This work was supported by EU Marie Curie Fellowship (EU/300686-InfO) to S.B. and a Research Prize from the United European Gastroenterology Foundation to H.C. We would like to thank Harry Begthel, Jeroen Korving and the Hubrecht Imaging Center for technical assistance, Meritxell Huch for help with initial organoid culture and Yana Zavros for discussion.

1. Establishment of Gastric Organoid Culture
Note: This protocol can be used for the isolation of gastric glands from mouse or human tissue. It is advised to use tissue of approximately 1 cm&#178;. Human tissue can be obtained from gastric resections or biopsies.
<ol>
	<li>Preparation of Material 
	Note: The used basement matrix is Matrigel. Keep the basement matrix on ice at all times. Store the basement matrix at -20 &#176;C and thaw on ice before use. Basal medium refers to Advanced DMEM/F12 supplemented with HEPES; an appropriate glutamine source such as Glutamax and appropriate antibiotics such as 1x Primocin. The incubator used is a standard cell culture incubator (37 &#176;C, humidified atmosphere, 5% CO2)
	<ol>
		<li>Sterilize preparation utensils by autoclaving or using 100% isopropyl alcohol: sharp forceps, scissors, a scalpel and a glass microscopy slide.</li>
		<li>The day before isolation, place a 24 well cell culture plate in the incubator.</li>
		<li>Prepare the basement matrix according to manufacturers&#8217; recommendation. Prepare aliquots of 1 ml to avoid repeated freeze thaw cycles.</li>
		<li>Prepare 500 ml chelating buffer and cool on ice. Prepare 1x buffer from sterile distilled water with 5.6 mM Na2HPO4, 8.0 mM KH2PO4, 96.2 mM NaCl, 1.6 mM KCl, 43.4 mM sucrose, 54.9 mM D-sorbitol, 0.5 mM DL-dithiothreitol (CAUTION), pH 7. If planning several isolations, prepare a 5x concentrated solution without the DL-dithiothreitol. Sterile filter the buffer. Before isolation, dilute the 5x buffer with sterile water to 1x and add DL-dithiothreitol just before isolation.</li>
		<li>Prepare and dilute all growth factors according to manufacturers&#8217; recommendations. Use small-sized aliquots and avoid freeze-thaw cycles. Functional growth factors are crucial for the results.</li>
		<li>Cool basal medium on ice and cool the centrifuge to 4 &#176;C.</li>
		<li>Warm another aliquot of basal medium to 37 &#176;C.</li>
	</ol>
	</li>
	<li>Isolation of Glands
	<ol>
		<li>Collect approximately 1 cm&#178; of tissue in ice cold basal medium. Keep on ice until preparation. While it is preferable to process tissue as soon as possible, store tissue in medium on ice if necessary.</li>
		<li>Place the tissue in a 10 cm Petri dish and cover it with cold 1x chelation buffer. Wash by gently moving back and forth.</li>
		<li>Place the tissue in a dry 10 cm Petri dish. Using forceps, carefully remove the mucus as well as the muscle layer under a stereomicroscope. Wash the tissue in cold 1x chelating buffer by gently moving back and forth.</li>
		<li>Place 1 cm2 tissue on a new, dry 10 cm Petri dish. Using scissors cut it into 20-50 small pieces of approximately 2-5 mm&#178; size.</li>
		<li>Using forceps, place all pieces into a 50 ml tube.</li>
		<li>Take a sterile 10 ml plastic pipette. Wet the pipette in 1x chelating buffer. Keep using this same pipette throughout the procedure.</li>
		<li>Add 10 ml cold 1x chelating buffer to the 50 ml tube. Wash the pieces by vigorously pipetting up and down 10 times. Let the pieces settle. Remove the supernatant.</li>
		<li>Repeat washing (step 1.2.7) until the supernatant is clear. This takes approximately 50-100 ml of 1x chelating buffer for 1 cm&#178; of human tissue.</li>
		<li>Incubate the tissue pieces in 20 ml 1x chelating buffer supplemented with 10 mM EDTA at RT for 10 min with gentle inverting every 2 min. 
		Note: Time and temperature of this incubation can be optimized for either speed and/or preservation of glandular architecture. They can range from several hours incubation at 4 &#176;C on a rolling platform to 5 min at 37 &#176;C in a shaker with 200 rpm. Good starting points for mouse stomach are 30 min at 4 &#176;C on a rolling platform and for human stomach, 10 min at RT.</li>
		<li>Pipette once gently up and down using the 10 ml pipette. Allow the pieces to settle. Discard the supernatant.</li>
		<li>Using the pipette, transfer the pieces to a clean 10 cm Petri dish. Remove the liquid.</li>
		<li>Place a glass microscopy slide on top of the tissue pieces. Observe the intact tissue under an inverted microscope for cell culture with 10X magnification.</li>
		<li>Apply pressure to the glass slide and Petri dish. Hold both in hand (with sterile gloves) and pressing the glass with the thumb. The rim of the tissue will appear cloudy indicating that glands are released out of the tissue.</li>
		<li>Observe the released glands under an inverted microscope for cell culture with 10X magnification.</li>
		<li>Collect glands and tissue in 30 ml cold basal medium. Let large tissue fragments settle.</li>
		<li>Collect the supernatant containing glands in two 15 ml tubes.</li>
		<li>Centrifuge 5 min at 200 x g and 4 &#176;C. Discard supernatant. The pellet contains isolated glands. Keep them on ice.</li>
	</ol>
	</li>
	<li>Seeding of Glands
	<ol>
		<li>For the seeding, keep basement matrix ice-cold at all times, so it will stay liquid.</li>
		<li>Alternative 1: Seed 6 wells of a dilution row.
		<ol>
			<li>Suspend the pellet in 60 &#181;l of basement matrix.</li>
			<li>Prepare 5 sterile 1.5 ml tubes on ice with each containing 50 &#181;l of basement matrix. Transfer 10 &#181;l of glands/basement matrix suspension into the first 1.5 ml tube. Suspend the glands and transfer 10 &#181;l of this solution to the next 1.5 ml tube. Repeat for the next tubes.</li>
		</ol>
		</li>
		<li>Alternative 2: Seed a calculated amount of glands per well. Start with 100 glands per 50 &#181;l basement matrix in one well of a 24 well plate.
		<ol>
			<li>Carefully suspend the pelleted glands in 10 ml basal medium. Place 50 &#181;l on a clean 10 ml Petri dish. Count number of glands under an inverted microscope for cell culture with 10X magnification.</li>
			<li>Calculate the concentration of glands in the solution. Transfer the volume that contains 400 glands to a new 15 ml tube.</li>
			<li>Centrifuge 5 min at 200 x g and 4 &#176;C. Discard supernatant and keep the tube on ice. Add 200 &#181;l basement matrix and carefully resuspend. Keep on ice.</li>
		</ol>
		</li>
		<li>Take the 37 &#176;C warm 24-well plate (see step 1.1.2) from the incubator. Place one drop of 50 &#181;l glands in basement matrix in the center of the well. The drop will form a dome.</li>
		<li>Carefully transfer the plate back to the cell culture incubator. Let the basement matrix solidify 10 min.</li>
		<li>Prepare warm medium with all growth factors.
		<ol>
			<li>For human glands: Supplement the basal medium with the following growth factors for human gastric organoids: 50 ng/ml EGF, 10% noggin-conditioned medium, 10% R-spondin1&#8211;conditioned medium, 50% Wnt-conditioned medium, 200 ng/ml fibroblast growth factor (FGF)10, 1 nM gastrin, and 2 &#181;M TGFbeta inhibitor and 10 &#181;M rho-associated coiled coil forming protein serine/threonine kinase inhibitor (RHOKi).</li>
			<li>For murine glands: Supplement the basal medium with the following growth factors for mouse gastric organoids: 50 ng/ml EGF, 10% noggin-conditioned medium, 10% R-spondin1&#8211;conditioned medium, 50% Wnt-conditioned medium, 100 ng/ml FGF10, 10 nM gastrin, 0.5 mM TGFbeta inhibitor and 10 &#181;M RHOKi.</li>
		</ol>
		</li>
		<li>Take the plate from the incubator. Carefully add 500 &#181;l medium with all growth factors (1.3.6) to each well without disturbing the basement matrix. Place it back to the incubator.</li>
		<li>Refresh the medium 3 times per week (every 2-3 days). For refreshing medium, remove the old medium with leaving the drop of basement matrix intact. Carefully add fresh, warm medium with all growth factors. Do not add RHOKi. Only add RHOKi directly after seeding of glands or after splitting of the organoids (step 2).</li>
	</ol>
	</li>
</ol>
2. Passage of Gastric Organoid Culture Before Microinjection.
Note: Every type of organoid culture has its own doubling time. Mouse intestinal as well as gastric cultures are usually split 1:5 every 5-7 days. Human intestinal cultures are split 1:5 every 10-12 days. Human gastric cultures are split 1:5 every 14 days. If initiated from single cells, human gastric organoids may also take 20 days to form properly. It is a good sign if budding structures surround the central lumen. In this protocol, organoids are split in 4 well plates for microinjection. Maintenance of organoids follows the same protocol, but can use any other cell culture plate, such as standard 24 well cell culture plates.
<ol>
	<li>Preparation of Material
	<ol>
		<li>Autoclave Pasteur pipettes.</li>
		<li>The day before passage, place a 4 well cell culture plate in the incubator at 37 &#176;C. The 4 well plates have low edges and allow micromanipulation.</li>
		<li>Prepare the basement matrix according to manufacturers&#8217; recommendation. On the day of passaging, thaw basement matrix on ice.</li>
		<li>Prepare and dilute all growth factors according to manufacturers&#8217; recommendations.</li>
		<li>Cool basal medium on ice and cool the centrifuge to 4 &#176;C.</li>
	</ol>
	</li>
	<li>Passage of Organoid Cultures
	<ol>
		<li>Take the plate with the organoids from the incubator. Remove medium from one well.</li>
		<li>Add 1 ml of cold basal medium to the basement matrix in the well. Using a 1 ml micropipette, vigorously pipette up and down until the basement matrix is broken up. Transfer to a 15 ml tube. Place on ice.</li>
		<li>Take a glass Pasteur pipette and a fire source such as a Bunsen burner.
		<ol>
			<li>Hold the tip of the pipette into the fire until the opening of the tip has narrowed from 1.5 mm to about 0.5 mm (Figure 1). Let the pipette cool to RT.</li>
			<li>Wet the pipette in basal medium. An optimally narrowed pipette will take up the medium visibly slower than an un-narrowed pipette, but it will still allow pipetting well.</li>
		</ol>
		</li>
		<li>Take up organoids in the pipette and vigorously pipette 10x up and down. The breaking of the organoids can be observed by eye.</li>
		<li>Add 9 ml of cold basal medium and centrifuge for 5 min at 200 x g and 4 &#176;C.</li>
		<li>Carefully discard all supernatant. Suspend the pellet in 250 &#181;l basement matrix. Keep on ice.</li>
		<li>Take the 37 &#176;C warm 4 well culture plate and place a drop of 50 &#181;l organoids/basement matrix in each well.</li>
		<li>Transfer the plate carefully back to the incubator. Let the basement matrix solidify at 37 &#176;C for 10 min.</li>
		<li>Prepare appropriate medium for either mouse or human organoids as listed in step 1.3.6.</li>
		<li>Take the plate from the incubator and overlay each basement matrix drop with 500 &#181;l medium.</li>
		<li>Transfer the plate to the incubator.</li>
		<li>Refresh the medium 3 times per week every 2-3 days (see 1.3.8.).</li>
		<li>For freezing of organoids, mechanically disrupt organoids as described for splitting in this protocol (Steps 2.2.1-2.2.5.). Suspend the organoid fragments in 500 ml&#160;freezing medium and freeze to -80 &#176;C using cryotubes and a freezing container. For long-term storage, transfer the tubes to liquid nitrogen.</li>
		<li>For thawing of organoids, prepare the culture plate, basement matrix, growth factors, cold and warm medium as outlined in steps 1.1.2, 1.1.3., 1.1.5., 1.1.6., 1.1.7. Warm the frozen vial using a water bath, and transfer cells immediately after thawing to a 15 ml tube with 10 ml cold basal medium. Centrifuge and plate the cells as outlined in 2.2.5 to 2.2.12. 
		Note: Microinjection of organoids is laborious, but allows the unique possibility to study interaction in 3D.</li>
		<li>If 3D studies are not needed, seed organoids in two dimensions. For this, disrupt the organoids as laid out in steps 2.2.1 to 2.2.6. Add 2,250 &#181;l cold medium with all growth factors to 250 &#181;l of basement matrix with organoid fragments.
		<ol>
			<li>Seed in 5 wells of a 24 well plate with 500 &#181;l per well. Change medium 3 times a week, with carefully replacing the upper 400 &#181;l only, to keep the basement matrix at the bottom of the plate undisturbed. 
			Note: Organoids will attach to the cell culture plate and expand in 2D. Electron microscopy has shown that the apical side of the cells faces the medium in the well (data not shown).</li>
			<li>Before infection, exchange all medium including basement matrix, to allow bacteria to attach to the cells. A similar protocol has also been described for infection with H. pylori14. 2D cell layers may contain not all cell types that are present in 3D organoids.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
3. Microinjection of Organoid Culture.
Note: This protocol can be used to microinject bacteria into organoids. It may be helpful to start the injection with organoids that are more permissive to microinjection. For example, mouse gastric organoids can grow into very large cystic organoids that are easy to target.
<ol>
	<li>Preparation of Material
	<ol>
		<li>Pull a glass capillary into two injection needles using a micropipette puller, according to manufacturers&#8217; recommendation. The micropipette puller will heat the glass capillary in the middle and will pull the capillary into two parts, thereby generating two glass needles. It is practical to pull several needles and store them in a clean petri dish.</li>
		<li>To allow bacterial infection, remove the antibiotics from all media for at least 3 medium changes (=one week). This will dilute antibiotics from basement matrix. If using a bacterial strain that is resistant to a specific antibiotic, add this specific antibiotic to minimize chances for contamination.</li>
		<li>Prepare the work bench for microinjections. For work at different biosafety levels it may be necessary to place a stereomicroscope inside a sterile bench. In this protocol, inject H. pylori under biosafety level 2 conditions under a stereomicroscope inside a sterile bench.</li>
		<li>Culture the bacteria according to standard protocols13,23.</li>
		<li>To estimate the multiplicity of infection (MOI), estimate two parameters: The number of bacteria and the number of cells per organoid as outlined below. The MOI can correlate with results, for example with hosts IL-8 mRNA expression13.
		<ol>
			<li>To calculate the bacterial density in the infection solution, first establish the standard curve of optical density and colony forming units (CFU) according to standard protocols24. An optical density of 0.1 at 550 nm should yield approximately 107&#160;CFU/ml.</li>
			<li>To estimate the number of cells per organoid, count number of organoids in 1 well. Disrupt organoids as outlined in steps 2.2.1-2.2.4. After centrifugation 5 min at 200 x g and 4 &#176;C, add 1 ml of enzymatic dissociation solution and resuspend.
			<ol>
				<li>Incubate at 37 &#176;C with repeated shaking for 5-10 min. Determine whether the cells have dissociated into single cells under the microscope (inverted microscope such as Leica DMIL at 10X magnification). If necessary prolong the incubation.</li>
				<li>Count cells per organoid using a hemocytometer and calculate the number of cells per organoid. Human gastric organoids with a diameter of about 200 &#181;m have approximately 4,000 cells. Injection of 0.2 &#181;l of a bacterial solution with 1 x 109 bacteria per ml results in an approximate MOI of 50.</li>
			</ol>
			</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Injection of Organoids. 
	Note: For microinjection, the glass needle is stabilized in a holder, which can be maneuvered in 3 dimensions by a micromanipulator. Organoids remain within the basement matrix within the well. Due to size and positioning in the well, not all organoids are equally amenable to injection. Usually, the 30 largest organoids in one well can be targeted in 5 min.
	<ol>
		<li>Harvest bacteria and wash them in basal medium according to standard protocols24.</li>
		<li>Calculate the number of bacteria per ml according to the optical density (see step 3.1.5.1). Dilute the bacteria to 1 x 109 bacteria per ml&#160;in basal medium.</li>
		<li>Take a glass needle. Using forceps break the tip so that the opening will be approximately 10 &#181;m wide.</li>
		<li>Insert the needle into the injection holder and fix it to the micromanipulator.</li>
		<li>Take up approximately 10 &#181;l bacterial solution into the needle.</li>
		<li>Place a 4 well plate with low edges containing organoid cultures under the stereomicroscope.</li>
		<li>Navigating with the micromanipulator, target a single organoids with the needle. Position the needle close to the organoid and then insert the needle into the organoid with one swift movement. Inject approximately 0.2 &#181;l bacterial solution into each organoid using the microinjector.</li>
	</ol>
	</li>
	<li>Harvest Organoids for Any Analysis.
	<ol>
		<li>As example, fix organoids after 4 hr. Remove supernatant and add 1 ml 2% formaldehyde and incubate 20 min at RT or O/N at 4 &#176;C. Organoids can be processed for immunohistochemistry according to standard procedures25.</li>
	</ol>
	</li>
</ol>

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R., 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=Identification+of+multipotent+luminal+progenitor+cells+in+human+prostate+organoid+cultures.">Identification of multipotent luminal progenitor cells in human prostate organoid cultures.</a> Cell. 159 (1), 163-175 (2014).</li><li>Bartfeld, S., 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=High-throughput+and+single-cell+imaging+of+NF-kappaB+oscillations+using+monoclonal+cell+lines.">High-throughput and single-cell imaging of NF-kappaB oscillations using monoclonal cell lines.</a> BMC cell. 11, 21 (2010).</li><li>Blanchard, T. G., Nedrud, J. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laboratory+Maintenance+of+Helicobacter+Species.">Laboratory Maintenance of Helicobacter Species.</a> Curr Protoc Microbiol. , (2006).</li><li>Van Es, J. H., de Geest, N., van de Born, M., Clevers, H., Hassan, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intestinal+stem+cells+lacking+the+Math1+tumour+suppressor+are+refractory+to+Notch+inhibitors.">Intestinal stem cells lacking the Math1 tumour suppressor are refractory to Notch inhibitors.</a> Nat Commun. 1 (2), 1-5 (2010).</li><li>Andersson-Rolf, A., Fink, J., Mustata, R. C., Koo, B. -. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Video+Protocol+of+Retroviral+Infection+in+Primary+Intestinal+Organoid+Culture.">A Video Protocol of Retroviral Infection in Primary Intestinal Organoid Culture.</a> J Vis Exp. (90), (2014).</li><li>Stange, D. E., Koo, B. -. K., 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=Differentiated+Troy++Chief+Cells+Act+as+Reserve+Stem+Cells+to+Generate+All+Lineages+of+the+Stomach+Epithelium.">Differentiated Troy+ Chief Cells Act as Reserve Stem Cells to Generate All Lineages of the Stomach Epithelium.</a> Cell. 155 (2), 357-368 (2013).</li><li>Van de Wetering, M., Sancho, E., 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=The+beta-catenin/TCF-4+complex+imposes+a+crypt+progenitor+phenotype+on+colorectal+cancer+cells.">The beta-catenin/TCF-4 complex imposes a crypt progenitor phenotype on colorectal cancer cells.</a> Cell. 111 (2), 241-250 (2002).</li><li>Schumacher, M. A., Aihara, E., 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=The+use+of+murine-derived+fundic+organoids+in+studies+of+gastric+physiology.">The use of murine-derived fundic organoids in studies of gastric physiology.</a> Journal Physiol. 593 (8), 1809-1827 (2015).</li><li>Schwank, G., Andersson-Rolf, A., Koo, B. -. K., Sasaki, N., Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+of+BAC+Transgenic+Epithelial+Organoids.">Generation of BAC Transgenic Epithelial Organoids.</a> PLoS ONE. 8 (10), e76871 (2013).</li><li>Koo, B. -. K., 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=Controlled+gene+expression+in+primary+Lgr5+organoid+cultures.">Controlled gene expression in primary Lgr5 organoid cultures.</a> Nat Meth. 9 (1), 81-83 (2012).</li><li>Schwank, G., 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=Functional+repair+of+CFTR+by+CRISPR/Cas9+in+intestinal+stem+cell+organoids+of+cystic+fibrosis+patients.">Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients.</a> Cell Stem Cell. 13 (6), 653-658 (2013).</li><li>Li, V. S. W., Ng, S. S., 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=Wnt+Signaling+through+Inhibition+of+&#946;-Catenin+Degradation+in+an+Intact+Axin1+Complex.">Wnt Signaling through Inhibition of &#946;-Catenin Degradation in an Intact Axin1 Complex.</a> Cell. 149 (6), 1245-1256 (2012).</li><li>Van de Wetering, M., 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=Prospective+derivation+of+a+'Living+Organoid+Biobank'+of+colorectal+cancer+patients.">Prospective derivation of a 'Living Organoid Biobank' of colorectal cancer patients.</a> Cell. 161 (4), 933-945 (2015).</li></ol>

Hans Clevers is an inventor on several patents for organoid culture. Otherwise the authors have nothing to disclose.

This protocol describes the use of ever-expanding, untransformed primary organoids from adult stem cells for infection biology. Critical steps are i) the isolation of viable glands, ii) expansion of organoids and iii) the microinjection. Below are some suggestions for modifications, troubleshooting and technical considerations. 
Compared to other isolation methods, which use vigorous shaking or pipetting to release glands and can be equally successful, the technique presented here has the adva...

The study of pathogens relies on adequate model systems to mimic the in vivo infection. For some infective agents, adequate model systems are lacking while some of the used systems are far from optimal. One example is the gastric bacterium&#160;Helicobacter pylori (H. pylori), which is causally related to development of gastric cancer. Yet in absence of a more suitable cell culture system, many studies that aim to analyze the molecular mechanisms underlying cancer development use cancer cell lines, which represent the endpoint of the cancerous cascade. Primary, non-transformed cells would be a better model for these studies. However, primary cells are only available from a small number of donors and cannot be cultured over longer periods of time. In recent years, stem cell research has made significant progress to provide new sources for primary cell cultures for the study of infection biology.
Cultures from three stem cell sources have been used: Embryonic stem cells (ESC), induced pluripotent stem cells (iPSC) or adult stem cells. They have been used to model infections with viruses, such as Cytomegalovirus1,2 or Hepatitis C Virus3&#8211;7, parasites, such as Plasmodium falciparum8 or Toxoplasma gondii9, and bacteria, such as Bacterioides thetaiotaomicron10 or Salmonella enterica11. Most recently, several approaches have been published to model infection with H. pylori with organoids derived from ESC or iPS cells12, mouse adult stem cells21,22 or human adult stem cells13&#8211;15.
The development of organoid cultures from adult stem cells originated from a study, in which single stem cells isolated from murine intestinal epithelium were seeded into a 3-dimensional matrix and embedded in medium that mimicked the environment of the intestinal stem cells containing EGF as mitogen, R-spondin to enhance Wnt signalling and Noggin to inhibit bone morphogenic protein (BMP) signalling16. Notably these cultures do not require co-culture with mesenchymal cells. In these conditions, the stem cells proliferate and form small structures with domains harboring cells of the intestinal crypts, and domains that contain the cells of the intestinal villus. The organoids thus self-organize to mimic the in vivo situation. Today, adult stem cells from many murine and humane tissues can be grown in vitro and self-organize into organoids that resemble their in vivo counterpart, such as small intestine and colon17, stomach13,18, liver19,20, pancreas21 and prostate22.
Here we provide a video protocol to culture mouse or human gastric organoids from adult stem cells and microinject them with H. pylori. This protocol is based on previous reports13,18. This method can be adapted for culturing and infecting other organoid cultures such as intestinal organoids.

<table><tbody><tr><td>&lt;strong&gt;Medium&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>HEPES</td><td>Invitrogen</td><td>15630-056</td><td></td></tr><tr><td>Advanced DMEM/F12</td><td>Invitrogen</td><td>12634-028</td><td></td></tr><tr><td>Matrigel, GFR, phenol free</td><td>BD</td><td>356231</td><td></td></tr><tr><td>GlutaMAX</td><td>Invitrogen</td><td>35050-079</td><td>Stock concentration 200 mM, final concentration 2 mM</td></tr><tr><td>B27</td><td>Invitrogen</td><td>17504-044</td><td>Stock concentration 50 x, final concentration 1x</td></tr><tr><td>N-Acetylcysteine</td><td>Sigma-Aldrich</td><td>A9165-5G</td><td>Stock concentration 500 mM, final concentration 1 mM</td></tr><tr><td>Murine recombinant EGF</td><td>Invitrogen</td><td>PMG8043</td><td>Stock concentration 500 &amp;micro;g/ml, final concentration 50 ng/ml</td></tr><tr><td>Human recombinant FGF10</td><td>Peprotech</td><td>100-26</td><td>Stock concentration 100 &amp;micro;g/ml, final concentration 200 ng/ml</td></tr><tr><td>TGF&amp;beta;i A-83-01</td><td>Tocris</td><td>2939</td><td>Stock concentration 500 &amp;micro;M, final concentration 2 &amp;micro;M&amp;nbsp;</td></tr><tr><td>Nicotinamide</td><td>Sigma-Aldrich</td><td>N0636</td><td>Stock concentration 1 M, final concentration 10 mM&amp;nbsp;</td></tr><tr><td>[Leu15]-Gastrin</td><td>Sigma-Aldrich</td><td>G9145</td><td>Stock concentration 100 &amp;micro;M, final concentration 1 nM</td></tr><tr><td>RHOKi Y-27632</td><td>Sigma-Aldrich</td><td>Y0503</td><td>Stock concentration 10 mM, final concentration 10 &amp;micro;M</td></tr><tr><td>Wnt3A conditioned medium</td><td></td><td></td><td>Stable cell line generated in the Clevers Lab. Final concentration 50%. Cells can be obtained from Hans Clevers.</td></tr><tr><td>R-spondin1 conditioned medium</td><td></td><td></td><td>Stable cell line generated in the Kuo Lab. Final concentration 10%. Cell line can be obtained from Calvin Kuo, Stanford.</td></tr><tr><td>Noggin conditioned medium</td><td></td><td></td><td>Stable cell line generated in the Clevers Lab. Final concentration 10%. Cells can be obtained from Hans Clevers.</td></tr><tr><td>R-spondin3</td><td>R&amp;amp;D</td><td>3500-RS/CF</td><td>Alternative source for R-spondin. This has been tested on human intestine organoids (1 &amp;micro;g/ml), but not yet on gastric organoids.</td></tr><tr><td>Noggin</td><td>Peprotech</td><td>120-10</td><td>Alternative source for noggin. This has been tested on human intestine organoids (100 ng/ml), but not yet on gastric organoids.</td></tr><tr><td>TrypLE express</td><td>Life Technologies</td><td>12605036</td><td>Enzymatic dissociation solution&amp;nbsp;</td></tr><tr><td>CoolCell&amp;reg; Alcohol-free Cell Freezing Containers</td><td>biocision</td><td>BCS-405</td><td></td></tr><tr><td>Recovery Cell Culture Freezing Medium</td><td>Invitrogen</td><td>12648-010</td><td></td></tr><tr><td>&lt;strong&gt;Antibiotics&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Primocin</td><td>Invivogen</td><td>ant-pm-1</td><td>An antibiotics composition agains bacteria and fungi. It is helpful after initiation of a culture. For long term culture you can switch to other antibiotics or none.</td></tr><tr><td>Penicillin/Streptomycin</td><td>Invitrogen</td><td>15140-122</td><td>Stock concentration 10,000/10,000 U/ml, final concentration 100/100 U/ml. Can be used alternatively to Primocin in long term culture.</td></tr><tr><td>&lt;strong&gt;Other&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Tweezers</td><td>Neolabs</td><td>2-1033</td><td>Tweezers with fine tips are helpful for the removal of muscle layer from the tissue.</td></tr><tr><td>4 Well Multidishes</td><td>Thermo Scientific</td><td>144444</td><td>You can use other Multidishes. These were particularly helpful for microinjections because they have a low outer rim and allow more mobility for the manipulator.</td></tr><tr><td>Micromanipulator</td><td>Narishige</td><td>M-152</td><td></td></tr><tr><td>Microinjector</td><td>Narishige</td><td>IM-5B</td><td></td></tr><tr><td>Stereomicroscope</td><td>Leica</td><td>MZ75</td><td></td></tr><tr><td>Workbench</td><td>Clean Air</td><td></td><td>Custom made to fit the stereomicroscope in ML2 condition</td></tr><tr><td>Capillaries</td><td>Harvard Apparatus</td><td>GC100T-10</td><td>1 mm outer diameter, 0.78 mm inner diameter.</td></tr><tr><td>Micropipette Puller</td><td>Sutter Instruments</td><td>Flaming Brown Micropipette Puller</td><td></td></tr><tr><td>anti Cag A antibody</td><td>Santa Cruz</td><td>sc-25766</td><td></td></tr></tbody></table>

organoids as model for infectious diseases: culture of human and murine stomach organoids and microinjection of helicobacter pylori

Recently infection biologists have employed stem cell derived cultures to answer the need for new and better models to study host-pathogen interactions. Three cellular sources have been used: Embryonic stem cells (ESC), induced pluripotent stem cells (iPSC) or adult stem cells. Here, culture of mouse and human gastric organoids derived from adult stem cells is described and used for infection with the gastric pathogen Helicobacter pylori. Human gastric glands are isolated from resection material, seeded in a basement matrix and embedded in medium containing growth factors epidermal growth factor (EGF), R-spondin, Noggin, Wnt, fibroblast growth factor (FGF) 10, gastrin and transforming growth factor (TGF) beta inhibitor. In these conditions, gastric glands grow into 3-dimensional organoids containing 4 lineages of the stomach. The organoids expand indefinitely and can be frozen and thawed similarly as cell lines. For infection studies, bacteria are microinjected into the lumen of the organoids. Infected organoids are processed for imaging. The described methods can be adapted to other organoids and infections with other bacteria, viruses or parasites. This allows the study of infection-induced changes in primary cells.

This protocol allows isolation of gastric glands (Figure 2). Glands are seeded into basement matrix, which solidifies as drop within a well, providing a 3 dimensional framework rich in laminin and collagen to allow the glands grow into organoids (Figure 3). Organoids typically start as small cysts and within 12-16 days, they expand into spheres with a diameter of 50-300 &#181;m (Figure 4). Some organoids will stay cystic, some will develop small buddings. The latter is u...

Watch this Scientific Journal Video about Organoids as Model for Infectious Diseases: Culture of Human and Murine Stomach Organoids and Microinjection of Helicobacter Pylori at JoVE.com

Organoids as Model for Infectious Diseases: Culture of Human and Murine Stomach Organoids and Microinjection of Helicobacter Pylori

Stem cell derived cultures harbor tremendous potential to model infectious diseases. Here, the culture of mouse and human gastric organoids derived from adult stem cells is described. The organoids are microinjected with the gastric pathogen Helicobacter pylori.

Recently infection biologists have employed stem cell derived cultures to answer the need for new and better models to study host-pathogen interactions. ...

organoids-as-model-for-infectious-diseases-culture-human-murine

Research

JoVE Journal

Immunology and Infection

35.2K Views.  University Medical Centre Utrecht. Stem cell derived cultures harbor tremendous potential to model infectious diseases. Here, the culture of mouse and human gastric organoids derived from adult stem cells is described. The organoids are microinjected with the gastric pathogen Helicobacter pylori.

Video: Organoids as Model for Infectious Diseases: Culture of Human and Murine Stomach Organoids and Microinjection of Helicobacter Pylori

Development of a Multicellular Three-dimensional Organotypic Model of the Human Intestinal Mucosa Grown Under Microgravity

Because cells growing in a three-dimensional (3-D) environment have the potential to bridge many gaps of cell cultivation in 2-D environments (e.g., flasks or dishes). In fact, it is widely recognized that cells grown in flasks or dishes tend to de-differentiate and lose specialized features of the tissues from which they were derived. Currently, there are mainly two types of 3-D culture systems where the cells are seeded into scaffolds mimicking the native extracellular matrix (ECM): (a) static models and (b) models using bioreactors. The first breakthrough was the static 3-D models. 3-D models using bioreactors such as the rotating-wall-vessel (RWV) bioreactors are a more recent development. The original concept of the RWV bioreactors was developed at NASA&#39;s Johnson Space Center in the early 1990s and is believed to overcome the limitations of static models such as the development of hypoxic, necrotic cores. The RWV bioreactors might circumvent this problem by providing fluid dynamics that allow the efficient diffusion of nutrients and oxygen. These bioreactors consist of a rotator base that serves to support and rotate two different formats of culture vessels that differ by their aeration source type: (1) Slow Turning Lateral Vessels (STLVs) with a co-axial oxygenator in the center, or (2) High Aspect Ratio Vessels (HARVs) with oxygenation via a flat, silicone rubber gas transfer membrane. These vessels allow efficient gas transfer while avoiding bubble formation and consequent turbulence. These conditions result in laminar flow and minimal shear force that models reduced gravity (microgravity) inside the culture vessel. Here we describe the development of a multicellular 3-D organotypic model of the human intestinal mucosa composed of an intestinal epithelial cell line and primary human lymphocytes, endothelial cells and fibroblasts cultured under microgravity provided by the RWV bioreactor.

Cells growing in a three-dimensional (3-D) environment represent a marked improvement over cell cultivation in 2-D environments (e.g., flasks or dishes). Here we describe the development of a multicellular 3-D organotypic model of the human intestinal mucosa cultured under microgravity provided by rotating-wall-vessel (RWV) bioreactors.

Because cells growing in a three-dimensional (3-D) environment have the potential to bridge many gaps of cell cultivation in 2-D environments (e.g., ...

Bioengineering

Mouse Models Of Helicobacter Infection And Gastric Pathologies

Helicobacter pylori is a gastric pathogen that is present in half of the global population and is a significant cause of morbidity and mortality in humans. Several mouse models of gastric Helicobacter infection have been developed to study the molecular and cellular mechanisms whereby H. pylori bacteria colonize the stomach of human hosts and cause disease. Herein, we describe protocols to: 1) prepare bacterial suspensions for the in vivo infection of mice via intragastric gavage; 2) determine bacterial colonization levels in mouse gastric tissues, by polymerase chain reaction (PCR) and viable counting; and 3) assess pathological changes, by histology. To establish Helicobacter infection in mice, specific pathogen-free (SPF) animals are first inoculated with suspensions (containing &#8805;105 colony-forming units, CFUs) of mouse-colonizing strains of either Helicobacter pylori or other gastric Helicobacter spp. from animals, such as Helicobacter felis. At the appropriate time-points post-infection, stomachs are excised and dissected sagittally into two equal tissue fragments, each comprising the antrum and body regions. One of these fragments is then used for either viable counting or DNA extraction, while the other is subjected to histological processing. Bacterial colonization and histopathological changes in the stomach may be assessed routinely in gastric tissue sections stained with Warthin-Starry, Giemsa or Haematoxylin and Eosin (H&#38;E) stains, as appropriate. Additional immunological analyses may also be undertaken by immunohistochemistry or immunofluorescence on mouse gastric tissue sections. The protocols described below are specifically designed to enable the assessment in mice of gastric pathologies resembling those in human-related H. pylori diseases, including inflammation, gland atrophy and lymphoid follicle formation. The inoculum preparation and intragastric gavage protocols may also be adapted to study the pathogenesis of other enteric human pathogens that colonize mice, such as Salmonella Typhimurium or Citrobacter rodentium.

Mouse Models Of Helicobacter Infection And Gastric Pathologies

Mice represent an invaluable in vivo model to study infection and diseases caused by gastrointestinal microorganisms. Here, we describe the methods used to study bacterial colonization and histopathological changes in mouse models of Helicobacter pylori-related disease.

Helicobacter pylori is a gastric pathogen that is present in half of the global population and is a significant cause of morbidity and mortality in ...

Using Human Induced Pluripotent Stem Cell-derived Intestinal Organoids to Study and Modify Epithelial Cell Protection Against Salmonella and Other Pathogens

The intestinal &#8216;organoid&#8217; (iHO) system, wherein 3-D structures representative of the epithelial lining of the human gut can be produced from human induced pluripotent stem cells (hiPSCs) and maintained in culture, provides an exciting opportunity to facilitate the modeling of the epithelial response to enteric infections. In vivo, intestinal epithelial cells (IECs) play a key role in regulating intestinal homeostasis and may directly inhibit pathogens, although the mechanisms by which this occurs are not fully elucidated. The cytokine interleukin-22 (IL-22) has been shown to play a role in the maintenance and defense of the gut epithelial barrier, including inducing a release of antimicrobial peptides and chemokines in response to infection.
We describe the differentiation of healthy control hiPSCs into iHOs via the addition of specific cytokine combinations to their culture medium before embedding them into a basement membrane matrix-based prointestinal culture system. Once embedded, the iHOs are grown in media supplemented with Noggin, R-spondin-1, epidermal growth factor (EGF), CHIR99021, prostaglandin E2, and Y-27632 dihydrochloride monohydrate. Weekly passages by manual disruption of the iHO ultrastructure lead to the formation of budded iHOs, with some exhibiting a crypt/villus structure. All iHOs demonstrate a differentiated epithelium consisting of goblet cells, enteroendocrine cells, Paneth cells, and polarized enterocytes, which can be confirmed via immunostaining for specific markers of each cell subset, transmission electron microscopy (TEM), and quantitative PCR (qPCR). To model infection, Salmonella enterica serovar Typhimurium SL1344 are microinjected into the lumen of the iHOs and incubated for 90 min at 37 &#176;C, and a modified gentamicin protection assay is performed to identify the levels of intracellular bacterial invasion. Some iHOs are also pretreated with recombinant human IL-22 (rhIL-22) prior to infection to establish whether this cytokine is protective against Salmonella infection.

Using Human Induced Pluripotent Stem Cell-derived Intestinal Organoids to Study and Modify Epithelial Cell Protection Against Salmonella and Other Pathogens

Human induced pluripotent stem cell (hiPSC)-derived intestinal organoids offer exciting opportunities to model enteric diseases in vitro. We demonstrate the differentiation of hiPSCs into intestinal organoids (iHOs), the stimulation of these iHOs with cytokines, and the microinjection of Salmonella Typhimurium into the iHO lumen, enabling the study of an epithelial invasion by this pathogen.

The intestinal &#8216;organoid&#8217; (iHO) system, wherein 3-D structures representative of the epithelial lining of the human gut can be produced from ...

Combining Human Organoids and Organ-on-a-Chip Technology to Model Intestinal Region-Specific Functionality

The intestinal mucosa is a complex physical and biochemical barrier that fulfills a myriad of important functions. It enables the transport, absorption, and metabolism of nutrients and xenobiotics while facilitating a symbiotic relationship with microbiota and restricting the invasion of microorganisms. Functional interaction between various cell types and their physical and biochemical environment is vital to establish and maintain intestinal tissue homeostasis. Modeling these complex interactions and integrated intestinal physiology in vitro is a formidable goal with the potential to transform the way new therapeutic targets and drug candidates are discovered and developed.
Organoids and Organ-on-a-Chip technologies have recently been combined to generate human-relevant intestine chips suitable for studying the functional aspects of intestinal physiology and pathophysiology in vitro. Organoids derived from the biopsies of the small (duodenum) and large intestine are seeded into the top compartment of an organ chip and then successfully expand&#160;as monolayers while preserving the distinct cellular, molecular, and functional features of each intestinal region. Human intestine tissue-specific microvascular endothelial cells are incorporated in the bottom compartment of the organ chip to recreate the epithelial-endothelial interface. This novel platform facilitates luminal exposure to nutrients, drugs, and microorganisms, enabling studies of intestinal transport, permeability, and host-microbe interactions.
Here, a detailed protocol is provided for the establishment of intestine chips representing the human duodenum (duodenum chip) and colon (colon chip), and their subsequent culture under continuous flow and peristalsis-like deformations. We demonstrate methods for assessing drug metabolism and CYP3A4 induction in duodenum chip using prototypical inducers and substrates. Lastly, we provide a step-by-step procedure&#160;for the in vitro modeling of interferon gamma (IFN&#947;)-mediated barrier disruption (leaky gut syndrome) in a colon chip, including methods for evaluating the alteration of paracellular permeability, changes in cytokine secretion, and transcriptomic profiling of the cells within the chip.

Biopsy-derived intestinal organoids and organ-on-a-chips technologies are combined into a microphysiological platform to recapitulate region-specific intestinal functionality.

The intestinal mucosa is a complex physical and biochemical barrier that fulfills a myriad of important functions. It enables the transport, absorption, ...

Adapting Gastrointestinal Organoids for Pathogen Infection and Single Cell Sequencing under Biosafety Level 3 (BSL-3) Conditions

Human intestinal organoids constitute the best cellular model to study pathogen infections of the gastrointestinal tract. These organoids can be derived from all sections of the GI tract (gastric, jejunum, duodenum, ileum, colon, rectum) and, upon differentiation, contain most of the cell types that are naturally found in each individual section. For example, intestinal organoids contain nutrient-absorbing enterocytes, secretory cells (Goblet, Paneth, and enteroendocrine), stem cells, as well as all lineage-specific differentiation intermediates (e.g.,&#160;early or immature cell types). The greatest advantage in using gastrointestinal tract-derived organoids to study infectious diseases is the possibility of precisely identifying which cell type is targeted by the enteric pathogen and to address whether the different sections of the gastrointestinal tract and their specific cell types similarly respond to pathogen challenges. Over the past years, gastrointestinal models, as well as organoids from other tissues, have been employed to study viral tropism and the mechanisms of pathogenesis. However, utilizing all the advantages of using organoids when employing highly pathogenic viruses represents a technical challenge and requires strict biosafety considerations. Additionally, as organoids are often grown in three dimensions, the basolateral side of the cells is facing the outside of the organoid while their apical side is facing the inside (lumen) of the organoids. This organization poses a challenge for enteric pathogens as many enteric infections initiate from the apical/luminal side of the cells following ingestion. The following manuscript will provide a comprehensive protocol to prepare human intestinal organoids for infection with enteric pathogens by considering the infection side (apical vs. basolateral) to perform single-cell RNA sequencing to characterize cell-type-specific host/pathogen interactions. This method details the preparation of the organoids as well as the considerations needed to perform this work under biosafety level 3 (BSL-3) containment conditions.

Adapting Gastrointestinal Organoids for Pathogen Infection and Single Cell Sequencing under Biosafety Level 3 BSL-3 Conditions

This protocol describes how to infect human intestinal organoids from either their apical or basolateral side to characterize host/pathogen interactions at the single-cell level using single-cell RNA sequencing (scRNAseq) technology.

Human intestinal organoids constitute the best cellular model to study pathogen infections of the gastrointestinal tract. These organoids can be derived ...

In Vitro Apical-Out Enteroid Model of Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is a devastating disease affecting preterm infants, characterized by intestinal inflammation and necrosis. Enteroids have recently emerged as a promising system to model gastrointestinal pathologies. However, currently utilized methods for enteroid manipulation either lack access to the apical surface of the epithelium (three-dimensional [3D]) or are time-consuming and resource-intensive (two-dimensional [2D] monolayers). These methods often require additional steps, such as microinjection, for the model to become physiologically translatable. Here, we describe a physiologically relevant and inexpensive protocol for studying NEC in vitro by reversing enteroid polarity, resulting in the apical surface facing outward (apical-out). An immunofluorescent staining protocol to examine enteroid barrier integrity and junctional protein expression following exposure to tumor necrosis factor-alpha (TNF-&#945;) or lipopolysaccharide (LPS) under normoxic or hypoxic conditions is also provided. The viability of 3D apical-out enteroids exposed to normoxic or hypoxic LPS or TNF-&#945; for 24 h is also evaluated. Enteroids exposed to either LPS or TNF-&#945;, in combination with hypoxia, exhibited disruption of epithelial architecture, a loss of adherens junction protein expression, and a reduction in cell viability. This protocol describes a new apical-out NEC-in-a-dish model which presents a physiologically relevant and cost-effective platform to identify potential epithelial targets for NEC therapies and study the preterm intestinal response to therapeutics.

In Vitro Apical-Out Enteroid Model of Necrotizing Enterocolitis

This protocol describes an apical-out necrotizing enterocolitis (NEC)-in-a-dish model utilizing small intestinal enteroids with reversed polarity, allowing access to the apical surface. We provide an immunofluorescent staining protocol to detect NEC-related epithelial disruption and a method to determine the viability of apical-out enteroids subjected to the NEC-in-a-dish protocol.

Necrotizing enterocolitis (NEC) is a devastating disease affecting preterm infants, characterized by intestinal inflammation and necrosis. Enteroids have ...

Medicine

Culture Methods to Study Apical-Specific Interactions using Intestinal Organoid Models

The lining of the gut epithelium is made up of a simple layer of specialized epithelial cells that expose their apical side to the lumen and respond to external cues. Recent optimization of in vitro culture conditions allows for the re-creation of the intestinal stem cell niche and the development of advanced 3-dimensional (3D) culture systems that recapitulate the cell composition and the organization of the epithelium. Intestinal organoids embedded in an extracellular matrix (ECM) can be maintained for long-term and self-organize to generate a well-defined, polarized epithelium that encompasses an internal lumen and an external exposed basal side. This restrictive nature of the intestinal organoids presents challenges in accessing the apical surface of the epithelium in vitro and limits the investigation of biological mechanisms such as nutrient uptake and host-microbiota/host-pathogen interactions. Here, we describe two methods that facilitate access to the apical side of the organoid epithelium and support the differentiation of specific intestinal cell types. First, we show how ECM removal induces an inversion of the epithelial cell polarity and allows for the generation of apical-out 3D organoids. Second, we describe how to generate 2-dimensional (2D) monolayers from single cell suspensions derived from intestinal organoids, comprised of&#160;mature and differentiated cell types. These techniques provide novel tools to study apical-specific interactions of the epithelium with external cues in vitro and promote the use of organoids as a platform to facilitate precision medicine.

Here we present two protocols that allow the modeling of intestinal apical-specific interactions. Organoid-derived intestinal monolayers and Air-Liquid Interface (ALI) cultures facilitate the generation of well-differentiated epithelia accessible from both luminal and basolateral sides, whereas polarity-inverted intestinal organoids expose their apical side and are amenable to high throughput assays.

The lining of the gut epithelium is made up of a simple layer of specialized epithelial cells that expose their apical side to the lumen and respond to ...

Biology

A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis

The human body is colonized by at least the same number of microbial cells as it is composed of human cells, and most of these microorganisms are located in the gut. Though the interplay between the gut microbiome and the host has been extensively studied, how the gut microbiome interacts with the enteric nervous system remains largely unknown. To date, a physiologically representative in vitro model to study gut microbiome-nervous system interactions does not exist. 
To fill this gap, we further developed the human-microbial crosstalk (HuMiX) gut-on-chip model by introducing induced pluripotent stem cell-derived enteric neurons into the device. The resulting model, 'neuroHuMiX', allows for the co-culture of bacterial, epithelial, and neuronal cells across microfluidic channels, separated by semi-permeable membranes. Despite separation of the different cell types, the cells can communicate with each other through soluble factors, simultaneously providing an opportunity to study each cell type separately. This setup allows for first insights into how the gut microbiome affects the enteric neuronal cells. This is a critical first step in studying and understanding the human gut microbiome-nervous system axis.

neuroHuMiX is an advanced gut-on-a-chip model to study the interactions of bacterial, epithelial, and neuronal cells under proximal and representative co-culture conditions. This model allows unravelling of the molecular mechanisms underlying the communication between the gut microbiome and the nervous system.

The human body is colonized by at least the same number of microbial cells as it is composed of human cells, and most of these microorganisms are located ...

Generating Human Gastric Organoids from Upper Endoscopy Biopsies

Establishment and Characterization of Patient-derived Gastric Organoids from Biopsies of Benign Gastric Body and Antral Epithelium

Gastric patient-derived organoids (PDOs) offer a unique tool for studying gastric biology and pathology. Consequently, these PDOs find increasing use in a wide array of research applications. However, a shortage of published approaches exists for producing gastric PDOs from single-cell digests while maintaining a standardized initial cell seeding density. In this protocol, the emphasis is on the initiation of gastric organoids from isolated single cells and the provision of a method for passaging organoids through fragmentation. Importantly, the protocol demonstrates that a standardized approach to the initial cell seeding density consistently yields gastric organoids from benign biopsy tissue and allows for standardized quantification of organoid growth. Finally, evidence supports the novel observation that gastric PDOs display varying rates of formation and growth based on whether the organoids originate from biopsies of the body or antral regions of the stomach. Specifically, it is revealed that the use of antral biopsy tissue for organoid initiation results in a greater number of organoids formed and more rapid organoid growth over a 20-day period when compared to organoids generated from biopsies of the gastric body. The protocol described herein offers investigators a timely and reproducible method for successfully generating and working with gastric PDOs.

Author Spotlight: Generation of and Comparison Between Patient-Derived Gastric Organoids from Different Regions of the Stomach 

Gastric patient-derived organoids find increasing use in research, yet formal protocols for generating human gastric organoids from single-cell digests with standardized seeding density are lacking. This protocol presents a detailed method for reliably creating gastric organoids from biopsy tissue obtained during upper endoscopy.

Gastric patient-derived organoids (PDOs) offer a unique tool for studying gastric biology and pathology. Consequently, these PDOs find increasing use in a ...

Generation of Apical-Out Intestinal Organoids and Assessment of Organoid Proliferation Rate Using EdU-Labeling

Here, we describe the generation of floating cultures of apical-out intestinal organoids from hydrogel-embedded intestinal organoid cultures. Concurrently, floating basal-out organoid cultures are established for direct comparison between apical-out and basal-out organoids. Apical-out and basal-out organoids are subsequently subjected to the thymidine analog 5-ethynyl-2&#39;-deoxyuridine (EdU), which is integrated into the newly synthesized DNA during the S-phase of cell division. This incorporation into DNA can be&#160;visualized&#160;in morphologically intact organoids using laser scanning confocal microscopy. Cells labeled with Hoechst33342 and EdU are then quantified in a semiautomatic manner using image analysis software. Calculation of the percentage of EdU-positive cells of the total number of cells allows for the analysis of cell proliferation in three-dimensional (3D) organoids. Despite being used here for the analysis of proliferation in intestinal organoids, the protocol is applicable to the analysis of nucleus-specific stainings of various sorts in other organoids or two-dimensional cell cultures as well.

Here, we describe a protocol for generating apical-out intestinal organoids from standard matrix-embedded organoid cultures. It also outlines the subsequent incorporation of EdU into actively proliferating cells and the semiautomatic quantification of EdU-positive cells.

Organoids as Model for Infectious Diseases: Culture of Human and Murine Stomach Organoids and Microinjection of Helicobacter Pylori

Summary

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In Vitro Apical-Out Enteroid Model of Necrotizing Enterocolitis

Culture Methods to Study Apical-Specific Interactions using Intestinal Organoid Models

A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis

Establishment and Characterization of Patient-derived Gastric Organoids from Biopsies of Benign Gastric Body and Antral Epithelium

Generation of Apical-Out Intestinal Organoids and Assessment of Organoid Proliferation Rate Using EdU-Labeling