Academic Appointments

Honors & Awards

  • NIH K01 Career Development Award, NIDDK (2017-2022)
  • Harvard Digestive Diseases Center P/F Award, Harvard (2017)
  • Barry R. and Irene Tilenius Bloom Fellowship, HSPH (2016)
  • NIH Ruth L. Kirschstein National Research Service Award, NIDDK (2012-2015)

Professional Education

  • Post Doctoral Fellowship, Harvard School of Public Health, Immunology and Infectious Diseases (2017)
  • Ph.D., Stanford University, Microbiology and Immunology (2011)
  • B.A., UC Berkeley, Molecular and Cell Biology (2002)

Current Research and Scholarly Interests

Our lab is broadly interested in how intestinal microbes shape our immune system to promote both health and disease. Recently we discovered that a type of intestinal epithelial cell, called tuft cells, act as sentinels stationed along the lining of the gut. Tuft cells respond to microbes, including parasites, to initiate type 2 immunity, remodel the epithelium, and alter gut physiology. Surprisingly, these changes to the intestine rely on the same chemosensory pathway found in oral taste cells. Currently, we aim to 1) elucidate the role of specific tuft cell receptors in microbial detection. 2) To understand how protozoa and bacteria within the microbiota impact host immunity. 3) Discover how tuft cells modulate surrounding cells and tissue.

2023-24 Courses

Stanford Advisees

All Publications

  • The abundance and morphology of human large intestinal goblet and tuft cells during chronic schistosomiasis. Parasite immunology Gologorsky, M. B., Mechler, C. M., Forgó, E., Charville, G. W., Howitt, M. R. 2023: e12981


    Schistosomiasis affects nearly 240 million people in predominately low- and middle-income countries and ranks second in the number of cases and socio-economic burden among all parasitic diseases. Despite the enormous burden posed by schistosomes, our understanding of how schistosomiasis impacts infected human tissues remains limited. Intestinal schistosomiasis in animal models leads to goblet cell hyperplasia, likely increasing mucus production and reflecting an intestinal type 2 immune response. However, it is unknown whether these same changes occur in schistosome-infected humans. Using immunofluorescence and light microscopy, we compared the abundance and morphology of goblet cells in patients diagnosed with schistosomiasis to uninfected controls. The mucin-containing vesicles in goblet cells from schistosome-infected patients were significantly larger (hypertrophic) than uninfected individuals, although goblet cell hyperplasia was absent in chronic human schistosomiasis. In addition, we examined tuft cells in the large intestinal epithelium of control and schistosome-infected patients. Tuft cell numbers expand during helminth infection in mice, but these cells have not been characterized in human parasite infections. We found no evidence of tuft cell hyperplasia during human schistosome infection. Thus, our study provides novel insight into schistosome-associated changes to the intestinal epithelium in humans, suggesting an increase in mucus production by large intestinal goblet cells but relatively minor effects on tuft cell numbers.

    View details for DOI 10.1111/pim.12981

    View details for PubMedID 37038837

  • Succinate and tuft cells: how does this sensory process interface with food allergy? The Journal of allergy and clinical immunology Nico, K. F., Tyner, M. D., Howitt, M. R. 2022

    View details for DOI 10.1016/j.jaci.2022.07.016

    View details for PubMedID 35934085

  • The Taste Receptor TAS1R3 Regulates Small Intestinal Tuft Cell Homeostasis. ImmunoHorizons Howitt, M. R., Cao, Y. G., Gologorsky, M. B., Li, J. A., Haber, A. L., Biton, M., Lang, J., Michaud, M., Regev, A., Garrett, W. S. 2020; 4 (1): 23–32


    Tuft cells are an epithelial cell type critical for initiating type 2 immune responses to parasites and protozoa in the small intestine. To respond to these stimuli, intestinal tuft cells use taste chemosensory signaling pathways, but the role of taste receptors in type 2 immunity is poorly understood. In this study, we show that the taste receptor TAS1R3, which detects sweet and umami in the tongue, also regulates tuft cell responses in the distal small intestine. BALB/c mice, which have an inactive form of TAS1R3, as well as Tas1r3-deficient C57BL6/J mice both have severely impaired responses to tuft cell-inducing signals in the ileum, including the protozoa Tritrichomonas muris and succinate. In contrast, TAS1R3 is not required to mount an immune response to the helminth Heligmosomoides polygyrus, which infects the proximal small intestine. Examination of uninfected Tas1r3-/- mice revealed a modest reduction in the number of tuft cells in the proximal small intestine but a severe decrease in the distal small intestine at homeostasis. Together, these results suggest that TAS1R3 influences intestinal immunity by shaping the epithelial cell landscape at steady-state.

    View details for DOI 10.4049/immunohorizons.1900099

    View details for PubMedID 31980480

  • A Tuft Act to Follow: Leukotrienes Take the Stage in Anti-worm Immunity. Immunity Fung, C. n., Howitt, M. R. 2020; 52 (3): 426–28


    Tuft cells are specialized taste-chemosensory cells that detect the presence of intestinal parasites and orchestrate type 2 immunity. In this issue of Immunity, McGinty et al. discover that parasitic worms, but not commensal protists, stimulate tuft cells to release cysteinyl leukotrienes to amplify anti-helminth immunity in the small intestine.

    View details for DOI 10.1016/j.immuni.2020.02.011

    View details for PubMedID 32187512

  • Tropism for tuft cells determines immune promotion of norovirus pathogenesis. Science (New York, N.Y.) Wilen, C. B., Lee, S., Hsieh, L. L., Orchard, R. C., Desai, C., Hykes, B. L., McAllaster, M. R., Balce, D. R., Feehley, T., Brestoff, J. R., Hickey, C. A., Yokoyama, C. C., Wang, Y. T., MacDuff, D. A., Kreamalmayer, D., Howitt, M. R., Neil, J. A., Cadwell, K., Allen, P. M., Handley, S. A., van Lookeren Campagne, M., Baldridge, M. T., Virgin, H. W. 2018; 360 (6385): 204-208


    Complex interactions between host immunity and the microbiome regulate norovirus infection. However, the mechanism of host immune promotion of enteric virus infection remains obscure. The cellular tropism of noroviruses is also unknown. Recently, we identified CD300lf as a murine norovirus (MNoV) receptor. In this study, we have shown that tuft cells, a rare type of intestinal epithelial cell, express CD300lf and are the target cell for MNoV in the mouse intestine. We found that type 2 cytokines, which induce tuft cell proliferation, promote MNoV infection in vivo. These cytokines can replace the effect of commensal microbiota in promoting virus infection. Our work thus provides insight into how the immune system and microbes can coordinately promote enteric viral infection.

    View details for DOI 10.1126/science.aar3799

    View details for PubMedID 29650672

  • A single-cell survey of the small intestinal epithelium. Nature Haber, A. L., Biton, M., Rogel, N., Herbst, R. H., Shekhar, K., Smillie, C., Burgin, G., Delorey, T. M., Howitt, M. R., Katz, Y., Tirosh, I., Beyaz, S., Dionne, D., Zhang, M., Raychowdhury, R., Garrett, W. S., Rozenblatt-Rosen, O., Shi, H. N., Yilmaz, O., Xavier, R. J., Regev, A. 2017; 551 (7680): 333-339


    Intestinal epithelial cells absorb nutrients, respond to microbes, function as a barrier and help to coordinate immune responses. Here we report profiling of 53,193 individual epithelial cells from the small intestine and organoids of mice, which enabled the identification and characterization of previously unknown subtypes of intestinal epithelial cell and their gene signatures. We found unexpected diversity in hormone-secreting enteroendocrine cells and constructed the taxonomy of newly identified subtypes, and distinguished between two subtypes of tuft cell, one of which expresses the epithelial cytokine Tslp and the pan-immune marker CD45, which was not previously associated with non-haematopoietic cells. We also characterized the ways in which cell-intrinsic states and the proportions of different cell types respond to bacterial and helminth infections: Salmonella infection caused an increase in the abundance of Paneth cells and enterocytes, and broad activation of an antimicrobial program; Heligmosomoides polygyrus caused an increase in the abundance of goblet and tuft cells. Our survey highlights previously unidentified markers and programs, associates sensory molecules with cell types, and uncovers principles of gut homeostasis and response to pathogens.

    View details for DOI 10.1038/nature24489

    View details for PubMedID 29144463

  • Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut SCIENCE Howitt, M. R., Lavoie, S., Michaud, M., Blum, A. M., Tran, S. V., Weinstock, J. V., Gallini, C. A., Redding, K., Margolskee, R. F., Osborne, L. C., Artis, D., Garrett, W. S. 2016; 351 (6279): 1329-1333


    The intestinal epithelium forms an essential barrier between a host and its microbiota. Protozoa and helminths are members of the gut microbiota of mammals, including humans, yet the many ways that gut epithelial cells orchestrate responses to these eukaryotes remain unclear. Here we show that tuft cells, which are taste-chemosensory epithelial cells, accumulate during parasite colonization and infection. Disruption of chemosensory signaling through the loss of TRMP5 abrogates the expansion of tuft cells, goblet cells, eosinophils, and type 2 innate lymphoid cells during parasite colonization. Tuft cells are the primary source of the parasite-induced cytokine interleukin-25, which indirectly induces tuft cell expansion by promoting interleukin-13 production by innate lymphoid cells. Our results identify intestinal tuft cells as critical sentinels in the gut epithelium that promote type 2 immunity in response to intestinal parasites.

    View details for DOI 10.1126/science.aaf1648

    View details for Web of Science ID 000372397700045

    View details for PubMedID 26847546

    View details for PubMedCentralID PMC5528851

  • Helicobacter pylori CheZHP and ChePep form a novel chemotaxis-regulatory complex distinct from the core chemotaxis signaling proteins and the flagellar motor. Molecular microbiology Lertsethtakarn, P., Howitt, M. R., Castellon, J., Amieva, M. R., Ottemann, K. M. 2015; 97 (6): 1063-1078


    Chemotaxis is important for Helicobacter pylori to colonize the stomach. Like other bacteria, H. pylori uses chemoreceptors and conserved chemotaxis proteins to phosphorylate the flagellar rotational response regulator, CheY, and modulate the flagellar rotational direction. Phosphorylated CheY is returned to its non-phosphorylated state by phosphatases such as CheZ. In previously studied cases, chemotaxis phosphatases localize to the cellular poles by interactions with either the CheA chemotaxis kinase or flagellar motor proteins. We report here that the H. pylori CheZ, CheZHP , localizes to the poles independently of the flagellar motor, CheA, and all typical chemotaxis proteins. Instead, CheZHP localization depends on the chemotaxis regulatory protein ChePep, and reciprocally, ChePep requires CheZHP for its polar localization. We furthermore show that these proteins interact directly. Functional domain mapping of CheZHP determined the polar localization motif lies within the central domain of the protein and that the protein has regions outside of the active site that participate in chemotaxis. Our results suggest that CheZHP and ChePep form a distinct complex. These results therefore suggest the intriguing idea that some phosphatases localize independently of the other chemotaxis and motility proteins, possibly to confer unique regulation on these proteins' activities.

    View details for DOI 10.1111/mmi.13086

    View details for PubMedID 26061894

  • The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T-reg Cell Homeostasis SCIENCE Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., Garrett, W. S. 2013; 341 (6145): 569-573


    Regulatory T cells (Tregs) that express the transcription factor Foxp3 are critical for regulating intestinal inflammation. Candidate microbe approaches have identified bacterial species and strain-specific molecules that can affect intestinal immune responses, including species that modulate Treg responses. Because neither all humans nor mice harbor the same bacterial strains, we posited that more prevalent factors exist that regulate the number and function of colonic Tregs. We determined that short-chain fatty acids, gut microbiota-derived bacterial fermentation products, regulate the size and function of the colonic Treg pool and protect against colitis in a Ffar2-dependent manner in mice. Our study reveals that a class of abundant microbial metabolites underlies adaptive immune microbiota coadaptation and promotes colonic homeostasis and health.

    View details for DOI 10.1126/science.1241165

    View details for Web of Science ID 000322586700059

    View details for PubMedID 23828891

    View details for PubMedCentralID PMC3807819

  • Exploring host-microbiota interactions in animal models and humans GENES & DEVELOPMENT Kostic, A. D., Howitt, M. R., Garrett, W. S. 2013; 27 (7): 701-718


    The animal and bacterial kingdoms have coevolved and coadapted in response to environmental selective pressures over hundreds of millions of years. The meta'omics revolution in both sequencing and its analytic pipelines is fostering an explosion of interest in how the gut microbiome impacts physiology and propensity to disease. Gut microbiome studies are inherently interdisciplinary, drawing on approaches and technical skill sets from the biomedical sciences, ecology, and computational biology. Central to unraveling the complex biology of environment, genetics, and microbiome interaction in human health and disease is a deeper understanding of the symbiosis between animals and bacteria. Experimental model systems, including mice, fish, insects, and the Hawaiian bobtail squid, continue to provide critical insight into how host-microbiota homeostasis is constructed and maintained. Here we consider how model systems are influencing current understanding of host-microbiota interactions and explore recent human microbiome studies.

    View details for DOI 10.1101/gad.212522.112

    View details for Web of Science ID 000317578000001

    View details for PubMedID 23592793

    View details for PubMedCentralID PMC3639412

  • A complex microworld in the gut Gut microbiota and cardiovascular disease connectivity NATURE MEDICINE Howitt, M. R., Garrett, W. S. 2012; 18 (8): 1188-1189

    View details for DOI 10.1038/nm.2895

    View details for Web of Science ID 000307469300022

    View details for PubMedID 22869188

  • ChePep Controls Helicobacter pylori Infection of the Gastric Glands and Chemotaxis in the Epsilonproteobacteria MBIO Howitt, M. R., Lee, J. Y., Lertsethtakarn, P., Vogelmann, R., Joubert, L., Ottemann, K. M., Amieva, M. R. 2011; 2 (4)


    Microbes use directed motility to colonize harsh and dynamic environments. We discovered that Helicobacter pylori strains establish bacterial colonies deep in the gastric glands and identified a novel protein, ChePep, necessary to colonize this niche. ChePep is preferentially localized to the flagellar pole. Although mutants lacking ChePep have normal flagellar ultrastructure and are motile, they have a slight defect in swarming ability. By tracking the movement of single bacteria, we found that ΔChePep mutants cannot control the rotation of their flagella and swim with abnormally frequent reversals. These mutants even sustain bursts of movement backwards with the flagella pulling the bacteria. Genetic analysis of the chemotaxis signaling pathway shows that ChePep regulates flagellar rotation through the chemotaxis system. By examining H. pylori within a microscopic pH gradient, we determined that ChePep is critical for regulating chemotactic behavior. The chePep gene is unique to the Epsilonproteobacteria but is found throughout this diverse group. We expressed ChePep from other members of the Epsilonproteobacteria, including the zoonotic pathogen Campylobacter jejuni and the deep sea hydrothermal vent inhabitant Caminibacter mediatlanticus, in H. pylori and found that ChePep is functionally conserved across this class. ChePep represents a new family of chemotaxis regulators unique to the Epsilonproteobacteria and illustrates the different strategies that microbes have evolved to control motility.Helicobacter pylori strains infect half of all humans worldwide and contribute to the development of peptic ulcers and gastric cancer. H. pylori cannot survive within the acidic lumen of the stomach and uses flagella to actively swim to and colonize the protective mucus and epithelium. The chemotaxis system allows H. pylori to navigate by regulating the rotation of its flagella. We identified a new protein, ChePep, which controls chemotaxis in H. pylori. ChePep mutants fail to colonize the gastric glands of mice and are completely outcompeted by normal H. pylori. Genes encoding ChePep are found only in the class Epsilonproteobacteria, which includes the human pathogen Campylobacter jejuni and environmental microbes like the deep-sea hydrothermal vent colonizer Caminibacter mediatlanticus, and we show that ChePep function is conserved in this class. Our study identifies a new colonization factor in H. pylori and also provides insight into the control and evolution of bacterial chemotaxis.

    View details for DOI 10.1128/mBio.00098-11

    View details for PubMedID 21791582