IFNγ, IL-13, and IL-22 uniquely affect RNA expression in organoids in a manner aligned to in vivo infection profiles 84 To assess in detail how IFNγ, IL-13, and IL-22 affect intestinal epithelial cells we performed bulk RNA-seq on 85 organoids treated with indicated cytokines for 24 hours compared to untreated controls. In a PCA plot, all four 86 conditions grouped separately, highlighting the different effector responses required for each type of immunity (Fig. 87 2A). This is further exemplified by uniquely induced genes for each condition (Fig. 2B) . Furthermore, IL-22 and 88 IL-13 induced genes associated with various cellular responses as determined by GO term analysis (Fig. S2A,B) . 89 In contrast, IFNγ induced genes associated primarily with antigen presentation, as the most significant GO terms 90 were related to this (Fig. 2C ). In support, flow cytometry analysis of IFNγ treated organoids showed that all cells 91 gain MHC-II and 90% gained MHC-I expression (Fig. 2D ). In vivo, during homeostasis, specifically Lgr5+ cells To test the effect of IFNγ, IL-13 and IL-22 on cell lineage differentiation, we used cell-type specific gene Goblet cell genes up in IL-22 Red nodes are found in the biological process GO-term "response to endoplasmatic reticulum". NES = normalised enrichment score, TPM = transcripts per million and NS = not significant. All images are projections of Z-stacks.
Cytokines utilize developmental signaling pathways to regulate effector responses 127 We were interested in how cytokine treatment leads to cellular effector responses. Intestinal epithelium relies 128 on NOTCH-, WNT-, BMP-and HIPPO-signaling to maintain homeostatic differentiation of cell lineages. We 129 hypothesized that cytokines may use these developmental pathways in directing epithelial cell differentiation. We BMP signaling is associated with IL-13 and limits tuft cell differentiation in vitro 150 We were somewhat surprised to find enrichment of BMP signaling upon IL-13 treatment (Fig. 4A ). BMP members 170 However, this model lacks any limiting factors that are needed to return back to homeostasis when the infection is 171 cleared. Our findings so far suggest that IL-13 treatment induces an epithelial-intrinsic feedback loop mediated by 172 BMP signaling. To further investigate this, we tested the ALK2 (BMP receptor) inhibitor dorsomorphin homolog 173 1 (DMH1) in combination with IL-13 (Mohedas et al. 2013). We found that DMH1 did not directly affect IL-174 13-induced Bmp2 expression (Fig. 6A ), but it did completely block the induction of canonical BMP target genes 175 Id1 /2 /3 (Fig. 6B) . Furthermore, the enrichment of BMP signaling pathway genes by IL-13 is blocked by DMH1, 176 without modulating the effect of IL-13 on HIPPO or NOTCH pathways genes (Fig. 6C) . Although DMH1 did not 177 change the number of tuft cells by itself, it did increase tuft cell numbers upon IL-13 co-treatment (Fig. 6D,E) .
IL-13+DMH1 also increased expression of tuft cell associated genes such as Dclk1, Pou2f3, Trpm5, and Alox5 179 (Fig. 6F ) as well as the overall tuft cell signature by GSEA (Fig. 6G ). Together, this supports a model in which 180 activation of BMP signaling limits IL-13-induced tuft cell differentiation, thus, providing a feedback loop to limit 181 tuft cell expansion and its associated type 2 immunity. 
The intestinal epithelium is capable of rapidly altering its cellular composition to defend against pathogens. Here, 184 we provide a comprehensive comparison of how different immune responses mechanistically drive changes in the 185 intestinal epithelium. Specifically, we find that key cytokines associated with different modes of immunity influence 186 developmental pathways to guide changes in epithelial composition.
culture well (Merenda, Fenderico, and Maurice 2019). This heterogeneity is readily visible in organoid morphology, 189 and in this study we successfully utilize a neural network to characterize these morphological differences by automat- limiting factors in this feed-forward loop, which is obviously required to resolve type 2 immunity. Here, we identify 202 how intestinal-epithelial intrinsic Bmp signaling can act as a brake on tuft cell expansion (Fig. 6 ). In addition, 203 we find that Il13ra1, which is involved in responding to type 2 cytokines, is uniquely expressed in tuft cells. We 204 would speculate that this is instrumental for tuft-cell specific signaling responses to type 2 cytokines, for example 205 to induce Bmp2.
In addition to our findings regarding cytokine-driven tuft cell expansion, we also provide data suggesting that Figure S1 : The image analysis pipeline performs well both in segmentation and classification of organoids, and is perfected by a manual verification step. A, A segmentation algorithm is used to find the outline and center of an organoid and the segmented organoid is classified by a neural network. An optional manual correction of organoid centers and classification can be performed. The organoids can then be segmented again which gives an updated segmentation following the manual correction. B, Comparison of automatic segmentation and automatic classification of organoids compared to manually verified segmentation and manually verified classification. Each circle represents one image. C, Minimal projections of small intestinal organoids treated with cytokines. Days since seeding. D, Distribution of circularity and mean gray value (higher value is whiter) of untreated small intestinal organoids. E, Image output from each step in the confocal image analysis pipeline. The center of each object of interest is marked with a square in a custom graphical user interface, and this information is used to separate even overlapping objects. Furthermore, objects in other channels, like Tuft cells, are analyzed to map which organoid they are inside. Here this association is shown by the organoids and the tuft cells that are within them having the same color in the last panel. This information is summarized and used to plot number of Tuft cells per organoid. 
In summary, the small intestine or distal colon of mouse was washed in ice-cold PBS and opened longitudinally. A 394 microscopy cover slip was used to gently scrape of excess mucus and villus before the intestine was cut into 2-4 mm 395 pieces. The fragments were resuspended in 30 mL ice-cold PBS and pipetted up and down with a 10 mL pipette.
Supernatant was discarded and this step was repeated 5-10 times until the supernatant was clear. The fragments 397 were incubated in 2 mM EDTA in PBS for small intestine, and 10 mM EDTA in PBS for colon, at 4°C for 30 398 min with gentle rocking. The supernatant was removed, 20 mL of ice-cold PBS was added and the fragments were 399 pipetted up and down. This washing step was repeated until the crypt fraction appeared as seen in a microscope. 
Bright field imaging and quantification of intestinal organoids 417 Z-stacks covering the entire matrigel droplet were captured using a EVOS2 microscope with CO 2 , temperature 418 and a humidity-controlled incubation chamber (Thermo-Fisher Scientific). 2D morphological properties of organoid 419 objects as well as their classification were gathered using a custom analysis program written in python based on 420 opencv2 (Bradski 2000) . The brightness of images were autoscaled to max brightness, and a canny edge detection 421 algorithm was run on each individual z-plane using the opencv2.canny function. Groups of pixels below a certain 422 size was removed and a minimal projection of the edges was generated. This image was used to define the contour 423 of objects. The implementation of opencv2s wathershed algorithm was used to split somewhat overlapping objects 424 from each other and the center of the object was defined as the pixel furthest from the edge of the object. Each 425 defined object contour was used to extract a 120x120 pixel picture of the object on a white background from 426 a minimal projection of the original z-stack. These images were used to classify the organoid as either "Junk", 427 "Budding" or "Spheroid" with a convolutional neural network implemented using Tensorflow and Keras (Abadi annotations were used to re-run the segmentation as described above, but this time the classification of the objects 433 were not changed and a watershed algorithm were used to segment object contours based on the manually curated 434 object centers. Finally, objects with a size less than 300 were filtered out of the data and plots were made with the Immunofluorescence staining of organoids and imaging 437 The matrigel used for organoids grown for immunofluorescent imaging were cultured in matrigel mixed with 25 % 438 BCM in eight-well slides (Ibidi, 80821). Media was removed and organoids were fixed in 300 µL 4% PFA with 2 % 439 sucrose for 30 minutes. Fixation solution was removed and 300 µL PBS was added, after 5 minutes the PBS was 440 removed. This washing step was done a total of two times. The PBS was removed and 0.2% Triton X-100 in PBS The harvested intestinal tissue was fixed with 10% formalin for 48 h at room temperature. Tissue was subsequently 459 dehydrated through a series of graded ethanol and then embedded in paraffin wax blocks. 5 µm thick sections 460 were cut using a microtome, floated in a 40°C water bath and transferred to a glass slide. After drying, the 461 tissue sections were kept in an oven at 60°C for 30 minutes and deparaffinized in two changes of Neo-clear (Xylene 462 substitute) for 5 min each, followed by graded ethanol (100 % ethanol 2 times with 3 min each, and next transfer 463 once through 95 %, 80 %, and 70 % ethanol and water 3 min each). Heat mediated antigen retrieval was performed 464 using citrate buffer. Tissue sections on glass slides were marked with hydrophobic pen (PAP pen, ab2601) to keep 465 staining reagents on the tissue section. Next, blocking buffer (1% BSA, 2% normal goat serum, 0.2% Triton X-100 466 in PBS) was added onto the sections of the slides and incubated in a humidified chamber at room temperature for 467 1 hour. Appropriately diluted primary antibody (antibody dilution buffer, e.g. 0.5 % bovine serum albumin, 1 % 468 normal goat serum, 0.05 % Tween 20 in PBS) was added to the sections on the slides and incubate in a humidified 469 VIII chamber at 4°C overnight. The slides were washed in 0.2 % Triton X-100 10 min each. Next, secondary antibody 470 conjugated with fluorochromes was added to the slides for 1 hour at room temperature in a humidified chamber.
Hoechst was used as counterstain and UEA1 was added to stain goblet cells. After rinsing three times with PBST 472 (0.2 % Triton X-100 in PBS) for 10 min each, slides were mounted in Fluoromount G. Complete tile scans were 473 acquired with a Zeiss Airyscan confocal microscope, using a 20x objective lens.
Quantification of immunofluorescence images 475 2D morphological properties of intestinal organoid objects in confocal images were gathered using a custom analysis 476 program written in python based on opencv2 (Bradski 2000) . Maximal projections of each channel were created 477 as well as a rgb composite of all channels, hereafter referred to as the combined channel. The center position of 478 all intestinal organoids as well as their class as either "budding" or "spheroid" were manually annotated in the 479 combined channel using a custom graphical user interface. A binary threshold individual to each channel was then 480 applied to create channel masks and additionally, these masks were added together to a combined mask. Contours 481 of objects were defined based on the outline in combined mask and they were split using a watershed algorithm 482 where the manual annotations were used as input. Only objects in the combined channel with a manual annotation