Michael R. Howitt

All Publications

• Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition. Cell Gerrick, E. R., Zlitni, S., West, P. T., Carter, M. M., Mechler, C. M., Olm, M. R., Caffrey, E. B., Li, J. A., Higginbottom, S. K., Severyn, C. J., Kracke, F., Spormann, A. M., Sonnenburg, J. L., Bhatt, A. S., Howitt, M. R. 2023

  Abstract

  The microbiota influences intestinal health and physiology, yet the contributions of commensal protists to the gut environment have been largely overlooked. Here, we discover human- and rodent-associated parabasalid protists, revealing substantial diversity and prevalence in nonindustrialized human populations. Genomic and metabolomic analyses of murine parabasalids from the genus Tritrichomonas revealed species-level differences in excretion of the metabolite succinate, which results in distinct small intestinal immune responses. Metabolic differences between Tritrichomonas species also determine their ecological niche within the microbiota. By manipulating dietary fibers and developing in vitro protist culture, we show that different Tritrichomonas species prefer dietary polysaccharides or mucus glycans. These polysaccharide preferences drive trans-kingdom competition with specific commensal bacteria, which affects intestinal immunity in a diet-dependent manner. Our findings reveal unappreciated diversity in commensal parabasalids, elucidate differences in commensal protist metabolism, and suggest how dietary interventions could regulate their impact on gut health.

  View details for DOI 10.1016/j.cell.2023.11.018

  View details for PubMedID 38096822

• Tuft cells mediate commensal remodeling of the small intestinal antimicrobial landscape. Proceedings of the National Academy of Sciences of the United States of America Fung, C., Fraser, L. M., Barrón, G. M., Gologorsky, M. B., Atkinson, S. N., Gerrick, E. R., Hayward, M., Ziegelbauer, J., Li, J. A., Nico, K. F., Tyner, M. D., DeSchepper, L. B., Pan, A., Salzman, N. H., Howitt, M. R. 2023; 120 (23): e2216908120

  Abstract

  Succinate produced by the commensal protist Tritrichomonas musculis (T. mu) stimulates chemosensory tuft cells, resulting in intestinal type 2 immunity. Tuft cells express the succinate receptor SUCNR1, yet this receptor does not mediate antihelminth immunity nor alter protist colonization. Here, we report that microbial-derived succinate increases Paneth cell numbers and profoundly alters the antimicrobial peptide (AMP) landscape in the small intestine. Succinate was sufficient to drive this epithelial remodeling, but not in mice lacking tuft cell chemosensory components required to detect this metabolite. Tuft cells respond to succinate by stimulating type 2 immunity, leading to interleukin-13-mediated epithelial and AMP expression changes. Moreover, type 2 immunity decreases the total number of mucosa-associated bacteria and alters the small intestinal microbiota composition. Finally, tuft cells can detect short-term bacterial dysbiosis that leads to a spike in luminal succinate levels and modulate AMP production in response. These findings demonstrate that a single metabolite produced by commensals can markedly shift the intestinal AMP profile and suggest that tuft cells utilize SUCNR1 and succinate sensing to modulate bacterial homeostasis.

  View details for DOI 10.1073/pnas.2216908120

  View details for PubMedID 37253002

• 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

  Abstract

  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

• Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation. Immunity Buquicchio, F. A., Fonseca, R., Yan, P. K., Wang, F., Evrard, M., Obers, A., Gutierrez, J. C., Raposo, C. J., Belk, J. A., Daniel, B., Zareie, P., Yost, K. E., Qi, Y., Yin, Y., Nico, K. F., Tierney, F. M., Howitt, M. R., Lareau, C. A., Satpathy, A. T., Mackay, L. K. 2024

  Abstract

  The memory CD8+ T cell pool contains phenotypically and transcriptionally heterogeneous subsets with specialized functions and recirculation patterns. Here, we examined the epigenetic landscape of CD8+ T cells isolated from seven non-lymphoid organs across four distinct infection models, alongside their circulating T cell counterparts. Using single-cell transposase-accessible chromatin sequencing (scATAC-seq), we found that tissue-resident memory T (TRM) cells and circulating memory T (TCIRC) cells develop along distinct epigenetic trajectories. We identified organ-specific transcriptional regulators of TRM cell development, including FOSB, FOS, FOSL1, and BACH2, and defined an epigenetic signature common to TRM cells across organs. Finally, we found that although terminal TEX cells share accessible regulatory elements with TRM cells, they are defined by TEX-specific epigenetic features absent from TRM cells. Together, this comprehensive data resource shows that TRM cell development is accompanied by dynamic transcriptome alterations and chromatin accessibility changes that direct tissue-adapted and functionally distinct T cell states.

  View details for DOI 10.1016/j.immuni.2024.06.014

  View details for PubMedID 39043184

• Tuft cell-derived acetylcholine promotes epithelial chloride secretion and intestinal helminth clearance. Immunity Billipp, T. E., Fung, C., Webeck, L. M., Sargent, D. B., Gologorsky, M. B., Chen, Z., McDaniel, M. M., Kasal, D. N., McGinty, J. W., Barrow, K. A., Rich, L. M., Barilli, A., Sabat, M., Debley, J. S., Wu, C., Myers, R., Howitt, M. R., von Moltke, J. 2024

  Abstract

  Epithelial cells secrete chloride to regulate water release at mucosal barriers, supporting both homeostatic hydration and the "weep" response that is critical for type 2 immune defense against parasitic worms (helminths). Epithelial tuft cells in the small intestine sense helminths and release cytokines and lipids to activate type 2 immune cells, but whether they regulate epithelial secretion is unknown. Here, we found that tuft cell activation rapidly induced epithelial chloride secretion in the small intestine. This response required tuft cell sensory functions and tuft cell-derived acetylcholine (ACh), which acted directly on neighboring epithelial cells to stimulate chloride secretion, independent of neurons. Maximal tuft cell-induced chloride secretion coincided with immune restriction of helminths, and clearance was delayed in mice lacking tuft cell-derived ACh, despite normal type 2 inflammation. Thus, we have uncovered an epithelium-intrinsic response unit that uses ACh to couple tuft cell sensing to the secretory defenses of neighboring epithelial cells.

  View details for DOI 10.1016/j.immuni.2024.03.023

  View details for PubMedID 38744291

• Intestinal tuft cell immune privilege enables norovirus persistence. Science immunology Strine, M. S., Fagerberg, E., Darcy, P. W., Barron, G. M., Filler, R. B., Alfajaro, M. M., D'Angelo-Gavrish, N., Wang, F., Graziano, V. R., Menasche, B. L., Damo, M., Wang, Y., Howitt, M. R., Lee, S., Joshi, N. S., Mucida, D., Wilen, C. B. 2024; 9 (93): eadi7038

  Abstract

  The persistent murine norovirus strain MNVCR6 is a model for human norovirus and enteric viral persistence. MNVCR6 causes chronic infection by directly infecting intestinal tuft cells, rare chemosensory epithelial cells. Although MNVCR6 induces functional MNV-specific CD8+ T cells, these lymphocytes fail to clear infection. To examine how tuft cells promote immune escape, we interrogated tuft cell interactions with CD8+ T cells by adoptively transferring JEDI (just EGFP death inducing) CD8+ T cells into Gfi1b-GFP tuft cell reporter mice. Unexpectedly, some intestinal tuft cells partially resisted JEDI CD8+ T cell-mediated killing-unlike Lgr5+ intestinal stem cells and extraintestinal tuft cells-despite seemingly normal antigen presentation. When targeting intestinal tuft cells, JEDI CD8+ T cells predominantly adopted a T resident memory phenotype with decreased effector and cytotoxic capacity, enabling tuft cell survival. JEDI CD8+ T cells neither cleared nor prevented MNVCR6 infection in the colon, the site of viral persistence, despite targeting a virus-independent antigen. Ultimately, we show that intestinal tuft cells are relatively resistant to CD8+ T cells independent of norovirus infection, representing an immune-privileged niche that can be leveraged by enteric microbes.

  View details for DOI 10.1126/sciimmunol.adi7038

  View details for PubMedID 38517952

• Commensal protists in reptiles display flexible host range and adaptation to ectothermic hosts. mBio Gerrick, E. R., DeSchepper, L. B., Mechler, C. M., Joubert, L. -., Dunker, F., Colston, T. J., Howitt, M. R. 2023: e0227323

  Abstract

  Environmental factors like climate change and captive breeding can impact the gut microbiota and host health. Therefore, conservation efforts for threatened species may benefit from understanding how these factors influence animal microbiomes. Parabasalid protists are members of the mammalian microbiota that can modulate the immune system and impact susceptibility to infections. However, little is known about parabasalids in reptiles. Here, we profile reptile-associated parabasalids in wild and captive reptiles and find that captivity has minimal impact on parabasalid prevalence or diversity. However, because reptiles are cold-blooded (ectothermic), their microbiotas experience wider temperature fluctuation than microbes in warm-blooded animals. To investigate whether extreme weather patterns affect parabasalid-host interactions, we analyzed the gene expression in reptile-associated parabasalids and found that temperature differences significantly alter genes associated with host health. These results expand our understanding of parabasalids in this vulnerable vertebrate group and highlight important factors to be taken into consideration for conservation efforts.

  View details for DOI 10.1128/mbio.02273-23

  View details for PubMedID 37962346

• 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

  Abstract

  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

  Abstract

  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

  Abstract

  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

  Abstract

  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

  Abstract

  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

• 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

  Abstract

  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

  Abstract

  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

  Abstract

  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)

  Abstract

  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