal, taking care not to disturb the tissue sections on the glass slides and using a pair of forceps to keep the slides from falling out of the Coplin jar. Replenish the Coplin jar with the remaining xylenes and incubate for 10 min at room temperature in the fume hood.</li>
		<li>Incubate the sections in 99.5% ethanol for 5 min at room temperature. After this incubation step, remove the slides from the Coplin jar, wipe the back of the slides on a laboratory wipe or paper towel, and briefly air-dry until the ethanol droplets are gone. 
		NOTE: Wiping the back of the slides enables better visualization of the drying progress.</li>
	</ol>
	</li>
	<li>Bacterial staining with FISH
	<ol>
		<li>Use a liquid blocker or PAP pen to limit the area of liquid expansion by circling the area of each tissue section. Ensure that the ink does not come in contact with the section itself. Create a circle as close to each tissue section as possible without contacting the tissue to minimize the surface area that needs to be covered by the hybridization solution.</li>
		<li>Prepare the hybridization solution: for every 50 &#181;L of pre-warmed hybridization solution, add 0.5 &#181;g probe (e.g., 0.5 &#181;L of 1 &#181;g/&#181;L probe). Pipette the hybridization solution onto the sections on the slide (~20 &#181;L/section, depending on the section/circle size). Protect the hybridization solution and the slides from light from this point onward during incubation steps and storage.</li>
		<li>Ensure that the volume of liquid used covers the entire section upon overlaying with a flexible plastic coverslip. Incubate the slide in a humid chamber to reduce evaporation. Create a humid chamber with a pipette tip box with wipes or paper towels at the bottom that have been soaked with excess hybridization solution or phosphate-buffered saline (PBS) to provide humidity. Incubate the sections at 45-50 &#176;C, depending on the probe set, for &#62;3 h.</li>
		<li>Warm up the FISH washing buffer: 20 mM Tris-HCl, pH 7.4; 0.9 M NaCl to 50 &#176;C during the incubation period. Prepare enough washing buffer to cover the slides in the Coplin jar.</li>
		<li>Remove the plastic coverslips; incubate the slides in FISH washing buffer in a&#160;Coplin jar, both pre-warmed&#160;to 50 &#176;C. Place the Coplin jar back into the 50 &#176;C oven for 10-20 min. For thick samples, remove the coverslips in the Coplin jar by adding the buffer and gently dislodging the coverslips to avoid smearing the slice.</li>
	</ol>
	</li>
	<li>Staining the mucus and host features
	<ol>
		<li>Prepare a general DNA/mucus counterstain in PBS: final 10 &#181;g/mL DAPI + 40 &#181;g/mL mucus stain UEA-1. Prepare enough counterstain to cover the spots in the absence of a coverslip to avoid damaging tissue with additional coverslips. 
		NOTE: Covering the spots in the absence of a coverslip will require larger volumes than the 20 &#181;L used in 3.3.2. For average-sized sections (~10 mm diameter), 200 &#181;L is enough to cover one spot; test this volume beforehand on a dummy slide.</li>
		<li>Remove the FISH washing buffer and replace it with PBS in the Coplin jar. Immediately after refilling the Coplin jar with PBS, decant the PBS.</li>
		<li>Remove the slides from the jar and pipette the counterstain on top of the section while ensuring to not touch the tissue with the pipette tip. Cover the entire section with a bubble. Incubate at 4 &#176;C for 45 min in the dark.</li>
		<li>Wash the stains 3 times quickly with fresh PBS: while holding the slides in place using tweezers, pour out the PBS in a sink and immediately refill with fresh PBS.</li>
		<li>Wiping the back of the slides against a wipe or paper towel, let most of the PBS evaporate off the sections, aided by a vacuum line connected to a pipette tip. Once again, avoid touching the section with the pipette tip.</li>
		<li>Mount the sections using a mounting medium (without DAPI) and let it set at room temperature covered by glass coverslips, ensuring that the coverslips are flat and there are no air bubbles in the mounting medium.</li>
		<li>Affix the coverslips to the slide by painting along the edges of the coverslip with clear nail polish, taking care to stay away from the edge of the slide to ensure that the slide will sit level in the microscope slide holder during imaging.</li>
		<li>Store the slides at 4 &#176;C in the dark for a few weeks before the fluorescence is depleted.</li>
	</ol>
	</li>
</ol>
4. Imaging and image analysis
<ol>
	<li>Visualizing the stains
	<ol>
		<li>Select an area of the tissue that contains both tissue and lumen to image the microbiota-host interface. For quantitative imaging of mucus thickness and luminal biogeography, select fields of view where the slices of the epithelial villi and/or crypts are longitudinal and not cross-sectional. Avoid areas with large gaps between the mucus and the epithelium to avoid sectioning artifacts.</li>
		<li>Locate tissue and correct the focal plane, utilizing the DAPI signal for locating and focusing to avoid photo-bleaching of the FISH fluorescence signal.</li>
		<li>Adjust the imaging settings. To visualize the bacterial DAPI stain, increase the laser power and gain to the point where the DAPI signal from epithelial cells is oversaturated or &#34;blown out.&#34; 
		NOTE: Do not oversaturate excessively, as this will lead to photobleaching and visual artifacts in the nuclei that cannot be recovered.</li>
		<li>For all other channels, use the minimum amount of laser power that will provide a clear signal above the background, and be careful not to oversaturate. 
		NOTE: This is especially important when performing tile-scans, as photobleaching will be problematic when the overlap between tiles is imaged.</li>
		<li>Use 40x or higher magnification to image individual bacteria.</li>
		<li>Acquire the images.
		<ol>
			<li>Acquire tile scans to obtain quantitative data on mucus thickness and spatial distribution of microbes within the lumen. Ensure 15% overlap between the tiles and check for vignetting/uneven illumination, which may be exacerbated by &#60;1x zoom. When setting up a tile scan, pay close attention to whether the tissue is in focus in all the tiles, as blurry/out-of-focus images cannot be analyzed (Figure 3B).</li>
			<li>If possible, minimize the number of tiles needed to image a given length of epithelium by rotating the scan area so that the epithelium and mucus layer are parallel to the tile and not at an angle. Otherwise, find a section of the epithelium that is parallel or perpendicular to the imaging area to achieve a similar effect.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>

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V., Calabresi, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Agar-gelatin+for+embedding+tissues+prior+to+paraffin+processing.">Agar-gelatin for embedding tissues prior to paraffin processing.</a> BioTechniques. 42 (5), 569-570 (2007).</li><li>Earle, K. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+imaging+of+gut+microbiota+spatial+organization.">Quantitative imaging of gut microbiota spatial organization.</a> Cell Host and Microbe. 18 (4), 478-488 (2015).</li><li>Jeckel, H., Drescher, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+and+opportunities+in+image+analysis+of+bacterial+cells+and+communities.">Advances and opportunities in image analysis of bacterial cells and communities.</a> FEMS Microbiology Reviews. , (2020).</li></ol>

The authors have no conflicts of interest.

The protocol described above provides a reproducible method to visualize the host-microbiota interface. These assays have considerably benefited from protocol development, starting from the optimization of FISH labeling18 to mucus preservation and imaging9. Fixation and embedding also provide useful storage of samples; furthermore, paraffin-infiltrated cassettes can be mailed without any restrictions, as the samples are completely fixed and inert.
Significance and alternative methods 
The combination of FISH and mucus staining enables the analysis of microbiota composition at specific tissue locations and the interaction between individual bacteria and the host. Alternative techniques that involve the analysis of specific sites within the microbiota are usually unable to explore the single-cell nature of these interactions, such as in the case of laser capture microdissection coupled with sequencing19. However, sequencing-based techniques have the advantage of being able to capture the genetic make-up of the microbiota at a finer level and more broadly than 16S rRNA probes.
A pitfall of the protocol presented is that it provides a single-time snapshot of the microbiota in relation to the host. For real-time imaging in live animals, special imaging techniques are required to facilitate the acquisition of a fluorescence signal in deep tissue (e.g., intravital two-photon microscopy and light-sheet fluorescence microscopy20,21). In these methods, the model organism is either colonized with bacteria that are stained with molecules that bind to their envelope20 or genetically modified bacteria that harbor fluorescent proteins21. In the latter case, the maturation of fluorescence proteins is a key issue as most standard fluorescent proteins require oxygen to emit light. Therefore, model organisms that have at least nanaerobic environments (nanomolar concentration of oxygen) are required, such as the aerobic zebrafish gut21.
In this protocol, methanol-Carnoy is used as a fixative instead of paraformaldehyde or formalin because it does not contain water. This prevents hydration, dehydration, and collapse of the mucus layer during processing and facilitates accurate measurements of mucus thickness. While methacarn fixation and paraffin embedding have become a standard in the field, different fixatives and embedding techniques have been investigated to optimize mucus preservation9,22, with some studies indicating that resins may be superior to paraffin embedding22. Another important limitation to paraffin embedding and methacarn fixation is the loss of fluorescent protein fluorescence, which can be avoided by using alternative fixatives (e.g., formalin or paraformaldehyde (PFA)) or modified embedding techniques23. Each fixative has benefits and drawbacks, and the choice of the fixative depends on the imaging priorities. Imaging modalities can be combined if biological replicates are fixed in either PFA and methacarn and images are obtained from both samples.
FISH has been combined with immunofluorescence in isolated instances with specific anti-Muc2C3 rabbit polyclonal antibodies9,24. These results have not been widely reproduced with other Muc2 antibodies, indicating that the choice of antibodies may be critical in the success of the FISH-immunofluorescence combination. The conditions for successful antibody staining for a given antibody may not permit retention of FISH staining.
Troubleshooting 
In this protocol, sample collection, sectioning, and staining represent critical steps to prevent the creation of imaging artifacts. For example, pressing on the tissue upon collection and before embedding can lead to mislocalization of the microbiota and affect mucus quality. Another important consideration is to avoid combining segments of very different thicknesses in a single cassette, such as a relatively empty piece of the small intestine and a pellet within the distal colon. The different thicknesses lead to difficulties in imaging: after embedding, transverse sectioning at a specific depth for one segment may be at the wrong depth for imaging for the other one (e.g., the lumen will be at different depths for each tissue) (Figure 1B,C and Figure 3A). Furthermore, for imaging animal model stool pellets, they may be wrapped in peritoneal membrane24. In this technique, a small section of freshly isolated peritoneum is gently folded around the stool and preserves the structure of the pellet during the wash steps outlined in the protocol.
Unlike processing animal tissue with contents, imaging human intestinal samples presents some challenges. Specifically, luminal contents and mucosal lining will likely be disrupted by the colonoscopy bowel preparation usually performed before intestinal biopsies or resection procedures. Additionally, when biopsies are collected, it is helpful to note the tissue orientation to aid in the identification of specific features (e.g., lumen vs. submucosa) in the absence of intestinal contents. Pre-embedding with 3% agar and/or agar:gelatin mixtures may be useful in maintaining tissue polarity25; however, there are issues with the dehydration and sectioning of agar, as reported in the literature, and processing times may need to be altered.
A key aspect to achieving good FISH staining comes from adjusting the formamide concentration for specific FISH probes. Formamide will control the hybridization stringency of FISH probes to their targets. It is important to ensure that a) the proper formamide concentration is chosen for staining a given community, and b) that a suitable formamide concentration is even possible for the probe combination that is being utilized-this may affect the optimal probe choice when utilizing multiple probes. Websites such as mathFISH (http://mathfish.cee.wisc.edu/) may help with calculating the proper formamide concentrations for a given probe. In the absence of information about appropriate formamide concentrations, this protocol can be tested with 0% and 10% formamide.
Sectioning the embedded samples requires cutting the block to a sufficient depth to obtain luminal slices, as sectioning too shallowly into a block will result in a cross-sectional view of the villi/crypts with no luminal contents (Figure 3A). Stain the samples soon after sectioning for optimal FISH signal, and use fresh DAPI (or DAPI stored at -20 &#176;C) to resolve background issues (Figure 3C). FISH staining of sections that are more than a month-old may result in poorer/inconsistent staining.
If the tissue or coverslip is not perfectly flat with respect to the slide, the sample may not be in focus at every position within a tile scan (Figure 3B), leading to wasted effort and potential photobleaching. This can be solved by taking smaller tile scans in which all positions have been verified to be in focus. Sectioning with dull blades can also lead to the detachment of the mucus and luminal contents, which appear as large dark areas while imaging. Finally, the evaporation of the solution or bubbles during the hybridization step can lead to uneven staining of the FISH probes in the tissue.
Another critical parameter that affects the efficiency of the FISH probe binding is the competition between different probes. A useful check to verify that the FISH probe is labeling bacteria is to examine the colocalization of the signal from the FISH probe with DAPI (Figure 2C,D). In samples that require the use of multiple rRNA probes, adjusting parameters such as hybridization temperature, probe concentration, and formamide becomes critical to ensure that the probes are binding to the correct species efficiently18.
Notes about imaging 
FISH-stained bacteria are best visualized using a confocal microscope and an objective of at least 40x magnification. While 63x magnification is preferred to image bacteria at the single-cell level, 40x magnification can also be used by maximizing the digital zoom or employing a super-resolution system. Systems equipped with super-resolution capabilities may also provide sub-cellular resolution of individual bacterial cells. Lower magnification objectives may be utilized to get a general sense of bacterial localization and mucus thickness.
Acquiring 16-bit images instead of 8-bit images is also highly recommended, as the higher dynamic range will help to capture the wide range of the DAPI signal from the extremely bright nuclei of the epithelium and the relatively weak signal of luminal bacteria. Aside from using the imaging setup described above, an important imaging consideration is the choice of fluorophores. For best separation between bacterial types, ensure that the fluorophores used do not overlap in excitation and emission spectra (unless imaging on a system with the ability to perform linear unmixing). Additionally, probes can be used in combination (e.g., the combination of a family-specific probe and a genus-specific probe) to identify additional community members. If using linear unmixing or unvalidated probes, it is essential to test the accuracy and level of FISH staining on pure cultures8,14.
Once the images are collected, multiple tools are available for the quantitative analysis of the host-microbiota interface, such as BacSpace26, HiPR-FISH8, and other segmentation tools27. BacSpace is a MATLAB software that allows the segmentation of the tissue and luminal components and the removal of plant material from images26. The program also provides analysis of mucus thickness in 2D and quantification of spatial distribution based on pixel distances in different channels26. Conversely, the HiPR-FISH Image Analysis software allows the segmentation of FISH-stained cells8. Finally, other bacterial segmentation tools that have been optimized for in vitro experiments27 could also be adapted to this application.
Conclusion 
In situ imaging enables the quantitative analysis of individual microbial taxa in the context of other community members and the various microenvironments created by diet, mucus, and host epithelial crypts. The interaction between organisms dictates the biology of host-associated microbial systems and provides an essential analysis of change in these structures during perturbation that has implications for health. Notably, the ability to image the microbiota in situ through the protocol described above provides an incredible window into the biogeography of the microbiota in relation to the animal host.

Microbial visualization techniques have origins that are as old as microbiology itself, when Antonie Van Leeuwenhoek used his microscope to observe bacteria (which he called &#34;animalcules&#34;) from tooth plaque and stool in the 17th century. Since then, numerous techniques have been developed to visualize the spatial organization of the consortium of bacteria, fungi, and viruses that live associated with a host-the microbiota1. Elucidating the localization of these microbes is essential to determining their function within their animal host. The biogeography of bacteria is important in commensal and pathogenic taxa alike, as proximity to specific locations (e.g., the epithelium), nutritional substrates, and specific microbes may dictate bacterial production of metabolites underlying interspecies and inter-kingdom interactions.
A key structure separating bacteria and the host tissues in several disparate body sites, such as the oral cavity, intestine, or lung, is the mucus - a host-produced layer that both prevents microbial translocation onto the host epithelial cells and serves as a nutritional resource for the microbiota2,3,4. Characterizing breaches and changes in this barrier is of key importance, leading to mechanistic insight into host-microbiota interactions that would not be obtained by sequencing alone5,6,7. For example, imaging enabled the discovery that antibiotic exposure can disrupt the mucus layer and microbiota organization7,8, and that laxatives may deplete the mucus, correlating with large changes in immune parameters5.
This protocol outlines a general framework for fixing, staining, and imaging the microbiota and the host tissue (Figure 1), built upon the work of Johansson and Hansson9. While this protocol is modeled in the context of intestinal sections, it can be easily adapted to other tissue types. This protocol enables the processing of either experimental animal or human clinical samples; notes for processing both types of samples have been included. In the example presented here, the host epithelium and luminal bacteria have been simultaneously labeled with 4&#8242;,6-diamidino-2-phenylindole (DAPI) staining, mucus with the fluorescein (FITC)-conjugated lectin, Ulex europaeus agglutinin I (UEA-1), and a specific bacterial taxon using FISH. FISH probes are usually designed against a taxon&#39;s 16S rRNA genes to ensure the high signal from binding a high-copy transcript.
In this example, the probe targets the 16S rRNA of the Muribaculaceae bacterial family (Figure 2). However, the stains are readily substituted with different FISH probes and/or lectins to accommodate the appropriate biological question. Previously validated FISH probes can be found on ProbeBase10, an online resource for rRNA-targeted oligonucleotide probes, or on SILVA11, a ribosomal RNA database. For the design of new probes, the reader may refer to new pipelines such as HiPR-FISH8 or Oligominer12. Using this protocol, it is possible to observe the close packing of bacteria in the intestinal lumen and the different features of intestinal mucus throughout the digestive tract. The workflow described here enables the quantitative analysis of the microbiota in the spatial context of its host environment.

<table><tbody><tr><td>Aluminum foil</td><td></td><td></td><td></td></tr><tr><td>Chloroform</td><td>Fisher</td><td>C298-500</td><td>Toxic</td></tr><tr><td>Coplin jar</td><td>Fisher</td><td>08-813E</td><td></td></tr><tr><td>Cover glass, 22 &amp;times; 22 mm, no #1</td><td>VWR</td><td>CA48366-227-1</td><td></td></tr><tr><td>DAPI</td><td>Sigma-Aldrich</td><td>D9542</td><td>Resuspended to 5 mg/mL</td></tr><tr><td>Empty pipette tip box(es)</td><td></td><td></td><td>To melt paraffin</td></tr><tr><td>Ethanol, anhydrous, molecular grade</td><td>--</td><td>--</td><td></td></tr><tr><td>FISH probes</td><td></td><td></td><td></td></tr><tr><td>FISH hybridization solution</td><td>--</td><td>--</td><td>20 mM Tris&amp;ndash;HCl pH 7.4, 0.9 M NaCl, 0.01% (w/v) SDS in nuclease-free water. Optional addition of 5&amp;ndash;50% (v/v) formamide</td></tr><tr><td>FISH washing buffer</td><td>--</td><td>--</td><td>20 mM Tris&amp;ndash;HCl pH 7.4, 0.9 M NaCl</td></tr><tr><td>Fluorescently-labeled Ulex Europaeus Agglutinin (UEA-1) lectin</td><td>Vector Laboratories</td><td>FL-1061 (Fluorescein-labeled) or RL-1062-2 (Rhodamine-labeled)</td><td>UEA-1 labels fucosylated glycans, so it is not appropriate for germ-free mice or for samples from fucosyltransferase 2 (FUT2)-deficient hosts.</td></tr><tr><td>Forceps</td><td></td><td></td><td></td></tr><tr><td>Formamide</td><td>Sigma-Aldrich</td><td>F9037</td><td></td></tr><tr><td>Fumehood</td><td></td><td></td><td></td></tr><tr><td>Glacial Acetic Acid</td><td>Fisher</td><td>A38-212</td><td>Corrosive and flammable</td></tr><tr><td>HybriSlip flexible plastic cover slips, 22 x 22 mm &amp;times; 0.25 mm</td><td>Sigma Aldrich</td><td>GBL722222</td><td>for FISH hybridization steps, can substitute glass coverslips</td></tr><tr><td>ImmEdge Hydrophobic Barrier PAP Pen</td><td>Vector Laboratories</td><td>H-4000</td><td></td></tr><tr><td>Kimwipes</td><td></td><td></td><td></td></tr><tr><td>Methanol</td><td>Fisher</td><td>A412</td><td>Toxic and flammable</td></tr><tr><td>Microtome</td><td></td><td></td><td>for sectioning</td></tr><tr><td>Multipurpose Specimen Storage Containers, 473 mL</td><td>Fisher</td><td>14-955-117A</td><td>Can substitute with a glass or polyethylene container of your choice. Methacarn is not compatible with polystyrene or metal.</td></tr><tr><td>Nail Polish</td><td>Electron Microscopy Sciences</td><td>72180</td><td>Any nail polish should work</td></tr><tr><td>Oven</td><td></td><td></td><td>Necessary range: 45-60 &amp;deg;C</td></tr><tr><td>Paraffin: Leica Paraplast</td><td>Leica</td><td>39601006</td><td></td></tr><tr><td>PBS, Phosphate-buffered Saline (10x solution)</td><td>Fisher</td><td>BP3991</td><td>Dilute to 1x for protocol</td></tr><tr><td>Sodium chloride</td><td>Fisher</td><td>S271</td><td></td></tr><tr><td>Sodium Dodecyl Sulfate (SDS), 20% Solution, RNase-free</td><td>Invitrogen</td><td>AM9820</td><td></td></tr><tr><td>Tissue-Loc HistoScreen Cassettes</td><td>Thermo Scientific</td><td>CA83009-999</td><td></td></tr><tr><td>Trizma hydrochloride solution, 1M Tris-HCl, pH 7.4</td><td>Sigma-Aldrich</td><td>T2663-1L</td><td></td></tr><tr><td>Vectashield</td><td>Vector Laboratories</td><td>H-1000</td><td></td></tr><tr><td>Water, nuclease-free</td><td>Fisher</td><td>BP2484100</td><td></td></tr><tr><td>Xylenes</td><td>Fisher</td><td>X3P-1GAL</td><td>Toxic and flammable</td></tr></tbody></table>

visualization of gut microbiota-host interactions via fluorescence in situ hybridization, lectin staining, and imaging

Measuring the localization of microbes within their in vivo context is an essential step in revealing the functional relationships between the microbiota and the vertebrate gut. The spatial landscape of the gut microbiota is tightly controlled by physical features - intestinal mucus, crypts, and folds - and is affected by host-controlled properties such as pH, oxygen availability, and immune factors. These properties limit the ability of commensal microbes and pathogens alike to colonize the gut stably. At the micron-scale, microbial organization determines the close-range interactions between different microbes as well as the interactions between microbes and their host. These interactions then affect large-scale organ function and host health.
This protocol enables the visualization of the gut microbiota spatial organization from distances between cells to organ-wide scales. The method is based on fixing gut tissues while preserving intestinal structure and mucus properties. The fixed samples are then embedded, sectioned, and stained to highlight specific bacterial species through fluorescence in situ hybridization (FISH). Host features, such as mucus and host cell components, are labeled with fluorescently labeled lectins. Finally, the stained sections are imaged using a confocal microscope utilizing tile-scan imaging at high magnification to bridge the micron to centimeter length scales. This type of imaging can be applied to intestinal sections from animal models and biopsies from human tissues to determine the biogeography of the microbiota in the gut in health and disease.

To investigate the localization of specific gut commensal bacteria in the mouse intestine, germ-free Swiss Webster mice that had been colonized with individual bacterial isolates were used in this study. For this experiment, the bacterial species labeled were i) a human isolate of the Muribaculaceae family5, Muribaculum intestinale, an abundant and prevalent family of bacteria in the murine microbiota15, as well as ii) Bacteroides thetaiotaomicron, a genetically tractable and common gut bacterium. Following two weeks of equilibration, the mice were euthanized, and a segment of the colon containing a fecal pellet was sectioned and fixed in freshly prepared methacarn. After two days of fixation, the sections were dehydrated by processing through methanol, ethanol, and xylenes, infiltrated with paraffin, embedded, and then sectioned to luminal 4 &#181;m slices. These samples were then stained with a FISH probe (3&#39; Cy3-tagged) specific for the Muribaculum isolate, designed using Oligominer software12, and checked for secondary and tertiary structure and minimal non-specific binding using NuPACK and mathFISH16,17. The samples were also counterstained with the Rhodamine-bound lectin UEA-1 (which stains fucosylated glycans in mucus) and DAPI. The stained sections were imaged using a 40x oil objective and super-resolution module.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/62646/62646fig01.jpg" /> 
Figure 1: Workflow of visualization of the microbiota-host interface in the intestine. (A) An illustrated workflow for the pipeline. (B) The two sectioning planes will yield either transverse sections (preferred for this pipeline) or cross-sectional &#34;doughnuts.&#34; (C) Embedding tissues of very different thicknesses may result in slices that are only optimal for one tissue or another. Abbreviations: FISH = fluorescence in situ hybridization; DAPI = 4&#8242;,6-diamidino-2-phenylindole. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/62646/62646fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/62646/62646fig02.jpg" /> 
Figure 2: Imaging the colon shows the localization of Muribaculum intestinale relative to mucus in a gnotobiotic mouse model. Sections were stained with DAPI (blue), Muribaculaceae FISH probe (red), and UEA-1 (green). (A) Distal colon of mouse mono-colonized with Muribaculum intestinale and&#160;(B) distal colon of mouse bi-colonized with Muribaculum intestinale and Bacteroides thetaiotaomicron. Scale bar = 20 &#181;m. (C and D) Cy3-FISH (left), DAPI (middle), and combined Cy3-FISH + DAPI channels for luminal inset portions of (A) and (B), respectively. Scale bar = 5 &#181;m. In (A) and (C), all bacteria-shaped and bacteria-sized DAPI signals are labeled with Cy3 (single arrowheads), and in (B) and (D), in addition to these Cy3- and DAPI-double-positive cells (single arrowheads), there are DAPI-stained bacterial cells that are Cy3-negative (double arrowheads), as expected for mono- and bi-colonization states. With the exception of longer filamentous bacteria, larger (&#62;4 &#181;m in length) DAPI-positive structures (blunt arrows) are plant material or nuclei from host cells. Abbreviations: FISH = fluorescence in situ hybridization; DAPI = 4&#8242;,6-diamidino-2-phenylindole. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/62646/62646fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/62646/62646fig03.jpg" /> 
Figure 3: Common problems. (A)&#160;Shallow sectioning will not provide luminal slices of the intestine. (Left) An intestinal segment that has been sectioned at a depth that provides a view of the lumen as well as longitudinal views of the epithelium. (Right) An intestinal segment that has been sectioned too shallowly, revealing only cross-sections of crypts and no constant mucus layer or bacteria. (B) Uneven tissue/coverslip coverage may result in blurry and unevenly illuminated tile-scans. A tile-scan was set up with positions that were out of focus (top right corner). (C) Example of normal background (left) and high background (right). In this example, for the DAPI signal-note the signal coming from the epithelium, outside the nuclei. All scale bars = 20 &#181;m. Abbreviation: DAPI = 4&#8242;,6-diamidino-2-phenylindole. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/62646/62646fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging at JoVE.com

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

This streamlined protocol details a workflow to detect and image bacteria in complex tissue samples, from fixing the tissue to staining microbes with fluorescent in situ hybridization.

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

Measuring the localization of microbes within their in vivo context is an essential step in revealing the functional relationships between the microbiota ...

visualization-gut-microbiota-host-interactions-via-fluorescence-situ

Universidad San Sebastian

Research

JoVE Journal

Immunology and Infection

7.8K Views.  University of British Columbia. This streamlined protocol details a workflow to detect and image bacteria in complex tissue samples, from fixing the tissue to staining microbes with fluorescent in situ hybridization. 

Video: Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization

Infectious diseases transmitted by arthropod vectors continue to pose a significant threat to human health worldwide. The pathogens causing these diseases, do not exist in isolation when they colonize the vector; rather, they likely engage in interactions with resident microorganisms in the gut lumen. The vector microbiota has been demonstrated to play an important role in pathogen transmission for several vector-borne diseases. Whether resident bacteria in the gut of the Ixodes scapularis tick, the vector of several human pathogens including Borrelia burgdorferi, influence tick transmission of pathogens is not determined. We require methods for characterizing the composition of the bacteria associated with the tick gut to facilitate a better understanding of potential interspecies interactions in the tick gut. Using whole-mount in situ hybridization to visualize RNA transcripts associated with particular bacterial species allows for the collection of qualitative data regarding the abundance and distribution of the microbiota in intact tissue. This technique can be used to examine changes in the gut microbiota milieu over the course of tick feeding and can also be applied to analyze expression of tick genes. Staining of whole tick guts yield information about the gross spatial distribution of target RNA in the tissue without the need for three-dimensional reconstruction and is less affected by environmental contamination, which often confounds the sequencing-based methods frequently used to study complex microbial communities. Overall, this technique is a valuable tool that can be used to better understand vector-pathogen-microbiota interactions and their role in disease transmission.

Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization

Here, we present a protocol to spatially and temporally assess the presence of viable microbiota in tick guts using a modified whole-mount in situ hybridization approach.

Infectious diseases transmitted by arthropod vectors continue to pose a significant threat to human health worldwide. The pathogens causing these ...

Genetics

Co-culture of Living Microbiome with Microengineered Human Intestinal Villi in a Gut-on-a-Chip Microfluidic Device

Here, we describe a protocol to perform long-term co-culture of multi-species human gut microbiome with microengineered intestinal villi in a human gut-on-a-chip microphysiological device. We recapitulate the intestinal lumen-capillary tissue interface in a microfluidic device, where physiological mechanical deformations and fluid shear flow are constantly applied to mimic peristalsis. In the lumen microchannel, human intestinal epithelial Caco-2 cells are cultured to form a &#39;germ-free&#39; villus epithelium and regenerate small intestinal villi. Pre-cultured microbial cells are inoculated into the lumen side to establish a host-microbe ecosystem. After microbial cells adhere to the apical surface of the villi, fluid flow and mechanical deformations are resumed to produce a steady-state microenvironment in which fresh culture medium is constantly supplied and unbound bacteria (as well as bacterial wastes) are continuously removed. After extended co-culture from days to weeks, multiple microcolonies are found to be randomly located between the villi, and both microbial and epithelial cells remain viable and functional for at least one week in culture. Our co-culture protocol can be adapted to provide a versatile platform for other host-microbiome ecosystems that can be found in various human organs, which may facilitate in vitro study of the role of human microbiome in orchestrating health and disease.

We describe an in vitro protocol to co-culture gut microbiome and intestinal villi for an extended period using a human gut-on-a-chip microphysiological system.

Here, we describe a protocol to perform long-term co-culture of multi-species human gut microbiome with microengineered intestinal villi in a human ...

Bioengineering

Investigation of Microbial Cooperation via Imaging Mass Spectrometry Analysis of Bacterial Colonies Grown on Agar and in Tissue During Infection

Understanding the metabolic consequences of microbial interactions that occur during infection presents a unique challenge to the field of biomedical imaging. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry represents a label-free, in situ imaging modality capable of generating spatial maps for a wide variety of metabolites. While thinly sectioned tissue samples are now routinely analyzed via this technology, imaging mass spectrometry analyses of non-traditional substrates, such as bacterial colonies commonly grown on agar in microbiology research, remain challenging due to the high water content and uneven topography of these samples. This paper demonstrates a sample preparation workflow to allow for imaging mass spectrometry analyses of these sample types. This process is exemplified using bacterial co-culture macrocolonies of two gastrointestinal pathogens: Clostridioides difficile and Enterococcus faecalis. Studying microbial interactions in this well-defined agar environment is also shown to complement tissue studies aimed at understanding microbial metabolic cooperation between these two pathogenic organisms in mouse models of infection. Imaging mass spectrometry analyses of the amino acid metabolites arginine and ornithine are presented as representative data. This method is broadly applicable to other analytes, microbial pathogens or diseases, and tissue types where a spatial measure of cellular or tissue biochemistry is desired.

Investigation of Microbial Cooperation via Imaging Mass Spectrometry Analysis of Bacterial Colonies Grown on Agar and in Tissue During Infection

A novel sample preparation method is demonstrated for the analysis of agar-based, bacterial macrocolonies via matrix-assisted laser desorption/ionization imaging mass spectrometry.

Understanding the metabolic consequences of microbial interactions that occur during infection presents a unique challenge to the field of biomedical ...

Biochemistry

Visualizing Bacteria in Nematodes using Fluorescent Microscopy

Symbioses, the living together of two or more organisms, are widespread throughout all kingdoms of life. As two of the most ubiquitous organisms on earth, nematodes and bacteria form a wide array of symbiotic associations that range from beneficial to pathogenic 1-3. One such association is the mutually beneficial relationship between Xenorhabdus bacteria and Steinernema nematodes, which has emerged as a model system of symbiosis 4. Steinernema nematodes are entomopathogenic, using their bacterial symbiont to kill insects 5. For transmission between insect hosts, the bacteria colonize the intestine of the nematode's infective juvenile stage 6-8. Recently, several other nematode species have been shown to utilize bacteria to kill insects 9-13, and investigations have begun examining the interactions between the nematodes and bacteria in these systems 9.
We describe a method for visualization of a bacterial symbiont within or on a nematode host, taking advantage of the optical transparency of nematodes when viewed by microscopy. The bacteria are engineered to express a fluorescent protein, allowing their visualization by fluorescence microscopy. Many plasmids are available that carry genes encoding proteins that fluoresce at different wavelengths (i.e. green or red), and conjugation of plasmids from a donor Escherichia coli strain into a recipient bacterial symbiont is successful for a broad range of bacteria. The methods described were developed to investigate the association between Steinernema carpocapsae and Xenorhabdus nematophila 14. Similar methods have been used to investigate other nematode-bacterium associations 9,15-18and the approach therefore is generally applicable.
The method allows characterization of bacterial presence and localization within nematodes at different stages of development, providing insights into the nature of the association and the process of colonization 14,16,19. Microscopic analysis reveals both colonization frequency within a population and localization of bacteria to host tissues 14,16,19-21. This is an advantage over other methods of monitoring bacteria within nematode populations, such as sonication 22or grinding 23, which can provide average levels of colonization, but may not, for example, discriminate populations with a high frequency of low symbiont loads from populations with a low frequency of high symbiont loads. Discriminating the frequency and load of colonizing bacteria can be especially important when screening or characterizing bacterial mutants for colonization phenotypes 21,24. Indeed, fluorescence microscopy has been used in high throughput screening of bacterial mutants for defects in colonization 17,18, and is less laborious than other methods, including sonication 22,25-27and individual nematode dissection 28,29.

To study the mutualism between Xenorhabdus bacteria and Steinernema nematodes, methods were developed to monitor bacterial presence and location within nematodes. The experimental approach, which can be applied to other systems, entails engineering bacteria to express the green fluorescent protein and visualizing, using fluorescence microscopy bacteria within the transparent nematode.

 
Symbioses, the living together of two or more organisms, are widespread throughout all kingdoms of life. As two of the most ubiquitous organisms on ...

Biology

Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization

Candida albicans is a fungal component of the gut microbiota in humans and many other mammals. Although C. albicans does not cause symptoms in most colonized hosts, the commensal reservoir does serve as a repository for infectious disease, and the presence of high fungal titers in the gut is associated with inflammatory bowel disease. Here, we describe a method to visualize C. albicans cell morphology and localization in a mouse model of stable gastrointestinal colonization. Colonization is established using a single dose of C. albicans in animals that have been treated with oral antibiotics. Segments of gut tissue are fixed in a manner that preserves the architecture of luminal contents (microorganisms and mucus) as well as the host mucosa. Finally, fluorescent in situ hybridization is performed using probes against fungal rRNA to stain for C. albicans and hyphae. A key advantage of this protocol is that it allows for simultaneous observation of C. albicans cell morphology and its spatial association with host structures during gastrointestinal colonization.

Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization

The purpose of this protocol is to visualize Candida albicans cell shape and localization in the mammalian gastrointestinal tract.

Candida albicans is a fungal component of the gut microbiota in humans and many other mammals. Although C. albicans does not cause symptoms in most ...

An Intestinal Gut Organ Culture System for Analyzing Host-Microbiota Interactions

The structure of the gut tissue facilitates close and mutualistic interactions between the host and the gut microbiota. These cross-talks are crucial for maintaining local and systemic homeostasis; changes to gut microbiota composition (dysbiosis) associate with a wide array of human diseases. Methods for dissecting host-microbiota interactions encompass an inherent tradeoff among preservation of physiological tissue structure (when using in vivo animal models) and the level of control over the experiment factors (as in simple in vitro cell culture systems). To address this tradeoff, Yissachar et al. recently developed an intestinal organ culture system. The system preserves a naive colon tissue construction and cellular mechanisms and it also permits tight experimental control, facilitating experimentations that cannot be readily performed in vivo. It is optimal for dissecting short-term responses of various gut components (such as epithelial, immunological and neuronal elements) to luminal perturbations (including anaerobic or aerobic microbes, whole microbiota samples from mice or humans, drugs and metabolites). Here, we present a detailed description of an optimized protocol for organ culture of multiple gut fragments using a custom-made gut culture device. Host responses to luminal perturbations can be visualized by immunofluorescence staining of tissue sections or whole-mount tissue fragments, fluorescence in-situ hybridization (FISH), or time-lapse imaging. This system supports a wide array of readouts, including next-generation sequencing, flow cytometry, and various cellular and biochemical assays. Overall, this three-dimensional organ culture system supports the culture of large, intact intestinal tissues and has broad applications for high-resolution analysis and visualization of host-microbiota interactions in the local gut environment.

This article presents a unique method for analyzing host-microbiome interactions using a novel gut organ culture system for ex vivo experiments.

The structure of the gut tissue facilitates close and mutualistic interactions between the host and the gut microbiota. These cross-talks are crucial for ...

Comprehensive Protocol for Cell Identification and Metabolic Analysis Using OPTIR-FISH

Optical Photothermal Infrared-Fluorescence In Situ Hybridization (OPTIR-FISH)

Understanding the metabolic activities of individual cells within complex communities is critical for unraveling their role in human disease. Here, we present a comprehensive protocol for simultaneous cell identification and metabolic analysis with the OPTIR-FISH platform by combining rRNA-tagged FISH probes and isotope-labeled substrates. Fluorescence imaging provides cell identification by the specific binding of rRNA-tagged FISH probes, while OPTIR imaging provides metabolic activities within single cells by isotope-induced red shift on OPTIR spectra. Using bacteria cultured with 13C-glucose as a test bed, the protocol outlines microbial culture with isotopic labeling, fluorescence in situ hybridization (FISH), sample preparation, optimization of the OPTIR-FISH imaging setup, and data acquisition. We also demonstrate how to perform image analysis and interpret spectral data at the single-cell level with high throughput. This protocol&#39;s standardized and detailed nature will greatly facilitate its adoption by researchers from diverse backgrounds and disciplines within the broad single-cell metabolism research community.

Author Spotlight: Integrated OPTIR-FISH for Single-Cell Metabolic and Identity Analysis in Complex Environments

Here, we present a protocol using optical photothermal infrared-fluorescence in situ hybridization (OPTIR-FISH), also known as mid-infrared photothermal-FISH (MIP-FISH), to identify individual cells and understand their metabolism. This methodology can be applied broadly for diverse applications, including mapping cellular metabolism with single-cell resolution.

Understanding the metabolic activities of individual cells within complex communities is critical for unraveling their role in human disease. Here, we ...

RNA Fluorescence in situ Hybridization (FISH) to Visualize Microbial Colonization and Infection in Caenorhabditis elegans Intestines

The intestines of wild Caenorhabditis nematodes are inhabited by a variety of microorganisms, including gut microbiome bacteria and pathogens, such as microsporidia and viruses. Because of the similarities between Caenorhabditis elegans and mammalian intestinal cells, as well as the power of the C. elegans system, this host has emerged as a model system to study host intestine-microbe interactions in vivo. While it is possible to observe some aspects of these interactions with bright-field microscopy, it is difficult to accurately classify microbes and characterize the extent of colonization or infection without more precise tools. RNA fluorescence in situ hybridization (FISH) can be used as a tool to identify and visualize microbes in nematodes from the wild or to experimentally characterize and quantify infection in nematodes infected with microbes in the lab. FISH probes, labeling the highly abundant small subunit ribosomal RNA, produce a bright signal for bacteria and microsporidian cells. Probes designed to target conserved regions of ribosomal RNA common to many species can detect a broad range of microbes, whereas targeting divergent regions of the ribosomal RNA is useful for narrower detection. Similarly, probes can be designed to label viral RNA. A protocol for RNA FISH staining with either paraformaldehyde (PFA) or acetone fixation is presented. PFA fixation is ideal for nematodes associated with bacteria, microsporidia, and viruses, whereas acetone fixation is necessary for the visualization of microsporida spores. Animals were first washed and fixed in paraformaldehyde or acetone. After fixation, FISH probes were incubated with samples to allow for the hybridization of probes to the desired target. The animals were again washed and then examined on microscope slides or using automated approaches. Overall, this FISH protocol enables detection, identification, and quantification of the microbes that inhabit the C. elegans intestine, including microbes for which there are no genetic tools available.

RNA Fluorescence in situ Hybridization FISH to Visualize Microbial Colonization and Infection in Caenorhabditis elegans Intestines

Intestinal microbes, including extracellular bacteria and intracellular pathogens like the Orsay virus and microsporidia (fungi), are often associated with wild Caenorhabditis nematodes. This article presents a protocol for detecting and quantifying microbes that colonize and/or infect C. elegans nematodes, and for measuring pathogen load after controlled infections in the lab.

The intestines of wild Caenorhabditis nematodes are inhabited by a variety of microorganisms, including gut microbiome bacteria and pathogens, such as ...

Detection of Tissue-resident Bacteria in Bladder Biopsies by 16S rRNA Fluorescence In Situ Hybridization

Visualization of the interaction of bacteria with host mucosal surfaces and tissues can provide valuable insight into mechanisms of pathogenesis. While visualization of bacterial pathogens in animal models of infection can rely on bacterial strains engineered to express fluorescent proteins such as GFP, visualization of bacteria within the mucosa of biopsies or tissue obtained from human patients requires an unbiased method. Here, we describe an efficient method for the detection of tissue-associated bacteria in human biopsy sections. This method utilizes fluorescent in situ hybridization (FISH) with a fluorescently labeled universal oligonucleotide probe for 16S rRNA to label tissue-associated bacteria within bladder biopsy sections acquired from patients suffering from recurrent urinary tract infection. Through use of a universal 16S rRNA probe, bacteria can be detected without prior knowledge of species, genera, or biochemical characteristics, such as lipopolysaccharide (LPS), that would be required for detection by immunofluorescence experiments. We describe a complete protocol for 16S rRNA FISH from biopsy fixation to imaging by confocal microscopy. This protocol can be adapted for use in almost any type of tissue and represents a powerful tool for the unbiased visualization of clinically-relevant bacterial-host interactions in patient tissue. Furthermore, using species or genera-specific probes, this protocol can be adapted for the detection of specific bacterial pathogens within patient tissue.

This protocol is for the unbiased detection of tissue-associated bacteria in patient biopsies by 16S rRNA in situ hybridization and confocal microscopy.

Visualization of the interaction of bacteria with host mucosal surfaces and tissues can provide valuable insight into mechanisms of pathogenesis. While ...

Imaging the Gut with "CLARITY"

CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging compatible Tissue hYdrogel) has recently evolved as a valuable technique involving acrylamide embedding to delipidate tissue (without sectioning) and to preserve the 3-D tissue structure for immunostaining. The technique is highly relevant in imaging the dynamic gut environment where different cell types interact during homeostasis and disease states. This method optimized for the mouse gut is described here, which helps to trace cell types like epithelia, enteroendocrine, neurons, glia, and the neuronal projections into the epithelia or enteroendocrine cells that mediate microbial sensing or nutrient chemo sensing respectively. The gut tissue (1-1.5 cm) is fixed in 4% paraformaldehyde (PFA) in phosphate buffered saline (PBS) at 4 &#176;C overnight on day 1. On day 2, PFA is discarded, and the tissue is washed thrice with PBS. The tissue is hydrogel embedded to preserve its integrity by incubation in 4% hydrogel (acrylamide) solution in PBS (diluted from 30% ProtoGel) overnight at 4 &#176;C. On day 3, the tissue-hydrogel solution is incubated at 37&#160;&#176;C for 1 h to allow hydrogel polymerization. Tissue is then washed thrice gently with PBS to remove excess hydrogel. The subsequent step of delipidation (clearing) involves tissue incubation in sodium dodecyl sulfate (8% SDS in PBS) at 37 &#176;C for 2 days (days 4 &#38; 5) on a shaker at room temperature (RT). On day 6, the cleared tissue is thoroughly washed with PBS to remove SDS. Tissue can be immunostained by incubation in primary antibodies (diluted in 0.5% normal donkey serum in PBS containing 0.3% Triton X-100), overnight at 4&#176;C, and subsequent incubation in appropriate secondary Alexa Fluor antibodies for 1.5 h at RT, and nuclear staining with DAPI (1: 10000). The tissue is transferred onto a clean glass slide and mounted using VectaShield for confocal imaging.

We describe the protocol for passive CLARITY (PACT) staining of mouse intestine to enable visualization of subepithelial tissues, including neurons, glia and enteroendocrine cells (EEC) without tissue sectioning. The protocol involves hydrogel embedding of formaldehyde-fixed tissue, and subsequent delipidation using an anionic detergent to "clear" the tissue.

CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging compatible Tissue hYdrogel) has recently evolved as a valuable technique involving ...

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

Summary

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Chapters in this video

Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization

Co-culture of Living Microbiome with Microengineered Human Intestinal Villi in a Gut-on-a-Chip Microfluidic Device

Investigation of Microbial Cooperation via Imaging Mass Spectrometry Analysis of Bacterial Colonies Grown on Agar and in Tissue During Infection

Visualizing Bacteria in Nematodes using Fluorescent Microscopy

Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization

An Intestinal Gut Organ Culture System for Analyzing Host-Microbiota Interactions

Optical Photothermal Infrared-Fluorescence In Situ Hybridization (OPTIR-FISH)

RNA Fluorescence in situ Hybridization (FISH) to Visualize Microbial Colonization and Infection in Caenorhabditis elegans Intestines

Detection of Tissue-resident Bacteria in Bladder Biopsies by 16S rRNA Fluorescence In Situ Hybridization

Imaging the Gut with "CLARITY"