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1.
Cell ; 177(5): 1217-1231.e18, 2019 05 16.
Artículo en Inglés | MEDLINE | ID: mdl-31006530

RESUMEN

The intestinal microbiota produces tens of thousands of metabolites. Here, we used host sensing of small molecules by G-protein coupled receptors (GPCRs) as a lens to illuminate bioactive microbial metabolites that impact host physiology. We screened 144 human gut bacteria against the non-olfactory GPCRome and identified dozens of bacteria that activated both well-characterized and orphan GPCRs, including strains that converted dietary histidine into histamine and shaped colonic motility; a prolific producer of the essential amino acid L-Phe, which we identified as an agonist for GPR56 and GPR97; and a species that converted L-Phe into the potent psychoactive trace amine phenethylamine, which crosses the blood-brain barrier and triggers lethal phenethylamine poisoning after monoamine oxidase inhibitor administration. These studies establish an orthogonal approach for parsing the microbiota metabolome and uncover multiple biologically relevant host-microbiota metabolome interactions.


Asunto(s)
Bacterias/crecimiento & desarrollo , Colon/microbiología , Microbioma Gastrointestinal/fisiología , Interacciones Microbiota-Huesped/fisiología , Receptores Acoplados a Proteínas G/metabolismo , Animales , Células HEK293 , Humanos , Ratones
2.
Nature ; 628(8006): 171-179, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38509360

RESUMEN

The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown1-3. Classical pathogens often invade host tissues and modulate immune responses through interactions with human extracellular and secreted proteins (the 'exoproteome'). Commensal microorganisms may also facilitate niche colonization and shape host biology by engaging host exoproteins; however, direct exoproteome-microbiota interactions remain largely unexplored. Here we developed and validated a novel technology, BASEHIT, that enables proteome-scale assessment of human exoproteome-microbiome interactions. Using BASEHIT, we interrogated more than 1.7 million potential interactions between 519 human-associated bacterial strains from diverse phylogenies and tissues of origin and 3,324 human exoproteins. The resulting interactome revealed an extensive network of transkingdom connectivity consisting of thousands of previously undescribed host-microorganism interactions involving 383 strains and 651 host proteins. Specific binding patterns within this network implied underlying biological logic; for example, conspecific strains exhibited shared exoprotein-binding patterns, and individual tissue isolates uniquely bound tissue-specific exoproteins. Furthermore, we observed dozens of unique and often strain-specific interactions with potential roles in niche colonization, tissue remodelling and immunomodulation, and found that strains with differing host interaction profiles had divergent interactions with host cells in vitro and effects on the host immune system in vivo. Overall, these studies expose a previously unexplored landscape of molecular-level host-microbiota interactions that may underlie causal effects of indigenous microorganisms on human health and disease.


Asunto(s)
Bacterias , Interacciones Microbiota-Huesped , Microbiota , Filogenia , Proteoma , Simbiosis , Animales , Femenino , Humanos , Ratones , Bacterias/clasificación , Bacterias/inmunología , Bacterias/metabolismo , Bacterias/patogenicidad , Interacciones Microbiota-Huesped/inmunología , Interacciones Microbiota-Huesped/fisiología , Tropismo al Anfitrión , Microbiota/inmunología , Microbiota/fisiología , Especificidad de Órganos , Unión Proteica , Proteoma/inmunología , Proteoma/metabolismo , Reproducibilidad de los Resultados
3.
Nature ; 615(7950): 168-174, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36813961

RESUMEN

Pancreatic ductal adenocarcinoma (PDAC) is expected to be the second most deadly cancer by 2040, owing to the high incidence of metastatic disease and limited responses to treatment1,2. Less than half of all patients respond to the primary treatment for PDAC, chemotherapy3,4, and genetic alterations alone cannot explain this5. Diet is an environmental factor that can influence the response to therapies, but its role in PDAC is unclear. Here, using shotgun metagenomic sequencing and metabolomic screening, we show that the microbiota-derived tryptophan metabolite indole-3-acetic acid (3-IAA) is enriched in patients who respond to treatment. Faecal microbiota transplantation, short-term dietary manipulation of tryptophan and oral 3-IAA administration increase the efficacy of chemotherapy in humanized gnotobiotic mouse models of PDAC. Using a combination of loss- and gain-of-function experiments, we show that the efficacy of 3-IAA and chemotherapy is licensed by neutrophil-derived myeloperoxidase. Myeloperoxidase oxidizes 3-IAA, which in combination with chemotherapy induces a downregulation of the reactive oxygen species (ROS)-degrading enzymes glutathione peroxidase 3 and glutathione peroxidase 7. All of this results in the accumulation of ROS and the downregulation of autophagy in cancer cells, which compromises their metabolic fitness and, ultimately, their proliferation. In humans, we observed a significant correlation between the levels of 3-IAA and the efficacy of therapy in two independent PDAC cohorts. In summary, we identify a microbiota-derived metabolite that has clinical implications in the treatment of PDAC, and provide a motivation for considering nutritional interventions during the treatment of patients with cancer.


Asunto(s)
Carcinoma Ductal Pancreático , Microbiota , Neoplasias Pancreáticas , Animales , Humanos , Ratones , Carcinoma Ductal Pancreático/dietoterapia , Carcinoma Ductal Pancreático/tratamiento farmacológico , Carcinoma Ductal Pancreático/metabolismo , Carcinoma Ductal Pancreático/microbiología , Glutatión Peroxidasa/metabolismo , Neoplasias Pancreáticas/dietoterapia , Neoplasias Pancreáticas/tratamiento farmacológico , Neoplasias Pancreáticas/metabolismo , Neoplasias Pancreáticas/microbiología , Peroxidasa/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Triptófano/metabolismo , Triptófano/farmacología , Triptófano/uso terapéutico , Neutrófilos/enzimología , Autofagia , Metagenoma , Metabolómica , Trasplante de Microbiota Fecal , Ácidos Indolacéticos/farmacología , Ácidos Indolacéticos/uso terapéutico , Modelos Animales de Enfermedad , Vida Libre de Gérmenes , Neoplasias Pancreáticas
4.
EMBO J ; 40(23): e108287, 2021 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-34676563

RESUMEN

Prevotella copri is a prevalent inhabitant of the human gut and has been associated with plant-rich diet consumption and diverse health states. The underlying genetic basis of these associations remains enigmatic due to the lack of genetic tools. Here, we developed a novel versatile genetic toolbox for rapid and efficient genetic insertion and allelic exchange applicable to P. copri strains from multiple clades. Enabled by the genetic platform, we systematically investigated the specificity of polysaccharide utilization loci (PULs) and identified four highly conserved PULs for utilizing arabinan, pectic galactan, arabinoxylan, and inulin, respectively. Further genetic and functional analysis of arabinan utilization systems illustrate that P. copri has evolved two distinct types of arabinan-processing PULs (PULAra ) and that the type-II PULAra is significantly enriched in individuals consuming a vegan diet compared to other diets. In summary, this genetic toolbox will enable functional genetic studies for P. copri in future.


Asunto(s)
Dieta Vegetariana , Microbioma Gastrointestinal , Sitios Genéticos , Genoma Bacteriano , Polisacáridos/metabolismo , Prevotella/genética , Prevotella/metabolismo , Heces/microbiología , Humanos , Prevotella/clasificación , Prevotella/aislamiento & purificación
5.
Mucosal Immunol ; 17(3): 431-449, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38159726

RESUMEN

Dedicator of cytokinesis 8 (DOCK8) mutations lead to a primary immunodeficiency associated with recurrent gastrointestinal infections and poor antibody responses but, paradoxically, heightened IgE to food antigens, suggesting that DOCK8 is central to immune homeostasis in the gut. Using Dock8-deficient mice, we found that DOCK8 was necessary for mucosal IgA production to multiple T cell-dependent antigens, including peanut and cholera toxin. Yet DOCK8 was not necessary in T cells for this phenotype. Instead, B cell-intrinsic DOCK8 was required for maintenance of antigen-specific IgA-secreting plasma cells (PCs) in the gut lamina propria. Unexpectedly, DOCK8 was not required for early B cell activation, migration, or IgA class switching. An unbiased interactome screen revealed novel protein partners involved in metabolism and apoptosis. Dock8-deficient IgA+ B cells had impaired cellular respiration and failed to engage glycolysis appropriately. These results demonstrate that maintenance of the IgA+ PC compartment requires DOCK8 and suggest that gut IgA+ PCs have unique metabolic requirements for long-term survival in the lamina propria.


Asunto(s)
Factores de Intercambio de Guanina Nucleótido , Inmunoglobulina A , Mucosa Intestinal , Ratones Noqueados , Células Plasmáticas , Animales , Ratones , Factores de Intercambio de Guanina Nucleótido/metabolismo , Factores de Intercambio de Guanina Nucleótido/genética , Inmunoglobulina A/metabolismo , Inmunoglobulina A/inmunología , Células Plasmáticas/inmunología , Células Plasmáticas/metabolismo , Mucosa Intestinal/inmunología , Mucosa Intestinal/metabolismo , Activación de Linfocitos , Linfocitos B/inmunología , Linfocitos B/metabolismo , Glucólisis , Ratones Endogámicos C57BL , Linfocitos T/inmunología , Linfocitos T/metabolismo
6.
Nat Microbiol ; 9(7): 1792-1811, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38862602

RESUMEN

The Klebsiella oxytoca species complex is part of the human microbiome, especially during infancy and childhood. K. oxytoca species complex strains can produce enterotoxins, namely, tilimycin and tilivalline, while also contributing to colonization resistance (CR). The relationship between these seemingly contradictory roles is not well understood. Here, by coupling ex vivo assays with CRISPR-mutagenesis and various mouse models, we show that K. oxytoca provides CR against Salmonella Typhimurium. In vitro, the antimicrobial activity against various Salmonella strains depended on tilimycin production and was induced by various simple carbohydrates. In vivo, CR against Salmonella depended on toxin production in germ-free mice, while it was largely toxin-independent in mice with residual microbiota. This was linked to the relative levels of toxin-inducing carbohydrates in vivo. Finally, dulcitol utilization was essential for toxin-independent CR in gnotobiotic mice. Together, this demonstrates that nutrient availability is key to both toxin-dependent and substrate-driven competition between K. oxytoca and Salmonella.


Asunto(s)
Klebsiella oxytoca , Infecciones por Salmonella , Salmonella typhimurium , Klebsiella oxytoca/genética , Klebsiella oxytoca/metabolismo , Animales , Ratones , Infecciones por Salmonella/microbiología , Salmonella typhimurium/genética , Salmonella typhimurium/metabolismo , Salmonella typhimurium/crecimiento & desarrollo , Salmonella typhimurium/efectos de los fármacos , Humanos , Modelos Animales de Enfermedad , Enterotoxinas/metabolismo , Enterotoxinas/genética , Femenino , Ratones Endogámicos C57BL , Infecciones por Klebsiella/microbiología , Microbiota , Microbioma Gastrointestinal , Antibiosis , Benzodiazepinonas
7.
JCI Insight ; 8(1)2023 01 10.
Artículo en Inglés | MEDLINE | ID: mdl-36625344

RESUMEN

A role of CD4+ T cells during the progression from nonalcoholic fatty liver disease (NAFLD) to nonalcoholic steatohepatitis (NASH) has been suggested, but which polarization state of these cells characterizes this progression and the development of fibrosis remain unclear. In addition, a gut-liver axis has been suggested to play a role in NASH, but the role of CD4+ T cells in this axis has just begun to be investigated. Combining single-cell RNA sequencing and multiple-parameter flow cytometry, we provide the first cell atlas to our knowledge focused on liver-infiltrating CD4+ T cells in patients with NAFLD and NASH, showing that NASH is characterized by a population of multicytokine-producing CD4+ T cells. Among these cells, only those with a Th17 polarization state were enriched in patients with advanced fibrosis. In parallel, we observed that Bacteroides appeared to be enriched in the intestine of NASH patients and to correlate with the frequency of multicytokine-producing CD4+ T cells. In short, we deliver a CD4+ T cell atlas of NAFLD and NASH, providing the rationale to target CD4+ T cells with a Th17 polarization state to block fibrosis development. Finally, our data offer an early indication to test whether multicytokine-producing CD4+ T cells are part of the gut-liver axis characterizing NASH.


Asunto(s)
Enfermedad del Hígado Graso no Alcohólico , Humanos , Linfocitos T CD4-Positivos , Fibrosis
8.
Cell Host Microbe ; 30(7): 988-1002.e6, 2022 07 13.
Artículo en Inglés | MEDLINE | ID: mdl-35640610

RESUMEN

The impacts of individual commensal microbes on immunity and disease can differ dramatically depending on the surrounding microbial context; however, the specific bacterial combinations that dictate divergent immunological outcomes remain largely undefined. Here, we characterize an immunostimulatory Allobaculum species from an inflammatory bowel disease patient that exacerbates colitis in gnotobiotic mice. Allobaculum inversely associates with the taxonomically divergent immunostimulatory species Akkermansia muciniphila in human-microbiota-associated mice and human cohorts. Co-colonization with A. muciniphila ameliorates Allobaculum-induced intestinal epithelial cell activation and colitis in mice, whereas Allobaculum blunts the A.muciniphila-specific systemic antibody response and reprograms the immunological milieu in mesenteric lymph nodes by blocking A.muciniphila-induced dendritic cell activation and T cell expansion. These studies thus identify a pairwise reciprocal interaction between human gut bacteria that dictates divergent immunological outcomes. Furthermore, they establish a generalizable framework to define the contextual cues contributing to the "incomplete penetrance" of microbial impacts on human disease.


Asunto(s)
Colitis , Enfermedades Inflamatorias del Intestino , Animales , Vida Libre de Gérmenes , Humanos , Enfermedades Inflamatorias del Intestino/microbiología , Intestinos/microbiología , Ratones , Verrucomicrobia
9.
Cell Host Microbe ; 29(1): 83-93.e3, 2021 01 13.
Artículo en Inglés | MEDLINE | ID: mdl-33385335

RESUMEN

The immunopathogenesis of inflammatory bowel disease (IBD) has been attributed to a combination of host genetics and intestinal dysbiosis. Previous work in a small cohort of IBD patients suggested that pro-inflammatory bacterial taxa are highly coated with secretory immunoglobulin IgA. Using bacterial fluorescence-activated cell sorting coupled with 16S rRNA gene sequencing (IgA-SEQ), we profiled IgA coating of intestinal microbiota in a large cohort of IBD patients and identified bacteria associated with disease and treatment. Forty-three bacterial taxa displayed significantly higher IgA coating in IBD compared with controls, including 8 taxa exhibiting differential IgA coating but similar relative abundance. Patients treated with anti-TNF-α therapies exhibited dramatically altered microbiota-specific IgA responses compared with controls. Furthermore, increased IgA coating of Oscillospira was associated with a delay in time to surgery. These results demonstrate that investigating IgA responses to microbiota can uncover potential disease-modifying taxa and reveal improved biomarkers of clinical course in IBD.


Asunto(s)
Bacterias/inmunología , Microbioma Gastrointestinal/inmunología , Microbioma Gastrointestinal/fisiología , Inmunoglobulina A Secretora/inmunología , Enfermedades Inflamatorias del Intestino/inmunología , Enfermedades Inflamatorias del Intestino/microbiología , Adulto , Bacterias/crecimiento & desarrollo , Clostridiales/crecimiento & desarrollo , Clostridiales/inmunología , Estudios de Cohortes , Colitis Ulcerosa/tratamiento farmacológico , Colitis Ulcerosa/inmunología , Colitis Ulcerosa/microbiología , Colitis Ulcerosa/fisiopatología , Enfermedad de Crohn/tratamiento farmacológico , Enfermedad de Crohn/inmunología , Enfermedad de Crohn/microbiología , Enfermedad de Crohn/fisiopatología , Progresión de la Enfermedad , Femenino , Humanos , Enfermedades Inflamatorias del Intestino/tratamiento farmacológico , Enfermedades Inflamatorias del Intestino/fisiopatología , Masculino , Factor de Necrosis Tumoral alfa/antagonistas & inhibidores
10.
Science ; 369(6501): 320-325, 2020 07 17.
Artículo en Inglés | MEDLINE | ID: mdl-32675374

RESUMEN

Restricted V(D)J recombination during fetal development was postulated to limit antibody repertoire breadth and prevent autoimmunity. However, newborn serum contains abundant autoantibodies, suggesting that B cell tolerance during gestation is not yet fully established. To investigate this apparent paradox, we evaluated the reactivities of more than 450 antibodies cloned from single B cells from human fetal liver, bone marrow, and spleen. We found that incomplete B cell tolerance in early human fetal life favored the accumulation of polyreactive B cells that bound both apoptotic cells and commensal bacteria from healthy adults. Thus, the restricted fetal preimmune repertoire contains potentially beneficial self-reactive innate-like B cell specificities that may facilitate the removal of apoptotic cells during development and shape gut microbiota assembly after birth.


Asunto(s)
Anticuerpos/inmunología , Linfocitos B/inmunología , Feto/inmunología , Autoanticuerpos/inmunología , Autoantígenos/inmunología , Autoinmunidad , Bacterias/inmunología , Femenino , Humanos , Inmunidad Innata , Especificidad de Órganos , Embarazo , Recombinación V(D)J
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