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Richards PJ, Almutrafy A, Liang L, Flaujac Lafontaine GM, King E, Fish NM, Connerton AJ, Connerton PL, Connerton IF. Prebiotic galactooligosaccharide feed modifies the chicken gut microbiota to efficiently clear Salmonella. mSystems 2024; 9:e0075424. [PMID: 39082804 PMCID: PMC11334501 DOI: 10.1128/msystems.00754-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 07/01/2024] [Indexed: 08/21/2024] Open
Abstract
Chicken meat is contaminated with Salmonella from the gut of infected chickens during slaughter. Eradication of Salmonella from broiler chickens through hygiene measures and/or vaccination is not cost-effective; complementary approaches are required. A mature gut microbiota obstructs Salmonella infection in chickens, and deliberate fortification of colonization resistance through prebiotic feed formulations would benefit public health and poultry production. Prebiotic galactooligosaccharides hastens Salmonella clearance from the gut of infected chickens. To better understand the role of galactooligosaccharides in colonization resistance, broiler chickens were raised on a wheat-soybean meal-based feed, with or without galactooligosaccharides for the first 24 days of life. Chickens were orally challenged with Salmonella enterica serovar Enteritidis at 20 days and the effect of supplementary galactooligosaccharides characterized by profiling Salmonella colonization, gut microbiota, innate immune response, and cecal short-chain fatty acid concentrations. Exposure to dietary galactooligosaccharides shortened the time to clear S. Enteritidis from the ceca. Differential abundance analysis of the cecal microbiota associated Salmonella challenge with a bacterial taxon belonging to the Acidaminococcaceae family (P < 0.005). Increased cecal concentrations of the short-chain fatty acids propionate and valerate were measured in Salmonella-challenged chickens sustained on either control or galactooligosaccharide-supplemented feed relative to mock-challenged controls; but far greater concentrations were detected in chickens fed a galactooligosaccharide-supplemented diet in early life. The abundance of the Acidaminococcaceae taxon exhibited a positive correlation with the cecal concentrations of propionate (ρ = 0.724, P = 0.008) and valerate (ρ = 0.71, P = 0.013). The absence of cecal pro-inflammatory transcriptional responses suggest that the rapid Salmonella clearance observed for the galactooligosaccharide-supplemented diet was not linked to innate immune function. IMPORTANCE Work presented here identifies bacterial taxa responsible for colonization resistance to Salmonella in broiler chickens. Deliberate cultivation of these taxa with prebiotic galactooligosaccharide has potential as a straight-forward, safe, and cost-effective intervention against Salmonella. We hypothesize that catabolism of galactooligosaccharide and its breakdown products by indigenous microorganisms colonizing the chicken gut produce excess levels of propionate. In the absence of gross inflammation, propionate is inimical to Salmonella and hastens intestinal clearance.
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Affiliation(s)
- Philip J. Richards
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Abeer Almutrafy
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Lu Liang
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Geraldine M. Flaujac Lafontaine
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Elizabeth King
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Neville M. Fish
- Saputo Dairy UK (c/o Simon Hunt), Saputo Dairy UK Innovation Centre, Harper Adams University, Edgmond, Newport, United Kingdom
| | - Amber J. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Phillippa L. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Ian F. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, United Kingdom
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Yu J, Tang H, Zhou N, Wang Z, Huang W, Chen Y, Wang D, Ni J, Lu J, Yao YF. Dietary L-arabinose-induced gut dysbiosis exacerbates Salmonella infection outcome. mSystems 2024; 9:e0052224. [PMID: 38980058 PMCID: PMC11334454 DOI: 10.1128/msystems.00522-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
The gut microbiota is essential for providing colonization resistance against pathogens. Dietary sugars markedly shift the composition of the intestinal microbiota and alter host susceptibility to enteric infections. Here, we demonstrate the effect of L-arabinose on bacterial infection by using a mouse infection model with Salmonella enterica serovar Typhimurium (S. Tm). In the presence of microbiota, L-arabinose induces a dramatic expansion of Enterobacteriaceae, thereby decreasing the microbiota diversity and causing more severe systemic infection. However, L-arabinose supplementation does not alter the disease progression of Salmonella infection in a microbiota-depleted mouse model. More importantly, short-term supplementation of L-arabinose fails to exert anti-diabetic effects in Salmonella-infected hyperglycemia mice and still promotes infection. Overall, our work reveals that a high intake of dietary L-arabinose supports a bloom of Enterobacteriaceae in Salmonella-infected gut, further accelerating the process of systemic infection.IMPORTANCEL-arabinose is a promising natural sweetener and food additive for the regulation of hyperglycemia. Since diabetic subjects are more susceptible to infections, the safety of dietary L-arabinose in diabetic patients experiencing infection remains a concern. Our findings reveal that L-arabinose exacerbates Salmonella infection outcome by inducing gut microbiota dysbiosis in mice. High dietary intake of L-arabinose may be deleterious for diabetic individuals undergoing infection.
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Affiliation(s)
- Jingchen Yu
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huang Tang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Zhou
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zuoqiang Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wanqiu Huang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yana Chen
- Department of Pediatrics, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Hefei, Anhui, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Lu
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
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3
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Albicoro FJ, Bessho S, Grando K, Olubajo S, Tam V, Tükel Ç. Lactate promotes the biofilm-to-invasive-planktonic transition in Salmonella enterica serovar Typhimurium via the de novo purine pathway. Infect Immun 2024:e0026624. [PMID: 39133016 DOI: 10.1128/iai.00266-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) infection triggers an inflammatory response that changes the concentration of metabolites in the gut impacting the luminal environment. Some of these environmental adjustments are conducive to S. Typhimurium growth, such as the increased concentrations of nitrate and tetrathionate or the reduced levels of Clostridia-produced butyrate. We recently demonstrated that S. Typhimurium can form biofilms within the host environment and respond to nitrate as a signaling molecule, enabling it to transition between sessile and planktonic states. To investigate whether S. Typhimurium utilizes additional metabolites to regulate its behavior, our study delved into the impact of inflammatory metabolites on biofilm formation. The results revealed that lactate, the most prevalent metabolite in the inflammatory environment, impedes biofilm development by reducing intracellular c-di-GMP levels, suppressing the expression of curli and cellulose, and increasing the expression of flagellar genes. A transcriptomic analysis determined that the expression of the de novo purine pathway increases during high lactate conditions, and a transposon mutagenesis genetic screen identified that PurA and PurG, in particular, play a significant role in the inhibition of curli expression and biofilm formation. Lactate also increases the transcription of the type III secretion system genes involved in tissue invasion. Finally, we show that the pyruvate-modulated two-component system BtsSR is activated in the presence of high lactate, which suggests that lactate-derived pyruvate activates BtsSR system after being exported from the cytosol. All these findings propose that lactate is an important inflammatory metabolite used by S. Typhimurium to transition from a biofilm to a motile state and fine-tune its virulence.IMPORTANCEWhen colonizing the gut, Salmonella enterica serovar Typhimurium (S. Typhimurium) adopts a dynamic lifestyle that alternates between a virulent planktonic state and a multicellular biofilm state. The coexistence of biofilm formers and planktonic S. Typhimurium in the gut suggests the presence of regulatory mechanisms that control planktonic-to-sessile transition. The signals triggering the transition of S. Typhimurium between these two lifestyles are not fully explored. In this work, we demonstrated that in the presence of lactate, the most dominant host-derived metabolite in the inflamed gut, there is a reduction of c-di-GMP in S. Typhimurium, which subsequently inhibits biofilm formation and induces the expression of its invasion machinery, motility genes, and de novo purine metabolic pathway genes. Furthermore, high levels of lactate activate the BtsSR two-component system. Collectively, this work presents new insights toward the comprehension of host metabolism and gut microenvironment roles in the regulation of S. Typhimurium biology during infection.
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Affiliation(s)
- Francisco J Albicoro
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Shingo Bessho
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Kaitlyn Grando
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Sophia Olubajo
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Vincent Tam
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Çagla Tükel
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
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Savage HP, Bays DJ, Tiffany CR, Gonzalez MAF, Bejarano EJ, Carvalho TP, Luo Z, Masson HLP, Nguyen H, Santos RL, Reagan KL, Thompson GR, Bäumler AJ. Epithelial hypoxia maintains colonization resistance against Candida albicans. Cell Host Microbe 2024; 32:1103-1113.e6. [PMID: 38838675 PMCID: PMC11239274 DOI: 10.1016/j.chom.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/01/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
Antibiotic treatment promotes the outgrowth of intestinal Candida albicans, but the mechanisms driving this fungal bloom remain incompletely understood. We identify oxygen as a resource required for post-antibiotic C. albicans expansion. C. albicans depleted simple sugars in the ceca of gnotobiotic mice but required oxygen to grow on these resources in vitro, pointing to anaerobiosis as a potential factor limiting growth in the gut. Clostridia species limit oxygen availability in the large intestine by producing butyrate, which activates peroxisome proliferator-activated receptor gamma (PPAR-γ) signaling to maintain epithelial hypoxia. Streptomycin treatment depleted Clostridia-derived butyrate to increase epithelial oxygenation, but the PPAR-γ agonist 5-aminosalicylic acid (5-ASA) functionally replaced Clostridia species to restore epithelial hypoxia and colonization resistance against C. albicans. Additionally, probiotic Escherichia coli required oxygen respiration to prevent a post-antibiotic bloom of C. albicans, further supporting the role of oxygen in colonization resistance. We conclude that limited access to oxygen maintains colonization resistance against C. albicans.
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Affiliation(s)
- Hannah P Savage
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Derek J Bays
- Department of Internal Medicine, Division of Infectious Diseases, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Mariela A F Gonzalez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Eli J Bejarano
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Thaynara P Carvalho
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; Departamento de Clinica e Cirurgia Veterinárias, Escola de Veterinária da Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627 Belo Horizonte, MG, Brazil
| | - Zheng Luo
- Department of Pathology Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Hugo L P Masson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Renato L Santos
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; Departamento de Clinica e Cirurgia Veterinárias, Escola de Veterinária da Universidade Federal de Minas Gerais, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627 Belo Horizonte, MG, Brazil
| | - Krystle L Reagan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95615, USA
| | - George R Thompson
- Department of Internal Medicine, Division of Infectious Diseases, School of Medicine, University of California, Davis, Sacramento, CA 95817, 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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5
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Osbelt L, Almási ÉDH, Wende M, Kienesberger S, Voltz A, Lesker TR, Muthukumarasamy U, Knischewski N, Nordmann E, Bielecka AA, Giralt-Zúñiga M, Kaganovitch E, Kühne C, Baier C, Pietsch M, Müsken M, Greweling-Pils MC, Breinbauer R, Flieger A, Schlüter D, Müller R, Erhardt M, Zechner EL, Strowig T. Klebsiella oxytoca inhibits Salmonella infection through multiple microbiota-context-dependent mechanisms. Nat Microbiol 2024; 9:1792-1811. [PMID: 38862602 PMCID: PMC11222139 DOI: 10.1038/s41564-024-01710-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/22/2024] [Indexed: 06/13/2024]
Abstract
The Klebsiella oxytoca species complex is part of the human microbiome, especially during infancy and childhood. K. oxytoca species complex strains can produce enterotoxins, namely, tilimycin and tilivalline, while also contributing to colonization resistance (CR). The relationship between these seemingly contradictory roles is not well understood. Here, by coupling ex vivo assays with CRISPR-mutagenesis and various mouse models, we show that K. oxytoca provides CR against Salmonella Typhimurium. In vitro, the antimicrobial activity against various Salmonella strains depended on tilimycin production and was induced by various simple carbohydrates. In vivo, CR against Salmonella depended on toxin production in germ-free mice, while it was largely toxin-independent in mice with residual microbiota. This was linked to the relative levels of toxin-inducing carbohydrates in vivo. Finally, dulcitol utilization was essential for toxin-independent CR in gnotobiotic mice. Together, this demonstrates that nutrient availability is key to both toxin-dependent and substrate-driven competition between K. oxytoca and Salmonella.
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Affiliation(s)
- Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Éva D H Almási
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Marie Wende
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Graz, Austria
| | - Alexander Voltz
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Nele Knischewski
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Elke Nordmann
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Agata A Bielecka
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - María Giralt-Zúñiga
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eugen Kaganovitch
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Caroline Kühne
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claas Baier
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Michael Pietsch
- Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Rolf Breinbauer
- BioTechMed-Graz, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| | - Antje Flieger
- Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Dirk Schlüter
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Marc Erhardt
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Graz, Austria
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany.
- Center for Individualized Infection Medicine, Hannover, Germany.
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6
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Yoo W, Shealy NG, Zieba JK, Torres TP, Baltagulov M, Thomas JD, Shelton CD, McGovern AG, Foegeding NJ, Olsan EE, Byndloss MX. Salmonella Typhimurium expansion in the inflamed murine gut is dependent on aspartate derived from ROS-mediated microbiota lysis. Cell Host Microbe 2024; 32:887-899.e6. [PMID: 38806059 PMCID: PMC11189616 DOI: 10.1016/j.chom.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/20/2024] [Accepted: 05/01/2024] [Indexed: 05/30/2024]
Abstract
Inflammation boosts the availability of electron acceptors in the intestinal lumen, creating a favorable niche for pathogenic Enterobacteriaceae. However, the mechanisms linking intestinal inflammation-mediated changes in luminal metabolites and pathogen expansion remain unclear. Here, we show that mucosal inflammation induced by Salmonella enterica serovar Typhimurium (S. Tm) infection increases intestinal levels of the amino acid aspartate. S. Tm used aspartate-ammonia lyase (aspA)-dependent fumarate respiration for growth in the murine gut only during inflammation. AspA-dependent growth advantage was abolished in the gut of germ-free mice and restored in gnotobiotic mice colonized with members of the classes Bacteroidia and Clostridia. Reactive oxygen species (ROS) produced during the host response caused lysis of commensal microbes, resulting in the release of microbiota-derived aspartate that was used by S. Tm, in concert with nitrate-dependent anaerobic respiration, to outcompete commensal Enterobacteriaceae. Our findings demonstrate the role of microbiota-derived amino acids in driving respiration-dependent S. Tm expansion during colitis.
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Affiliation(s)
- Woongjae Yoo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Nicolas G Shealy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jacob K Zieba
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Teresa P Torres
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madi Baltagulov
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Julia D Thomas
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Catherine D Shelton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Anna G McGovern
- 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
| | - Erin E Olsan
- Department of Biological Sciences, California State University, Sacramento, CA 95819, 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 Digestive Disease Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, TN 37235, USA; Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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7
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Muramatsu MK, Winter SE. Nutrient acquisition strategies by gut microbes. Cell Host Microbe 2024; 32:863-874. [PMID: 38870902 PMCID: PMC11178278 DOI: 10.1016/j.chom.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
The composition and function of the gut microbiota are intimately tied to nutrient acquisition strategies and metabolism, with significant implications for host health. Both dietary and host-intrinsic factors influence community structure and the basic modes of bacterial energy metabolism. The intestinal tract is rich in carbon and nitrogen sources; however, limited access to oxygen restricts energy-generating reactions to fermentation. By contrast, increased availability of electron acceptors during episodes of intestinal inflammation results in phylum-level changes in gut microbiota composition, suggesting that bacterial energy metabolism is a key driver of gut microbiota function. In this review article, we will illustrate diverse examples of microbial nutrient acquisition strategies in the context of habitat filters and anatomical location and the central role of energy metabolism in shaping metabolic strategies to support bacterial growth in the mammalian gut.
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Affiliation(s)
- Matthew K Muramatsu
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis, Davis, CA 95616, USA
| | - Sebastian E Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis, Davis, CA 95616, USA.
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8
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Rojas VK, Winter MG, Jimenez AG, Tanner NW, Crockett SL, Spiga L, Hendrixson DR, Winter SE. Infection-associated gene regulation of L-tartrate metabolism in Salmonella enterica serovar Typhimurium. mBio 2024; 15:e0035024. [PMID: 38682906 PMCID: PMC11237755 DOI: 10.1128/mbio.00350-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Enteric pathogens such as Salmonella enterica serovar Typhimurium experience spatial and temporal changes to the metabolic landscape throughout infection. Host reactive oxygen and nitrogen species non-enzymatically convert monosaccharides to alpha hydroxy acids, including L-tartrate. Salmonella utilizes L-tartrate early during infection to support fumarate respiration, while L-tartrate utilization ceases at later time points due to the increased availability of exogenous electron acceptors such as tetrathionate, nitrate, and oxygen. It remains unknown how Salmonella regulates its gene expression to metabolically adapt to changing nutritional environments. Here, we investigated how the transcriptional regulation for L-tartrate metabolism in Salmonella is influenced by infection-relevant cues. L-tartrate induces the transcription of ttdBAU, genes involved in L-tartrate utilization. L-tartrate metabolism is negatively regulated by two previously uncharacterized transcriptional regulators TtdV (STM3357) and TtdW (STM3358), and both TtdV and TtdW are required for the sensing of L-tartrate. The electron acceptors nitrate, tetrathionate, and oxygen repress ttdBAU transcription via the two-component system ArcAB. Furthermore, the regulation of L-tartrate metabolism is required for optimal fitness in a mouse model of Salmonella-induced colitis. TtdV, TtdW, and ArcAB allow for the integration of two cues, i.e., substrate availability and availability of exogenous electron acceptors, to control L-tartrate metabolism. Our findings provide novel insights into how Salmonella prioritizes the utilization of different electron acceptors for respiration as it experiences transitional nutrient availability throughout infection. IMPORTANCE Bacterial pathogens must adapt their gene expression profiles to cope with diverse environments encountered during infection. This coordinated process is carried out by the integration of cues that the pathogen senses to fine-tune gene expression in a spatiotemporal manner. Many studies have elucidated the regulatory mechanisms of how Salmonella sense metabolites in the gut to activate or repress its virulence program; however, our understanding of how Salmonella coordinates its gene expression to maximize the utilization of carbon and energy sources found in transitional nutrient niches is not well understood. In this study, we discovered how Salmonella integrates two infection-relevant cues, substrate availability and exogenous electron acceptors, to control L-tartrate metabolism. From our experiments, we propose a model for how L-tartrate metabolism is regulated in response to different metabolic cues in addition to characterizing two previously unknown transcriptional regulators. This study expands our understanding of how microbes combine metabolic cues to enhance fitness during infection.
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Affiliation(s)
- Vivian K. Rojas
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Maria G. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Angel G. Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Natasha W. Tanner
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Stacey L. Crockett
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David R. Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sebastian E. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, California, USA
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9
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Gao Y, Yu L, Ye Z, Zhang C, Gong Y, Zhang Q, Zhang C, Zhao J, Narbad A, Chen W, Zhai Q, Tian F. In vitro batch fermentation demonstrates variations in the regulation of gut microbiota and metabolic functions by β-glucans of differing structures. Food Res Int 2024; 186:114287. [PMID: 38729740 DOI: 10.1016/j.foodres.2024.114287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/03/2024] [Accepted: 03/27/2024] [Indexed: 05/12/2024]
Abstract
The gut microbiota is widely acknowledged as a crucial factor in regulating host health. The structure of dietary fibers determines changes in the gut microbiota and metabolic differences resulting from their fermentation, which in turn affect gut microbe-related health effects. β-Glucan (BG) is a widely accessible dietary fiber to humans, and its structural characteristics vary depending on the source. However, the interactions between different structural BGs and gut microbiota remain unclear. This study used an in vitro fermentation model to investigate the effects of BG on gut microbiota, and microbiomics and metabolomics techniques to explore the relationship between the structure of BG, bacterial communities, and metabolic profiles. The four sources of BG (barley, yeast, algae, and microbial fermentation) contained different types and proportions of glycosidic bonds, which differentially altered the bacterial community. The BG from algal sources, which contained only β(1 → 4) glycosidic bonds, was the least metabolized by the gut microbiota and caused limited metabolic changes. The other three BGs contain more diverse glycosidic bonds and can be degraded by bacteria from multiple genera, causing a wider range of metabolic changes. This work also suggested potential synergistic degradation relationships between gut bacteria based on BG. Overall, this study deepens the structural characterization-microbial-functional understanding of BGs and provides theoretical support for the development of gut microbiota-targeted foods.
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Affiliation(s)
- Yuhang Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Zi Ye
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chuan Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuhong Gong
- Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences / Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing / Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China.
| | - Qingsong Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Arjan Narbad
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China; Gut Health and Microbiome Institute Strategic Programme, Quadram Institute Bioscience, Norwich 16 NR4 7UQ, UK.
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
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10
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Cherrak Y, Salazar MA, Yilmaz K, Kreuzer M, Hardt WD. Commensal E. coli limits Salmonella gut invasion during inflammation by producing toxin-bound siderophores in a tonB-dependent manner. PLoS Biol 2024; 22:e3002616. [PMID: 38865418 PMCID: PMC11168627 DOI: 10.1371/journal.pbio.3002616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/05/2024] [Indexed: 06/14/2024] Open
Abstract
The gastrointestinal tract is densely colonized by a polymicrobial community known as the microbiota which serves as primary line of defence against pathogen invasion. The microbiota can limit gut-luminal pathogen growth at different stages of infection. This can be traced to specific commensal strains exhibiting direct or indirect protective functions. Although these mechanisms hold the potential to develop new approaches to combat enteric pathogens, they remain far from being completely described. In this study, we investigated how a mouse commensal Escherichia coli can outcompete Salmonella enterica serovar Typhimurium (S. Tm). Using a salmonellosis mouse model, we found that the commensal E. coli 8178 strain relies on a trojan horse trap strategy to limit S. Tm expansion in the inflamed gut. Combining mutants and reporter tools, we demonstrated that inflammation triggers the expression of the E. coli 8178 antimicrobial microcin H47 toxin which, when fused to salmochelin siderophores, can specifically alter S. Tm growth. This protective function was compromised upon disruption of the E. coli 8178 tonB-dependent catecholate siderophore uptake system, highlighting a previously unappreciated crosstalk between iron intake and microcin H47 activity. By identifying the genetic determinants mediating S. Tm competition, our work not only provides a better mechanistic understanding of the protective function displayed by members of the gut microbiota but also further expands the general contribution of microcins in bacterial antagonistic relationships. Ultimately, such insights can open new avenues for developing microbiota-based approaches to better control intestinal infections.
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Affiliation(s)
- Yassine Cherrak
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Miguel Angel Salazar
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Koray Yilmaz
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Markus Kreuzer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
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11
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Thomas SC, Guo Y, Xu F, Saxena D, Li X. A novel SUCNR1 inhibitor alleviates dysbiosis through inhibition of host responses without direct interaction with host microbiota. Mol Oral Microbiol 2024; 39:80-90. [PMID: 37715517 PMCID: PMC10939988 DOI: 10.1111/omi.12431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
Type 2 diabetes (T2D) is a chronic metabolic disorder in which insulin resistance and impaired insulin secretion result in altered metabolite balance, specifically elevated levels of circulating glucose and succinate, which increases the risk of many pathologies, including periodontitis. Succinate, a tricarboxylic acid (TCA) cycle intermediate, can be produced and metabolized by both host cells and host microbiota, where elevated levels serve as an inflammation and pathogen threat signal through activating the succinate G protein-coupled receptor, SUCNR1. Modulating succinate-induced SUCNR1 signaling remains a promising therapeutic approach for pathologies resulting in elevated levels of succinate, such as T2D and periodontitis. Here, we demonstrate hyperglycemia and elevated intracellular succinate in a T2D mouse model and determine gut microbiome composition. Drawing on previous work demonstrating the ability of a novel SUCNR1 antagonist, compound 7a, to block inflammation and alleviate dysbiosis in a mouse model, we examined if compound 7a has an impact on the growth and virulence gene expression of bacterial and fungal human microbiota in vitro, and if 7a could reduce bone loss in a periodontitis-induced mouse model. T2D mice harbored a significantly different gut microbiome, suggesting the altered metabolite profile of T2D causes shifts in host-microbial community structure, with enrichment in succinate producers and consumers and mucin-degrading bacteria. Bacterial and fungal cultures showed that 7a did not influence growth or virulence gene expression, suggesting the therapeutic effects of 7a are a direct result of 7a interacting with host cells and that alterations in microbial community structure are driven by reduced host SUCNR1 signaling. This work further suggests that targeting SUCNR1 signaling is a promising therapeutic approach in metabolic, inflammatory, or immune disorders with elevated succinate levels.
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Affiliation(s)
- Scott C. Thomas
- Department of Molecular Pathobiology, New York University College of Dentistry; New York, NY 10010
| | - Yuqi Guo
- Department of Molecular Pathobiology, New York University College of Dentistry; New York, NY 10010
| | - Fangxi Xu
- Department of Molecular Pathobiology, New York University College of Dentistry; New York, NY 10010
| | - Deepak Saxena
- Department of Molecular Pathobiology, New York University College of Dentistry; New York, NY 10010
- Department of Surgery, New York University Grossman School of Medicine; New York, NY 10016
- Perlmutter Cancer Institute, New York University Langone Medical Center; New York, NY 10016
| | - Xin Li
- Department of Molecular Pathobiology, New York University College of Dentistry; New York, NY 10010
- Department of Urology, New York University Grossman School of Medicine; New York, NY 10016
- Perlmutter Cancer Institute, New York University Langone Medical Center; New York, NY 10016
- Lead Contact
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12
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Kapur N, Alam MA, Hassan SA, Patel PH, Wempe LA, Bhogoju S, Goretsky T, Kim JH, Herzog J, Ge Y, Awuah SG, Byndloss M, Baumler AJ, Zadeh MM, Sartor RB, Barrett T. Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.584471. [PMID: 38559035 PMCID: PMC10979996 DOI: 10.1101/2024.03.14.584471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background Mitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative anaerobes (eg. Proteobacteria ) and restricts obligate anaerobes (eg. Firmicutes ). Dysbiotic metabolites negatively affect host metabolism and immunity. Our novel compound (AuPhos) upregulates intestinal epithelial cell (IEC) mito function, attenuates colitis and corrects dysbiosis in humanized Il10-/- mice. We posit that AuPhos corrects IBD-associated dysbiotic metabolism. Methods Primary effect of AuPhos on mucosal Mito respiration and healing process was studied in ex vivo treated human colonic biopsies and piroxicam-accelerated (Px) Il10-/- mice. Secondary effect on microbiome was tested in DSS-colitis WT B6 and germ-free 129.SvEv WT or Il10-/- mice reconstituted with human IBD stool (Hu- Il10-/- ). Mice were treated orally with AuPhos (10- or 25- mg/kg; q3d) or vehicle, stool samples collected for fecal lipocalin-2 (f-LCN2) assay and microbiome analyses using 16S rRNA sequencing. AuPhos effect on microbial metabolites was determined using untargeted global metabolomics. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 staining in sections from pimonidazole HCl-infused DSS-mice. Effect of AuPhos on enteric oxygenation was assessed by E. coli Nissle 1917 WT (aerobic respiration-proficient) and cytochrome oxidase (cydA) mutant (aerobic respiration-deficient). Results Metagenomic (16S) analysis revealed AuPhos reduced relative abundances of Proteobacteria and increased blooms of Firmicutes in uninflamed B6 WT, DSS-colitis, Hu-WT and Hu- Il10-/- mice. AuPhos also increased hypoxyprobe-1 staining in surface IECs suggesting enhanced O2 utilization. AuPhos-induced anaerobiosis was confirmed by a significant increase in cydA mutant compared to WT (O2-utlizing) E.coli . Ex vivo treatment of human biopsies with AuPhos showed significant increase in Mito mass, and complexes I and IV. Further, gene expression analysis of AuPhos-treated biopsies showed increase in stem cell markers (Lgr4, Lgr5, Lrig1), with concomitant decreases in pro-inflammatory markers (IL1β,MCP1, RankL). Histological investigation of AuPhos-fed Px- Il10-/- mice showed significantly decreased colitis score in AuPhos-treated Px- Il10-/- mice, with decrease in mRNA of pro-inflammatory cytokines and increase in Mito complexes ( ND5 , ATP6 ). AuPhos significantly altered microbial metabolites associated with SCFA synthesis, FAO, TCA cycle, tryptophan and polyamine biosynthesis pathways. AuPhos increased pyruvate, 4-hydroxybutyrate, 2-hydroxyglutarate and succinate, suggesting an upregulation of pyruvate and glutarate pathways of butyrate production. AuPhos reduced IBD-associated primary bile acids (BA) with concomitant increase in secondary BA (SBA). AuPhos treatment significantly decreased acylcarnitines and increased L-carnitine reflective of enhanced FAO. AuPhos increases TCA cycle intermediates and creatine, energy reservoir substrates indicating enhanced OxPHOS. Besides, AuPhos also upregulates tryptophan metabolism, decreases Kynurenine and its derivatives, and increases polyamine biosynthesis pathway (Putresceine and Spermine). Conclusion These findings indicate that AuPhos-enhanced IEC mitochondrial function reduces enteric O2 delivery, which corrects disease-associated metabolomics by restoring short-chain fatty acids, SBA, AA and IEC energy metabolism. Graphical abstract
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13
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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.06.561241. [PMID: 37873088 PMCID: PMC10592638 DOI: 10.1101/2023.10.06.561241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to insertion "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M. Kirsch
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
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14
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Schubert C, Unden G. Regulation of Aerobic Succinate Transporter dctA of E. coli by cAMP-CRP, DcuS-DcuR, and EIIAGlc: Succinate as a Carbon Substrate and Signaling Molecule. Microb Physiol 2024; 34:108-120. [PMID: 38432210 DOI: 10.1159/000538095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
INTRODUCTION C4-dicarboxylates (C4-DC) have emerged as significant growth substrates and signaling molecules for various Enterobacteriaceae during their colonization of mammalian hosts. Particularly noteworthy is the essential role of fumarate respiration during colonization of pathogenic bacteria. To investigate the regulation of aerobic C4-DC metabolism, the study explored the transcriptional control of the main aerobic C4-DC transporter, dctA, under different carbohydrate conditions. In addition, mutants related to carbon catabolite repression (CCR) and C4-DC regulation (DcuS-DcuR) were examined to better understand the regulatory integration of aerobic C4-DC metabolism into CCR. For initial insight into posttranslational regulation, the interaction between the aerobic C4-DC transporter DctA and EIIAGlc from the glucose-specific phosphotransferase system was investigated. METHODS The expression of dctA was characterized in the presence of various carbohydrates and regulatory mutants affecting CCR. This was accomplished by fusing the dctA promoter (PdctA) to the lacZ reporter gene. Additionally, the interaction between DctA and EIIAGlc of the glucose-specific phosphotransferase system was examined in vivo using a bacterial two-hybrid system. RESULTS The dctA promoter region contains a class I cAMP-CRP-binding site at position -81.5 and a DcuR-binding site at position -105.5. DcuR, the response regulator of the C4-DC-activated DcuS-DcuR two-component system, and cAMP-CRP stimulate dctA expression. The expression of dctA is subject to the influence of various carbohydrates via cAMP-CRP, which differently modulate cAMP levels. Here we show that EIIAGlc of the glucose-specific phosphotransferase system strongly interacts with DctA, potentially resulting in the exclusion of C4-DCs when preferred carbon substrates, such as sugars, are present. In contrast to the classical inducer exclusion known for lactose permease LacY, inhibition of C4-DC uptake into the cytoplasm affects only its role as a substrate, but not as an inducer since DcuS detects C4-DCs in the periplasmic space ("substrate exclusion"). The work shows an interplay between cAMP-CRP and the DcuS-DcuR regulatory system for the regulation of dctA at both transcriptional and posttranslational levels. CONCLUSION The study highlights a hierarchical interplay between global (cAMP-CRP) and specific (DcuS-DcuR) regulation of dctA at the transcriptional and posttranslational levels. The integration of global and specific transcriptional regulation of dctA, along with the influence of EIIAGlc on DctA, fine-tunes C4-DC catabolism in response to the availability of other preferred carbon sources. It attributes DctA a central role in the control of aerobic C4-DC catabolism and suggests a new role to EIIAGlc on transporters (control of substrate uptake by substrate exclusion).
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Affiliation(s)
- Christopher Schubert
- Institute for Molecular Physiology (IMP), Microbiology and Wine Research, Johannes Gutenberg-University, Mainz, Germany
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Gottfried Unden
- Institute for Molecular Physiology (IMP), Microbiology and Wine Research, Johannes Gutenberg-University, Mainz, Germany,
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15
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Lee C, Lee S, Yoo W. Metabolic Interaction Between Host and the Gut Microbiota During High-Fat Diet-Induced Colorectal Cancer. J Microbiol 2024; 62:153-165. [PMID: 38625645 DOI: 10.1007/s12275-024-00123-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 04/17/2024]
Abstract
Colorectal cancer (CRC) is the second-highest cause of cancer-associated mortality among both men and women worldwide. One of the risk factors for CRC is obesity, which is correlated with a high-fat diet prevalent in Western dietary habits. The association between an obesogenic high-fat diet and CRC has been established for several decades; however, the mechanisms by which a high-fat diet increases the risk of CRC remain unclear. Recent studies indicate that gut microbiota strongly influence the pathogenesis of both high-fat diet-induced obesity and CRC. The gut microbiota is composed of hundreds of bacterial species, some of which are implicated in CRC. In particular, the expansion of facultative anaerobic Enterobacteriaceae, which is considered a microbial signature of intestinal microbiota functional imbalance (dysbiosis), is associated with both high-fat diet-induced obesity and CRC. Here, we review the interaction between the gut microbiome and its metabolic byproducts in the context of colorectal cancer (CRC) during high-fat diet-induced obesity. In addition, we will cover how a high-fat diet can drive the expansion of genotoxin-producing Escherichia coli by altering intestinal epithelial cell metabolism during gut inflammation conditions.
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Affiliation(s)
- Chaeeun Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Seungrin Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Woongjae Yoo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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16
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Moreira de Gouveia MI, Bernalier-Donadille A, Jubelin G. Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease. BIOLOGY 2024; 13:142. [PMID: 38534413 DOI: 10.3390/biology13030142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/28/2024]
Abstract
The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom.
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Affiliation(s)
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000 Clermont-Ferrand, France
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17
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Beutler M, Eberl C, Garzetti D, Herp S, Münch P, Ring D, Dolowschiak T, Brugiroux S, Schiller P, Hussain S, Basic M, Bleich A, Stecher B. Contribution of bacterial and host factors to pathogen "blooming" in a gnotobiotic mouse model for Salmonella enterica serovar Typhimurium-induced enterocolitis. Infect Immun 2024; 92:e0031823. [PMID: 38189339 PMCID: PMC10863408 DOI: 10.1128/iai.00318-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Inflammation has a pronounced impact on the intestinal ecosystem by driving an expansion of facultative anaerobic bacteria at the cost of obligate anaerobic microbiota. This pathogen "blooming" is also a hallmark of enteric Salmonella enterica serovar Typhimurium (S. Tm) infection. Here, we analyzed the contribution of bacterial and host factors to S. Tm "blooming" in a gnotobiotic mouse model for S. Tm-induced enterocolitis. Mice colonized with the Oligo-Mouse-Microbiota (OMM12), a minimal bacterial community, develop fulminant colitis by day 4 after oral infection with wild-type S. Tm but not with an avirulent mutant. Inflammation leads to a pronounced reduction in overall intestinal bacterial loads, distinct microbial community shifts, and pathogen blooming (relative abundance >50%). S. Tm mutants attenuated in inducing gut inflammation generally elicit less pronounced microbiota shifts and reduction in total bacterial loads. In contrast, S. Tm mutants in nitrate respiration, salmochelin production, and ethanolamine utilization induced strong inflammation and S. Tm "blooming." Therefore, individual Salmonella-specific inflammation-fitness factors seem to be of minor importance for competition against this minimal microbiota in the inflamed gut. Finally, we show that antibody-mediated neutrophil depletion normalized gut microbiota loads but not intestinal inflammation or microbiota shifts. This suggests that neutrophils equally reduce pathogen and commensal bacterial loads in the inflamed gut.
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Affiliation(s)
- Markus Beutler
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Claudia Eberl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Debora Garzetti
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Simone Herp
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Philipp Münch
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Tamas Dolowschiak
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zürich, Switzerland
| | - Sandrine Brugiroux
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Patrick Schiller
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Saib Hussain
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marijana Basic
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - André Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
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18
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Rojas VK, Winter MG, Jimenez AG, Tanner NW, Crockett SL, Spiga L, Hendrixson DR, Winter SE. Gene regulation of infection-associated L-tartrate metabolism in Salmonella enterica serovar Typhimurium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578992. [PMID: 38370731 PMCID: PMC10871181 DOI: 10.1101/2024.02.05.578992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Enteric pathogens such as Salmonella enterica serovar Typhimurium experience spatial and temporal changes to the metabolic landscape throughout infection. Host reactive oxygen and nitrogen species non-enzymatically convert monosaccharides to alpha hydroxy acids, including L-tartrate. Salmonella utilizes L-tartrate early during infection to support fumarate respiration, while L-tartrate utilization ceases at later time points due to the increased availability of exogenous electron acceptors such as tetrathionate, nitrate, and oxygen. It remains unknown how Salmonella regulates its gene expression to metabolically adapt to changing nutritional environments. Here, we investigated how the transcriptional regulation for L-tartrate metabolism in Salmonella is influenced by infection-relevant cues. L-tartrate induces the transcription of ttdBAU, genes involved in L-tartrate utilization. L-tartrate metabolism is negatively regulated by two previously uncharacterized transcriptional regulators TtdV (STM3357) and TtdW (STM3358), and both TtdV and TtdW are required for sensing of L-tartrate. The electron acceptors nitrate, tetrathionate, and oxygen repress ttdBAU transcription via the two-component system ArcAB. Furthermore, regulation of L-tartrate metabolism is required for optimal fitness in a mouse model of Salmonella-induced colitis. TtdV, TtdW, and ArcAB allow for the integration of two cues, substrate availability and availability of exogenous electron acceptors, to control L-tartrate metabolism. Our findings provide novel insights into how Salmonella prioritizes utilization of different electron acceptors for respiration as it experiences transitional nutrient availability throughout infection.
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Affiliation(s)
- Vivian K. Rojas
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, CA, USA
| | - Maria G. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, CA, USA
| | - Angel G. Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Infectious Diseases, Genentech, South San Francisco, California, USA
| | - Natasha W. Tanner
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, CA, USA
| | - Stacey L. Crockett
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David R. Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sebastian E. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, CA, USA
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA, USA
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19
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Kellogg TD, Ceglia S, Mortzfeld BM, Zeamer AL, Foley SE, Ward DV, Bhattarai SK, McCormick BA, Reboldi A, Bucci V. Microbiota encoded fatty-acid metabolism expands tuft cells to protect tissues homeostasis during Clostridioides difficile infection in the large intestine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.574039. [PMID: 38352546 PMCID: PMC10862725 DOI: 10.1101/2024.01.29.574039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Metabolic byproducts of the intestinal microbiota are crucial in maintaining host immune tone and shaping inter-species ecological dynamics. Among these metabolites, succinate is a driver of tuft cell (TC) differentiation and consequent type 2 immunity-dependent protection against invading parasites in the small intestine. Succinate is also a growth enhancer of the nosocomial pathogen Clostridioides difficile in the large intestine. To date, no research has shown the role of succinate in modulating TC dynamics in the large intestine, or the relevance of this immune pathway to C. difficile pathophysiology. Here we reveal the existence of a three-way circuit between commensal microbes, C. difficile and host epithelial cells which centers around succinate. Through selective microbiota depletion experiments we demonstrate higher levels of type 2 cytokines leading to expansion of TCs in the colon. We then demonstrate the causal role of the microbiome in modulating colonic TC abundance and subsequent type 2 cytokine induction using rational supplementation experiments with fecal transplants and microbial consortia of succinate-producing bacteria. We show that administration of a succinate-deficient Bacteroides thetaiotaomicron knockout (Δfrd) significantly reduces the enhanced type 2 immunity in mono-colonized mice. Finally, we demonstrate that mice prophylactically administered with the consortium of succinate-producing bacteria show reduced C. difficile-induced morbidity and mortality compared to mice administered with heat-killed bacteria or the vehicle. This effect is reduced in a partial tuft cell knockout mouse, Pou2f3+/-, and nullified in the tuft cell knockout mouse, Pou2f3-/-, confirming that the observed protection occurs via the TC pathway. Succinate is an intermediary metabolite of the production of short-chain fatty acids, and its concentration often increases during dysbiosis. The first barrier to enteric pathogens alike is the intestinal epithelial barrier, and host maintenance and strengthening of barrier integrity is vital to homeostasis. Considering our data, we propose that activation of TC by the microbiota-produced succinate in the colon is a mechanism evolved by the host to counterbalance microbiome-derived cues that facilitate invasion by intestinal pathogens.
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Affiliation(s)
- Tasia D. Kellogg
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
| | - Simona Ceglia
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
- Department of Pathology, UMass Chan Medical School, Worcester, MA, USA
| | - Benedikt M. Mortzfeld
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
| | - Abigail L. Zeamer
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
| | - Sage E. Foley
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Current address: Transformational and Translational Immunology Discovery Department, AbbVie, Cambridge, MA, USA
| | - Doyle V. Ward
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
| | - Shakti K. Bhattarai
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
| | - Beth A. McCormick
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
| | - Andrea Reboldi
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
- Department of Pathology, UMass Chan Medical School, Worcester, MA, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
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20
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Leleiwi I, Kokkinias K, Kim Y, Baniasad M, Shaffer M, Sabag-Daigle A, Daly RA, Flynn RM, Wysocki VH, Ahmer BMM, Borton MA, Wrighton KC. Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575907. [PMID: 38293109 PMCID: PMC10827160 DOI: 10.1101/2024.01.16.575907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella -infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella- induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.
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21
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Lee SM, Thapa Magar R, Jung MK, Kong HG, Song JY, Kwon JH, Choi M, Lee HJ, Lee SY, Khan R, Kim JF, Lee SW. Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health. THE ISME JOURNAL 2024; 18:wrae120. [PMID: 38952008 PMCID: PMC11253211 DOI: 10.1093/ismejo/wrae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.
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Affiliation(s)
- Sang-Moo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Roniya Thapa Magar
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Min Kyeong Jung
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyun Gi Kong
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Joo Hwan Kwon
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Minseo Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyoung Ju Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Jihyun F Kim
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Microbiome Initiative, Yonsei University, Seoul 03722, Republic of Korea
| | - Seon-Woo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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22
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Spiga L, Winter MG, Muramatsu MK, Rojas VK, Chanin RB, Zhu W, Hughes ER, Taylor SJ, Faber F, Porwollik S, Carvalho TF, Qin T, Santos RL, Andrews-Polymenis H, McClelland M, Winter SE. Byproducts of inflammatory radical metabolism provide transient nutrient niches for microbes in the inflamed gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570695. [PMID: 38106073 PMCID: PMC10723490 DOI: 10.1101/2023.12.08.570695] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Louis Pasteur's experiments on tartaric acid laid the foundation for our understanding of molecular chirality, but major questions remain. By comparing the optical activity of naturally-occurring tartaric acid with chemically-synthesized paratartaric acid, Pasteur realized that naturally-occurring tartaric acid contained only L-tartaric acid while paratartaric acid consisted of a racemic mixture of D- and L-tartaric acid. Curiously, D-tartaric acid has no known natural source, yet several gut bacteria specifically degrade D-tartaric acid. Here, we investigated the oxidation of monosaccharides by inflammatory reactive oxygen and nitrogen species. We found that this reaction yields an array of alpha hydroxy carboxylic acids, including tartaric acid isomers. Utilization of inflammation- derived D- and L-tartaric acid enhanced colonization by Salmonella Typhimurium and E. coli in murine models of gut inflammation. Our findings suggest that byproducts of inflammatory radical metabolism, such as tartrate and other alpha hydroxy carboxylic acids, create transient nutrient niches for enteric pathogens and other potentially harmful bacteria. Furthermore, this work illustrates that inflammatory radicals generate a zoo of molecules, some of which may erroneously presumed to be xenobiotics.
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23
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Wang A, Guan B, Zhang H, Xu H. Danger-associated metabolites trigger metaflammation: A crowbar in cardiometabolic diseases. Pharmacol Res 2023; 198:106983. [PMID: 37931790 DOI: 10.1016/j.phrs.2023.106983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Cardiometabolic diseases (CMDs) are characterized by a series of metabolic disorders and chronic low-grade inflammation. CMDs contribute to a high burden of mortality and morbidity worldwide. Host-microbial metabolic regulation that triggers metaflammation is an emerging field of study that promotes a new perspective for perceiving cardiovascular risks. The term metaflammation denotes the entire cascade of immune responses activated by a new class of metabolites known as "danger-associated metabolites" (DAMs). It is being proposed by the present review for the first time. We summarize current studies covering bench to bedside aspects of DAMs to better understand CMDs in the context of DAMs. We have focused on the involvement of DAMs in the pathophysiological development of CMDs, including the disruption of immune homeostasis and chronic inflammation-triggered damage leading to CMD-related adverse events, as well as emerging therapeutic approaches for targeting DAM metabolism in CMDs.
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Affiliation(s)
- Anlu Wang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China; National Clinical Research Center for Chinese Medicine Cardiology, Beijing 100091, China
| | - Baoyi Guan
- Department of Internal Medicine-Cardiovascular, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - He Zhang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China; National Clinical Research Center for Chinese Medicine Cardiology, Beijing 100091, China
| | - Hao Xu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China; National Clinical Research Center for Chinese Medicine Cardiology, Beijing 100091, China.
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24
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Spiga L, Fansler RT, Perera YR, Shealy NG, Munneke MJ, David HE, Torres TP, Lemoff A, Ran X, Richardson KL, Pudlo N, Martens EC, Folta-Stogniew E, Yang ZJ, Skaar EP, Byndloss MX, Chazin WJ, Zhu W. Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection. Cell Host Microbe 2023; 31:1639-1654.e10. [PMID: 37776864 PMCID: PMC10599249 DOI: 10.1016/j.chom.2023.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/06/2023] [Accepted: 08/29/2023] [Indexed: 10/02/2023]
Abstract
During intestinal inflammation, host nutritional immunity starves microbes of essential micronutrients, such as iron. Pathogens scavenge iron using siderophores, including enterobactin; however, this strategy is counteracted by host protein lipocalin-2, which sequesters iron-laden enterobactin. Although this iron competition occurs in the presence of gut bacteria, the roles of commensals in nutritional immunity involving iron remain unexplored. Here, we report that the gut commensal Bacteroides thetaiotaomicron acquires iron and sustains its resilience in the inflamed gut by utilizing siderophores produced by other bacteria, including Salmonella, via a secreted siderophore-binding lipoprotein XusB. Notably, XusB-bound enterobactin is less accessible to host sequestration by lipocalin-2 but can be "re-acquired" by Salmonella, allowing the pathogen to evade nutritional immunity. Because the host and pathogen have been the focus of studies of nutritional immunity, this work adds commensal iron metabolism as a previously unrecognized mechanism modulating the host-pathogen interactions and nutritional immunity.
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Affiliation(s)
- Luisella Spiga
- 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
| | - Ryan T Fansler
- 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
| | - Yasiru R Perera
- Departments of Biochemistry and Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Nicolas G Shealy
- 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
| | - Matthew J Munneke
- 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
| | - Holly E David
- 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
| | - Teresa P Torres
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew Lemoff
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xinchun Ran
- Departments of Chemistry, Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Katrina L Richardson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicholas Pudlo
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ewa Folta-Stogniew
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, CT 06511, USA
| | - Zhongyue J Yang
- Departments of Chemistry, Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Eric P Skaar
- 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
| | - 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
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
| | - Wenhan Zhu
- 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.
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25
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Ben-Arosh H, Avraham R. Tissue-specific macrophage immunometabolism. Curr Opin Immunol 2023; 84:102369. [PMID: 37473458 DOI: 10.1016/j.coi.2023.102369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023]
Abstract
Macrophages are phagocytic cells distributed across tissues that sustain homeostasis by constantly probing their local environment. Upon perturbations, macrophages rewire their energy metabolism to execute their immune programs. Intensive research in the field of immunometabolism highlights cell-intrinsic immunometabolites such as succinate and itaconate as immunomodulatory signals. A role for cell-extrinsic stimuli now emerges with evidence for signals that shape macrophages' metabolism in a tissue-specific manner. In this review, we will cover macrophage immunometabolism in the gut, a complex metabolic and immunologically active tissue. During homeostasis, gut macrophages are constantly exposed to pro-inflammatory ligands from the microbiota, and in contrast, are balanced by microbiota-derived anti-inflammatory metabolites. Given their extensive metabolic changes during activation, spatial analyses of the tissue will allow the characterization of metabolic niches of macrophage in the gut. Identifying metabolic perturbations of macrophage subsets during chronic inflammation and infection can direct future tissue-specific metabolotherapies.
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Affiliation(s)
- Hadar Ben-Arosh
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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26
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Pokorzynski ND, Groisman EA. How Bacterial Pathogens Coordinate Appetite with Virulence. Microbiol Mol Biol Rev 2023; 87:e0019822. [PMID: 37358444 PMCID: PMC10521370 DOI: 10.1128/mmbr.00198-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.
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Affiliation(s)
- Nick D. Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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27
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Winter MG, Hughes ER, Muramatsu MK, Jimenez AG, Chanin RB, Spiga L, Gillis CC, McClelland M, Andrews-Polymenis H, Winter SE. Formate oxidation in the intestinal mucus layer enhances fitness of Salmonella enterica serovar Typhimurium. mBio 2023; 14:e0092123. [PMID: 37498116 PMCID: PMC10470504 DOI: 10.1128/mbio.00921-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/12/2023] [Indexed: 07/28/2023] Open
Abstract
Salmonella enterica serovar Typhimurium induces intestinal inflammation to create a niche that fosters the outgrowth of the pathogen over the gut microbiota. Under inflammatory conditions, Salmonella utilizes terminal electron acceptors generated as byproducts of intestinal inflammation to generate cellular energy through respiration. However, the electron donating reactions in these electron transport chains are poorly understood. Here, we investigated how formate utilization through the respiratory formate dehydrogenase-N (FdnGHI) and formate dehydrogenase-O (FdoGHI) contribute to gut colonization of Salmonella. Both enzymes fulfilled redundant roles in enhancing fitness in a mouse model of Salmonella-induced colitis, and coupled to tetrathionate, nitrate, and oxygen respiration. The formic acid utilized by Salmonella during infection was generated by its own pyruvate-formate lyase as well as the gut microbiota. Transcription of formate dehydrogenases and pyruvate-formate lyase was significantly higher in bacteria residing in the mucus layer compared to the lumen. Furthermore, formate utilization conferred a more pronounced fitness advantage in the mucus, indicating that formate production and degradation occurred predominantly in the mucus layer. Our results provide new insights into how Salmonella adapts its energy metabolism to the local microenvironment in the gut. IMPORTANCE Bacterial pathogens must not only evade immune responses but also adapt their metabolism to successfully colonize their host. The microenvironments encountered by enteric pathogens differ based on anatomical location, such as small versus large intestine, spatial stratification by host factors, such as mucus layer and antimicrobial peptides, and distinct commensal microbial communities that inhabit these microenvironments. Our understanding of how Salmonella populations adapt its metabolism to different environments in the gut is incomplete. In the current study, we discovered that Salmonella utilizes formate as an electron donor to support respiration, and that formate oxidation predominantly occurs in the mucus layer. Our experiments suggest that spatially distinct Salmonella populations in the mucus layer and the lumen differ in their energy metabolism. Our findings enhance our understanding of the spatial nature of microbial metabolism and may have implications for other enteric pathogens as well as commensal host-associated microbial communities.
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Affiliation(s)
- Maria G. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Elizabeth R. Hughes
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Matthew K. Muramatsu
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Angel G. Jimenez
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Rachael B. Chanin
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Luisella Spiga
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Caroline C. Gillis
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, UC Irvine, Irvine, California, USA
| | - Helene Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, Texas A&M College of Medicine, College Station, Texas, USA
| | - Sebastian E. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
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Turner M, Van Hulzen L, Pietri JE. The gut microbiota induces melanin deposits that act as substrates for fimA-mediated aggregation of Salmonella Typhimurium and enhance infection of the German cockroach vector. Microbiol Spectr 2023; 11:e0211923. [PMID: 37606369 PMCID: PMC10580948 DOI: 10.1128/spectrum.02119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/28/2023] [Indexed: 08/23/2023] Open
Abstract
When Salmonella Typhimurium is ingested by German cockroaches, the bacteria replicate in the gut and persist for at least 7 d, enabling transmission in the feces. However, the mechanisms that facilitate survival and persistence in the cockroach gut remain poorly detailed. We previously reported the formation of biofilm-like aggregate populations of S. Typhimurium in the gut of cockroaches upon ingestion. We also reported that deletion of the type-1 fimbrial subunit of S. Typhimurium, fimA, leads to a reduced bacterial load in the cockroach gut. Here, we link these observations and provide further insight into the mechanism and function of S. Typhimurium aggregation in the gut of the cockroach. We show that S. Typhimurium but not Escherichia coli forms aggregated populations in the cockroach gut, and that aggregate formation requires fimA but not the biofilm formation-related genes csgA and csgD. Furthermore, we show that S. Typhimurium aggregates are formed using small granular deposits present in the cockroach gut, which exhibit properties consistent with melanin, as substrates. These melanin deposits are prevalent in the guts of both immature and adult cockroaches from laboratory colonies and are correlated with increased gut bacterial density while being entirely absent in gnotobiotic cockroaches reared without exposure to environmental bacteria, indicating they are induced as a response to the gut microbiota. When cockroaches lacking melanin deposits in the gut are fed S. Typhimurium, they exhibit lower rates of infection than those harboring melanin deposits, demonstrating that microbiota-induced melanin deposits enhance infection of the gut of the vector. IMPORTANCE Cockroaches, including the German cockroach (Blattella germanica), can be both mechanical and biological vectors of pathogenic bacteria. Together, our data reveal a novel mechanism by which S. Typhimurium interacts with the cockroach gut and its microbiota that promotes infection of the vector. These findings exemplify the emerging but underappreciated complexity of the relationship between cockroaches and S. Typhimurium.
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Affiliation(s)
- Matthew Turner
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
| | - Landen Van Hulzen
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
| | - Jose E. Pietri
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
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Nagarajan A, Scoggin K, Gupta J, Threadgill DW, Andrews-Polymenis HL. Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome. MICROBIOME 2023; 11:149. [PMID: 37420306 PMCID: PMC10329326 DOI: 10.1186/s40168-023-01552-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/18/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND The human gut microbiota is a complex community comprised of trillions of bacteria and is critical for the digestion and absorption of nutrients. Bacterial communities of the intestinal microbiota influence the development of several conditions and diseases. We studied the effect of host genetics on gut microbial composition using Collaborative Cross (CC) mice. CC mice are a panel of mice that are genetically diverse across strains, but genetically identical within a given strain allowing repetition and deeper analysis than is possible with other collections of genetically diverse mice. RESULTS 16S rRNA from the feces of 167 mice from 28 different CC strains was sequenced and analyzed using the Qiime2 pipeline. We observed a large variance in the bacterial composition across CC strains starting at the phylum level. Using bacterial composition data, we identified 17 significant Quantitative Trait Loci (QTL) linked to 14 genera on 9 different mouse chromosomes. Genes within these intervals were analyzed for significant association with pathways and the previously known human GWAS database using Enrichr analysis and Genecards database. Multiple host genes involved in obesity, glucose homeostasis, immunity, neurological diseases, and many other protein-coding genes located in these regions may play roles in determining the composition of the gut microbiota. A subset of these CC mice was infected with Salmonella Typhimurium. Using infection outcome data, an increase in abundance of genus Lachnospiraceae and decrease in genus Parasutterella correlated with positive health outcomes after infection. Machine learning classifiers accurately predicted the CC strain and the infection outcome using pre-infection bacterial composition data from the feces. CONCLUSION Our study supports the hypothesis that multiple host genes influence the gut microbiome composition and homeostasis, and that certain organisms may influence health outcomes after S. Typhimurium infection. Video Abstract.
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Affiliation(s)
- Aravindh Nagarajan
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - Kristin Scoggin
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
| | - Jyotsana Gupta
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - David W. Threadgill
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX USA
- Department of Biochemistry & Biophysics and Department of Nutrition, Texas A&M University, College Station, TX USA
| | - Helene L. Andrews-Polymenis
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
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Spiga L, Fansler RT, Perera YR, Shealy NG, Munneke MJ, Torres TP, David HE, Lemoff A, Ran X, Richardson KL, Pudlo N, Martens EC, Yang ZJ, Skaar EP, Byndloss MX, Chazin WJ, Zhu W. Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.546471. [PMID: 37425782 PMCID: PMC10326984 DOI: 10.1101/2023.06.25.546471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
During intestinal inflammation, host nutritional immunity starves microbes of essential micronutrients such as iron. Pathogens scavenge iron using siderophores, which is counteracted by the host using lipocalin-2, a protein that sequesters iron-laden siderophores, including enterobactin. Although the host and pathogens compete for iron in the presence of gut commensal bacteria, the roles of commensals in nutritional immunity involving iron remain unexplored. Here, we report that the gut commensal Bacteroides thetaiotaomicron acquires iron in the inflamed gut by utilizing siderophores produced by other bacteria including Salmonella, via a secreted siderophore-binding lipoprotein termed XusB. Notably, XusB-bound siderophores are less accessible to host sequestration by lipocalin-2 but can be "re-acquired" by Salmonella , allowing the pathogen to evade nutritional immunity. As the host and pathogen have been the focus of studies of nutritional immunity, this work adds commensal iron metabolism as a previously unrecognized mechanism modulating the interactions between pathogen and host nutritional immunity.
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Leleiwi I, Rodriguez-Ramos J, Shaffer M, Sabag-Daigle A, Kokkinias K, Flynn RM, Daly RA, Kop LFM, Solden LM, Ahmer BMM, Borton MA, Wrighton KC. Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers. MICROBIOME 2023; 11:114. [PMID: 37210515 PMCID: PMC10199544 DOI: 10.1186/s40168-023-01529-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/21/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. RESULTS Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. CONCLUSIONS This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.
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Affiliation(s)
- Ikaia Leleiwi
- Department of Cell and Molecular Biology, The Colorado State University, Fort Collins, CO USA
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Josué Rodriguez-Ramos
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Graduate Degree Program in Ecology, The Colorado State University, Fort Collins, CO USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH USA
| | - Katherine Kokkinias
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Department of Microbiology, Immunology, and Pathology, The Colorado State University, Fort Collins, CO USA
| | - Rory M. Flynn
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Rebecca A. Daly
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Linnea F. M. Kop
- Department of Microbiology, RIBES, Radbound University, Nijmegen, The Netherlands
- Department of Microbiology and Biophysics, The Ohio State University, Columbus, OH USA
| | - Lindsey M. Solden
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Brian M. M. Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH USA
| | - Mikayla A. Borton
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Kelly C. Wrighton
- Department of Cell and Molecular Biology, The Colorado State University, Fort Collins, CO USA
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Graduate Degree Program in Ecology, The Colorado State University, Fort Collins, CO USA
- Department of Microbiology, Immunology, and Pathology, The Colorado State University, Fort Collins, CO USA
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Liu XF, Shao JH, Liao YT, Wang LN, Jia Y, Dong PJ, Liu ZZ, He DD, Li C, Zhang X. Regulation of short-chain fatty acids in the immune system. Front Immunol 2023; 14:1186892. [PMID: 37215145 PMCID: PMC10196242 DOI: 10.3389/fimmu.2023.1186892] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
A growing body of research suggests that short-chain fatty acids (SCFAs), metabolites produced by intestinal symbiotic bacteria that ferment dietary fibers (DFs), play a crucial role in the health status of symbiotes. SCFAs act on a variety of cell types to regulate important biological processes, including host metabolism, intestinal function, and immune function. SCFAs also affect the function and fate of immune cells. This finding provides a new concept in immune metabolism and a better understanding of the regulatory role of SCFAs in the immune system, which impacts the prevention and treatment of disease. The mechanism by which SCFAs induce or regulate the immune response is becoming increasingly clear. This review summarizes the different mechanisms through which SCFAs act in cells. According to the latest research, the regulatory role of SCFAs in the innate immune system, including in NLRP3 inflammasomes, receptors of TLR family members, neutrophils, macrophages, natural killer cells, eosinophils, basophils and innate lymphocyte subsets, is emphasized. The regulatory role of SCFAs in the adaptive immune system, including in T-cell subsets, B cells, and plasma cells, is also highlighted. In addition, we discuss the role that SCFAs play in regulating allergic airway inflammation, colitis, and osteoporosis by influencing the immune system. These findings provide evidence for determining treatment options based on metabolic regulation.
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Affiliation(s)
- Xiao-feng Liu
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Jia-hao Shao
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Yi-Tao Liao
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Li-Ning Wang
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yuan Jia
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Peng-jun Dong
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Zhi-zhong Liu
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Dan-dan He
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Chao Li
- Department of Spine, Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Xian Zhang
- Department of Spine, Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
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Iverson TM, Singh PK, Cecchini G. An evolving view of Complex II - non-canonical complexes, megacomplexes, respiration, signaling, and beyond. J Biol Chem 2023; 299:104761. [PMID: 37119852 DOI: 10.1016/j.jbc.2023.104761] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/01/2023] Open
Abstract
Mitochondrial Complex II is traditionally studied for its participation in two key respiratory processes: the electron transport chain and the Krebs cycle. There is now a rich body of literature explaining how Complex II contributes to respiration. However, more recent research shows that not all of the pathologies associated with altered Complex II activity clearly correlate with this respiratory role. Complex II activity has now been shown to be necessary for a range of biological processes peripherally-related to respiration, including metabolic control, inflammation, and cell fate. Integration of findings from multiple types of studies suggests that Complex II both participates in respiration and controls multiple succinate-dependent signal transduction pathways. Thus, the emerging view is that the true biological function of Complex II is well beyond respiration. This review uses a semi-chronological approach to highlight major paradigm shifts that occurred over time. Special emphasis is given to the more recently identified functions of Complex II and its subunits because these findings have infused new directions into an established field.
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Affiliation(s)
- T M Iverson
- Departments of Pharmacology, Vanderbilt University, Nashville, TN 37232; Departments of Biochemistry, Vanderbilt University, Nashville, TN 37232; Departments of Center for Structural Biology, Vanderbilt University, Nashville, TN 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232.
| | - Prashant K Singh
- Departments of Pharmacology, Vanderbilt University, Nashville, TN 37232; Departments of Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158.
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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Zhang Y, Chen R, Zhang D, Qi S, Liu Y. Metabolite interactions between host and microbiota during health and disease: Which feeds the other? Biomed Pharmacother 2023; 160:114295. [PMID: 36709600 DOI: 10.1016/j.biopha.2023.114295] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Metabolites produced by the host and microbiota play a crucial role in how human bodies develop and remain healthy. Most of these metabolites are produced by microbiota and hosts in the digestive tract. Metabolites in the gut have important roles in energy metabolism, cellular communication, and host immunity, among other physiological activities. Although numerous host metabolites, such as free fatty acids, amino acids, and vitamins, are found in the intestine, metabolites generated by gut microbiota are equally vital for intestinal homeostasis. Furthermore, microbiota in the gut is the sole source of some metabolites, including short-chain fatty acids (SCFAs). Metabolites produced by microbiota, such as neurotransmitters and hormones, may modulate and significantly affect host metabolism. The gut microbiota is becoming recognized as a second endocrine system. A variety of chronic inflammatory disorders have been linked to aberrant host-microbiota interplays, but the precise mechanisms underpinning these disturbances and how they might lead to diseases remain to be fully elucidated. Microbiome-modulated metabolites are promising targets for new drug discovery due to their endocrine function in various complex disorders. In humans, metabolotherapy for the prevention or treatment of various disorders will be possible if we better understand the metabolic preferences of bacteria and the host in specific tissues and organs. Better disease treatments may be possible with the help of novel complementary therapies that target host or bacterial metabolism. The metabolites, their physiological consequences, and functional mechanisms of the host-microbiota interplays will be highlighted, summarized, and discussed in this overview.
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Affiliation(s)
- Yan Zhang
- Department of Anethesiology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - Rui Chen
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - DuoDuo Zhang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China.
| | - Shuang Qi
- Department of Anethesiology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - Yan Liu
- Department of Hand and Foot Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
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Bogomolnaya L, Talamantes M, Rocha J, Nagarajan A, Zhu W, Spiga L, Winter MG, Konganti K, Adams LG, Winter S, Andrews-Polymenis H. Taxonomic and Metagenomic Analyses Define the Development of the Microbiota in the Chick. mBio 2023; 14:e0244422. [PMID: 36475774 PMCID: PMC9973254 DOI: 10.1128/mbio.02444-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
Chicks are ideal to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Taxonomic/metagenomic analyses captured the development of the chick microbiota in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm) during development. Taxonomic analysis suggests that colonization by the chicken microbiota takes place in several waves. The cecal microbiota stabilizes at day 12 posthatch with prominent Gammaproteobacteria and Clostridiales. Introduction of S. Typhimurium at day 4 posthatch disrupted the expected waves of intestinal colonization. Taxonomic and metagenomic shotgun sequencing analyses allowed us to identify species present in uninfected chicks. Untargeted metabolomics suggested different metabolic activities in infected chick microbiota. This analysis and gas chromatography-mass spectrometry on ingesta confirmed that lactic acid in cecal content coincides with the stable presence of enterococci in STm-infected chicks. Unique metabolites, including 2-isopropylmalic acid, an intermediate in the biosynthesis of leucine, were present only in the cecal content of STm-infected chicks. The metagenomic data suggested that the microbiota in STm-infected chicks contained a higher abundance of genes, from STm itself, involved in branched-chain amino acid synthesis. We generated an ilvC deletion mutant (STM3909) encoding ketol-acid-reductoisomerase, a gene required for the production of l-isoleucine and l-valine. ΔilvC mutants are disadvantaged for growth during competitive infection with the wild type. Providing the ilvC gene in trans restored the growth of the ΔilvC mutant. Our integrative approach identified biochemical pathways used by STm to establish a colonization niche in the chick intestine during development. IMPORTANCE Chicks are an ideal model to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Using taxonomic and metagenomic analyses, we captured the development of chick microbiota to 19 days posthatch in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm). We show that normal development of the microbiota takes place in waves and is altered in the presence of a pathogen. Metagenomics and metabolomics suggested that branched-chain amino acid biosynthesis is especially important for Salmonella growth in the infected chick intestine. Salmonella mutants unable to make l-isoleucine and l-valine colonize the chick intestine poorly. Restoration of the pathway for biosynthesis of these amino acids restored the colonizing ability of Salmonella. Integration of multiple analyses allowed us to correctly identify biochemical pathways used by Salmonella to establish a niche for colonization in the chick intestine during development.
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Affiliation(s)
- Lydia Bogomolnaya
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, Texas, USA
- Deparment of Biomedical Sciences, Marshall University, Huntington, West Virginia, USA
| | - Marissa Talamantes
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, Texas, USA
| | - Joana Rocha
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, Texas, USA
| | - Aravindh Nagarajan
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, Texas, USA
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, USA
| | - Wenhan Zhu
- Department of Microbiology and Immunology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Luisella Spiga
- Department of Microbiology and Immunology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Maria G. Winter
- Department of Microbiology and Immunology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Kranti Konganti
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M, College Station, Texas, USA
| | - L. Garry Adams
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M, College Station, Texas, USA
| | - Sebastian Winter
- Department of Microbiology and Immunology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Helene Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, Texas, USA
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, USA
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The Colorectal Cancer Gut Environment Regulates Activity of the Microbiome and Promotes the Multidrug Resistant Phenotype of ESKAPE and Other Pathogens. mSphere 2023; 8:e0062622. [PMID: 36847529 PMCID: PMC10117110 DOI: 10.1128/msphere.00626-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The human gut microbiota in colorectal cancer patients have a distinct population compared to heathy counterparts. However, the activity (gene expression) of this community has not been investigated.
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Cruz E, Haeberle AL, Westerman TL, Durham ME, Suyemoto MM, Knodler LA, Elfenbein JR. Nonredundant Dimethyl Sulfoxide Reductases Influence Salmonella enterica Serotype Typhimurium Anaerobic Growth and Virulence. Infect Immun 2023; 91:e0057822. [PMID: 36722978 PMCID: PMC9933680 DOI: 10.1128/iai.00578-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 02/02/2023] Open
Abstract
Facultative anaerobic enteric pathogens can utilize a diverse array of alternate electron acceptors to support anaerobic metabolism and thrive in the hypoxic conditions within the mammalian gut. Dimethyl sulfoxide (DMSO) is produced by methionine catabolism and can act as an alternate electron acceptor to support anaerobic respiration. The DMSO reductase complex consists of three subunits, DmsA, DmsB, and DmsC, and allows bacteria to grow anaerobically with DMSO as an electron acceptor. The genomes of nontyphoidal Salmonella enterica encode three putative dmsABC operons, but the impact of the apparent genetic redundancy in DMSO reduction on the fitness of nontyphoidal S. enterica during infection remains unknown. We hypothesized that DMSO reduction would be needed for S. enterica serotype Typhimurium to colonize the mammalian gut. We demonstrate that an S. Typhimurium mutant with loss of function in all three putative DMSO reductases (ΔdmsA3) poorly colonizes the mammalian intestine when the microbiota is intact and when inflammation is absent. DMSO reduction enhances anaerobic growth through nonredundant contributions of two of the DMSO reductases. Furthermore, DMSO reduction influences virulence by increasing expression of the type 3 secretion system 2 and reducing expression of the type 3 secretion system 1. Collectively, our data demonstrate that the DMSO reductases of S. Typhimurium are functionally nonredundant and suggest DMSO is a physiologically relevant electron acceptor that supports S. enterica fitness in the gut.
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Affiliation(s)
- E. Cruz
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - A. L. Haeberle
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - T. L. Westerman
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - M. E. Durham
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - M. M. Suyemoto
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - L. A. Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - J. R. Elfenbein
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Food Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Fuke N, Yamashita T, Shimizu S, Matsumoto M, Sawada K, Jung S, Tokuda I, Misawa M, Suzuki S, Ushida Y, Mikami T, Itoh K, Suganuma H. Association of Plasma Lipopolysaccharide-Binding Protein Concentration with Dietary Factors, Gut Microbiota, and Health Status in the Japanese General Adult Population: A Cross-Sectional Study. Metabolites 2023; 13:metabo13020250. [PMID: 36837869 PMCID: PMC9965710 DOI: 10.3390/metabo13020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The influx of intestinal bacteria-derived lipopolysaccharide (LPS) into the blood has attracted attention as a cause of diseases. The aim of this study is investigating the associations between the influx of LPS, dietary factors, gut microbiota, and health status in the general adult population. Food/nutrient intake, gut microbiota, health status and plasma LPS-binding protein (LBP; LPS exposure indicator) were measured in 896 residents (58.1% female, mean age 54.7 years) of the rural Iwaki district of Japan, and each correlation was analyzed. As the results, plasma LBP concentration correlated with physical (right/left arms' muscle mass [β = -0.02, -0.03]), renal (plasma renin activity [β = 0.27], urine albumin creatinine ratio [β = 0.50]), adrenal cortical (cortisol [β = 0.14]), and thyroid function (free thyroxine [β = 0.05]), iron metabolism (serum iron [β = -0.14]), and markers of lifestyle-related diseases (all Qs < 0.20). Plasma LBP concentration were mainly negatively correlated with vegetables/their nutrients intake (all βs ≤ -0.004, Qs < 0.20). Plasma LBP concentration was positively correlated with the proportion of Prevotella (β = 0.32), Megamonas (β = 0.56), and Streptococcus (β = 0.65); and negatively correlated with Roseburia (β = -0.57) (all Qs < 0.20). Dietary factors correlated with plasma LBP concentration correlated with positively (all βs ≥ 0.07) or negatively (all βs ≤ -0.07) the proportion of these bacteria (all Qs < 0.20). Our results suggested that plasma LBP concentration in the Japanese general adult population was associated with various health issues, and that dietary habit was associated with plasma LBP concentration in relation to the intestinal bacteria.
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Affiliation(s)
- Nobuo Fuke
- Innovation Division, KAGOME Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
- Correspondence: ; Tel.: +81-80-1573-5815
| | - Takahiro Yamashita
- Innovation Division, KAGOME Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
| | - Sunao Shimizu
- Innovation Division, KAGOME Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
- Department of Vegetable Life Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Mai Matsumoto
- Innovation Division, KAGOME Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
| | - Kaori Sawada
- Innovation Center for Health Promotion, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Songee Jung
- Innovation Center for Health Promotion, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
- Department of Digital Nutrition and Health Sciences, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Itoyo Tokuda
- Innovation Center for Health Promotion, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Mina Misawa
- Center of Innovation Research Initiatives Organization, Hirosaki University, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Shigenori Suzuki
- Innovation Division, KAGOME Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
| | - Yusuke Ushida
- Innovation Division, KAGOME Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
| | - Tatsuya Mikami
- Innovation Center for Health Promotion, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Ken Itoh
- Department of Vegetable Life Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Hiroyuki Suganuma
- Innovation Division, KAGOME Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
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Michaels M, Madsen KL. Immunometabolism and microbial metabolites at the gut barrier: Lessons for therapeutic intervention in inflammatory bowel disease. Mucosal Immunol 2023; 16:72-85. [PMID: 36642380 DOI: 10.1016/j.mucimm.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 01/15/2023]
Abstract
The concept of immunometabolism has emerged recently whereby the repolarizing of inflammatory immune cells toward anti-inflammatory profiles by manipulating cellular metabolism represents a new potential therapeutic approach to controlling inflammation. Metabolic pathways in immune cells are tightly regulated to maintain immune homeostasis and appropriate functional specificity. Because effector and regulatory immune cell populations have different metabolic requirements, this allows for cellular selectivity when regulating immune responses based on metabolic pathways. Gut microbes have a major role in modulating immune cell metabolic profiles and functional responses through extensive interactions involving metabolic products and crosstalk between gut microbes, intestinal epithelial cells, and mucosal immune cells. Developing strategies to target metabolic pathways in mucosal immune cells through the modulation of gut microbial metabolism has the potential for new therapeutic approaches for human autoimmune and inflammatory diseases, such as inflammatory bowel disease. This review will give an overview of the relationship between metabolic reprogramming and immune responses, how microbial metabolites influence these interactions, and how these pathways could be harnessed in the treatment of inflammatory bowel disease.
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Affiliation(s)
- Margret Michaels
- University of Alberta, Department of Medicine, Edmonton, Alberta, Canada
| | - Karen L Madsen
- University of Alberta, Department of Medicine, Edmonton, Alberta, Canada; IMPACTT: Integrated Microbiome Platforms for Advancing Causation Testing & Translation, Edmonton, Alberta, Canada.
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Schubert C, Unden G. Fumarate, a central electron acceptor for Enterobacteriaceae beyond fumarate respiration and energy conservation. Adv Microb Physiol 2023; 82:267-299. [PMID: 36948656 DOI: 10.1016/bs.ampbs.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
C4-dicarboxylates (C4-DCs) such as fumarate, l-malate and l-aspartate are key substrates for Enterobacteria such as Escherichia coli or Salmonella typhimurium during anaerobic growth. In general, C4-DCs are oxidants during biosynthesis, e.g., of pyrimidine or heme, acceptors for redox balancing, a high-quality nitrogen source (l-aspartate) and electron acceptor for fumarate respiration. Fumarate reduction is required for efficient colonization of the murine intestine, even though the colon contains only small amounts of C4-DCs. However, fumarate can be produced endogenously by central metabolism, allowing autonomous production of an electron acceptor for biosynthesis and redox balancing. Bacteria possess a complex set of transporters for the uptake (DctA), antiport (DcuA, DcuB, TtdT) and excretion (DcuC) of C4-DCs. DctA and DcuB exert regulatory functions and link transport to metabolic control through interaction with regulatory proteins. The sensor kinase DcuS of the C4-DC two-component system DcuS-DcuR forms complexes with DctA (aerobic) or DcuB (anaerobic), representing the functional state of the sensor. Moreover, EIIAGlc from the glucose phospho-transferase system binds to DctA and presumably inhibits C4-DC uptake. Overall, the function of fumarate as an oxidant in biosynthesis and redox balancing explains the pivotal role of fumarate reductase for intestinal colonization, while the role of fumarate in energy conservation (fumarate respiration) is of minor importance.
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Affiliation(s)
- Christopher Schubert
- Institute for Molecular Physiology (IMP), Microbiology and Biotechnology; Johannes Gutenberg-University, Mainz, Germany; Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
| | - Gottfried Unden
- Institute for Molecular Physiology (IMP), Microbiology and Biotechnology; Johannes Gutenberg-University, Mainz, Germany.
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Chen H, Wu X, Sun R, Lu H, Lin R, Gao X, Li G, Feng Z, Zhu R, Yao Y, Feng B, Liu Z. Dysregulation of CD177 + neutrophils on intraepithelial lymphocytes exacerbates gut inflammation via decreasing microbiota-derived DMF. Gut Microbes 2023; 15:2172668. [PMID: 36729914 PMCID: PMC9897772 DOI: 10.1080/19490976.2023.2172668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Neutrophils synergize with intestinal resident intraepithelial lymphocytes (IELs) to serve as the first-line defense and maintain intestinal homeostasis. However, the underlying mechanisms whereby neutrophils regulate IELs to inhibit intestinal inflammation are still not completely understood. Here, we found that depletion of neutrophils (especially CD177+ subset) caused expansion of colitogenic TCRγδ+CD8αα+ IELs, increased intestinal inflammation, and dysbiosis after dextran sulfate sodium exposure or Citrobacter rodentium infection in mice. scRNA-seq analysis revealed a pyroptosis-related gene signature and hyperresponsiveness to microbiota in TCRγδ+CD8αα+ IELs from colitic Cd177-/- mice. Microbiota-derived fumarate and its derivative dimethyl fumarate (DMF), as well as fumarate-producing microbiotas, decreased in the feces of colitic Cd177-/- mice. Elimination of dysbiosis by antibiotics treatment or co-housing procedure and DMF supplementation restrained TCRγδ+CD8αα+ IEL activation. Consistently, DMF significantly alleviated intestinal mucosal inflammation in mice through restricting gasdermin D (GSDMD)-induced pyroptosis of TCRγδ+CD8αα+ IELs. Therefore, our data reveal that neutrophils inhibit intestinal inflammation by promoting microbiota-derived DMF to regulate TCRγδ+CD8αα+ IEL activation in a GSDMD-mediated pyroptosis-dependent manner, and that DMF may serve as a therapeutic target for the management of intestinal inflammation.
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Affiliation(s)
- Huimin Chen
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaohan Wu
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruicong Sun
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huiying Lu
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ritian Lin
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiang Gao
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Gengfeng Li
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhongsheng Feng
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruixin Zhu
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yao Yao
- Department of Gastroenterology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Baisui Feng
- Department of Gastroenterology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhanju Liu
- Center for Inflammatory Bowel Disease Research, The Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China,Department of Gastroenterology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Division of Immunology, School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, China,CONTACT Zhanju Liu Center for IBD Research, The Shanghai Tenth People’s Hospital of Tongji University, Shanghai, China
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Abstract
Succinate is a circulating metabolite, and the relationship between abnormal changes in the physiological concentration of succinate and inflammatory diseases caused by the overreaction of certain immune cells has become a research focus. Recent investigations have shown that succinate produced by the gut microbiota has the potential to regulate host homeostasis and treat diseases such as inflammation. Gut microbes are important for maintaining intestinal homeostasis. Microbial metabolites serve as nutrients in energy metabolism, and act as signal molecules that stimulate host cell and organ function and affect the structural balance between symbiotic gut microorganisms. This review focuses on succinate as a metabolite of both host cells and gut microbes and its involvement in regulating the gut - immune tissue axis by activating intestinal mucosal cells, including macrophages, dendritic cells, and intestinal epithelial cells. We also examined its role as the mediator of microbiota - host crosstalk and its potential function in regulating intestinal microbiota homeostasis. This review explores feasible ways to moderate succinate levels and provides new insights into succinate as a potential target for microbial therapeutics for humans.
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Affiliation(s)
- Yi-Han Wei
- College of Animal Science, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiang-Chao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, USA
| | - Xiu-Qi Wang
- College of Animal Science, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - Chun-Qi Gao
- College of Animal Science, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
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Fan HH, Fang SB, Chang YC, Huang ST, Huang CH, Chang PR, Chang WC, Yang LTL, Lin PC, Cheng HY. Effects of colonization-associated gene yqiC on global transcriptome, cellular respiration, and oxidative stress in Salmonella Typhimurium. J Biomed Sci 2022; 29:102. [PMID: 36457101 PMCID: PMC9714038 DOI: 10.1186/s12929-022-00885-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/20/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND yqiC is required for colonizing the Salmonella enterica serovar Typhimurium (S. Typhimurium) in human cells; however, how yqiC regulates nontyphoidal Salmonella (NTS) genes to influence bacteria-host interactions remains unclear. METHODS The global transcriptomes of S. Typhimurium yqiC-deleted mutant (ΔyqiC) and its wild-type strain SL1344 after 2 h of in vitro infection with Caco-2 cells were obtained through RNA sequencing to conduct comparisons and identify major yqiC-regulated genes, particularly those involved in Salmonella pathogenicity islands (SPIs), ubiquinone and menaquinone biosynthesis, electron transportation chains (ETCs), and carbohydrate/energy metabolism. A Seahorse XFp Analyzer and assays of NADH/NAD+ and H2O2 were used to compare oxygen consumption and extracellular acidification, glycolysis parameters, adenosine triphosphate (ATP) generation, NADH/NAD+ ratios, and H2O2 production between ΔyqiC and SL1344. RESULTS After S. Typhimurium interacts with Caco-2 cells, yqiC represses gene upregulation in aspartate carbamoyl transferase, type 1 fimbriae, and iron-sulfur assembly, and it is required for expressing ilvB operon, flagellin, tdcABCD, and dmsAB. Furthermore, yqiC is required for expressing mainly SPI-1 genes and specific SPI-4, SPI-5, and SPI-6 genes; however, it diversely regulates SPI-2 and SPI-3 gene expression. yqiC significantly contributes to menD expression in menaquinone biosynthesis. A Kyoto Encyclopedia of Genes and Genomes analysis revealed the extensive association of yqiC with carbohydrate and energy metabolism. yqiC contributes to ATP generation, and the analyzer results demonstrate that yqiC is required for maintaining cellular respiration and metabolic potential under energy stress and for achieving glycolysis, glycolytic capacity, and glycolytic reserve. yqiC is also required for expressing ndh, cydA, nuoE, and sdhB but suppresses cyoC upregulation in the ETC of aerobically and anaerobically grown S. Typhimurium; priming with Caco-2 cells caused a reversed regulation of yiqC toward upregulation in these ETC complex genes. Furthermore, yqiC is required for maintaining NADH/NAD+ redox status and H2O2 production. CONCLUSIONS Specific unreported genes that were considerably regulated by the colonization-associated gene yqiC in NTS were identified, and the key role and tentative mechanisms of yqiC in the extensive modulation of virulence factors, SPIs, ubiquinone and menaquinone biosynthesis, ETCs, glycolysis, and oxidative stress were discovered.
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Affiliation(s)
- Hung-Hao Fan
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan ,grid.412896.00000 0000 9337 0481Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan ,grid.412955.e0000 0004 0419 7197Department of Emergency Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shiuh-Bin Fang
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan ,grid.412896.00000 0000 9337 0481Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan ,grid.412896.00000 0000 9337 0481Master Program for Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yu-Chu Chang
- grid.412896.00000 0000 9337 0481Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Tung Huang
- grid.412087.80000 0001 0001 3889Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Chih-Hung Huang
- grid.412087.80000 0001 0001 3889Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Pei-Ru Chang
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan ,grid.412896.00000 0000 9337 0481Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chiao Chang
- grid.412896.00000 0000 9337 0481Master Program for Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Lauderdale Tsai-Ling Yang
- grid.59784.370000000406229172National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Pei-Chun Lin
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan
| | - Hung-Yen Cheng
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan
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Song Y, Chen K, Lv L, Xiang Y, Du X, Zhang X, Zhao G, Xiao Y. Uncovering the biogeography of the microbial commmunity and its association with nutrient metabolism in the intestinal tract using a pig model. Front Nutr 2022; 9:1003763. [PMID: 36238459 PMCID: PMC9552906 DOI: 10.3389/fnut.2022.1003763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is a complex ecosystem that is essential for the metabolism, immunity and health of the host. The gut microbiota also plays a critical role in nutrient absorption and metabolism, and nutrients can influence the growth and composition of the gut microbiota. To gain a better understanding of the relationship between the gut microbial composition and nutrient metabolism, we used a pig model by collecting the contents of the different intestinal locations from six pigs to investigate microbial composition in different intestinal locations based on 16S rRNA gene sequencing and the concentrations of short-chain fatty acids (SCFAs), amino acids, fat, and crude ash in different intestinal locations using gas chromatography and chemical analysis. The results showed that the richness and diversity of intestinal microbial communities gradually increased from the small intestine to the large intestine. The relative abundance of Proteobacteria was higher in the jejunum and ileum, whereas the proportion of Firmicutes was higher in the cecum and colon. The concentrations of SCFAs were higher in the cecum and colon (P < 0.05). The concentrations of amino acids were higher in the small intestine than in the large intestine, while the amino acid content was significantly higher in the ascending colon than in the transverse colon and descending colon. The correlation analysis revealed that Ruminococcaceae UCG-005, Coriobacteriaceae_uncultured, [Eubacterium] hallii group, Mogibacterium and Lachnospiraceae AC2044 group had a higher positive correlation with SCFAs, crude ash and fat but had a negative correlation with amino acids in different gut locations of pigs. These findings may serve as fundamental data for using nutrient metabolism to regulate human and animal gut microbes and health and provide guidance for exploring host-microbe bidirectional interaction mechanisms and driving pathways.
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Affiliation(s)
- Yuanyuan Song
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Kai Chen
- Quality and Safety of Animal Products Group, Zhejiang Center of Animal Disease Control, Hangzhou, China
| | - Lu Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yun Xiang
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Xizhong Du
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Xiaojun Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Guangmin Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Yingping Xiao
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The Feed Additive Potassium Diformate Prevents Salmonella enterica Serovar Pullorum Infection and Affects Intestinal Flora in Chickens. Antibiotics (Basel) 2022; 11:antibiotics11091265. [PMID: 36140044 PMCID: PMC9495629 DOI: 10.3390/antibiotics11091265] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Extensive studies have shown that potassium diformate (KDF), an antibiotic substitute used as a feed additive, improves animal growth performance, although there is less direct evidence of its preventive effect on bacterial infections and its influence on the intestinal flora of animals. In this study, the inhibition effect of KDF on Salmonella enterica serovar Pullorum, an important enteric pathogen causing pullorum disease, was investigated in vitro and on a chicken infection model. The effect of KDF on the diversities and structures of chicken duodenal and cecum flora were also investigated using 16S rRNA gene sequencing. The results showed that addition of 0.5% KDF in feed or 0.1% KDF in drinking water significantly reduced the bacterial loads and the degree of pathological changes in the cecum, improved digestion and reduced the pH of the gastrointestinal tract of chickens infected with S. pullorum. KDF also significantly modified the diversity and abundance of intestinal microflorae in chickens. In particular, it promoted the colonization of several probiotics, such as Bacteroides, Blautia, Ruminococcus_torques_group and Faecalibacteriumm, which are involved in maintenance of the intestinal barrier, modulation of inflammation, energy supply for intestinal cells and pathogen resistance. These results enrich the theoretical basis for the clinical application of KDF in chickens.
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Lopez LR, Ahn JH, Alves T, Arthur JC. Microenvironmental Factors that Shape Bacterial Metabolites in Inflammatory Bowel Disease. Front Cell Infect Microbiol 2022; 12:934619. [PMID: 35959366 PMCID: PMC9362432 DOI: 10.3389/fcimb.2022.934619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a significant global health problem that involves chronic intestinal inflammation and can involve severe comorbidities, including intestinal fibrosis and inflammation-associated colorectal cancer (CRC). Disease-associated alterations to the intestinal microbiota often include fecal enrichment of Enterobacteriaceae, which are strongly implicated in IBD development. This dysbiosis of intestinal flora accompanies changes in microbial metabolites, shaping host:microbe interactions and disease risk. While there have been numerous studies linking specific bacterial taxa with IBD development, our understanding of microbial function in the context of IBD is limited. Several classes of microbial metabolites have been directly implicated in IBD disease progression, including bacterial siderophores and genotoxins. Yet, our microbiota still harbors thousands of uncharacterized microbial products. In-depth discovery and characterization of disease-associated microbial metabolites is necessary to target these products in IBD treatment strategies. Towards improving our understanding of microbiota metabolites in IBD, it is important to recognize how host relevant factors influence microbiota function. For example, changes in host inflammation status, metal availability, interbacterial community structure, and xenobiotics all play an important role in shaping gut microbial ecology. In this minireview, we outline how each of these factors influences gut microbial function, with a specific focus on IBD-associated Enterobacteriaceae metabolites. Importantly, we discuss how altering the intestinal microenvironment could improve the treatment of intestinal inflammation and associated disorders, like intestinal fibrosis and CRC.
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Affiliation(s)
- Lacey R. Lopez
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ju-Hyun Ahn
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Tomaz Alves
- Division of Comprehensive Oral Health, Adams School of Dentistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Gastrointestinal Biology and Disease, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Janelle C. Arthur,
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Wu Z, Xu Q, Gu S, Chen Y, Lv L, Zheng B, Wang Q, Wang K, Wang S, Xia J, Yang L, Bian X, Jiang X, Zheng L, Li L. Akkermansia muciniphila Ameliorates Clostridioides difficile Infection in Mice by Modulating the Intestinal Microbiome and Metabolites. Front Microbiol 2022; 13:841920. [PMID: 35663882 PMCID: PMC9159907 DOI: 10.3389/fmicb.2022.841920] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridioides difficile is a common cause of nosocomial infection. Antibiotic-induced dysbiosis in the intestinal microbiota is a core cause of C. difficile infection (CDI). Akkermansia muciniphila plays an active role in maintaining gastrointestinal balance and might offer the protective effects on CDI as probiotics. Here, we investigated the effects and mechanisms of A. muciniphila on CDI. C57BL/6 mice (n = 29) were administered A. muciniphila Muc T (3 × 109 CFUs, 0.2 mL) or phosphate-buffered saline (PBS) by oral gavage for 2 weeks. Mice were pretreated with an antibiotic cocktail and subsequently challenged with the C. difficile strain VPI 10463. A. muciniphila treatment prevented weight loss in mice and reduced the histological injury of the colon. And it also alleviated inflammation and improved the barrier function of the intestine. The administration effects of A. muciniphila may be associated with an increase in short-chain fatty acid production and the maintenance of bile acids' steady-state. Our results provide evidence that administration of A. muciniphila to CDI mice, with an imbalance in the microbial community structure, lead to a decrease in abundance of members of the Enterobacteriaceae and Enterococcaceae. In short, A. muciniphila shows a potential anti-CDI role by modulating gut microbiota and the metabolome.
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Affiliation(s)
- Zhengjie Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiaomai Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Silan Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiangqiang Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kaicen Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuting Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiafeng Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liya Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyuan Bian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianwan Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisi Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Bacterial Research Platform, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
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49
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Nadimpalli ML, Lanza VF, Montealegre MC, Sultana S, Fuhrmeister ER, Worby CJ, Teichmann L, Caduff L, Swarthout JM, Crider YS, Earl AM, Brown J, Luby SP, Islam MA, Julian TR, Pickering AJ. Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children. Nat Microbiol 2022; 7:620-629. [PMID: 35422497 PMCID: PMC9249080 DOI: 10.1038/s41564-022-01101-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/24/2022] [Indexed: 02/07/2023]
Abstract
Healthy development of the gut microbiome provides long-term health benefits. Children raised in countries with high infectious disease burdens are frequently exposed to diarrhoeal pathogens and antibiotics, which perturb gut microbiome assembly. A recent cluster-randomized trial leveraging >4,000 child observations in Dhaka, Bangladesh, found that automated water chlorination of shared taps effectively reduced child diarrhoea and antibiotic use. In this substudy, we leveraged stool samples collected from 130 children 1 year after chlorine doser installation to examine differences between treatment and control children's gut microbiota. Water chlorination was associated with increased abundance of several bacterial genera previously linked to improved gut health; however, we observed no effects on the overall richness or diversity of taxa. Several clinically relevant antibiotic resistance genes were relatively more abundant in the gut microbiome of treatment children, possibly due to increases in Enterobacteriaceae. While further studies on the long-term health impacts of drinking chlorinated water would be valuable, we conclude that access to chlorinated water did not substantially impact child gut microbiome development in this setting, supporting the use of chlorination to increase global access to safe drinking water.
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Affiliation(s)
- Maya L. Nadimpalli
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
| | - Val F. Lanza
- Bioinformatics Unit, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain,Network Research Center for Infectious Diseases (CIBERINFEC), Spain
| | | | - Sonia Sultana
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Erica R. Fuhrmeister
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Colin J. Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA
| | - Lisa Teichmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jenna M. Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Yoshika S. Crider
- Energy and Resources Group, University of California Berkeley, Berkeley, CA, USA,King Center on Global Development, Stanford University, Stanford, CA, USA
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen P. Luby
- Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Mohammad Aminul Islam
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland,Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Timothy R. Julian
- Network Research Center for Infectious Diseases (CIBERINFEC), Spain,Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Amy J. Pickering
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA,Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA,Blum Center for Developing Economies, University of California, Berkeley, CA, USA,Correspondence and requests for materials should be addressed to Dr. Amy Pickering () and Dr. Tim Julian ()
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50
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Schubert C, Unden G. C 4-Dicarboxylates as Growth Substrates and Signaling Molecules for Commensal and Pathogenic Enteric Bacteria in Mammalian Intestine. J Bacteriol 2022; 204:e0054521. [PMID: 34978458 PMCID: PMC9017328 DOI: 10.1128/jb.00545-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The C4-dicarboxylates (C4-DC) l-aspartate and l-malate have been identified as playing an important role in the colonization of mammalian intestine by enteric bacteria, such as Escherichia coli and Salmonella enterica serovar Typhimurium, and succinate as a signaling molecule for host-enteric bacterium interaction. Thus, endogenous and exogenous fumarate respiration and related functions are required for efficient initial growth of the bacteria. l-Aspartate represents a major substrate for fumarate respiration in the intestine and a high-quality substrate for nitrogen assimilation. During nitrogen assimilation, DcuA catalyzes an l-aspartate/fumarate antiport and serves as a nitrogen shuttle for the net uptake of ammonium only, whereas DcuB acts as a redox shuttle that catalyzes the l-malate/succinate antiport during fumarate respiration. The C4-DC two-component system DcuS-DcuR is active in the intestine and responds to intestinal C4-DC levels. Moreover, in macrophages and in mice, succinate is a signal that promotes virulence and survival of S. Typhimurium and pathogenic E. coli. On the other hand, intestinal succinate is an important signaling molecule for the host and activates response and protective programs. Therefore, C4-DCs play a major role in supporting colonization of enteric bacteria and as signaling molecules for the adaptation of host physiology.
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Affiliation(s)
- Christopher Schubert
- Institute for Molecular Physiology (IMP), Microbiology and Wine Research, Johannes Gutenberg University, Mainz, Germany
| | - Gottfried Unden
- Institute for Molecular Physiology (IMP), Microbiology and Wine Research, Johannes Gutenberg University, Mainz, Germany
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