NKS is supported by NIH award K08 AI108690.

All studies were conducted under strict review and guidelines according to the Institutional Animal Care and Use Committee (IACUC) at Harvard Medical School, which meets the veterinary standards set by the American Association for Laboratory Animal Science (AALAS).
1. Horizontal Transmission of Bacteria via Co-housing (Optional)&#160;
<ol>
	<li>To minimize exogenous contamination (particularly if using gnotobiotic mice), practice aseptic technique while assembling sterile disposable cages, using food and water that have both been autoclaved.</li>
	<li>Use ear punches or tags to individually mark 6 week old C57BL/6 mice that harbor different microbiotas and house them in the same cage. Given that mice are coprophagic and eat fecal pellets from the cage floor, microbes will naturally be transmitted horizontally between the mice.</li>
	<li>Co-house mice for &#8805;1 week to allow time for microbial transfer and immunologic change prior to analysis.</li>
</ol>
2. Preparation of a Single Cell Suspension from the Small-intestinal Intraepithelial Layer and Lamina Propria
<ol>
	<li>Preparation of Solutions
	<ol>
		<li>Prepare extraction media (per small intestine): 30 ml RPMI + 93 &#181;l 5% (w/v) dithiothreitol (DTT) + 60 &#181;l 0.5 M EDTA + 500 &#181;l fetal bovine serum (FBS). Add the DTT immediately before use.</li>
		<li>Prepare digestion media (per small intestine): 25 ml RPMI + 12.5 mg dispase + 37.5 mg collagenase II + 300 &#181;l FBS. Add the dispase and collagenase immediately before use.</li>
		<li>For all incubations performed at 37 &#176;C, prewarm solutions to 37 &#176;C.</li>
	</ol>
	</li>
	<li>Euthanize the mouse by CO2 asphyxiation followed by cervical dislocation.</li>
	<li>Place the mouse dorsal side down and spray the abdomen with 70% ethanol. Use scissors to perform a laparotomy by sequentially cutting the skin and then peritoneal fascia along the ventral midline from the pubic symphysis to the xiphoid process, thus exposing the peritoneal cavity.</li>
	<li>Use scissors to separate the small intestine from the stomach by transecting the pyloric sphincter. Gently remove the small intestine from the peritoneum, teasing away the mesenteric fat.
	<ol>
		<li>To fully remove the small intestine, make a second cut at the ileo-cecal junction. Place the isolated small intestine into cold (i.e., 4 &#176;C) RPMI containing 10% FBS to maximize cell viability.</li>
	</ol>
	</li>
	<li>Gently remove large pieces of fat using curved forceps. Use caution to avoid tearing the intestinal tissue itself while trying to remove fat.</li>
	<li>To remove intestinal contents, gently flush intestines with 15 - 20 ml of cold PBS using an 18 G feeding needle affixed to a syringe.</li>
	<li>Use scissors to excise PPs, and place them into cold RPMI containing 5% FBS. PPs are located on the antimesenteric side of the small intestine and appear as a multi-lobulated white mass. Depending on the specific strain, a mouse typically has 8 - 12 PPs.</li>
	<li>Cut the small intestine into 3 - 4 inch segments.</li>
	<li>Remove residual fat by rolling each small-intestinal segment on a paper towel moistened with RPMI, using a dull scalpel to tease the fat away from the tissue.</li>
	<li>Turn the tissue inside out by cannulating the intestinal segments with curved forceps and grasping the distal end of the tissue. Then use a pair of straight forceps to gently remove the tissue segment from the curved forceps (beginning at the proximal end), resulting in the tissue being inverted.</li>
	<li>Place tissue segments in a cup containing 30 ml of extraction media and a stir bar. Secure the lid on the cup, and stir at 500 rpm for 15 min at 37 &#176;C; stirring should be vigorous but not turbulent.</li>
	<li>After incubation, use a steel strainer to separate tissue pieces from the epithelium-containing supernatant, which should appear cloudy. This supernatant contains intraepithelial lymphocytes that can be further analyzed, if desired, by proceeding to filtering the sample in steps 2.18 - 2.23.</li>
	<li>Manually agitate the tissue pieces in RPMI to wash away residual extraction media.</li>
	<li>Place tissue on a dry paper towel and flip it end over end several times to facilitate removal of residual mucus that was not liberated by the extraction medium.</li>
	<li>Place tissue fragments in a 1.5 ml tube with 600 &#181;l of digestion medium.</li>
	<li>Use scissors to mince the tissue until pieces no longer stick to the scissors and the solution appears homogenous. This step is critical to ensure complete enzymatic digestion of the tissue.</li>
	<li>Add the minced small intestine to a cup containing 25 ml of digestion media. Stir at 500 rpm for 30 min at 37 &#176;C. Halfway through the digestion (i.e., at 15 min), pipet up and down with a serological pipet to help break up any large chunks of tissue.</li>
	<li>Filter digested tissue (or epithelial layer from step 2.12 if processing IELs) through a 100 &#181;m cell strainer into a 50 ml tube. Rinse the strainer with 20 ml of RPMI containing 10% FBS.</li>
	<li>Centrifuge the filtered solution at 500 x g for 10 min at 4 &#176;C.</li>
	<li>Carefully decant supernatant and resuspend pellet in 1 ml of RPMI containing 10% FBS.</li>
	<li>Filter resuspended cells through a 40 &#181;m cell strainer into a 50 ml tube. Rinse strainer with 20 ml of RPMI containing 10% FBS.</li>
	<li>Centrifuge filtered solution at 500 x g for 10 min at 4 &#176;C.</li>
	<li>Carefully decant supernatant, and resuspend pellet in 1 ml of RPMI containing 2% FBS.</li>
</ol>
3. Preparation of a Single Cell Suspension from Peyer&#39;s Patches
<ol>
	<li>Transfer excised PPs to a cup with 25 ml of digestion media and a stir bar. Secure lid, and spin at 500 rpm for 10 min at 37 &#176;C.</li>
	<li>Filter digested PPs through a 40 &#181;m cell strainer into a 50 ml tube. If any clumps remain, press them through the strainer using the flat end of the plunger from a 1 ml syringe.</li>
	<li>Rinse strainer with 10 ml of RPMI containing 10% FBS.</li>
	<li>Centrifuge filtered solution at 500 x g for 10 min at 4 &#176;C.</li>
	<li>Carefully decant supernatant, and resuspend pellet in 1 ml of RPMI containing 2% FBS.</li>
</ol>
4. Surface Staining for Flow Cytometry
<ol>
	<li>Aliquot appropriate volume of cells (e.g., 200 &#181;l of LPLs) into a 96-well round-bottom plate.</li>
	<li>Centrifuge at 500 x g for 5 min at 4 &#176;C. Decant supernatant by inverting the plate.</li>
	<li>Resuspend cells in 90 &#181;l of RPMI containing 2% FBS and a 1:100 dilution of anti-CD16/32 (Fc block). Incubate for 10 min at 4 &#176;C.</li>
	<li>Add 10 &#181;l PBS. Centrifuge at 500 x g for 5 min at 4 &#176;C. Decant supernatant by inverting the plate.</li>
	<li>Resuspend cells in 250 &#181;l PBS. Centrifuge at 500 x g for 5 min at 4 &#176;C. Decant supernatant by inverting the plate.</li>
	<li>(Optional) Stain cells with viability dye, if desired, by following the manufacturer&#39;s protocol.</li>
	<li>Resuspend cells in 100 &#181;l 1% formalin to fix the cells. Incubate for 1 hr&#160;in the dark at 4 &#176;C.</li>
	<li>Add 200 &#181;l PBS. Centrifuge at 500 x g for 5 min at 4 &#176;C. Decant supernatant by inverting the plate.</li>
	<li>Resuspend cells in 250 &#181;l PBS. Centrifuge at 500 x g for 5 min at 4 &#176;C. Decant supernatant by inverting the plate.</li>
	<li>Resuspend cells in 200 &#181;l PBS. Analyze cells using a flow cytometer.</li>
</ol>

<ol>
	<li>Cummings, D. E., Overduin, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gastrointestinal+regulation+of+food+intake.">Gastrointestinal regulation of food intake.</a> J Clin Invest. 117 (1), 13-23 (2007).</li><li>Mowat, A. M., Agace, W. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regional+specialization+within+the+intestinal+immune+system.">Regional specialization within the intestinal immune system.</a> Nat Rev Immunol. 14 (10), 667-685 (2014).</li><li>Round, J. L., Mazmanian, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+gut+microbiota+shapes+intestinal+immune+responses+during+health+and+disease.">The gut microbiota shapes intestinal immune responses during health and disease.</a> Nat Rev Immunol. 9 (5), 313-323 (2009).</li><li>Sartor, R. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+influences+in+inflammatory+bowel+diseases.">Microbial influences in inflammatory bowel diseases.</a> Gastroenterology. 134 (2), 577-594 (2008).</li><li>Tlaskalova-Hogenova, H., 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=Commensal+bacteria+(normal+microflora),+mucosal+immunity+and+chronic+inflammatory+and+autoimmune+diseases.">Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases.</a> Immunol Lett. 93 (2-3), 97-108 (2004).</li><li>Wen, L., 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=Innate+immunity+and+intestinal+microbiota+in+the+development+of+Type+1+diabetes.">Innate immunity and intestinal microbiota in the development of Type 1 diabetes.</a> Nature. 455 (7216), 1109-1113 (2008).</li><li>Pabst, R., Russell, M. W., Brandtzaeg, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+distribution+of+lymphocytes+and+plasma+cells+and+the+role+of+the+gut.">Tissue distribution of lymphocytes and plasma cells and the role of the gut.</a> Trends Immunol. 29 (5), 206-208 (2008).</li><li>Surana, N. K., Kasper, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+yin+yang+of+bacterial+polysaccharides:+lessons+learned+from+B.+fragilis+PSA.">The yin yang of bacterial polysaccharides: lessons learned from B. fragilis PSA.</a> Immunol Rev. 245 (1), 13-26 (2012).</li><li>Surana, N. K., Kasper, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deciphering+the+tete-a-tete+between+the+microbiota+and+the+immune+system.">Deciphering the tete-a-tete between the microbiota and the immune system.</a> J Clin Invest. 124 (10), 4197-4203 (2014).</li><li>Gauguet, 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=Intestinal+microbiota+of+mice+influences+resistance+to+Staphylococcus+aureus+pneumonia.">Intestinal microbiota of mice influences resistance to Staphylococcus aureus pneumonia.</a> Infect Immun. , (2015).</li><li>Ochoa-Reparaz, J., 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=A+polysaccharide+from+the+human+commensal+Bacteroides+fragilis+protects+against+CNS+demyelinating+disease.">A polysaccharide from the human commensal Bacteroides fragilis protects against CNS demyelinating disease.</a> Mucosal Immunol. 3 (5), 487-495 (2010).</li><li>Wu, H. J., 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=Gut-residing+segmented+filamentous+bacteria+drive+autoimmune+arthritis+via+T+helper+17+cells.">Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells.</a> Immunity. 32 (6), 815-827 (2010).</li><li>Goodyear, A. W., Kumar, A., Dow, S., Ryan, E. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+of+murine+small+intestine+leukocyte+isolation+for+global+immune+phenotype+analysis.">Optimization of murine small intestine leukocyte isolation for global immune phenotype analysis.</a> J Immunol Methods. 405, 97-108 (2014).</li><li>Chung, H., 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=Gut+immune+maturation+depends+on+colonization+with+a+host-specific+microbiota.">Gut immune maturation depends on colonization with a host-specific microbiota.</a> Cell. 149 (7), 1578-1593 (2012).</li><li>Resendiz-Albor, A. A., Esquivel, R., Lopez-Revilla, R., Verdin, L., Moreno-Fierros, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Striking+phenotypic+and+functional+differences+in+lamina+propria+lymphocytes+from+the+large+and+small+intestine+of+mice.">Striking phenotypic and functional differences in lamina propria lymphocytes from the large and small intestine of mice.</a> Life Sci. 76 (24), 2783-2803 (2005).</li><li>Carrasco, 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=Comparison+of+lymphocyte+isolation+methods+for+endoscopic+biopsy+specimens+from+the+colonic+mucosa.">Comparison of lymphocyte isolation methods for endoscopic biopsy specimens from the colonic mucosa.</a> J Immunol Methods. 389 (1-2), 29-37 (2013).</li><li>Van Damme, N., 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=Chemical+agents+and+enzymes+used+for+the+extraction+of+gut+lymphocytes+influence+flow+cytometric+detection+of+T+cell+surface+markers.">Chemical agents and enzymes used for the extraction of gut lymphocytes influence flow cytometric detection of T cell surface markers.</a> J Immunol Methods. 236 (1-2), 27-35 (2000).</li></ol>

No conflicts of interest declared.

We present a protocol for the isolation and flow cytometric characterization of small-intestinal lymphocytes, including the LPLs, IELs, and lymphocytes in the PPs. For those interested in evaluating how changes in the microbiota affect the small-intestinal immune system, we detail the straightforward steps involved in the horizontal transmission of organisms between mice harboring different microbiotas. Although this protocol focuses on the small intestine, the procedure is the same for analysis of the large intestine, with the only difference being that there are no PPs to remove (although colonic patches are present, these are typically not grossly visible).
There are several key steps in achieving optimal isolation of lymphocytes from small-intestinal tissue. Meticulous removal of adipose tissue is absolutely critical to ensuring lymphocyte viability and optimal yield. Additionally, DTT is a crucial mucolytic used in the extraction of epithelial cells. Given its unstable nature, we suggest storing single-use aliquots of a 5% solution at &#8804;-20 &#176;C and not re-freezing any unused volume. Although EDTA is used in the extraction medium to aid in the removal of epithelial cells15, its presence &#8212;&#160;as well as excess FBS or mucus &#8212;&#160;during the digestion process can inhibit the collagenase. The concentration of collagenase used has been demonstrated to differentially affect surface marker expression and cell viability13,16,17. Moreover, depending on the surface marker of interest, it may be that a different formulation of collagenase (e.g., collagenase type I, II, VI, or VIII) is optimal13,17. Some empiric optimization may be required depending on the specific experimental question and, owing to lot-to-lot variation, the specific lot and relative activity level of collagenase. Furthermore, additional optimization may be required depending on the specific strain and age of mouse used. For example, the times listed here have been optimized for a ~6 week old C57BL/6 mouse; for a ~8 week old Swiss Webster mouse, the digestion time may be increased to 40 minutes.
In summary, we have provided a detailed protocol for the isolation of small-intestinal lymphocytes from the lamina propria, intraepithelial layer, and PPs. Once mastered, one can reasonably process 4 mice and have single cell suspensions ready for staining in ~4 hr. Although we describe the immediate staining of these cells for flow cytometric characterization, one can alternatively stimulate these cells to assess cytokine production, sort cells for transcriptional and/or proteomic analyses, or culture the cells to look at in vitro interactions with other cell types. Moreover, while we focused on the lymphocyte population, this protocol can also be used to examine myeloid cells. Taken together, this streamlined approach to isolating single cell populations from various intestinal compartments allows one to interrogate both how various factors (e.g., microbiota, dietary antigens) influence the ontogeny of the intestinal immune system and also how these cells may be relevant in extra-intestinal diseases.

The principal task of the small intestine is often considered to be the digestion and absorption of nutrients1. While this metabolic function is clearly essential, the small intestine has an equally significant role in protecting the host from the continual barrage of environmental antigens found within the lumen2. The intestinal tract separates the outside world (e.g., luminal antigens) from the internal environment of the host with an epithelial layer that is only a single cell layer thick. As such, the small-intestinal immune system has the formidable task of balancing its threshold for reactivity, allowing foreign antigens from the diet and commensal microbes to enter the mucosa with minimal, if any, immune response while mounting a robust response against invading pathogens and other &#34;harmful&#34; antigens. Excessive or inappropriate immune responses to these antigens can lead to pathologic disease (e.g., inflammatory bowel disease, type I diabetes, multiple sclerosis) and must be avoided3-6.
Overall, the gastrointestinal tract is thought to represent the largest immune organ in the body, containing over 70% of all antibody-secreting cells7. The small-intestinal immune system is comprised of 3 main compartments&#160;&#8212;&#160;the lamina propria (LP), the intraepithelial layer, and Peyer&#39;s patches (PPs) &#8212;&#160;that each contains a distinctive group of lymphocytes2. The LP lymphocytes (LPLs) are primarily TCR&#945;&#946;+ T cells with ~20% B cells; intraepithelial lymphocytes (IELs) contain very few B cells with more TCR&#947;&#948;+ T cells than TCR&#945;&#946;+ T cells; and PPs, which are secondary lymphoid organs embedded in the small-intestinal wall, contain ~80% B cells. Although each of these anatomical regions has slightly distinct functions and ontological bases, they function in a harmonized fashion to protect the host from pathogenic insults.
Furthermore, there is growing appreciation that the microbiota is a critical determinant for the development of the intestinal immune system, with increasing recognition of the cognate relationship between specific microbes and the ontogeny of particular cell lineages8,9. Moreover, given that education of the intestinal immune system affects immune responses in anatomically distant sites (e.g., arthritis, multiple sclerosis, pneumonia), it has become clear that development of the intestinal immune system is relevant to more disease processes than previously recognized10-12. As such, interest in quantitatively assessing the intestinal immune system has extended beyond host-pathogen interactions to now include host-commensal interactions and the pathogenesis of many systemic diseases as well.
Given the variability of current methods in the isolation of intestinal lymphocytes, a method that is optimized for yield, viability, and consistency while balancing the time required is increasingly critical. Protocols that involve Percoll gradients are time and labor intensive and potentially more prone to human error, leading to variable yield and viability13. Herein, we provide an optimized protocol for the isolation and characterization of lymphocytes from all 3 small-intestinal immune compartments. Additionally, given increasing interest in microbe-induced alterations in the mucosal immune system, we include steps that can be used to allow for the horizontal transmission of microorganisms between mice to assess how these changes quantitatively affect the intestinal immune system.

<table>
	<tbody>
		<tr>
			<td>Sterile Gloves</td>
			<td>Kimberly-Clark</td>
			<td>555092</td>
			<td></td>
		</tr>
		<tr>
			<td>sterile mouse cage</td>
			<td>Innovive</td>
			<td>MS2-AD</td>
			<td>contains lid, cage bottom, and alpha-dri bedding</td>
		</tr>
		<tr>
			<td>metal feeder</td>
			<td>Innovive</td>
			<td>M-FEED</td>
			<td></td>
		</tr>
		<tr>
			<td>water bottle</td>
			<td>Innovive</td>
			<td>M-WB-300</td>
			<td></td>
		</tr>
		<tr>
			<td>card holder</td>
			<td>Innovive</td>
			<td>CRD-HLD-H</td>
			<td></td>
		</tr>
		<tr>
			<td>autoclavable rodent chow (NIH-31M)</td>
			<td>Zeigler</td>
			<td>4131207530</td>
			<td></td>
		</tr>
		<tr>
			<td>RPMI medium 1640</td>
			<td>Gibco</td>
			<td>11875-119</td>
			<td></td>
		</tr>
		<tr>
			<td>dithiothreitol (DTT)</td>
			<td>Sigma</td>
			<td>D5545-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>0.5 M EDTA (pH 8.0)</td>
			<td>Ambion</td>
			<td>AM9262</td>
			<td></td>
		</tr>
		<tr>
			<td>fetal bovine serum (FBS)</td>
			<td>GemBio</td>
			<td>100-510</td>
			<td></td>
		</tr>
		<tr>
			<td>dispase II</td>
			<td>Invitrogen</td>
			<td>17105-041</td>
			<td>the concentration in the protocol is based on an activity level of 1.878 U/mg</td>
		</tr>
		<tr>
			<td>collagenase, type II&#160;</td>
			<td>Invitrogen</td>
			<td>17101-015</td>
			<td>the concentration in the protocol is based on an activity level of 245 U/mg</td>
		</tr>
		<tr>
			<td>dissecting scissors</td>
			<td>Roboz</td>
			<td>RS-5882</td>
			<td></td>
		</tr>
		<tr>
			<td>feeding needle (18 G, 2&#34; length)</td>
			<td>Roboz</td>
			<td>FN-7905</td>
			<td></td>
		</tr>
		<tr>
			<td>10 ml syringe</td>
			<td>BD</td>
			<td>305482</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Gibco</td>
			<td>14190-250</td>
			<td></td>
		</tr>
		<tr>
			<td>Disposable Scalpel (15 blade)</td>
			<td>Miltex</td>
			<td>4-415</td>
			<td></td>
		</tr>
		<tr>
			<td>curved forceps</td>
			<td>Roboz</td>
			<td>RS-5211</td>
			<td></td>
		</tr>
		<tr>
			<td>straight forceps</td>
			<td>Roboz</td>
			<td>RS-5132</td>
			<td></td>
		</tr>
		<tr>
			<td>multi-purpose cups, 120 ml</td>
			<td>VWR</td>
			<td>89009-662</td>
			<td></td>
		</tr>
		<tr>
			<td>stir bar</td>
			<td>VWR</td>
			<td>58949-062</td>
			<td></td>
		</tr>
		<tr>
			<td>multi-position stir plate, 9-position</td>
			<td>VWR</td>
			<td>12621-048</td>
			<td></td>
		</tr>
		<tr>
			<td>stainless steel conical strainer, 3 inch&#160;</td>
			<td>RSVP</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 ml tube</td>
			<td>Eppendorf</td>
			<td>0030 125.150</td>
			<td></td>
		</tr>
		<tr>
			<td>100 &#956;m cell strainer</td>
			<td>Falcon</td>
			<td>08-771-19</td>
			<td></td>
		</tr>
		<tr>
			<td>40 &#956;m cell strainer</td>
			<td>Falcon</td>
			<td>08-771-1</td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL conical tube</td>
			<td>Falcon</td>
			<td>352098</td>
			<td></td>
		</tr>
		<tr>
			<td>1 ml syringe</td>
			<td>BD</td>
			<td>309659</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plate, round-bottom</td>
			<td>Corning</td>
			<td>3799</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-mouse CD16/32 (Fc block)</td>
			<td>Biolegend</td>
			<td>101320</td>
			<td></td>
		</tr>
		<tr>
			<td>(optional) fixable viability dye eFluor 780</td>
			<td>eBiosciences</td>
			<td>65-0865-18</td>
			<td></td>
		</tr>
		<tr>
			<td>10% formalin, neutral buffered</td>
			<td>Thermo Scientific</td>
			<td>5725</td>
			<td></td>
		</tr>
	</tbody>
</table>

isolation and flow cytometric characterization of murine small intestinal lymphocytes

The intestines &#8212; which contain the largest number of immune cells of any organ in the body &#8212; are constantly exposed to foreign antigens, both microbial and dietary. Given an increasing understanding that these luminal antigens help shape the immune response and that education of immune cells within the intestine is critical for a number of systemic diseases, there has been increased interest in characterizing the intestinal immune system. However, many published protocols are arduous and time-consuming. We present here a simplified protocol for the isolation of lymphocytes from the small-intestinal lamina propria, intraepithelial layer, and Peyer&#39;s patches that is rapid, reproducible, and does not require laborious Percoll gradients. Although the protocol focuses on the small intestine, it is also suitable for analysis of the colon. Moreover, we highlight some aspects that may need additional optimization depending on the specific scientific question. This approach results in the isolation of large numbers of viable lymphocytes that can subsequently be used for flow cytometric analysis or alternate means of characterization.

Flow cytometric analysis of single cell suspensions of small-intestinal lymphocytes should yield a discrete population of cells that have similar forward and side scatter characteristics as splenocytes (Figures 1A and 1B). The lymphocytes may begin to die if the tissue is not maintained at 4 &#176;C during the initial stages of the isolation, resulting in the lymphocyte population having a lower forward scatter and being more difficult to separate from other epithelial and dead cells (Figure 1C). Moreover, if the small-intestinal tissue is not completely cleaned of its mesenteric fat, there is virtually a complete loss of lymphocytes (Figure 1D). These features illustrate how working quickly (i.e., not allowing the tissue to warm up) and paying attention to detail (i.e., removing even small amounts of mesenteric fat) is necessary to ensure sample quality. Typically, we obtain ~80% viability for small-intestinal LPLs (Figure 1E).
Figure 2A demonstrates how the composition of the microbiota can greatly affect the numbers of specific cell populations. As we have previously demonstrated, germ-free (GF) mice, which are completely devoid of any microorganisms, have a small-intestinal immune system that is markedly immature as compared to specific pathogen-free (SPF) mice, and colonization of GF mice with a normal mouse microbiota (MMb) results in restoration of the small-intestinal immune system14. In contrast, gnotobiotic mice harboring a normal human microbiota (HMb) &#8212;&#160;and that have a similar number and diversity of fecal bacteria as MMb mice &#8212;&#160;have a small-intestinal immune system that is indistinguishable from that of GF mice14.
Taking advantage of the coprophagic nature of mice, co-housing mice together represents a simple, yet powerful method for allowing horizontal transmission of organisms between mice. This approach allows one to test whether the resulting change in the microbiota affects the small-intestinal immune system. As an example, we demonstrated that co-housing HMb mice with MMb mice for 4 weeks resulted in the normalization of the number of CD3+ CD8+ T cells in the SI LP (Figure 2B)14. This result confirms that the differences between MMb and HMb mice observed in Figure 2A is due to variations in the microbiota between these mice &#8212;&#160;variations that are overcome by co-housing the mice together.
<img alt="Figure 1" src="/files/ftp_upload/54114/54114fig1.jpg" /> 
Figure 1. Intestinal Lymphocytes have FSC and SSC Characteristics Similar to Splenocytes. A - D. Dot plots depicting SSC and FSC for optimally prepared splenocytes (A) and small-intestinal lamina propria (SI LP) cells (B - D). B. The SI LP sample was prepared according to the described protocol. C. The intestinal tissue was intentionally allowed to warm to demonstrate that SI LP cells begin to have a lower FSC. D. The mesenteric fat was not cleaned off the small intestine prior to preparing single cells, resulting in the loss of a discernible SI LP lymphocyte population. E. The sample depicted in panel B was stained in step 4.7 with fixable viability dye (e.g., eFluor 780) according to the manufacturer&#39;s instructions. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54114/54114fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/54114/54114fig2.jpg" /> 
Figure 2. The Microbiota Impacts Maturation of the Small-intestinal Immune System. A. CD3+&#160;CD8+ T cells were enumerated in the SI LP of SPF, MMb, HMb, and GF mice. B. HMb mice were co-housed with MMb mice for 4 weeks prior to enumerating CD3+&#160;CD8+ T cells in the SI LP. MMb and HMb mice that were not co-housed were analyzed for comparison. Each data point represents an individual mouse, and the horizontal bars reflect the mean. NS, not significant; *, p &#60;0.05; **, p &#60;0.01; ***, p &#60;0.001. Figures are reproduced-with permission-from reference 14, with slight modification of B. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54114/54114fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

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Isolation and Flow Cytometric Characterization of Murine Small Intestinal Lymphocytes

There is growing interest in the quantitative characterization of intestinal lymphocytes owing to increasing recognition that these cells play a critical role in a variety of intestinal and systemic diseases. In this protocol, we describe how to isolate single cell populations from different small-intestinal compartments for subsequent flow cytometric characterization.

The intestines &#8212; which contain the largest number of immune cells of any organ in the body &#8212; are constantly exposed to foreign antigens, both ...

isolation-flow-cytometric-characterization-murine-small-intestinal

Nanyang Technological University

Research

JoVE Journal

Immunology and Infection

27.3K Views.  Boston Children’s Hospital. There is growing interest in the quantitative characterization of intestinal lymphocytes owing to increasing recognition that these cells play a critical role in a variety of intestinal and systemic diseases. In this protocol, we describe how to isolate single cell populations from different small-intestinal compartments for subsequent flow cytometric characterization. 

Video: Isolation and Flow Cytometric Characterization of Murine Small Intestinal Lymphocytes

Flow Cytometric Isolation of Primary Murine Type II Alveolar Epithelial Cells for Functional and Molecular Studies

Throughout the last years, the contribution of alveolar type II epithelial cells (AECII) to various aspects of immune regulation in the lung has been increasingly recognized. AECII have been shown to participate in cytokine production in inflamed airways and to even act as antigen-presenting cells in both infection and T-cell mediated autoimmunity 1-8. Therefore, they are especially interesting also in clinical contexts such as airway hyper-reactivity to foreign and self-antigens as well as infections that directly or indirectly target AECII. However, our understanding of the detailed immunologic functions served by alveolar type II epithelial cells in the healthy lung as well as in inflammation remains fragmentary. Many studies regarding AECII function are performed using mouse or human alveolar epithelial cell lines 9-12. Working with cell lines certainly offers a range of benefits, such as the availability of large numbers of cells for extensive analyses. However, we believe the use of primary murine AECII allows a better understanding of the role of this cell type in complex processes like infection or autoimmune inflammation. Primary murine AECII can be isolated directly from animals suffering from such respiratory conditions, meaning they have been subject to all additional extrinsic factors playing a role in the analyzed setting. As an example, viable AECII can be isolated from mice intranasally infected with influenza A virus, which primarily targets these cells for replication 13. Importantly, through ex vivo infection of AECII isolated from healthy mice, studies of the cellular responses mounted upon infection can be further extended.
Our protocol for the isolation of primary murine AECII is based on enzymatic digestion of the mouse lung followed by labeling of the resulting cell suspension with antibodies specific for CD11c, CD11b, F4/80, CD19, CD45 and CD16/CD32. Granular AECII are then identified as the unlabeled and sideward scatter high (SSChigh) cell population and are separated by fluorescence activated cell sorting 3.
In comparison to alternative methods of isolating primary epithelial cells from mouse lungs, our protocol for flow cytometric isolation of AECII by negative selection yields untouched, highly viable and pure AECII in relatively short time. Additionally, and in contrast to conventional methods of isolation by panning and depletion of lymphocytes via binding of antibody-coupled magnetic beads 14, 15, flow cytometric cell-sorting allows discrimination by means of cell size and granularity. Given that instrumentation for flow cytometric cell sorting is available, the described procedure can be applied at relatively low costs. Next to standard antibodies and enzymes for lung disintegration, no additional reagents such as magnetic beads are required. The isolated cells are suitable for a wide range of functional and molecular studies, which include in vitro culture and T-cell stimulation assays as well as transcriptome, proteome or secretome analyses 3, 4.

We describe the rapid isolation of primary murine type II alveolar epithelial cells (AECII) by flow cytometric negative selection. These AECII show high viability and purity and are suitable for a wide range of functional and molecular studies regarding their role in respiratory conditions such as autoimmune or infectious diseases.

Throughout  the last years, the contribution of alveolar type II epithelial cells (AECII)  to various aspects of immune regulation in the lung has been ...

Isolation of Lymphocytes from Mouse Genital Tract Mucosa

Mucosal surfaces, including in the gastrointestinal, urogenital, and respiratory tracts, provide portals of entry for pathogens, such as viruses and bacteria 1. Mucosae are also inductive sites in the host to generate immunity against pathogens, such as the Peyers patches in the intestinal tract and the nasal-associated lymphoreticular tissue in the respiratory tract. This unique feature brings mucosal immunity as a crucial player of the host defense system. Many studies have been focused on gastrointestinal and respiratory mucosal sites. However, there has been little investigation of reproductive mucosal sites. The genital tract mucosa is the primary infection site for sexually transmitted diseases (STD), including bacterial and viral infections. STDs are one of the most critical health challenges facing the world today. Centers for Disease Control and Prevention estimates that there are 19 million new infectious every year in the United States. STDs cost the U.S. health care system $17 billion every year 2, and cost individuals even more in immediate and life-long health consequences. In order to confront this challenge, a greater understanding of reproductive mucosal immunity is needed and isolating lymphocytes is an essential component of these studies. Here, we present a method to reproducibly isolate lymphocytes from murine female genital tracts for immunological studies that can be modified for adaption to other species. The method described below is based on one mouse.&#x2003;

An efficient way to isolate lymphocytes from mouse genital tract is described. This method takes advantage of enzyme digestion and Percoll gradient separation to allow efficient isolation. This technique is also adaptable to for use in other species

Mucosal surfaces, including in the gastrointestinal, urogenital, and respiratory tracts, provide portals of entry for pathogens, such as viruses and ...

Isolation and Th17 Differentiation of Na&iuml;ve CD4 T Lymphocytes

Th17 cells are a distinct subset of T cells that have been found to produce interleukin 17 (IL-17), and differ in function from the other T cell subsets including Th1, Th2, and regulatory T cells. Th17 cells have emerged as a central culprit in overzealous inflammatory immune responses associated with many autoimmune disorders. In this method we purify T lymphocytes from the spleen and lymph nodes of C57BL/6 mice, and stimulate purified CD4+ T cells under control and Th17-inducing environments. The Th17-inducing environment includes stimulation in the presence of anti-CD3 and anti-CD28 antibodies, IL-6, and TGF-&#946;. After incubation for at least 72 hours and for up to five days at 37 &#176;C, cells are subsequently analyzed for the capability to produce IL-17 through flow cytometry, qPCR, and ELISAs. Th17 differentiated CD4+CD25- T cells can be utilized to further elucidate the role that Th17 cells play in the onset and progression of autoimmunity and host defense. Moreover, Th17 differentiation of CD4+CD25- lymphocytes from distinct murine knockout/disease models can contribute to our understanding of cell fate plasticity.

Isolation and Th17 Differentiation of Na&#239;ve CD4 T Lymphocytes

With effector functions distinct from other T cell subsets, Th17 cells have been centrally implicated in inflammatory autoimmunity. This in vitro Th17 differentiation protocol provides a means to determine whether na&#239;ve CD4+ T lymphocytes can differentiate into Th17 cells, and to further examine their role in autoimmunity and host response.

Th17 cells are a distinct subset of T cells that have been found to produce interleukin 17 (IL-17), and differ in function from the other T cell subsets ...

Isolation and Flow Cytometric Analysis of Immune Cells from the Ischemic Mouse Brain

Ischemic stroke initiates a robust inflammatory response that starts in the intravascular compartment and involves rapid activation of brain resident cells. A key mechanism of this inflammatory response is the migration of circulating immune cells to the ischemic brain facilitated by chemokine release and increased endothelial adhesion molecule expression. Brain-invading leukocytes are well-known contributing to early-stage secondary ischemic injury, but their significance for the termination of inflammation and later brain repair has only recently been noticed.
Here, a simple protocol for the efficient isolation of immune cells from the ischemic mouse brain is provided. After transcardial perfusion, brain hemispheres are dissected and mechanically dissociated. Enzymatic digestion with Liberase&#160;is followed by density gradient (such as Percoll) centrifugation to remove myelin and cell debris. One major advantage of this protocol is the single-layer density gradient procedure which does not require time-consuming preparation of gradients and can be reliably performed. The approach yields highly reproducible cell counts per brain hemisphere and allows for measuring several flow cytometry panels in one biological replicate. Phenotypic characterization and quantification of brain-invading leukocytes after experimental stroke may contribute to a better understanding of their multifaceted roles in ischemic injury and repair.

Inflammation plays a central role in the pathogenesis of ischemic stroke. Increasing evidence suggests that it acts as a double-edged sword which exacerbates early brain injury, but also contributes to later repair. This protocol describes the isolation of immune cells from the ischemic brain and their subsequent flow cytometric phenotyping.

Ischemic stroke initiates a robust inflammatory response that starts in the intravascular compartment and involves rapid activation of brain resident ...

Isolation and Flow Cytometric Analysis of Glioma-infiltrating Peripheral Blood Mononuclear Cells

Our laboratory has recently demonstrated that natural killer (NK) cells are capable of eradicating orthotopically implanted mouse GL26 and rat CNS-1 malignant gliomas soon after intracranial engraftment if the cancer cells are rendered deficient in their expression of the &#946;-galactoside-binding lectin galectin-1 (gal-1). More recent work now shows that a population of Gr-1+/CD11b+ myeloid cells is critical to this effect. To better understand the mechanisms by which NK and myeloid cells cooperate to confer gal-1-deficient tumor rejection we have developed a comprehensive protocol for the isolation and analysis of glioma-infiltrating peripheral blood mononuclear cells (PBMC). The method is demonstrated here by comparing PBMC infiltration into the tumor microenvironment of gal-1-expressing GL26 gliomas with those rendered gal-1-deficient via shRNA knockdown. The protocol begins with a description of&#160;how to culture and prepare GL26 cells for inoculation into the syngeneic C57BL/6J mouse brain. It then explains the steps involved in the isolation and flow cytometric analysis of glioma-infiltrating PBMCs from the early brain tumor microenvironment. The method is adaptable to a number of in vivo experimental designs in which temporal data on immune infiltration into the brain is required. The method is sensitive and highly reproducible, as glioma-infiltrating PBMCs can be isolated from intracranial tumors as soon as 24 hr post-tumor engraftment with similar cell counts observed from time point matched tumors throughout independent experiments. A single experimentalist can perform the method from brain harvesting to flow cytometric analysis of glioma-infiltrating PBMCs in roughly 4-6 hr depending on the number of samples to be analyzed. Alternative glioma models and/or cell-specific detection antibodies may also be used at the experimentalists&#8217; discretion to assess the infiltration of several other immune cell types of interest without the need for alterations to the overall procedure.

Presented here is a straightforward method for the isolation and flow cytometric analysis of glioma-infiltrating peripheral blood mononuclear cells that yields time-dependent quantitative data on the number and activation status of immune cells entering the early brain tumor microenvironment.

Our laboratory has recently demonstrated that natural killer (NK) cells are capable of eradicating orthotopically implanted mouse GL26 and rat CNS-1 ...

Isolation and Activation of Murine Lymphocytes

B and T cells, with their extremely diverse antigen-receptor repertoires, have the ability to mount specific immune responses against almost any invading pathogen1,2. Understandably, such intricate abilities are controlled by a large number of molecules involved in various cellular processes to ensure timely and spatially regulated immune responses3. Here, we describe experimental procedures that allow rapid isolation of highly purified murine lymphocytes using magnetic cell sorting technology. The resulting purified lymphocytes can then be subjected to various in vitro or in vivo functional assays, such as the determination of lymphocyte signaling capacity upon stimulation by immunoblotting4 and the investigation of proliferative abilities by 3H-thymidine incorporation or carboxyfluorescein diacetate succinimidyl ester (CFSE) labeling5-7. In addition to comparing the functional capacities of control and genetically modified lymphocytes, we can also determine the T cell stimulatory capacity of antigen-presenting cells (APCs) in vivo, as shown in our representative results using transplanted CFSE-labeled OT-I T cells.

Lymphocytes are the major players in adaptive immune responses. Here, we present a lymphocyte purification protocol to determine the physiological functions of the desired molecules in lymphocyte activation in vitro and in vivo. The described experimental procedures are suitable for comparing functional capacities between control and genetically modified lymphocytes.

B and T cells, with their extremely diverse antigen-receptor repertoires, have the ability to mount specific immune responses against almost any invading ...

Flow Cytometric Analysis of Particle-bound Bet v 1 Allergen in PM10

Flow cytometry is a method widely used to quantify suspended solids such as cells or bacteria in a size range from 0.5 to several tens of micrometers in diameter. In addition to a characterization of forward and sideward scatter properties, it enables the use of fluorescent labeled markers like antibodies to detect respective structures. Using indirect antibody staining, flow cytometry is employed here to quantify birch pollen allergen (precisely Bet v 1)-loaded particles of 0.5 to 10 &#181;m in diameter in inhalable particulate matter (PM10, particle size &#8804;10 &#181;m in diameter). PM10 particles may act as carriers of adsorbed allergens possibly transporting them to the lower respiratory tract, where they could trigger allergic reactions.
So far the allergen content of PM10 has been studied by means of enzyme linked immunosorbent assays (ELISAs) and scanning electron microscopy. ELISA measures the dissolved and not the particle-bound allergen. Compared to scanning electron microscopy, which can visualize allergen-loaded particles, flow cytometry may additionally quantify them. As allergen content of ambient air can deviate from birch pollen count, allergic symptoms might perhaps correlate better with allergen exposure than with pollen count. In conjunction with clinical data, the presented method offers the opportunity to test in future experiments whether allergic reactions to birch pollen antigens are associated with the Bet v 1 allergen content of PM10 particles &#62;0.5 &#181;m.

Here, we present a protocol to quantify allergen-loaded particles by flow cytometry. Ambient particulate matter particles may act as carriers of adsorbed allergens. We show here that flow cytometry, a method widely used to characterize suspended solids &#62;0.5 &#181;m in diameter, can be used to measure these allergen-loaded particles.

Flow cytometry is a method widely used to quantify suspended solids such as cells or bacteria in a size range from 0.5 to several tens of micrometers in ...

Isolation and Flow Cytometric Analysis of Human Endocervical Gamma Delta T Cells

The female reproductive tract (FRT) mucosal immune system serves as the first line of defense. Better knowledge of the genital mucosa is therefore essential for understanding pathogenicity of different pathogens including HIV. Gamma delta (GD) T cells are the prototype of &#39;unconventional&#39; T cells and represent a relatively small subset of T cells defined by their expression of heterodimeric T-cell receptors (TCRs) composed of gamma and delta chains. This sets them apart from the classical and much better known CD4+ helper T cells and CD8+ cytotoxic T cells that are defined by alpha-beta TCRs. GD T cells often show tissue-specific localization and are enriched in epithelium. GD T cells orchestrate immune responses in inflammation, tumor surveillance, infectious disease, and autoimmunity.
Here, we present a method to reproducibly isolate and analyze human endocervical intraepithelial GD T lymphocytes. We have used endocervical cytobrush samples from women participating in the Women&#39;s Interagency HIV Infection Study (WIHS). Knowledge about GD T cells interactions during conditions in which there is an insult to the vaginal mucosal could be applied to any clinical study in which mucosal vulnerability is addressed, including the development of vaginal microbicides.In addition, knowledge about mucosal GD T cell responses has potential for application of GD T cell-based immune therapy in treating infectious diseases.

We describe here an isolation method to obtain human endocervical intraepithelial lymphocytes for the analysis of intraepithelial gamma delta T cells. This protocol can be extended for the purification of endocervical gamma delta T cells by magnetic beads or by cell sorting.

The female reproductive tract (FRT) mucosal immune system serves as the first line of defense. Better knowledge of the genital mucosa is therefore ...

Isolating Lymphocytes from the Mouse Small Intestinal Immune System

The intestinal immune system plays an essential role in maintaining the barrier function of the gastrointestinal tract by generating tolerant responses to dietary antigens and commensal bacteria while mounting effective immune responses to enteropathogenic microbes. In addition, it has become clear that local intestinal immunity has a profound impact on distant and systemic immunity. Therefore, it is important to study how an intestinal immune response is induced and what the immunologic outcome of the response is. Here, a detailed protocol is described for the isolation of lymphocytes from small intestine inductive sites like the gut-associated lymphoid tissue Peyer&#39;s patches and the draining mesenteric lymph nodes and effector sites like the lamina propria and the intestinal epithelium. This technique ensures isolation of a large numbers of lymphocytes from small intestinal tissues with optimal purity and viability and minimal cross compartmental contamination within acceptable time constraints. The technical capability to isolate lymphocytes and other immune cells from intestinal tissues enables the understanding of immune responses to gastrointestinal infections, cancers, and inflammatory diseases.

Here we describe a detailed protocol for the isolation of lymphocytes from the inductive sites including the gut-associated lymphoid tissue Peyer&#39;s patches and the draining mesenteric lymph nodes, and the effector sites including the lamina propria and the intestinal epithelium of the small intestinal immune system.

The intestinal immune system plays an essential role in maintaining the barrier function of the gastrointestinal tract by generating tolerant responses to ...

Isolation and In Vitro Culture of Murine and Human Alveolar Macrophages

Alveolar macrophages are terminally differentiated, lung-resident macrophages of prenatal origin. Alveolar macrophages are unique in their long life and their important role in lung development and function, as well as their lung-localized responses to infection and inflammation. To date, no unified method for identification, isolation, and handling of alveolar macrophages from humans and mice exists. Such a method is needed for studies on these important innate immune cells in various experimental settings. The method described here, which can be easily adopted by any laboratory, is a simplified approach to harvesting alveolar macrophages from bronchoalveolar lavage fluid or from lung tissue and maintaining them in vitro. Because alveolar macrophages primarily occur as adherent cells in the alveoli, the focus of this method is on dislodging them prior to harvest and identification. The lung is a highly vascularized organ, and various cell types of myeloid and lymphoid origin inhabit, interact, and are influenced by the lung microenvironment. By using the set of surface markers described here, researchers can easily and unambiguously distinguish alveolar macrophages from other leukocytes, and purify them for downstream applications. The culture method developed herein supports both human and mouse alveolar macrophages for in vitro growth, and is compatible with cellular and molecular studies.

Isolation and In Vitro Culture of Murine and Human Alveolar Macrophages

This communication describes methodologies for isolation and culture of alveolar macrophages from humans and murine models for experimental purposes.

Alveolar macrophages are terminally differentiated, lung-resident macrophages of prenatal origin. Alveolar macrophages are unique in their long life and ...