1
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Lee JY, Tiffany CR, Mahan SP, Kellom M, Rogers AWL, Nguyen H, Stevens ET, Masson HLP, Yamazaki K, Marco ML, Eloe-Fadrosh EA, Turnbaugh PJ, Bäumler AJ. High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota. Cell 2024; 187:1191-1205.e15. [PMID: 38366592 PMCID: PMC11023689 DOI: 10.1016/j.cell.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 09/27/2023] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
Carbohydrate intolerance, commonly linked to the consumption of lactose, fructose, or sorbitol, affects up to 30% of the population in high-income countries. Although sorbitol intolerance is attributed to malabsorption, the underlying mechanism remains unresolved. Here, we show that a history of antibiotic exposure combined with high fat intake triggered long-lasting sorbitol intolerance in mice by reducing Clostridia abundance, which impaired microbial sorbitol catabolism. The restoration of sorbitol catabolism by inoculation with probiotic Escherichia coli protected mice against sorbitol intolerance but did not restore Clostridia abundance. Inoculation with the butyrate producer Anaerostipes caccae restored a normal Clostridia abundance, which protected mice against sorbitol-induced diarrhea even when the probiotic was cleared. Butyrate restored Clostridia abundance by stimulating epithelial peroxisome proliferator-activated receptor-gamma (PPAR-γ) signaling to restore epithelial hypoxia in the colon. Collectively, these mechanistic insights identify microbial sorbitol catabolism as a potential target for approaches for the diagnosis, treatment, and prevention of sorbitol intolerance.
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Affiliation(s)
- Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Scott P Mahan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Matthew Kellom
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Andrew W L Rogers
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Eric T Stevens
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616, USA
| | - Hugo L P Masson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kohei Yamazaki
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA; Laboratory of Veterinary Public Health, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Maria L Marco
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616, USA
| | - Emiley A Eloe-Fadrosh
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA.
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2
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Abstract
The gut microbiota prevents infection by crowding out pathogens.
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Affiliation(s)
- Lauren C Radlinski
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
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3
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Winter SE, Bäumler AJ. Gut dysbiosis: Ecological causes and causative effects on human disease. Proc Natl Acad Sci U S A 2023; 120:e2316579120. [PMID: 38048456 PMCID: PMC10722970 DOI: 10.1073/pnas.2316579120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/02/2023] [Indexed: 12/06/2023] Open
Abstract
The gut microbiota plays a role in many human diseases, but high-throughput sequence analysis does not provide a straightforward path for defining healthy microbial communities. Therefore, understanding mechanisms that drive compositional changes during disease (gut dysbiosis) continues to be a central goal in microbiome research. Insights from the microbial pathogenesis field show that an ecological cause for gut dysbiosis is an increased availability of host-derived respiratory electron acceptors, which are dominant drivers of microbial community composition. Similar changes in the host environment also drive gut dysbiosis in several chronic human illnesses, and a better understanding of the underlying mechanisms informs approaches to causatively link compositional changes in the gut microbiota to an exacerbation of symptoms. The emerging picture suggests that homeostasis is maintained by host functions that control the availability of resources governing microbial growth. Defining dysbiosis as a weakening of these host functions directs attention to the underlying cause and identifies potential targets for therapeutic intervention.
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Affiliation(s)
- Sebastian E. Winter
- Department of Medicine, Division of Infectious Diseases, University of California, Davis, CA95616
- Department of Medical Microbiology and Immunology, University of California, Davis, CA95616
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, University of California, Davis, CA95616
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4
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Savage HP, Bays DJ, Gonzalez MAF, Bejarano EJ, Nguyen H, Masson HLP, Carvalho TP, Santos RL, Thompson GR, Bäumler AJ. 5-ASA can functionally replace Clostridia to prevent a post-antibiotic bloom of Candida albicans by maintaining epithelial hypoxia. bioRxiv 2023:2023.04.17.537218. [PMID: 37131682 PMCID: PMC10153110 DOI: 10.1101/2023.04.17.537218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Antibiotic prophylaxis sets the stage for an intestinal bloom of Candida albicans , which can progress to invasive candidiasis in patients with hematologic malignancies. Commensal bacteria can reestablish microbiota-mediated colonization resistance after completion of antibiotic therapy, but they cannot engraft during antibiotic prophylaxis. Here we use a mouse model to provide a proof of concept for an alternative approach, which replaces commensal bacteria functionally with drugs to restore colonization resistance against C. albicans . Streptomycin treatment, which depletes Clostridia from the gut microbiota, disrupted colonization resistance against C. albicans and increased epithelial oxygenation in the large intestine. Inoculating mice with a defined community of commensal Clostridia species reestablished colonization resistance and restored epithelial hypoxia. Notably, these functions of commensal Clostridia species could be replaced functionally with the drug 5-aminosalicylic acid (5-ASA), which activates mitochondrial oxygen consumption in the epithelium of the large intestine. When streptomycin-treated mice received 5-ASA, the drug reestablished colonization resistance against C. albicans and restored physiological hypoxia in the epithelium of the large intestine. We conclude that 5-ASA treatment is a non-biotic intervention that restores colonization resistance against C. albicans without requiring the administration of live bacteria.
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5
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Jossi SE, Arcuri M, Alshayea A, Persaud RR, Marcial-Juárez E, Palmieri E, Di Benedetto R, Pérez-Toledo M, Pillaye J, Channell WM, Schager AE, Lamerton RE, Cook CN, Goodall M, Haneda T, Bäumler AJ, Jackson-Jones LH, Toellner KM, MacLennan CA, Henderson IR, Micoli F, Cunningham AF. Vi polysaccharide and conjugated vaccines afford similar early, IgM or IgG-independent control of infection but boosting with conjugated Vi vaccines sustains the efficacy of immune responses. Front Immunol 2023; 14:1139329. [PMID: 37033932 PMCID: PMC10076549 DOI: 10.3389/fimmu.2023.1139329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Vaccination with Vi capsular polysaccharide (Vi-PS) or protein-Vi typhoid conjugate vaccine (TCV) can protect adults against Salmonella Typhi infections. TCVs offer better protection than Vi-PS in infants and may offer better protection in adults. Potential reasons for why TCV may be superior in adults are not fully understood. Methods and results Here, we immunized wild-type (WT) mice and mice deficient in IgG or IgM with Vi-PS or TCVs (Vi conjugated to tetanus toxoid or CRM197) for up to seven months, with and without subsequent challenge with Vi-expressing Salmonella Typhimurium. Unexpectedly, IgM or IgG alone were similarly able to reduce bacterial burdens in tissues, and this was observed in response to conjugated or unconjugated Vi vaccines and was independent of antibody being of high affinity. Only in the longer-term after immunization (>5 months) were differences observed in tissue bacterial burdens of mice immunized with Vi-PS or TCV. These differences related to the maintenance of antibody responses at higher levels in mice boosted with TCV, with the rate of fall in IgG titres induced to Vi-PS being greater than for TCV. Discussion Therefore, Vi-specific IgM or IgG are independently capable of protecting from infection and any superior protection from vaccination with TCV in adults may relate to responses being able to persist better rather than from differences in the antibody isotypes induced. These findings suggest that enhancing our understanding of how responses to vaccines are maintained may inform on how to maximize protection afforded by conjugate vaccines against encapsulated pathogens such as S. Typhi.
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Affiliation(s)
- Siân E. Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Melissa Arcuri
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
- GSK Vaccines Institute for Global Health SRL, Siena, Italy
| | - Areej Alshayea
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Ruby R. Persaud
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Edith Marcial-Juárez
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Elena Palmieri
- GSK Vaccines Institute for Global Health SRL, Siena, Italy
| | | | - Marisol Pérez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jamie Pillaye
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Will M. Channell
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Anna E. Schager
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Rachel E. Lamerton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Charlotte N. Cook
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Margaret Goodall
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Takeshi Haneda
- Laboratory of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, United States
| | - Lucy H. Jackson-Jones
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - Kai-Michael Toellner
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Calman A. MacLennan
- Bill & Melinda Gates Foundation, London, United Kingdom
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ian R. Henderson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Adam F. Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
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6
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English BC, Savage HP, Mahan SP, Diaz-Ochoa VE, Young BM, Abuaita BH, Sule G, Knight JS, O’Riordan MX, Bäumler AJ, Tsolis RM. The IRE1α-XBP1 Signaling Axis Promotes Glycolytic Reprogramming in Response to Inflammatory Stimuli. mBio 2023; 14:e0306822. [PMID: 36475773 PMCID: PMC9973330 DOI: 10.1128/mbio.03068-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022] Open
Abstract
Immune cells must be able to adjust their metabolic programs to effectively carry out their effector functions. Here, we show that the endoplasmic reticulum (ER) stress sensor Inositol-requiring enzyme 1 alpha (IRE1α) and its downstream transcription factor X box binding protein 1 (XBP1) enhance the upregulation of glycolysis in classically activated macrophages (CAMs). The IRE1α-XBP1 signaling axis supports this glycolytic switch in macrophages when activated by lipopolysaccharide (LPS) stimulation or infection with the intracellular bacterial pathogen Brucella abortus. Importantly, these different inflammatory stimuli have distinct mechanisms of IRE1α activation; while Toll-like receptor 4 (TLR4) supports glycolysis under both conditions, TLR4 is required for activation of IRE1α in response to LPS treatment but not B. abortus infection. Though IRE1α and XBP1 are necessary for maximal induction of glycolysis in CAMs, activation of this pathway is not sufficient to increase the glycolytic rate of macrophages, indicating that the cellular context in which this pathway is activated ultimately dictates the cell's metabolic response and that IRE1α activation may be a way to fine-tune metabolic reprogramming. IMPORTANCE The immune system must be able to tailor its response to different types of pathogens in order to eliminate them and protect the host. When confronted with bacterial pathogens, macrophages, frontline defenders in the immune system, switch to a glycolysis-driven metabolism to carry out their antibacterial functions. Here, we show that IRE1α, a sensor of ER stress, and its downstream transcription factor XBP1 support glycolysis in macrophages during infection with Brucella abortus or challenge with Salmonella LPS. Interestingly, these stimuli activate IRE1α by independent mechanisms. While the IRE1α-XBP1 signaling axis promotes the glycolytic switch, activation of this pathway is not sufficient to increase glycolysis in macrophages. This study furthers our understanding of the pathways that drive macrophage immunometabolism and highlights a new role for IRE1α and XBP1 in innate immunity.
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Affiliation(s)
- Bevin C. English
- Department of Medical Microbiology and Immunology, University of California—Davis, Davis, California, USA
| | - Hannah P. Savage
- Department of Medical Microbiology and Immunology, University of California—Davis, Davis, California, USA
| | - Scott P. Mahan
- Department of Medical Microbiology and Immunology, University of California—Davis, Davis, California, USA
| | - Vladimir E. Diaz-Ochoa
- Department of Medical Microbiology and Immunology, University of California—Davis, Davis, California, USA
| | - Briana M. Young
- Department of Medical Microbiology and Immunology, University of California—Davis, Davis, California, USA
| | - Basel H. Abuaita
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gautam Sule
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason S. Knight
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Mary X. O’Riordan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, University of California—Davis, Davis, California, USA
| | - Renée M. Tsolis
- Department of Medical Microbiology and Immunology, University of California—Davis, Davis, California, USA
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7
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Abstract
Changes in the composition of gut-associated microbial communities are associated with many human illnesses, but the factors driving dysbiosis remain incompletely understood. One factor governing the microbiota composition in the gut is bile. Bile acids shape the microbiota composition through their antimicrobial activity and by activating host signaling pathways that maintain gut homeostasis. Although bile acids are host-derived, their functions are integrally linked to bacterial metabolism, which shapes the composition of the intestinal bile acid pool. Conditions that change the size or composition of the bile acid pool can trigger alterations in the microbiota composition that exacerbate inflammation or favor infection with opportunistic pathogens. Therefore, manipulating the composition or size of the bile acid pool might be a promising strategy to remediate dysbiosis.
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Affiliation(s)
- Anaïs B. Larabi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Hugo L. P. Masson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
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8
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Alugupalli AS, Cravens MP, Walker JA, Gulandijany D, Dickinson GS, Debes GF, Schifferli DM, Bäumler AJ, Alugupalli KR, Alugupalli KR. The Lack of Natural IgM Increases Susceptibility and Impairs Anti-Vi Polysaccharide IgG Responses in a Mouse Model of Typhoid. Immunohorizons 2022; 6:807-816. [PMID: 36480484 DOI: 10.4049/immunohorizons.2200088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating IgM present in the body prior to any apparent Ag exposure is referred to as natural IgM. Natural IgM provides protective immunity against a variety of pathogens. Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of typhoid fever in humans. Because mice are not permissive to S. Typhi infection, we employed a murine model of typhoid using S. enterica serovar Typhimurium expressing the Vi polysaccharide (ViPS) of S. Typhi (S. Typhimurium strain RC60) to evaluate the role of natural IgM in pathogenesis. We found that natural mouse IgM binds to S. Typhi and S. Typhimurium. The severity of S. Typhimurium infection in mice is dependent on presence of the natural resistance-associated macrophage protein 1 (Nramp1) allele; therefore, we infected mice deficient in secreted form of IgM (sIgM) on either a Nramp1-resistant (129S) or -susceptible (C57BL/6J) background. We found that the lack of natural IgM results in a significantly increased susceptibility and an exaggerated liver pathology regardless of the route of infection or the Nramp1 allele. Reconstitution of sIgM-/- mice with normal mouse serum or purified polyclonal IgM restored the resistance to that of sIgM+/+ mice. Furthermore, immunization of sIgM-/- mice with heat-killed S. Typhi induced a significantly reduced anti-ViPS IgG and complement-dependent bactericidal activity against S. Typhi in vitro, compared with that of sIgM+/+ mice. These findings indicate that natural IgM is an important factor in reducing the typhoid severity and inducing an optimal anti-ViPS IgG response to vaccination.
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Affiliation(s)
- Akhil S Alugupalli
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA.,Department of Microbiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA
| | - Matthew P Cravens
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Justin A Walker
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Dania Gulandijany
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Gregory S Dickinson
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Gudrun F Debes
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Dieter M Schifferli
- Department of Microbiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA; and
| | - Kishore R Alugupalli
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Kishore R Alugupalli
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
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9
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Abstract
Changes in the composition of the gut microbiota are associated with many human diseases. So far, however, we have failed to define homeostasis or dysbiosis by the presence or absence of specific microbial species. The composition and function of the adult gut microbiota is governed by diet and host factors that regulate and direct microbial growth. The host delivers oxygen and nitrate to the lumen of the small intestine, which selects for bacteria that use respiration for energy production. In the colon, by contrast, the host limits the availability of oxygen and nitrate, which results in a bacterial community that specializes in fermentation for growth. Although diet influences microbiota composition, a poor diet weakens host control mechanisms that regulate the microbiota. Hence, quantifying host parameters that control microbial growth could help define homeostasis or dysbiosis and could offer alternative strategies to remediate dysbiosis.
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Affiliation(s)
- Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
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10
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Liou MJ, Miller BM, Litvak Y, Nguyen H, Natwick DE, Savage HP, Rixon JA, Mahan SP, Hiyoshi H, Rogers AWL, Velazquez EM, Butler BP, Collins SR, McSorley SJ, Harshey RM, Byndloss MX, Simon SI, Bäumler AJ. Host cells subdivide nutrient niches into discrete biogeographical microhabitats for gut microbes. Cell Host Microbe 2022; 30:836-847.e6. [PMID: 35568027 PMCID: PMC9187619 DOI: 10.1016/j.chom.2022.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 03/15/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022]
Abstract
Changes in the microbiota composition are associated with many human diseases, but factors that govern strain abundance remain poorly defined. We show that a commensal Escherichia coli strain and a pathogenic Salmonella enterica serovar Typhimurium isolate both utilize nitrate for intestinal growth, but each accesses this resource in a distinct biogeographical niche. Commensal E. coli utilizes epithelial-derived nitrate, whereas nitrate in the niche occupied by S. Typhimurium is derived from phagocytic infiltrates. Surprisingly, avirulent S. Typhimurium was shown to be unable to utilize epithelial-derived nitrate because its chemotaxis receptors McpB and McpC exclude the pathogen from the niche occupied by E. coli. In contrast, E. coli invades the niche constructed by S. Typhimurium virulence factors and confers colonization resistance by competing for nitrate. Thus, nutrient niches are not defined solely by critical resources, but they can be further subdivided biogeographically within the host into distinct microhabitats, thereby generating new niche opportunities for distinct bacterial species.
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Affiliation(s)
- Megan J Liou
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Brittany M Miller
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Yael Litvak
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem 9190401, Israel
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Dean E Natwick
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Hannah P Savage
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Jordan A Rixon
- Center for Immunology and Infectious Diseases and Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Scott P Mahan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Hirotaka Hiyoshi
- Department of Bacteriology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Andrew W L Rogers
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Eric M Velazquez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Brian P Butler
- Department of Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Sean R Collins
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Stephen J McSorley
- Center for Immunology and Infectious Diseases and Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Rasika M Harshey
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mariana X Byndloss
- Vanderbilt Institute for Infection, Immunology and Inflammation and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Scott I Simon
- Department of Biomedical Engineering, College of Engineering and Department of Dermatology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA.
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11
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Abstract
Listeria monocytogenes uses respiration to sustain a risky fermentative lifestyle during infection.
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Affiliation(s)
- Lauren C Radlinski
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, United States
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, United States
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12
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Alfonso-Garcia A, Cevallos SA, Lee JY, Li C, Bec J, Bäumler AJ, Marcu L. Assessment of Murine Colon Inflammation Using Intraluminal Fluorescence Lifetime Imaging. Molecules 2022; 27:1317. [PMID: 35209104 PMCID: PMC8875403 DOI: 10.3390/molecules27041317] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 01/22/2023] Open
Abstract
Inflammatory bowel disease (IBD) is typically diagnosed by exclusion years after its onset. Current diagnostic methods are indirect, destructive, or target overt disease. Screening strategies that can detect low-grade inflammation in the colon would improve patient prognosis and alleviate associated healthcare costs. Here, we test the feasibility of fluorescence lifetime imaging (FLIm) to detect inflammation from thick tissue in a non-destructive and label-free approach based on tissue autofluorescence. A pulse sampling FLIm instrument with 355 nm excitation was coupled to a rotating side-viewing endoscopic probe for high speed (10 mm/s) intraluminal imaging of the entire mucosal surface (50-80 mm) of freshly excised mice colons. Current results demonstrate that tissue autofluorescence lifetime was sensitive to the colon anatomy and the colonocyte layer. Moreover, mice under DSS-induced colitis and 5-ASA treatments showed changes in lifetime values that were qualitatively related to inflammatory markers consistent with alterations in epithelial bioenergetics (switch between β-oxidation and aerobic glycolysis) and physical structure (colon length). This study demonstrates the ability of intraluminal FLIm to image mucosal lifetime changes in response to inflammatory treatments and supports the development of FLIm as an in vivo imaging technique for monitoring the onset, progression, and treatment of inflammatory diseases.
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Affiliation(s)
- Alba Alfonso-Garcia
- Biomedical Engineering Department, University of California, Davis, CA 95616, USA; (C.L.); (J.B.); (L.M.)
| | - Stephanie A. Cevallos
- Medical Microbiology and Immunology Department, University of California, Davis, CA 95616, USA; (S.A.C.); (J.-Y.L.); (A.J.B.)
| | - Jee-Yon Lee
- Medical Microbiology and Immunology Department, University of California, Davis, CA 95616, USA; (S.A.C.); (J.-Y.L.); (A.J.B.)
| | - Cai Li
- Biomedical Engineering Department, University of California, Davis, CA 95616, USA; (C.L.); (J.B.); (L.M.)
| | - Julien Bec
- Biomedical Engineering Department, University of California, Davis, CA 95616, USA; (C.L.); (J.B.); (L.M.)
| | - Andreas J. Bäumler
- Medical Microbiology and Immunology Department, University of California, Davis, CA 95616, USA; (S.A.C.); (J.-Y.L.); (A.J.B.)
| | - Laura Marcu
- Biomedical Engineering Department, University of California, Davis, CA 95616, USA; (C.L.); (J.B.); (L.M.)
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13
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Hiyoshi H, English BC, Diaz-Ochoa VE, Wangdi T, Zhang LF, Sakaguchi M, Haneda T, Tsolis RM, Bäumler AJ. Virulence factors perforate the pathogen-containing vacuole to signal efferocytosis. Cell Host Microbe 2022; 30:163-170.e6. [PMID: 34951948 PMCID: PMC8831471 DOI: 10.1016/j.chom.2021.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/20/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022]
Abstract
Intracellular pathogens commonly reside within macrophages to find shelter from humoral defenses, but host cell death can expose them to the extracellular milieu. We find intracellular pathogens solve this dilemma by using virulence factors to generate a complement-dependent find-me signal that initiates uptake by a new phagocyte through efferocytosis. During macrophage death, Salmonella uses a type III secretion system to perforate the membrane of the pathogen-containing vacuole (PCV), thereby triggering complement deposition on bacteria entrapped in pore-induced intracellular traps (PITs). In turn, complement activation signals neutrophil efferocytosis, a process that shelters intracellular bacteria from the respiratory burst. Similarly, Brucella employs its type IV secretion system to perforate the PCV membrane, which induces complement deposition on bacteria entrapped in PITs. Collectively, this work identifies virulence factor-induced perforation of the PCV as a strategy of intracellular pathogens to generate a find-me signal for efferocytosis.
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Affiliation(s)
- Hirotaka Hiyoshi
- Department of Bacteriology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Department of Medical Microbiology and Immunology, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Bevin C English
- Department of Medical Microbiology and Immunology, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Vladimir E Diaz-Ochoa
- Department of Medical Microbiology and Immunology, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Tamding Wangdi
- Department of Medical Microbiology and Immunology, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Lillian F Zhang
- Department of Medical Microbiology and Immunology, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Miako Sakaguchi
- Central Laboratory, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Takeshi Haneda
- Laboratory of Microbiology, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, University of California at Davis, One Shields Ave, Davis, CA 95616, USA.
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14
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Chang CS, Liao YC, Huang CT, Lin CM, Cheung CHY, Ruan JW, Yu WH, Tsai YT, Lin IJ, Huang CH, Liou JS, Chou YH, Chien HJ, Chuang HL, Juan HF, Huang HC, Chan HL, Liao YC, Tang SC, Su YW, Tan TH, Bäumler AJ, Kao CY. Identification of a gut microbiota member that ameliorates DSS-induced colitis in intestinal barrier enhanced Dusp6-deficient mice. Cell Rep 2021; 37:110016. [PMID: 34818535 DOI: 10.1016/j.celrep.2021.110016] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/30/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Strengthening the gut epithelial barrier is a potential strategy for management of gut microbiota-associated illnesses. Here, we demonstrate that dual-specificity phosphatase 6 (Dusp6) knockout enhances baseline colon barrier integrity and ameliorates dextran sulfate sodium (DSS)-induced colonic injury. DUSP6 mutation in Caco-2 cells enhances the epithelial feature and increases mitochondrial oxygen consumption, accompanied by altered glucose metabolism and decreased glycolysis. We find that Dusp6-knockout mice are more resistant to DSS-induced dysbiosis, and the cohousing and fecal microbiota transplantation experiments show that the gut/fecal microbiota derived from Dusp6-knockout mice also confers protection against colitis. Further culturomics and mono-colonialization experiments show that one gut microbiota member in the genus Duncaniella confers host protection from DSS-induced injury. We identify Dusp6 deficiency as beneficial for shaping the gut microbiota eubiosis necessary to protect against gut barrier-related diseases.
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Affiliation(s)
- Cherng-Shyang Chang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Yi-Chu Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Chih-Ting Huang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Chiao-Mei Lin
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | | | - Jhen-Wei Ruan
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Wen-Hsuan Yu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Ting Tsai
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - I-Jung Lin
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, 30062, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, 30062, Taiwan
| | - Ya-Hsien Chou
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Hung-Jen Chien
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Hsiao-Li Chuang
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei, 11571, Taiwan
| | - Hsueh-Fen Juan
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan; Center for Computational and Systems Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Hong-Lin Chan
- Institute of Bioinformatics and Structural Biology and Department of Medical Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Shiue-Cheng Tang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Wen Su
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Cheng-Yuan Kao
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan; Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
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15
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Yoo W, Zieba JK, Foegeding NJ, Torres TP, Shelton CD, Shealy NG, Byndloss AJ, Cevallos SA, Gertz E, Tiffany CR, Thomas JD, Litvak Y, Nguyen H, Olsan EE, Bennett BJ, Rathmell JC, Major AS, Bäumler AJ, Byndloss MX. High-fat diet-induced colonocyte dysfunction escalates microbiota-derived trimethylamine N-oxide. Science 2021; 373:813-818. [PMID: 34385401 DOI: 10.1126/science.aba3683] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/18/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022]
Abstract
A Western-style, high-fat diet promotes cardiovascular disease, in part because it is rich in choline, which is converted to trimethylamine (TMA) by the gut microbiota. However, whether diet-induced changes in intestinal physiology can alter the metabolic capacity of the microbiota remains unknown. Using a mouse model of diet-induced obesity, we show that chronic exposure to a high-fat diet escalates Escherichia coli choline catabolism by altering intestinal epithelial physiology. A high-fat diet impaired the bioenergetics of mitochondria in the colonic epithelium to increase the luminal bioavailability of oxygen and nitrate, thereby intensifying respiration-dependent choline catabolism of E. coli In turn, E. coli choline catabolism increased levels of circulating trimethlamine N-oxide, which is a potentially harmful metabolite generated by gut microbiota.
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Affiliation(s)
- Woongjae Yoo
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jacob K Zieba
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nora J Foegeding
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Teresa P Torres
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Catherine D Shelton
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicolas G Shealy
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Austin J Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Stephanie A Cevallos
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Erik Gertz
- Department of Biological Sciences, California State University, Sacramento, CA 95819, USA.,Agriculture Research Service (ARS-USDA), University of California at Davis, Davis, CA 95616, USA.,Department of Nutrition, University of California at Davis, Davis, CA 95616, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Julia D Thomas
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yael Litvak
- Department of Nutrition, University of California at Davis, Davis, CA 95616, USA.,Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem 9190401, Israel
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Erin E Olsan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA.,Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA.,Department of Biological Sciences, California State University, Sacramento, CA 95819, USA
| | - Brian J Bennett
- Department of Biological Sciences, California State University, Sacramento, CA 95819, USA.,Agriculture Research Service (ARS-USDA), University of California at Davis, Davis, CA 95616, USA.,Department of Nutrition, University of California at Davis, Davis, CA 95616, USA
| | - Jeffrey C Rathmell
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Amy S Major
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Agriculture Research Service (ARS-USDA), University of California at Davis, Davis, CA 95616, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA.
| | - Mariana X Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA. .,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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16
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Tiffany CR, Lee JY, Rogers AWL, Olsan EE, Morales P, Faber F, Bäumler AJ. The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum. Microbiome 2021; 9:174. [PMID: 34412707 PMCID: PMC8375055 DOI: 10.1186/s40168-021-01123-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/25/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND The catabolic activity of the microbiota contributes to health by aiding in nutrition, immune education, and niche protection against pathogens. However, the nutrients consumed by common taxa within the gut microbiota remain incompletely understood. METHODS Here we combined microbiota profiling with an un-targeted metabolomics approach to determine whether depletion of small metabolites in the cecum of mice correlated with the presence of specific bacterial taxa. Causality was investigated by engrafting germ-free or antibiotic-treated mice with complex or defined microbial communities. RESULTS We noted that a depletion of Clostridia and Erysipelotrichia from the gut microbiota triggered by antibiotic treatment was associated with an increase in the cecal concentration of sugar acids and sugar alcohols (polyols). Notably, when we inoculated germ-free mice with a defined microbial community of 14 Clostridia and 3 Erysipelotrichia isolates, we observed the inverse, with a marked decrease in the concentrations of sugar acids and polyols in cecal contents. The carbohydrate footprint produced by the defined microbial community was similar to that observed in gnotobiotic mice receiving a cecal microbiota transplant from conventional mice. Supplementation with sorbitol, a polyol used as artificial sweetener, increased cecal sorbitol concentrations in antibiotic-treated mice, which was abrogated after inoculation with a Clostridia isolate able to grow on sorbitol in vitro. CONCLUSIONS We conclude that consumption of sugar alcohols by Clostridia and Erysipelotrichia species depletes these metabolites from the intestinal lumen during homeostasis. Video abstract.
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Affiliation(s)
- Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Andrew W L Rogers
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Erin E Olsan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
- Present Address: Department of Biological Sciences, California State University Sacramento, 6000 J Street, Sacramento, CA, 95819, USA
| | - Pavel Morales
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Franziska Faber
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
- Present Address: Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, Josef-Schneider-Street 2/D15, 97080, Würzburg, Germany
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
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17
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Miller BM, Liou MJ, Zhang LF, Nguyen H, Litvak Y, Schorr EM, Jang KK, Tiffany CR, Butler BP, Bäumler AJ. Anaerobic Respiration of NOX1-Derived Hydrogen Peroxide Licenses Bacterial Growth at the Colonic Surface. Cell Host Microbe 2021; 28:789-797.e5. [PMID: 33301718 DOI: 10.1016/j.chom.2020.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/14/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022]
Abstract
The colonic microbiota exhibits cross-sectional heterogeneity, but the mechanisms that govern its spatial organization remain incompletely understood. Here we used Citrobacter rodentium, a pathogen that colonizes the colonic surface, to identify microbial traits that license growth and survival in this spatial niche. Previous work showed that during colonic crypt hyperplasia, type III secretion system (T3SS)-mediated intimate epithelial attachment provides C. rodentium with oxygen for aerobic respiration. However, we find that prior to the development of colonic crypt hyperplasia, T3SS-mediated intimate attachment is not required for aerobic respiration but for hydrogen peroxide (H2O2) respiration using cytochrome c peroxidase (Ccp). The epithelial NADPH oxidase NOX1 is the primary source of luminal H2O2 early after C. rodentium infection and is required for Ccp-dependent growth. Our results suggest that NOX1-derived H2O2 is a resource that governs bacterial growth and survival in close proximity to the mucosal surface during gut homeostasis.
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Affiliation(s)
- Brittany M Miller
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Megan J Liou
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Lillian F Zhang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA; Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem 9190401, Israel
| | - Eva-Magdalena Schorr
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kyung Ku Jang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA; Present address: Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Brian P Butler
- Department of Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA.
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18
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Abstract
An imbalance in the microbiota may contribute to many human illnesses, which has prompted efforts to rebalance it by targeting the microbes themselves. However, by supplying the habitat, the host wields a prominent influence over microbial growth at body surfaces, raising the possibility that rebalancing the microbiota by targeting our immune system would be a viable alternative. Host control mechanisms that sculpt the microbial habitat form a functional unit with the microbiota, termed microbiota-nourishing immunity, that confers colonization resistance against pathogens. The host components of microbiota-nourishing immunity can be viewed as habitat filters that select for microbial traits licensing growth and survival in host habitat patches. Here we review current knowledge of how host-derived habitat filters shape the size, species composition, and spatial heterogeneity of the microbiota and discuss whether these host control mechanisms could be harnessed for developing approaches to rebalance microbial communities during dysbiosis.
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Affiliation(s)
- Brittany M Miller
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA;
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA;
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19
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Lee JY, Cevallos SA, Byndloss MX, Tiffany CR, Olsan EE, Butler BP, Young BM, Rogers AWL, Nguyen H, Kim K, Choi SW, Bae E, Lee JH, Min UG, Lee DC, Bäumler AJ. High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease. Cell Host Microbe 2020; 28:273-284.e6. [PMID: 32668218 DOI: 10.1016/j.chom.2020.06.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/25/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022]
Abstract
The clinical spectra of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) intersect to form a scantily defined overlap syndrome, termed pre-IBD. We show that increased Enterobacteriaceae and reduced Clostridia abundance distinguish the fecal microbiota of pre-IBD patients from IBS patients. A history of antibiotics in individuals consuming a high-fat diet was associated with the greatest risk for pre-IBD. Exposing mice to these risk factors resulted in conditions resembling pre-IBD and impaired mitochondrial bioenergetics in the colonic epithelium, which triggered dysbiosis. Restoring mitochondrial bioenergetics in the colonic epithelium with 5-amino salicylic acid, a PPAR-γ (peroxisome proliferator-activated receptor gamma) agonist that stimulates mitochondrial activity, ameliorated pre-IBD symptoms. As with patients, mice with pre-IBD exhibited notable expansions of Enterobacteriaceae that exacerbated low-grade mucosal inflammation, suggesting that remediating dysbiosis can alleviate inflammation. Thus, environmental risk factors cooperate to impair epithelial mitochondrial bioenergetics, thereby triggering microbiota disruptions that exacerbate inflammation and distinguish pre-IBD from IBS.
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Affiliation(s)
- Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA; Chaum Life Center, CHA Bundang Medical Center, School of Medicine, CHA University, Seoul 06062, Republic of Korea; Department of Family Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Stephanie A Cevallos
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Erin E Olsan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Brian P Butler
- School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Briana M Young
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Andrew W L Rogers
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kyongchol Kim
- Chaum Life Center, CHA Bundang Medical Center, School of Medicine, CHA University, Seoul 06062, Republic of Korea
| | - Sang-Woon Choi
- Chaum Life Center, CHA Bundang Medical Center, School of Medicine, CHA University, Seoul 06062, Republic of Korea
| | - Eunsoo Bae
- Chaum Life Center, CHA Bundang Medical Center, School of Medicine, CHA University, Seoul 06062, Republic of Korea
| | - Je Hee Lee
- ChunLab, Inc., Seoul 06725, Republic of Korea
| | - Ui-Gi Min
- ChunLab, Inc., Seoul 06725, Republic of Korea
| | - Duk-Chul Lee
- Department of Family Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA.
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20
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Tsolis RM, Bäumler AJ. Gastrointestinal host-pathogen interaction in the age of microbiome research. Curr Opin Microbiol 2020; 53:78-89. [PMID: 32344325 DOI: 10.1016/j.mib.2020.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
The microbiota is linked to human health by governing susceptibility to infection. However, the interplay between enteric pathogens, the host, and its microbiota is complex, encompassing host cell manipulation by virulence factors, immune responses, and a diverse gut ecosystem. The host represents a foundation species that uses its immune system as a habitat filter to shape the gut microbiota. In turn, the gut microbiota protects against ecosystem invasion by opportunistic pathogens through priority effects that are based on niche modification or niche preemption. Frank pathogens can overcome these priority effects by using their virulence factors to manipulate host-derived habitat filters, thereby constructing new nutrient-niches in the intestinal lumen that support ecosystem invasion. The emerging picture identifies pathogens as ecosystem engineers and suggests that virulence factors are useful tools for identifying host-derived habitat filters that balance the microbiota.
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Affiliation(s)
- Renée M Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA.
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21
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Pusceddu MM, Barboza M, Keogh CE, Schneider M, Stokes P, Sladek JA, Kim HJD, Torres-Fuentes C, Goldfild LR, Gillis SE, Brust-Mascher I, Rabasa G, Wong KA, Lebrilla C, Byndloss MX, Maisonneuve C, Bäumler AJ, Philpott DJ, Ferrero RL, Barrett KE, Reardon C, Gareau MG. Nod-like receptors are critical for gut-brain axis signalling in mice. J Physiol 2019; 597:5777-5797. [PMID: 31652348 DOI: 10.1113/jp278640] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
KEY POINTS •Nucleotide binding oligomerization domain (Nod)-like receptors regulate cognition, anxiety and hypothalamic-pituitary-adrenal axis activation. •Nod-like receptors regulate central and peripheral serotonergic biology. •Nod-like receptors are important for maintenance of gastrointestinal physiology. •Intestinal epithelial cell expression of Nod1 receptors regulate behaviour. ABSTRACT Gut-brain axis signalling is critical for maintaining health and homeostasis. Stressful life events can impact gut-brain signalling, leading to altered mood, cognition and intestinal dysfunction. In the present study, we identified nucleotide binding oligomerization domain (Nod)-like receptors (NLR), Nod1 and Nod2, as novel regulators for gut-brain signalling. NLR are innate immune pattern recognition receptors expressed in the gut and brain, and are important in the regulation of gastrointestinal physiology. We found that mice deficient in both Nod1 and Nod2 (NodDKO) demonstrate signs of stress-induced anxiety, cognitive impairment and depression in the context of a hyperactive hypothalamic-pituitary-adrenal axis. These deficits were coupled with impairments in the serotonergic pathway in the brain, decreased hippocampal cell proliferation and immature neurons, as well as reduced neural activation. In addition, NodDKO mice had increased gastrointestinal permeability and altered serotonin signalling in the gut following exposure to acute stress. Administration of the selective serotonin reuptake inhibitor, fluoxetine, abrogated behavioural impairments and restored serotonin signalling. We also identified that intestinal epithelial cell-specific deletion of Nod1 (VilCre+ Nod1f/f ), but not Nod2, increased susceptibility to stress-induced anxiety-like behaviour and cognitive impairment following exposure to stress. Together, these data suggest that intestinal epithelial NLR are novel modulators of gut-brain communication and may serve as potential novel therapeutic targets for the treatment of gut-brain disorders.
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Affiliation(s)
- Matteo M Pusceddu
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Mariana Barboza
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Ciara E Keogh
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Melinda Schneider
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Patricia Stokes
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Jessica A Sladek
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Hyun Jung D Kim
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Cristina Torres-Fuentes
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.,Department of Food Science & Technology, University of California Davis, Davis, CA, USA
| | - Lily R Goldfild
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Shane E Gillis
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Ingrid Brust-Mascher
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Gonzalo Rabasa
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Kyle A Wong
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Carlito Lebrilla
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA
| | | | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA
| | - Dana J Philpott
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Richard L Ferrero
- Hudson Institute of Medical Research, Department of Molecular and Translational Science and Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Kim E Barrett
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Colin Reardon
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Mélanie G Gareau
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
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22
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Abstract
Advances in data collection technologies reveal that an imbalance (dysbiosis) in the composition of host-associated microbial communities (microbiota) is linked to many human illnesses. This association makes dysbiosis a central concept for understanding how the human microbiota contributes to health and disease. However, it remains problematic to define the term dysbiosis by cataloguing microbial species names. Here, we discuss how incorporating the germ-organ concept, ecological assumptions, and immunological principles into a theoretical framework for microbiota research provides a functional definition for dysbiosis. The generation of such a framework suggests that the next logical step in microbiota research will be to illuminate the mechanistic underpinnings of dysbiosis, which often involves a weakening of immune mechanisms that balance our microbial communities.
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Affiliation(s)
- Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis California
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis California
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23
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Cevallos SA, Lee JY, Tiffany CR, Byndloss AJ, Johnston L, Byndloss MX, Bäumler AJ. Increased Epithelial Oxygenation Links Colitis to an Expansion of Tumorigenic Bacteria. mBio 2019; 10:e02244-19. [PMID: 31575772 PMCID: PMC6775460 DOI: 10.1128/mbio.02244-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022] Open
Abstract
Intestinal inflammation is a risk factor for colorectal cancer formation, but the underlying mechanisms remain unknown. Here, we investigated whether colitis alters the colonic microbiota to enhance its cancer-inducing activity. Colitis increased epithelial oxygenation in the colon of mice and drove an expansion of Escherichia coli within the gut-associated microbial community through aerobic respiration. An aerobic expansion of colibactin-producing E. coli was required for the cancer-inducing activity of this pathobiont in a mouse model of colitis-associated colorectal cancer formation. We conclude that increased epithelial oxygenation in the colon is associated with an expansion of a prooncogenic driver species, thereby increasing the cancer-inducing activity of the microbiota.IMPORTANCE One of the environmental factors important for colorectal cancer formation is the gut microbiota, but the habitat filters that control its cancer-inducing activity remain unknown. Here, we show that chemically induced colitis elevates epithelial oxygenation in the colon, thereby driving an expansion of colibactin-producing Escherichia coli, a prooncogenic driver species. These data suggest that elevated epithelial oxygenation is a potential risk factor for colorectal cancer formation because the consequent changes in the gut habitat escalate the cancer-inducing activity of the microbiota.
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Affiliation(s)
- Stephanie A Cevallos
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Austin J Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Luana Johnston
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
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24
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25
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Hiyoshi H, Wangdi T, Lock G, Saechao C, Raffatellu M, Cobb BA, Bäumler AJ. Mechanisms to Evade the Phagocyte Respiratory Burst Arose by Convergent Evolution in Typhoidal Salmonella Serovars. Cell Rep 2019; 22:1787-1797. [PMID: 29444431 PMCID: PMC5826628 DOI: 10.1016/j.celrep.2018.01.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 12/20/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022] Open
Abstract
Typhoid fever caused by Salmonella enterica serovar (S.) Typhi differs in its clinical presentation from gastroenteritis caused by S. Typhimurium and other non-typhoidal Salmonella serovars. The different clinical presentations are attributed in part to the virulence-associated capsular polysaccharide (Vi antigen) of S. Typhi, which prevents phagocytes from triggering a respiratory burst by preventing antibody-mediated complement activation. Paradoxically, the Vi antigen is absent from S. Paratyphi A, which causes a disease that is indistinguishable from typhoid fever. Here, we show that evasion of the phagocyte respiratory burst by S. Paratyphi A required very long O antigen chains containing the O2 antigen to inhibit antibody binding. We conclude that the ability to avoid the phagocyte respiratory burst is a property distinguishing typhoidal from non-typhoidal Salmonella serovars that was acquired by S. Typhi and S. Paratyphi A independently through convergent evolution.
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Affiliation(s)
- Hirotaka Hiyoshi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Tamding Wangdi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA.
| | - Gabriel Lock
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Cheng Saechao
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Manuela Raffatellu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian A Cobb
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA.
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26
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Abstract
An imbalance in our microbiota may contribute to many human diseases, but the mechanistic underpinnings of dysbiosis remain poorly understood. We argue that dysbiosis is secondary to a defect in microbiota-nourishing immunity, a part of our immune system that balances the microbiota to attain colonization resistance against environmental exposure to microorganisms. We discuss this new hypothesis and its implications for ulcerative colitis, an inflammatory bowel disease of the large intestine.
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Affiliation(s)
- Mariana X Byndloss
- Vanderbilt Institute for Infection, Immunology, and Inflammation and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
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27
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Abstract
An imbalance in the colonic microbiota might underlie many human diseases, but the mechanisms that maintain homeostasis remain elusive. Recent insights suggest that colonocyte metabolism functions as a control switch, mediating a shift between homeostatic and dysbiotic communities. During homeostasis, colonocyte metabolism is directed toward oxidative phosphorylation, resulting in high epithelial oxygen consumption. The consequent epithelial hypoxia helps to maintain a microbial community dominated by obligate anaerobic bacteria, which provide benefit by converting fiber into fermentation products absorbed by the host. Conditions that alter the metabolism of the colonic epithelium increase epithelial oxygenation, thereby driving an expansion of facultative anaerobic bacteria, a hallmark of dysbiosis in the colon. Enteric pathogens subvert colonocyte metabolism to escape niche protection conferred by the gut microbiota. The reverse strategy, a metabolic reprogramming to restore colonocyte hypoxia, represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.
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Affiliation(s)
- Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.
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28
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Velazquez EM, Nguyen H, Heasley KT, Saechao CH, Gil LM, Rogers AWL, Miller BM, Rolston MR, Lopez CA, Litvak Y, Liou MJ, Faber F, Bronner DN, Tiffany CR, Byndloss MX, Byndloss AJ, Bäumler AJ. Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection. Nat Microbiol 2019; 4:1057-1064. [PMID: 30911125 PMCID: PMC6533147 DOI: 10.1038/s41564-019-0407-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 02/11/2019] [Indexed: 12/16/2022]
Abstract
Lack of reproducibility is a prominent problem in biomedical research. An important source of variation in animal experiments is the microbiome, but little is known about specific changes in the microbiota composition that cause phenotypic differences. Here we show that genetically similar laboratory mice obtained from four different commercial vendors exhibited marked phenotypic variation in their susceptibility to Salmonella infection. Fecal microbiota transplantation into germ-free mice replicated donor susceptibility, revealing that variability was due to changes in the gut microbiota composition. Co-housing of mice only partially transferred protection against Salmonella infection, suggesting that minority species within the gut microbiota might confer this trait. Consistent with this idea, we identified endogenous Enterobacteriaceae, a low abundance taxon, as keystone species responsible for variation in the susceptibility to Salmonella infection. Protection conferred by endogenous Enterobacteriaceae could be modeled by inoculating mice with probiotic Escherichia coli, which conferred resistance by using its aerobic metabolism to compete with Salmonella for resources. We conclude that a mechanistic understanding of phenotypic variation can accelerate development of strategies for enhancing the reproducibility of animal experiments.
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Affiliation(s)
- Eric M Velazquez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Keaton T Heasley
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Cheng H Saechao
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Lindsey M Gil
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andrew W L Rogers
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Brittany M Miller
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Matthew R Rolston
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Megan J Liou
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Franziska Faber
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Denise N Bronner
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Austin J Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.
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29
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Affiliation(s)
- Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United States of America
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United States of America
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30
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Sorbara MT, Dubin K, Littmann ER, Moody TU, Fontana E, Seok R, Leiner IM, Taur Y, Peled JU, van den Brink MRM, Litvak Y, Bäumler AJ, Chaubard JL, Pickard AJ, Cross JR, Pamer EG. Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification. J Exp Med 2018; 216:84-98. [PMID: 30563917 PMCID: PMC6314524 DOI: 10.1084/jem.20181639] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/26/2018] [Accepted: 12/07/2018] [Indexed: 12/17/2022] Open
Abstract
Klebsiella pneumoniae, Escherichia coli, and other members of the Enterobacteriaceae family are common human pathogens that have acquired broad antibiotic resistance, rendering infection by some strains virtually untreatable. Enterobacteriaceae are intestinal residents, but generally represent <1% of the adult colonic microbiota. Antibiotic-mediated destruction of the microbiota enables Enterobacteriaceae to expand to high densities in the colon, markedly increasing the risk of bloodstream invasion, sepsis, and death. Here, we demonstrate that an antibiotic-naive microbiota suppresses growth of antibiotic-resistant clinical isolates of Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis by acidifying the proximal colon and triggering short chain fatty acid (SCFA)-mediated intracellular acidification. High concentrations of SCFAs and the acidic environment counter the competitive edge that O2 and NO3 respiration confer upon Enterobacteriaceae during expansion. Reestablishment of a microbiota that produces SCFAs enhances clearance of Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis from the intestinal lumen and represents a potential therapeutic approach to enhance clearance of antibiotic-resistant pathogens.
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Affiliation(s)
- Matthew T Sorbara
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY .,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Krista Dubin
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Eric R Littmann
- Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Thomas U Moody
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emily Fontana
- Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ruth Seok
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ingrid M Leiner
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.,Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Taur
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Jonathan U Peled
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, University of California, Davis School of Medicine, Davis, CA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, University of California, Davis School of Medicine, Davis, CA
| | - Jean-Luc Chaubard
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amanda J Pickard
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eric G Pamer
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY .,Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
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31
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Abstract
Dual RNA-seq has emerged as a genome-wide expression profiling technique, simultaneously measuring RNA transcript levels in a given host and its pathogen during an infection. Recently, the method was transferred from cell culture to in vivo models of bacterial infections; however, specific host cell-type resolution has not yet been achieved. Here we present a detailed protocol that describes the application of Dual RNA-seq to murine colonocytes isolated from mice infected with the enteric pathogen Salmonella Typhimurium. At day 5 after oral infection, the mice were humanely euthanized, their colons extracted, and colonocytes isolated and fixed. Upon antibody staining of cell type-specific surface markers, the fraction of Salmonella-invaded colonocytes was collected by fluorescence-activated cell sorting based on a fluorescent signal emitted by the internalized bacteria. Total RNA was extracted from cells enriched by this method, and ribosomal transcripts from host and microbial cells were removed prior to cDNA synthesis and library generation. We compared different protocols for library preparation and discuss their respective advantages and caveats when applied to minute RNA amounts that constitute an inherent challenge for in vivo transcriptomics. Our results introduce an ultralow input protocol that holds promise for cell type-specific in vivo Dual RNA-seq for charting gene expression of a bacterial pathogen within its respective in vivo niche, along with the consequent host response.
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Affiliation(s)
- Lutz Frönicke
- University of California Davis Genome Center, Davis, CA, United States
| | - Denise N Bronner
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Bridget McLaughlin
- Comprehensive Cancer Center Flow Cytometry Shared Resource, University of California Davis, Davis, CA, United States
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Alexander J Westermann
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany.
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32
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Byndloss MX, Pernitzsch SR, Bäumler AJ. Healthy hosts rule within: ecological forces shaping the gut microbiota. Mucosal Immunol 2018; 11:1299-1305. [PMID: 29743614 DOI: 10.1038/s41385-018-0010-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/05/2018] [Indexed: 02/04/2023]
Abstract
A balanced gut microbiota is important for human health, but the mechanisms that maintain homeostasis are incompletely understood. Recent insights suggest the host plays a key role in shaping its gut microbiota to be beneficial. While host control in the small intestine curbs bacterial numbers to avoid competition for simple sugars and amino acids, the host limits oxygen availability in the large intestine to obtain microbial fermentation products from fiber. Epithelial cells are major players in imposing ecological control mechanisms, which involves the release of antimicrobial peptides by small-intestinal Paneth cells and maintenance of luminal anaerobiosis by epithelial hypoxia in the colon. Harnessing these epithelial control mechanisms for therapeutic means could provide a novel lynchpin for strategies to remediate dysbiosis.
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Affiliation(s)
- Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | | | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
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33
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Bronner DN, Faber F, Olsan EE, Byndloss MX, Sayed NA, Xu G, Yoo W, Kim D, Ryu S, Lebrilla CB, Bäumler AJ. Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease. Cell Host Microbe 2018; 23:266-273.e4. [PMID: 29447698 DOI: 10.1016/j.chom.2018.01.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 11/11/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
Abstract
Salmonella enterica serovar (S.) Typhi is an extraintestinal pathogen that evolved from Salmonella serovars causing gastrointestinal disease. Compared with non-typhoidal Salmonella serovars, the genomes of typhoidal serovars contain various loss-of-function mutations. However, the contribution of these genetic differences to this shift in pathogen ecology remains unknown. We show that the ydiQRSTD operon, which is deleted in S. Typhi, enables S. Typhimurium to utilize microbiota-derived butyrate during gastrointestinal disease. Unexpectedly, genetic ablation of butyrate utilization reduces S. Typhimurium epithelial invasion and attenuates intestinal inflammation. Deletion of ydiD renders S. Typhimurium sensitive to butyrate-mediated repression of invasion gene expression. Combined with the gain of virulence-associated (Vi) capsular polysaccharide and loss of very-long O-antigen chains, two features characteristic of S. Typhi, genetic ablation of butyrate utilization abrogates S. Typhimurium-induced intestinal inflammation. Thus, the transition from a gastrointestinal to an extraintestinal pathogen involved discrete genetic changes, providing insights into pathogen evolution and emergence.
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Affiliation(s)
- Denise N Bronner
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Franziska Faber
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Erin E Olsan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Nada A Sayed
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Gege Xu
- Department of Chemistry, College of Letters and Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Woongjae Yoo
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Dajeong Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Carlito B Lebrilla
- Department of Chemistry, College of Letters and Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
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Sheng L, Jena PK, Liu HX, Hu Y, Nagar N, Bronner DN, Settles ML, Bäumler AJ, Wan YJY. Obesity treatment by epigallocatechin-3-gallate-regulated bile acid signaling and its enriched Akkermansia muciniphila. FASEB J 2018; 32:fj201800370R. [PMID: 29882708 PMCID: PMC6219838 DOI: 10.1096/fj.201800370r] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/14/2018] [Indexed: 12/21/2022]
Abstract
Dysregulated bile acid (BA) synthesis is accompanied by dysbiosis, leading to compromised metabolism. This study analyzes the effect of epigallocatechin-3-gallate (EGCG) on diet-induced obesity through regulation of BA signaling and gut microbiota. The data revealed that EGCG effectively reduced diet-increased obesity, visceral fat, and insulin resistance. Gene profiling data showed that EGCG had a significant impact on regulating genes implicated in fatty acid uptake, adipogenesis, and metabolism in the adipose tissue. In addition, metabolomics analysis revealed that EGCG altered the lipid and sugar metabolic pathways. In the intestine, EGCG reduced the FXR agonist chenodeoxycholic acid, as well as the FXR-regulated pathway, suggesting intestinal FXR deactivation. However, in the liver, EGCG increased the concentration of FXR and TGR-5 agonists and their regulated signaling. Furthermore, our data suggested that EGCG activated Takeda G protein receptor (TGR)-5 based on increased GLP-1 release and elevated serum PYY level. EGCG and antibiotics had distinct antibacterial effects. They also differentially altered body weight and BA composition. EGCG, but not antibiotics, increased Verrucomicrobiaceae, under which EGCG promoted intestinal bloom of Akkermansia muciniphila. Excitingly, A. muciniphila was as effective as EGCG in treating diet-induced obesity. Together, EGCG shifts gut microbiota and regulates BA signaling thereby having a metabolic beneficial effect.-Sheng, L., Jena, P. K., Liu, H.-X., Hu, Y., Nagar, N., Bronner, D. N., Settles, M. L., Bäumler, A. J. Wan, Y.-J. Y. Obesity treatment by epigallocatechin-3-gallate-regulated bile acid signaling and its enriched Akkermansia muciniphila.
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Affiliation(s)
- Lili Sheng
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Prasant Kumar Jena
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Hui-Xin Liu
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Ying Hu
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Nidhi Nagar
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Denise N. Bronner
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Matthew L. Settles
- Bioinformatics Core Facility in the Genome Center, University of California, Davis, Davis, California, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Yu-Jui Yvonne Wan
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
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Hiyoshi H, Tiffany CR, Bronner DN, Bäumler AJ. Typhoidal Salmonella serovars: ecological opportunity and the evolution of a new pathovar. FEMS Microbiol Rev 2018; 42:527-541. [DOI: 10.1093/femsre/fuy024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/19/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Hirotaka Hiyoshi
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Connor R Tiffany
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Denise N Bronner
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
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Abstract
Gut dysbiosis is associated with many non-communicable human diseases, but the mechanisms maintaining homeostasis remain incompletely understood. Recent insights suggest that during homeostasis, epithelial hypoxia limits oxygen availability in the colon, thereby maintaining a balanced microbiota that functions as a microbial organ, producing metabolites contributing to host nutrition, immune education and niche protection. Dysbiosis is characterized by a shift in the microbial community structure from obligate to facultative anaerobes, suggesting oxygen as an important ecological driver of microbial organ dysfunction. The ensuing disruption of gut homeostasis can lead to non- communicable disease because microbiota-derived metabolites are either depleted or generated at harmful concentrations. This Opinion article describes the concept that host control over the microbial ecosystem in the colon is critical for the composition and function of our microbial organ, which provides a theoretical framework for linking microorganisms to non-communicable diseases.
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Affiliation(s)
- Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA
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Zhu W, Winter MG, Byndloss MX, Spiga L, Duerkop BA, Hughes ER, Büttner L, de Lima Romão E, Behrendt CL, Lopez CA, Sifuentes-Dominguez L, Huff-Hardy K, Wilson RP, Gillis CC, Tükel Ç, Koh AY, Burstein E, Hooper LV, Bäumler AJ, Winter SE. Precision editing of the gut microbiota ameliorates colitis. Nature 2018; 553:208-211. [PMID: 29323293 DOI: 10.1038/nature25172] [Citation(s) in RCA: 325] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/24/2017] [Indexed: 12/30/2022]
Abstract
Inflammatory diseases of the gastrointestinal tract are frequently associated with dysbiosis, characterized by changes in gut microbial communities that include an expansion of facultative anaerobic bacteria of the Enterobacteriaceae family (phylum Proteobacteria). Here we show that a dysbiotic expansion of Enterobacteriaceae during gut inflammation could be prevented by tungstate treatment, which selectively inhibited molybdenum-cofactor-dependent microbial respiratory pathways that are operational only during episodes of inflammation. By contrast, we found that tungstate treatment caused minimal changes in the microbiota composition under homeostatic conditions. Notably, tungstate-mediated microbiota editing reduced the severity of intestinal inflammation in mouse models of colitis. We conclude that precision editing of the microbiota composition by tungstate treatment ameliorates the adverse effects of dysbiosis in the inflamed gut.
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Affiliation(s)
- Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Breck A Duerkop
- Department of Immunology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Elizabeth R Hughes
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Lisa Büttner
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Everton de Lima Romão
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Cassie L Behrendt
- Department of Immunology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Luis Sifuentes-Dominguez
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Kayci Huff-Hardy
- Department of Internal Medicine, Division of Digestive & Liver Diseases, University of Texas Southwestern Medical Center 75390, 5323 Harry Hines Boulevard, Dallas, Texas, USA
| | - R Paul Wilson
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, 1801 North Broad Street, Philadelphia, Pennsylvania 19122, USA
| | - Caroline C Gillis
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Çagla Tükel
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, 1801 North Broad Street, Philadelphia, Pennsylvania 19122, USA
| | - Andrew Y Koh
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Ezra Burstein
- Department of Internal Medicine, Division of Digestive & Liver Diseases, University of Texas Southwestern Medical Center 75390, 5323 Harry Hines Boulevard, Dallas, Texas, USA
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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Byndloss MX, Olsan EE, Rivera-Chávez F, Tiffany CR, Cevallos SA, Lokken KL, Torres TP, Byndloss AJ, Faber F, Gao Y, Litvak Y, Lopez CA, Xu G, Napoli E, Giulivi C, Tsolis RM, Revzin A, Lebrilla CB, Bäumler AJ. Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 2017; 357:570-575. [PMID: 28798125 DOI: 10.1126/science.aam9949] [Citation(s) in RCA: 634] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/22/2017] [Indexed: 12/12/2022]
Abstract
Perturbation of the gut-associated microbial community may underlie many human illnesses, but the mechanisms that maintain homeostasis are poorly understood. We found that the depletion of butyrate-producing microbes by antibiotic treatment reduced epithelial signaling through the intracellular butyrate sensor peroxisome proliferator-activated receptor γ (PPAR-γ). Nitrate levels increased in the colonic lumen because epithelial expression of Nos2, the gene encoding inducible nitric oxide synthase, was elevated in the absence of PPAR-γ signaling. Microbiota-induced PPAR-γ signaling also limits the luminal bioavailability of oxygen by driving the energy metabolism of colonic epithelial cells (colonocytes) toward β-oxidation. Therefore, microbiota-activated PPAR-γ signaling is a homeostatic pathway that prevents a dysbiotic expansion of potentially pathogenic Escherichia and Salmonella by reducing the bioavailability of respiratory electron acceptors to Enterobacteriaceae in the lumen of the colon.
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Affiliation(s)
- Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Erin E Olsan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Fabian Rivera-Chávez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Stephanie A Cevallos
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Kristen L Lokken
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Teresa P Torres
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Austin J Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Franziska Faber
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Yandong Gao
- Department of Biomedical Engineering, College of Engineering, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Gege Xu
- Department of Chemistry, College of Letters and Sciences, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Alexander Revzin
- Department of Biomedical Engineering, College of Engineering, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, College of Letters and Sciences, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
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Litvak Y, Byndloss MX, Tsolis RM, Bäumler AJ. Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction. Curr Opin Microbiol 2017; 39:1-6. [PMID: 28783509 DOI: 10.1016/j.mib.2017.07.003] [Citation(s) in RCA: 329] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/14/2017] [Indexed: 12/19/2022]
Abstract
A balanced gut microbiota is important for health, but the mechanisms maintaining homeostasis are incompletely understood. Anaerobiosis of the healthy colon drives the composition of the gut microbiota towards a dominance of obligate anaerobes, while dysbiosis is often associated with a sustained increase in the abundance of facultative anaerobic Proteobacteria, indicative of a disruption in anaerobiosis. The colonic epithelium is hypoxic, but intestinal inflammation or antibiotic treatment increases epithelial oxygenation in the colon, thereby disrupting anaerobiosis to drive a dysbiotic expansion of facultative anaerobic Proteobacteria through aerobic respiration. These observations suggest a dysbiotic expansion of Proteobacteria is a potential diagnostic microbial signature of epithelial dysfunction, a hypothesis that could spawn novel preventative or therapeutic strategies for a broad spectrum of human diseases.
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Affiliation(s)
- Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA.
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Abstract
Carbapenemase-producing Enterobacteriaceae are an emerging threat to hospitals worldwide, and antibiotic exposure is a risk factor for developing fecal carriage that may lead to nosocomial infection. Here, we review how antibiotics reduce colonization resistance against Enterobacteriaceae to pinpoint possible control points for curbing their spread. Recent work identifies host-derived respiratory electron acceptors as a critical resource driving a post-antibiotic expansion of Enterobacteriaceae within the large bowel. By providing a conceptual framework for colonization resistance against Enterobacteriaceae, these mechanistic insights point to the metabolism of epithelial cells as a possible target for intervention strategies.
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Affiliation(s)
- Erin E Olsan
- From the Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California 95616
| | - Mariana X Byndloss
- From the Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California 95616
| | - Franziska Faber
- From the Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California 95616
| | - Fabian Rivera-Chávez
- From the Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California 95616
| | - Renée M Tsolis
- From the Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California 95616
| | - Andreas J Bäumler
- From the Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California 95616
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Abstract
Changes in the composition of gut-associated microbial communities may underlie many inflammatory and allergic diseases. However, the processes that help maintain a stable community structure are poorly understood. Here we review topical work elucidating the nutrient-niche occupied by facultative anaerobic bacteria of the family Enterobacteriaceae, whose predominance within the gut-associated microbial community is a common marker of dysbiosis. A paucity of exogenous respiratory electron acceptors limits growth of Enterobacteriaceae within a balanced gut-associated microbial community. However, recent studies suggest that the availability of oxygen in the large bowel is markedly elevated by changes in host physiology that accompany antibiotic treatment or infection with enteric pathogens, such as Salmonella serovars or attaching and effacing (AE) pathogens. The resulting increase in oxygen availability, alone or in conjunction with other electron acceptors, drives an uncontrolled luminal expansion of Enterobacteriaceae. Insights into the underlying mechanisms provide important clues about factors that control the balance between the host and its resident microbial communities.
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Affiliation(s)
- Fabian Rivera-Chávez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA.
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Elfenbein JR, Knodler LA, Schaeffer AR, Faber F, Bäumler AJ, Andrews-Polymenis HL. A Salmonella Regulator Modulates Intestinal Colonization and Use of Phosphonoacetic Acid. Front Cell Infect Microbiol 2017; 7:69. [PMID: 28361036 PMCID: PMC5351497 DOI: 10.3389/fcimb.2017.00069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/23/2017] [Indexed: 11/21/2022] Open
Abstract
Many microorganisms produce phosphonates, molecules characterized by stable carbon-phosphorus bonds that store phosphorus or act as antimicrobials. The role of phosphonates in the marine biosphere is well characterized but the role of these molecules in the intestine is poorly understood. Salmonella enterica uses its virulence factors to influence the host immune response to compete with the host and normal microflora for nutrients. Salmonella cannot produce phosphonates but encodes the enzymes to use them suggesting that it is exposed to phosphonates during its life cycle. The role of phosphonates during enteric salmonellosis is unexplored. We have previously shown that STM3602, encoding a putative regulator of phosphonate metabolism, is needed for colonization in calves. Here, we report that the necessity of STM3602 in colonization of the murine intestine results from multiple factors. STM3602 is needed for full activation of the type-3 secretion system-1 and for optimal invasion of epithelial cells. The ΔSTM3602 mutant grows poorly in phosphonoacetic acid (PA) as the sole phosphorus source, but can use 2-aminoethylphosphonate. PhnA, an enzyme required for PA breakdown, is not controlled by STM3602 suggesting an additional mechanism for utilization of PA in S. Typhimurium. Finally, the requirement of STM3602 for intestinal colonization differs depending on the composition of the microflora. Our data suggest that STM3602 has multiple regulatory targets that are necessary for survival within the microbial community in the intestine. Determination of the members of the STM3602 regulon may illuminate new pathways needed for colonization of the host.
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Affiliation(s)
- Johanna R Elfenbein
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University Health Science CenterBryan, TX, USA; Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State UniversityRaleigh, NC, USA
| | - Leigh A Knodler
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University Pullman, WA, USA
| | - Allison R Schaeffer
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University Health Science Center Bryan, TX, USA
| | - Franziska Faber
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis Davis, CA, USA
| | - Andreas J Bäumler
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis Davis, CA, USA
| | - Helene L Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University Health Science Center Bryan, TX, USA
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Byndloss MX, Rivera-Chávez F, Tsolis RM, Bäumler AJ. How bacterial pathogens use type III and type IV secretion systems to facilitate their transmission. Curr Opin Microbiol 2017; 35:1-7. [DOI: 10.1016/j.mib.2016.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 10/21/2022]
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Faber F, Thiennimitr P, Spiga L, Byndloss MX, Litvak Y, Lawhon S, Andrews-Polymenis HL, Winter SE, Bäumler AJ. Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis. PLoS Pathog 2017; 13:e1006129. [PMID: 28056091 PMCID: PMC5215881 DOI: 10.1371/journal.ppat.1006129] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/14/2016] [Indexed: 12/16/2022] Open
Abstract
Intestinal inflammation caused by Salmonella enterica serovar Typhimurium increases the availability of electron acceptors that fuel a respiratory growth of the pathogen in the intestinal lumen. Here we show that one of the carbon sources driving this respiratory expansion in the mouse model is 1,2-propanediol, a microbial fermentation product. 1,2-propanediol utilization required intestinal inflammation induced by virulence factors of the pathogen. S. Typhimurium used both aerobic and anaerobic respiration to consume 1,2-propanediol and expand in the murine large intestine. 1,2-propanediol-utilization did not confer a benefit in germ-free mice, but the pdu genes conferred a fitness advantage upon S. Typhimurium in mice mono-associated with Bacteroides fragilis or Bacteroides thetaiotaomicron. Collectively, our data suggest that intestinal inflammation enables S. Typhimurium to sidestep nutritional competition by respiring a microbiota-derived fermentation product. Salmonella enterica serovar Typhimurium induces intestinal inflammation to induce the generation of host-derived respiratory electron acceptors, thereby driving a respiratory pathogen expansion, which aids infectious transmission by the fecal oral route. However, the identity of nutrients serving as electron donors to enable S. Typhimurium to edge out competing microbes in the competitive environment of the gut are just beginning to be worked out. Here we demonstrate that aerobic and anaerobic respiratory pathways cooperate to promote growth of Salmonella on the microbial fermentation product 1,2-propanediol. We propose that pathogen-induced intestinal inflammation enables Salmonella to sidestep nutritional competition with the largely anaerobic microbiota by respiring a microbe-derived metabolite that cannot be consumed by fermentation.
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Affiliation(s)
- Franziska Faber
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States of America
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Mariana X. Byndloss
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States of America
| | - Yael Litvak
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States of America
| | - Sara Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, United States of America
| | - Helene L. Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, United States of America
| | - Sebastian E. Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Andreas J. Bäumler
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States of America
- * E-mail:
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45
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Abstract
In recent years, many spore-forming commensal Clostridia found in the gut have been discovered to promote host physiology, immune development, and protection against infections. We provide a detailed protocol for rapid enrichment of spore-forming bacteria from murine intestine. Briefly, contents from the intestinal cecum are collected aerobically, diluted and finally treated with chloroform to enrich for Clostridia spores.
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Affiliation(s)
- Eric M Velazquez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Fabian Rivera-Chávez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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46
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Rivera-Chávez F, Zhang LF, Faber F, Lopez CA, Byndloss MX, Olsan EE, Xu G, Velazquez EM, Lebrilla CB, Winter SE, Bäumler AJ. Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella. Cell Host Microbe 2016; 19:443-54. [PMID: 27078066 DOI: 10.1016/j.chom.2016.03.004] [Citation(s) in RCA: 518] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/17/2016] [Accepted: 03/17/2016] [Indexed: 12/18/2022]
Abstract
The mammalian intestine is host to a microbial community that prevents pathogen expansion through unknown mechanisms, while antibiotic treatment can increase susceptibility to enteric pathogens. Here we show that streptomycin treatment depleted commensal, butyrate-producing Clostridia from the mouse intestinal lumen, leading to decreased butyrate levels, increased epithelial oxygenation, and aerobic expansion of Salmonella enterica serovar Typhimurium. Epithelial hypoxia and Salmonella restriction could be restored by tributyrin treatment. Clostridia depletion and aerobic Salmonella expansion were also observed in the absence of streptomycin treatment in genetically resistant mice but proceeded with slower kinetics and required the presence of functional Salmonella type III secretion systems. The Salmonella cytochrome bd-II oxidase synergized with nitrate reductases to drive luminal expansion, and both were required for fecal-oral transmission. We conclude that Salmonella virulence factors and antibiotic treatment promote pathogen expansion through the same mechanism: depletion of butyrate-producing Clostridia to elevate epithelial oxygenation, allowing aerobic Salmonella growth.
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Affiliation(s)
- Fabian Rivera-Chávez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Lillian F Zhang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Franziska Faber
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Erin E Olsan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Gege Xu
- Department of Chemistry, College of Letters and Sciences, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Eric M Velazquez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, College of Letters and Sciences, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
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47
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Costa LF, Mol JPS, Silva APC, Macêdo AA, Silva TMA, Alves GES, Winter S, Winter MG, Velazquez EM, Byndloss MX, Bäumler AJ, Tsolis RM, Paixão TA, Santos RL. Iron acquisition pathways and colonization of the inflamed intestine by Salmonella enterica serovar Typhimurium. Int J Med Microbiol 2016; 306:604-610. [PMID: 27760693 DOI: 10.1016/j.ijmm.2016.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Salmonella enterica serotype Typhimurium is able to expand in the lumen of the inflamed intestine through mechanisms that have not been fully resolved. Here we utilized streptomycin-pretreated mice and dextran sodium sulfate (DSS)-treated mice to investigate how pathways for S. Typhimurium iron acquisition contribute to pathogen expansion in the inflamed intestine. Competitive infection with an iron uptake-proficient S. Typhimurium strain and mutant strains lacking tonB feoB, feoB, tonB or iroN in streptomycin pretreated mice demonstrated that ferric iron uptake requiring IroN and TonB conferred a fitness advantage during growth in the inflamed intestine. However, the fitness advantage conferred by ferrous iron uptake mechanisms was independent of inflammation and was only apparent in models where the normal microbiota composition had been disrupted by antibiotic treatment.
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Affiliation(s)
- Luciana F Costa
- Departamento de Patologia, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Juliana P S Mol
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária da Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ana Patricia C Silva
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária da Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
| | - Auricélio A Macêdo
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária da Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
| | - Teane M A Silva
- Departamento de Patologia, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Geraldo E S Alves
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária da Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sebastian Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eric M Velazquez
- Department of Medical Microbiology and Immunology, University of California at Davis, Davis, CA, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, University of California at Davis, Davis, CA, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, University of California at Davis, Davis, CA, USA
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, University of California at Davis, Davis, CA, USA.
| | - Tatiane A Paixão
- Departamento de Patologia, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Renato L Santos
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária da Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil.
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48
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Lopez CA, Miller BM, Rivera-Chávez F, Velazquez EM, Byndloss MX, Chávez-Arroyo A, Lokken KL, Tsolis RM, Winter SE, Bäumler AJ. Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration. Science 2016; 353:1249-53. [PMID: 27634526 PMCID: PMC5127919 DOI: 10.1126/science.aag3042] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/05/2016] [Indexed: 12/20/2022]
Abstract
Citrobacter rodentium uses a type III secretion system (T3SS) to induce colonic crypt hyperplasia in mice, thereby gaining an edge during its competition with the gut microbiota through an unknown mechanism. Here, we show that by triggering colonic crypt hyperplasia, the C. rodentium T3SS induced an excessive expansion of undifferentiated Ki67-positive epithelial cells, which increased oxygenation of the mucosal surface and drove an aerobic C. rodentium expansion in the colon. Treatment of mice with the γ-secretase inhibitor dibenzazepine to diminish Notch-driven colonic crypt hyperplasia curtailed the fitness advantage conferred by aerobic respiration during C. rodentium infection. We conclude that C. rodentium uses its T3SS to induce histopathological lesions that generate an intestinal microenvironment in which growth of the pathogen is fueled by aerobic respiration.
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Affiliation(s)
- Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Brittany M Miller
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Fabian Rivera-Chávez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Eric M Velazquez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Alfredo Chávez-Arroyo
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Kristen L Lokken
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, USA.
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49
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Abstract
The microbiome has an important role in human health. Changes in the microbiota can confer resistance to or promote infection by pathogenic bacteria. Antibiotics have a profound impact on the microbiota that alters the nutritional landscape of the gut and can lead to the expansion of pathogenic populations. Pathogenic bacteria exploit microbiota-derived sources of carbon and nitrogen as nutrients and regulatory signals to promote their own growth and virulence. By eliciting inflammation, these bacteria alter the intestinal environment and use unique systems for respiration and metal acquisition to drive their expansion. Unravelling the interactions between the microbiota, the host and pathogenic bacteria will produce strategies for manipulating the microbiota against infectious diseases.
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Affiliation(s)
- Andreas J Bäumler
- Department of Medical Microbiology and Immunology, University of California, Davis, School of Medicine, Davis, California 95616, USA
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9048, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, USA
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50
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Song J, Wilhelm CL, Wangdi T, Maira-Litran T, Lee SJ, Raetz M, Sturge CR, Mirpuri J, Pei J, Grishin NV, McSorley SJ, Gewirtz AT, Bäumler AJ, Pier GB, Galán JE, Yarovinsky F. Absence of TLR11 in Mice Does Not Confer Susceptibility to Salmonella Typhi. Cell 2016; 164:827-8. [PMID: 26919416 DOI: 10.1016/j.cell.2016.02.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Indexed: 11/15/2022]
Affiliation(s)
- Jeongmin Song
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Cara L Wilhelm
- Department of Immunology, University of Texas Southwestern Medical Center, TX 75390, USA
| | - Tamding Wangdi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Tomas Maira-Litran
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Seung-Joo Lee
- Center for Comparative Medicine, Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Megan Raetz
- Department of Immunology, University of Texas Southwestern Medical Center, TX 75390, USA
| | - Carolyn R Sturge
- Department of Immunology, University of Texas Southwestern Medical Center, TX 75390, USA
| | - Julie Mirpuri
- Department of Immunology, University of Texas Southwestern Medical Center, TX 75390, USA
| | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, TX 75390, USA; Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, TX 75390, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, TX 75390, USA; Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, TX 75390, USA
| | - Stephen J McSorley
- Center for Comparative Medicine, Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity and Infection, Georgia State University, Atlanta, GA 30303, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
| | - Felix Yarovinsky
- Department of Immunology, University of Texas Southwestern Medical Center, TX 75390, USA; David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, NY 14642, USA.
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