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1. Preparation of bacterial cells
- Streak glycerol stocked fluorescent bacteria (such as GFP expressing S. Typhimurium) on LB an agar plate containing 100 μg/ml of ampicillin.
- Culture a single colony from LB agar overnight in 2 ml of new LB medium.
- Add 0.5 ml of bacterial culture to 4.5 ml of new LB medium and incubate until optical density of 1.0 at 600 nm is reached.
- Harvest bacterial cells by centrifugation (3,000 x g, 5 min, 4°C).
- Discard the supernatant and wash twice with 5.0 ml of sterile phosphate buffer saline (PBS).
- Resuspend bacterial pellet with 5 ml of PBS, and use 50 μl of the suspension containing approximately 107 colony forming unit (CFU) as the inoculum.
- In case of using fluorescently labeled bacteria, the bacterial cells were labeled by fluorescence labeling reagent according to standard protocol.
2. Anesthesia
- Fill a small plastic box (10 x 10 x 5 cm) with 5% (v/v) vaporized isoflurane mixed with air (flow rate: 200 ml/min).
- Anesthetize eight- to sixteen-weak-old male or female mice in the box.
- Move the mice to an autopsy table after anesthesia.
- Continuously anesthetize the mice by 2% (v/v) vaporized isoflurane mixed with air (flow rate: 200 ml/min) (Figure 1). This is a terminal procedure.
3. Ligated Peyer's patch loop assay
- Incise 1cm of the abdominal skin and then cut the abdominal peritoneum of an anesthetized mouse and take out the small intestine containing the Peyer's patch.
- Ligate the intestine with sewing yarn, taking care to avoid blood vessels. Note: only bind one side of the intestine, and leave the other side loose.
- Inject 50 μl of bacterial suspension or PBS (control) with a syringe into ligated Peyer's patch loop on the loose side of the intestine (Figure 2).
- Bind loose side, and close the mouse's abdomen with a clip.
- After 1 h, remove the ligated Peyer's patch loop, and euthanize the mouse by cervical dislocation.
- Excise Peyer's patch from ligated Peyer's patch loop.
- Flashing the apical side of Peyer's patch by 1ml of PBS with using syringe attached to a needle to remove excess mucosal fluid and bacteria. Flashing the Peyer's patch an additional two times.
4. Whole mount staining and confocal microscopic analysis of Peyer's patch
- Fix Peyer's patch in BD Cytofix/Cytoperm solution on ice for 1 hr.
- Wash Peyer's patch three times with 1ml of BD Perm/Wash buffer for 5 min, and then block with 1 ml of blocking buffer containing 0.1% (w/v) saponin, 0.2% (w/v) BSA in PBS for 30 min on ice.
- Add 200-fold diluted anti-mouse GP2 monoclonal antibody (5 μg/ml) to the specimen to detect M cells.
- Incubate for 2 hrs at room temperature or overnight at 4°C.
- Wash three times with 1 ml of cold PBS, then add 200-fold diluted anti-rat IgG antibody conjugated with DyLight549 (20 μg/ml)to the specimen.
- Incubate sample on ice for 2 hrs.
- Wash three times with 1 ml of cold PBS, then add 50-fold diluted Alexa 633 conjugated Phalloidin to the specimen to detect F-actin.
- Incubate on ice for 2 hrs.
- Wash lightly with 1 ml of cold PBS. Then place three to four pieces of circular cover glass on a slide, and embed the specimens in a 30% solution of glycerol in PBS on the slide (Figure 3).
- Observe specimens with a DM-IRE2 confocal laser scanning microscope or a DeltaVision Restoration deconvolution microscope.
5. Representative Results:
The specimen example of a mouse ligated Peyer's patch loop assay with GFP-S. Typhimurium was observed with a DeltaVision Restoration deconvolution microscope (Figure 4). GFP-S. Typhimurium is transcytosed by GP2+M cells. A mouse Peyer's patch intestinal loop assay can identify the kind of commensal or pathogenic bacteria that can be transcytosed by M cells.

Figure 1. Anesthesia of mice under vaporized isoflurane condition. Vaporized isoflurane was supplied by an anesthesia-dedicated apparatus (left side).

Figure 2. Summary of ligated Peyer's patch intestinal loop assay. The fluorescent bacterial suspension was injected by syringe into ligated Peyer's patch loop on the loose side of the intestine.

Figure 3. Mount of the specimens. The specimens were embedded in a 30% solution of glycerol in PBS on a special slide in which a perforated plastic plate (1mm thick) was bound by adhesive agent on a glass slide.

Figure 4. Example of a mouse ligated Peyer's patch loop assay with GFP-S. Typhimurium. GP2, which is reported as M cell specific marker5, was stained with anti-mouse GP2 antibody (Red).The specimen was observed with a DeltaVision Restoration deconvolution microscope. GFP-expressing S. Typhimurium was co-localized with GP2 on the apical plasma membrane of M cell and in the subapical cytoplasmic vesicles (arrowheads). Top, apical view. Bottom and side, lateral views. Scale bar: 10 μm.