1
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Chen L, Xue J, He Y, Zhao L, Zhang Y, Yin L, Fu S, Yu W, Ma X, Wang Y, Tang Y, Gao Z. Serum metabolomics profile identifies patients with community-acquired pneumonia infected by bacteria, fungi, and viruses. Ann Med 2024; 56:2399320. [PMID: 39283042 PMCID: PMC11407381 DOI: 10.1080/07853890.2024.2399320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
PURPOSE Patients with bacterial, fungal, and viral community-acquired pneumonia (CAP) were studied to determine their metabolic profiles. METHODS Loop-mediated isothermal amplification technology and nucleic acid sequence-dependent amplification combined with microfluidic chip technology were applied to screen multiple pathogens from respiratory tract samples. Eighteen patients with single bacterial infection (B-CAP), fifteen with single virus infection (V-CAP), twenty with single fungal infection (F-CAP), and twenty controls were enrolled. UHPLC-MS/MS analysis of untargeted serum samples for metabolic profiles. Multiple linear regression and Spearman's rank correlation analysis were used to determine associations between metabolites and clinical parameters. The sensitivity and specificity of the screened metabolites were also examined, along with their area under the curve. RESULTS The metabolic signatures of patients with CAP infected by bacteria, viruses, and fungi were markedly different from those of controls. The abundances of 45, 56, and 79 metabolites were significantly unbalanced. Among these differential metabolites, 11, 13, and 29 were unique to the B-CAP, V-CAP, and F-CAP groups, respectively. Bacterial infections were the only known causes of disturbances in the pentose and glucuronate and aldarate and ascorbate metabolism interconversions metabolic pathway. CONCLUSIONS Serum metabolomic techniques based on UHPLC-MS/MS may identify differences between individuals with CAP who have been infected by various pathogens, and they can also build a metabolite signature for early detection of the origin of infection and prompt care.
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Affiliation(s)
- Li Chen
- Department of Respiratory, Beijing Ditan Hospital, Capital Medical University, Beijing, People's Republic of China
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Jianbo Xue
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yukun He
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Lili Zhao
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Ying Zhang
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Lu Yin
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Shining Fu
- Department of Respiratory and Critical Care Medicine, Beijing Jishuitan Hospital, Beijing, China
| | - Wenyi Yu
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Xinqian Ma
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yu Wang
- Department of Respiratory, Beijing Ditan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yanfen Tang
- Department of Respiratory, Beijing Ditan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Zhancheng Gao
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, China
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2
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Ma G, Tao Q, Li X, Han Y, Du H, Hu Q, Xiao H. Metabolomics study of dietary Pleurotus eryngii β-type glycosidic polysaccharide on colitis induced by dextran sodium sulfate in mice - Exploration for the potential metabolic indicators in urine and serum. Food Chem 2024; 458:140195. [PMID: 38954951 DOI: 10.1016/j.foodchem.2024.140195] [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: 03/22/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Pleurotus eryngii, an edible mushroom recognized for its potent polysaccharides, demonstrates significant regulatory effects on metabolic processes. β-glucan (WPEP) derived from P. eryngii has been noted for its therapeutic potential, exhibiting notable benefits in alleviating colonic inflammation and restructuring gut microbiota in mice treated with dextran sodium sulfate (DSS). This study focuses on utilizing DSS-induced colitis mice to explore the efficacy and underlying mechanisms of WPEP in ameliorating colitis, employing a metabolomics approach analyzing urine and serum. The findings reveal that WPEP administration effectively regulates metabolic imbalances in DSS mice, impacting purine metabolism, pentose and glucuronic acid interconversion, amino acid metabolism, primary bile acid biosynthesis, citric acid cycle, and lipid metabolism. Furthermore, WPEP demonstrates a capacity to modulate colitis by regulating diverse metabolic pathways, consequently influencing intestinal barrier integrity, motility, inflammation, oxidative stress, and immunity. These insights suggest that WPEP is a promising food component for managing inflammatory bowel diseases.
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Affiliation(s)
- Gaoxing Ma
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, People's Republic of China
| | - Qi Tao
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, People's Republic of China
| | - Xinyi Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, People's Republic of China
| | - Yanhui Han
- Department of Food Science, University of Massachusetts, Amherst, MA 01002, USA
| | - Hengjun Du
- Department of Food Science, University of Massachusetts, Amherst, MA 01002, USA
| | - Qiuhui Hu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, People's Republic of China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, MA 01002, USA.
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3
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Singh S, Gola C, Singh B, Agrawal V, Chaba R. D-galactonate metabolism in enteric bacteria: a molecular and physiological perspective. Curr Opin Microbiol 2024; 81:102524. [PMID: 39137493 DOI: 10.1016/j.mib.2024.102524] [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: 05/30/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024]
Abstract
D-galactonate, a widely prevalent sugar acid, was first reported as a nutrient source for enteric bacteria in the 1970s. Since then, decades of research enabled a description of the modified Entner-Doudoroff pathway involved in its degradation and reported the structural and biochemical features of its metabolic enzymes, primarily in Escherichia coli K-12. However, only in the last few years, the D-galactonate transporter has been characterized, and the regulation of the dgo operon, encoding the structural genes for the transporter and enzymes of D-galactonate metabolism, has been detailed. Notably, in recent years, multiple evolutionary studies have identified the dgo operon as a dominant target for adaptation of E. coli in the mammalian gut. Despite considerable research on dgo operon, numerous fundamental questions remain to be addressed. The emerging relevance of the dgo operon in host-bacterial interactions further necessitates the study of D-galactonate metabolism in other enterobacterial strains.
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Affiliation(s)
- Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Chetna Gola
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Vishal Agrawal
- Amity School of Biological Sciences, Amity University Punjab, Mohali, SAS Nagar, Punjab 140306, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India.
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4
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Cherrak Y, Salazar MA, Näpflin N, Malfertheiner L, Herzog MKM, Schubert C, von Mering C, Hardt WD. Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut. Nat Microbiol 2024; 9:2696-2709. [PMID: 39160293 PMCID: PMC11445065 DOI: 10.1038/s41564-024-01775-x] [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: 10/02/2023] [Accepted: 07/04/2024] [Indexed: 08/21/2024]
Abstract
Resource competition is a driver of gut microbiota composition. Bacteria can outcompete metabolically similar rivals through the limitation of shared growth-fuelling nutrients. The mechanisms underlying this remain unclear for bacteria with identical sets of metabolic genes. Here we analysed the lactose utilization operon in the murine commensal Escherichia coli 8178. Using in vitro and in vivo approaches, we showed that translation of the lactose utilization repressor gene lacI from its native non-canonical GTG start codon increases the basal expression of the lactose utilization cluster, enhancing adaptation to lactose consumption. Consequently, a strain carrying the wild type lacI GTG start codon outperformed the lacI ATG start codon mutant in the mouse intestine. This advantage was attenuated upon limiting host lactose intake through diet shift or altering the mutant frequency, emphasizing the context-dependent effect of a single nucleotide change on the bacterial fitness of a common member of the gut microbiota. Coupled with a genomic analysis highlighting the selection of non-ATG start codons in sugar utilization regulator genes across the Enterobacteriaceae family, our data exposed an unsuspected function of non-canonical start codons in metabolic competition.
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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
| | - Nicolas Näpflin
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Mathias K-M Herzog
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christopher Schubert
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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5
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Fan X, Liu X, Yan Y, Hua D, Luo K, Hao S, Zhu D, Zhou D, Liu H. Widely targeted metabolomics analysis reveals the effect of soybean hull polysaccharides on nonvolatile components of plant-based yogurt and its metabolic pattern. Int J Biol Macromol 2024; 279:135144. [PMID: 39208892 DOI: 10.1016/j.ijbiomac.2024.135144] [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: 05/23/2024] [Revised: 08/09/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Soybean hull polysaccharides (SHPS) enhance the physicochemical properties of plant-based yogurt. However, their effects on the nutritional profile and biochemical mechanisms remain unclear. This study aimed to assess the impact of SHPS addition on the nonvolatile components of plant-based yogurt and its underlying mechanisms through widely targeted metabolomics analysis. The results demonstrated that the addition of SHPS (0.2 %-1.0 % w/v) enhanced the levels of free amino acids, sugars, and organic acids, with the addition of 0.6 % w/v being particularly effective in improving yogurt quality. Widely targeted metabolomics analysis revealed 278 differential metabolites between yogurt supplemented with 0.6 % SHPS (SPY) and the control sample. SHPS increased the content of various metabolites, including amino acids and derivatives, saccharides, organic acids, and flavonoids, among others. Key metabolic pathways affected by SHPS included pantothenate and CoA biosynthesis; valine, leucine, and isoleucine biosynthesis; and benzoate degradation. As the primary component of SHPS, galacturonic acid affected the metabolic products in yogurt by participating in the pentose and glucuronate interconversions and ascorbate and aldarate metabolism pathways. These findings elucidate the role of SHPS in modulating the nutritional composition of plant-based yogurt, offering valuable insights into its functional mechanisms in food processing.
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Affiliation(s)
- Xiangrong Fan
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Xiaoqing Liu
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Yaxin Yan
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Dong Hua
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Ke Luo
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Sijia Hao
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Danshi Zhu
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China
| | - Dayu Zhou
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China.
| | - He Liu
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China.
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6
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Beekman CN, Penumutchu S, Peterson R, Han G, Belenky M, Hasan MH, Belenky A, Beura LK, Belenky P. Spatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment. Cell Rep 2024; 43:114572. [PMID: 39116202 DOI: 10.1016/j.celrep.2024.114572] [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: 01/30/2024] [Revised: 06/05/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Antibiotics cause collateral damage to resident microbes that is associated with various health risks. To date, studies have largely focused on the impacts of antibiotics on large intestinal and fecal microbiota. Here, we employ a gastrointestinal (GI) tract-wide integrated multiomic approach to show that amoxicillin (AMX) treatment reduces bacterial abundance, bile salt hydrolase activity, and unconjugated bile acids in the small intestine (SI). Losses of fatty acids (FAs) and increases in acylcarnitines in the large intestine (LI) correspond with spatially distinct expansions of Proteobacteria. Parasutterella excrementihominis engage in FA biosynthesis in the SI, while multiple Klebsiella species employ FA oxidation during expansion in the LI. We subsequently demonstrate that restoration of unconjugated bile acids can mitigate losses of commensals in the LI while also inhibiting the expansion of Proteobacteria during AMX treatment. These results suggest that the depletion of bile acids and lipids may contribute to AMX-induced dysbiosis in the lower GI tract.
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Affiliation(s)
- Chapman N Beekman
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Rachel Peterson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Geongoo Han
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Marina Belenky
- Felicitex Therapeutics Inc., 27 Strathmore Road, Natick, MA 01760, USA
| | - Mohammad H Hasan
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Alexei Belenky
- Felicitex Therapeutics Inc., 27 Strathmore Road, Natick, MA 01760, USA
| | - Lalit K Beura
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
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7
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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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8
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Chen Y, Xiao L, Zhou M, Zhang H. The microbiota: a crucial mediator in gut homeostasis and colonization resistance. Front Microbiol 2024; 15:1417864. [PMID: 39165572 PMCID: PMC11333231 DOI: 10.3389/fmicb.2024.1417864] [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: 04/15/2024] [Accepted: 07/23/2024] [Indexed: 08/22/2024] Open
Abstract
The gut microbiota is a complex and diverse community of microorganisms that colonizes the human gastrointestinal tract and influences various aspects of human health. These microbes are closely related to enteric infections. As a foreign entity for the host, commensal microbiota is restricted and regulated by the barrier and immune system in the gut and contributes to gut homeostasis. Commensals also effectively resist the colonization of pathogens and the overgrowth of indigenous pathobionts by utilizing a variety of mechanisms, while pathogens have developed strategies to subvert colonization resistance. Dysbiosis of the microbial community can lead to enteric infections. The microbiota acts as a pivotal mediator in establishing a harmonious mutualistic symbiosis with the host and shielding the host against pathogens. This review aims to provide a comprehensive overview of the mechanisms underlying host-microbiome and microbiome-pathogen interactions, highlighting the multi-faceted roles of the gut microbiota in preventing enteric infections. We also discuss the applications of manipulating the microbiota to treat infectious diseases in the gut.
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Affiliation(s)
- Yiding Chen
- Department of Gastroenterology, West China Tianfu Hospital, Sichuan University, Chengdu, China
| | - Ling Xiao
- Department of Gastroenterology, West China Tianfu Hospital, Sichuan University, Chengdu, China
| | - Min Zhou
- Department of Gastroenterology, West China Tianfu Hospital, Sichuan University, Chengdu, China
| | - Hu Zhang
- Department of Gastroenterology, West China Tianfu Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
- Center for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China
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9
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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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10
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Cottam C, White RT, Beck LC, Stewart CJ, Beatson SA, Lowe EC, Grinter R, Connolly JPR. Metabolism of L-arabinose converges with virulence regulation to promote enteric pathogen fitness. Nat Commun 2024; 15:4462. [PMID: 38796512 PMCID: PMC11127945 DOI: 10.1038/s41467-024-48933-7] [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: 12/18/2023] [Accepted: 05/16/2024] [Indexed: 05/28/2024] Open
Abstract
Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified an uncharacterised transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full competitive fitness in the mouse gut and highly expressed during human infection. Discovery of this transporter suggested that EHEC strains have an enhanced ability to scavenge ʟ-arabinose and therefore prompted us to investigate the impact of this nutrient on pathogenesis. Accordingly, we discovered that ʟ-arabinose enhances expression of the EHEC type 3 secretion system, increasing its ability to colonise host cells, and that the underlying mechanism is dependent on products of its catabolism rather than the sensing of ʟ-arabinose as a signal. Furthermore, using the murine pathogen Citrobacter rodentium, we show that ʟ-arabinose metabolism provides a fitness benefit during infection via virulence factor regulation, as opposed to supporting pathogen growth. Finally, we show that this mechanism is not restricted to ʟ-arabinose and extends to other pentose sugars with a similar metabolic fate. This work highlights the importance integrating central metabolism with virulence regulation in order to maximise competitive fitness of enteric pathogens within the host-niche.
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Affiliation(s)
- Curtis Cottam
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Rhys T White
- Institute of Environmental Science and Research, Wellington, New Zealand
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lauren C Beck
- Newcastle University Translation and Clinical Research Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Christopher J Stewart
- Newcastle University Translation and Clinical Research Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elisabeth C Lowe
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - James P R Connolly
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK.
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11
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Rosay T, Jimenez AG, Sperandio V. Glucuronic acid confers colonization advantage to enteric pathogens. Proc Natl Acad Sci U S A 2024; 121:e2400226121. [PMID: 38502690 PMCID: PMC10990124 DOI: 10.1073/pnas.2400226121] [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: 01/04/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Glucuronidation is a detoxification process to eliminate endo- and xeno-biotics and neurotransmitters from the host circulation. Glucuronosyltransferase binds these compounds to glucuronic acid (GlcA), deactivating them and allowing their elimination through the gastrointestinal (GI) tract. However, the microbiota produces β-glucuronidases that release GlcA and reactivate these compounds. Enteric pathogens such as enterohemorrhagic Escherichia coli (EHEC) and Citrobacter rodentium sense and utilize galacturonic acid (GalA), an isomer of GlcA, to outcompete the microbiota promoting gut colonization. However, the role of GlcA in pathogen colonization has not been explored. Here, we show that treatment of mice with a microbial β-glucuronidase inhibitor (GUSi) decreased C. rodentium's colonization of the GI tract, without modulating bacterial virulence or host inflammation. Metagenomic studies indicated that GUSi did not change the composition of the intestinal microbiota in these animals. GlcA confers an advantage for pathogen expansion through its utilization as a carbon source. Congruently mutants unable to catabolize GlcA depict lower GI colonization compared to wild type and are not sensitive to GUSi. Germfree mice colonized with a commensal E. coli deficient for β-glucuronidase production led to a decrease of C. rodentium tissue colonization, compared to animals monocolonized with an E. coli proficient for production of this enzyme. GlcA is not sensed as a signal and doesn't activate virulence expression but is used as a metabolite. Because pathogens can use GlcA to promote their colonization, inhibitors of microbial β-glucuronidases could be a unique therapeutic against enteric infections without disturbing the host or microbiota physiology.
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Affiliation(s)
- Thibaut Rosay
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI53706
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Angel G. Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Vanessa Sperandio
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI53706
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX75390
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12
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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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13
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Bin P, Liu W, Zhang X, Liu B, Zhu G. A novel antibacterial strategy for targeting the bacterial methionine biosynthesis pathway. Int J Antimicrob Agents 2024; 63:107057. [PMID: 38072168 DOI: 10.1016/j.ijantimicag.2023.107057] [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: 06/10/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024]
Abstract
Bacterial pathogens reprogramme their metabolic networks to support growth and establish infection at specific sites. Bacterial central metabolism has been considered attractive for developing antimicrobial drugs; however, most metabolic enzymes are conserved between humans and bacteria. This study found that blockade of methionine biosynthesis in Citrobacter rodentium and Salmonella enteritidis inhibited bacterial growth and activity of the type III secretion system, resulting in severe defects in colonization and pathogenicity. In addition, α-methyl-methionine was found to inhibit the activity of methionine biosynthetic enzyme MetA, and consequently reduce the virulence and pathogenicity of enteric pathogens. These findings highlight the crucial role of methionine in bacterial virulence, and describe a potential new drug target.
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Affiliation(s)
- Peng Bin
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China; College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wanyang Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiaojie Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Baobao Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
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14
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Doranga S, Krogfelt KA, Cohen PS, Conway T. Nutrition of Escherichia coli within the intestinal microbiome. EcoSal Plus 2024:eesp00062023. [PMID: 38417452 DOI: 10.1128/ecosalplus.esp-0006-2023] [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: 11/03/2023] [Indexed: 03/01/2024]
Abstract
In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.
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Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Karen A Krogfelt
- Department of Science and Environment, Pandemix Center Roskilde University, Roskilde, Denmark
| | - Paul S Cohen
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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15
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Spragge F, Bakkeren E, Jahn MT, B N Araujo E, Pearson CF, Wang X, Pankhurst L, Cunrath O, Foster KR. Microbiome diversity protects against pathogens by nutrient blocking. Science 2023; 382:eadj3502. [PMID: 38096285 DOI: 10.1126/science.adj3502] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023]
Abstract
The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonization of two major bacterial pathogens, both in vitro and in gnotobiotic mice. Whereas single species alone had negligible effects, colonization resistance greatly increased with community diversity. Moreover, this community-level resistance rested critically upon certain species being present. We explained these ecological patterns through the collective ability of resistant communities to consume nutrients that overlap with those used by the pathogen. Furthermore, we applied our findings to successfully predict communities that resist a novel target strain. Our work provides a reason why microbiome diversity is beneficial and suggests a route for the rational design of pathogen-resistant communities.
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Affiliation(s)
- Frances Spragge
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Erik Bakkeren
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Martin T Jahn
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Claire F Pearson
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Xuedan Wang
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louise Pankhurst
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Olivier Cunrath
- CNRS, UMR7242, Biotechnology and Cell Signaling, University of Strasbourg, Illkirch, France
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
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16
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Fang F, Xue Y, Xu X, Fang D, Liu W, Zhong Y, Han J, Li Y, Tao Q, Lu R, Ma C, Kumar A, Wang D. L-glutamine protects against enterohemorrhagic Escherichia coli infection by inhibiting bacterial virulence and enhancing host defense concurrently. Microbiol Spectr 2023; 11:e0097523. [PMID: 37815335 PMCID: PMC10714755 DOI: 10.1128/spectrum.00975-23] [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: 03/07/2023] [Accepted: 08/24/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE The type 3 secretion system (T3SS) was obtained in many Gram-negative bacterial pathogens, and it is crucial for their pathogenesis. Environmental signals were found to be involved in the expression regulation of T3SS, which was vital for successful bacterial infection in the host. Here, we discovered that L-glutamine (Gln), the most abundant amino acid in the human body, could repress enterohemorrhagic Escherichia coli (EHEC) T3SS expression via nitrogen metabolism and therefore had potential as an antivirulence agent. Our in vitro and in vivo evidence demonstrated that Gln could decline EHEC infection by attenuating bacterial virulence and enhancing host defense simultaneously. We repurpose Gln as a potential treatment for EHEC infection accordingly.
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Affiliation(s)
- Fang Fang
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
| | - Yunxin Xue
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
| | - Xuefang Xu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Dingli Fang
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
| | - Weijia Liu
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
| | - Ying Zhong
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
| | - Jinping Han
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
| | - Yunhe Li
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
| | - Qian Tao
- Department of Pathology, Women and Children's Hospital, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, Fujian Province, China
| | - Rong Lu
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
| | - Cong Ma
- Department of Nephrology, Lishan Hospital, Anshan Central Hospital, Anshan, Liaoning Province, China
| | | | - Dai Wang
- Department of Laboratory Medicine, Xiamen Key Laboratory of Perinatal-Neonatal Infection, Women and Children's Hospital, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedical Laboratory, School of Public Health and School of Medicine, Xiamen University, Xiamen, Fujian Province, China
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17
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Honda K, Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta D, Hasegawa N, Ohya T, Bhattarai S, Sasajima S, Yoshimasa A, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridooshi Y, Sugita K, Stražar M, Skelly A, Suda W, Hattori M, Nakamoto N, Caballero S, Norman J, Olle B, Tanoue T, Arita M, Bucci V, Atarashi K, Xavier R. Rationally-defined microbial consortia suppress multidrug-resistant proinflammatory Enterobacteriaceae via ecological control. RESEARCH SQUARE 2023:rs.3.rs-3462622. [PMID: 37961431 PMCID: PMC10635318 DOI: 10.21203/rs.3.rs-3462622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Persistent colonization and outgrowth of pathogenic organisms in the intestine may occur due to long-term antibiotic usage or inflammatory conditions, which perpetuate dysregulated immunity and tissue damage1,2. Gram-negative Enterobacteriaceae gut pathobionts are particularly recalcitrant to conventional antibiotic treatment3,4, though an emerging body of evidence suggests that manipulation of the commensal microbiota may be a practical alternative therapeutic strategy5-7. In this study, we rationally isolated and down-selected commensal bacterial consortia from healthy human stool samples capable of strongly and specifically suppressing intestinal Enterobacteriaceae. One of the elaborated consortia, consisting of 18 commensal strains, effectively controlled ecological niches by regulating gluconate availability, thereby reestablishing colonization resistance and alleviating antibiotic-resistant Klebsiella-driven intestinal inflammation in mice. Harnessing these microbial activities in the form of live bacterial therapeutics may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant bacterial infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Aoto Yoshimasa
- JSR-Keio University Medical and Chemical Innovation Center
| | | | | | | | | | | | | | | | | | | | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences
| | | | | | - Silvia Caballero
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
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18
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Yang W, Sun H, Yan J, Kang C, Wu J, Yang B. Enterohemorrhagic Escherichia coli senses microbiota-derived nicotinamide to increase its virulence and colonization in the large intestine. Cell Rep 2023; 42:112638. [PMID: 37294635 DOI: 10.1016/j.celrep.2023.112638] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/05/2023] [Accepted: 05/25/2023] [Indexed: 06/11/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen that specifically colonizes and infects the human large intestine. EHEC O157:H7 engages intricate regulatory pathways to detect host intestinal signals and regulate virulence-related gene expression during colonization and infection. However, the overall EHEC O157:H7 virulence regulatory network in the human large intestine remains incompletely understood. Here, we report a complete signal regulatory pathway where the EvgSA two-component system responds to high-nicotinamide levels produced by microbiota in the large intestine and directly activates loci of enterocyte effacement genes to promote EHEC O157:H7 adherence and colonization. This EvgSA-mediated nicotinamide signaling regulatory pathway is conserved and widespread among several other EHEC serotypes. Moreover, disruption of this virulence-regulating pathway by the deletion of evgS or evgA significantly decreased EHEC O157:H7 adherence and colonization in the mouse intestinal tract, indicating that these genes could be potential targets for the development of new therapeutics for EHEC O157:H7 infection.
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Affiliation(s)
- Wen Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Hongmin Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Jun Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Chenbo Kang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Junli Wu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China.
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19
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Caballero-Flores G, Pickard JM, Núñez G. Microbiota-mediated colonization resistance: mechanisms and regulation. Nat Rev Microbiol 2023; 21:347-360. [PMID: 36539611 PMCID: PMC10249723 DOI: 10.1038/s41579-022-00833-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 12/24/2022]
Abstract
A dense and diverse microbial community inhabits the gut and many epithelial surfaces. Referred to as the microbiota, it co-evolved with the host and is beneficial for many host physiological processes. A major function of these symbiotic microorganisms is protection against pathogen colonization and overgrowth of indigenous pathobionts. Dysbiosis of the normal microbial community increases the risk of pathogen infection and overgrowth of harmful pathobionts. The protective mechanisms conferred by the microbiota are complex and include competitive microbial-microbial interactions and induction of host immune responses. Pathogens, in turn, have evolved multiple strategies to subvert colonization resistance conferred by the microbiota. Understanding the mechanisms by which microbial symbionts limit pathogen colonization should guide the development of new therapeutic approaches to prevent or treat disease.
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Affiliation(s)
- Gustavo Caballero-Flores
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Joseph M Pickard
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA.
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20
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Feng Y, Li D, Ma C, Hu X, Chen F. Barley Leaf Ameliorates Citrobacter-rodentium-Induced Colitis through Arginine Enrichment. Nutrients 2023; 15:nu15081890. [PMID: 37111109 PMCID: PMC10145403 DOI: 10.3390/nu15081890] [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: 03/25/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Inflammatory bowel disease (IBD) has become a global public health challenge. Our previous study showed that barley leaf (BL) significantly reduces Citrobacter-rodentium (CR)-induced colitis, but its mechanism remains elusive. Thus, in this study, we used non-targeted metabolomics techniques to search for potentially effective metabolites. Our results demonstrated that dietary supplementation with BL significantly enriched arginine and that arginine intervention significantly ameliorated CR-induced colitis symptoms such as reduced body weight, shortened colon, wrinkled cecum, and swollen colon wall in mice; in addition, arginine intervention dramatically ameliorated CR-induced histopathological damage to the colon. The gut microbial diversity analysis showed that arginine intervention significantly decreased the relative abundance of CR and significantly increased the relative abundance of Akkermansia, Blautia, Enterorhabdus, and Lachnospiraceae, which modified the CR-induced intestinal flora disorder. Notably, arginine showed a dose-dependent effect on the improvement of colitis caused by CR.
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Affiliation(s)
- Yu Feng
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Daotong Li
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Chen Ma
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Fang Chen
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
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21
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Genomic Island-Encoded Histidine Kinase and Response Regulator Coordinate Mannose Utilization with Virulence in Enterohemorrhagic Escherichia coli. mBio 2023; 14:e0315222. [PMID: 36786613 PMCID: PMC10128022 DOI: 10.1128/mbio.03152-22] [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: 02/15/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is a highly adaptive pathogen and has acquired diverse genetic elements, such as genomic islands and prophages, via horizontal gene transfer to promote fitness in vivo. Two-component signaling systems (TCSs) allow bacteria to sense, respond to, and adapt to various environments. This study identified a putative two-component signaling system composed of the histidine kinase EDL5436 (renamed LmvK) and the response regulator EDL5428 (renamed LmvR) in EHEC. lmvK and lmvR along with EDL5429 to EDL5434 (EDL5429-5434) between them constitute the OI167 genomic island and are highly associated with the EHEC pathotype. EDL5429-5434 encode transporters and metabolic enzymes that contribute to growth on mannose and are directly upregulated by LmvK/LmvR in the presence of mannose, as revealed by quantitative PCR (qPCR) and DNase I footprint assays. Moreover, LmvR directly activates the expression of the type III secretion system in response to mannose and promotes the formation of attaching and effacing lesions on HeLa cells. Using human colonoid and mouse infection models, we show that lmvK and lmvR contributed greatly to adherence and microcolony (MC) formation ex vivo and colonization in vivo. Finally, RNA sequencing and chromatin immunoprecipitation coupled with sequencing analyses identified additional direct targets of LmvR, most of which are involved in metabolism. Given that mannose is a mucus-derived sugar that induces virulence and is preferentially used by EHEC during infection, our data revealed a previously unknown mechanism by which EHEC recognizes the host metabolic landscape and regulates virulence expression accordingly. Our findings provide insights into how pathogenic bacteria evolve by acquiring genetic elements horizontally to adapt to host environments. IMPORTANCE The gastrointestinal tract represents a complex and challenging environment for enterohemorrhagic Escherichia coli (EHEC). However, EHEC is a highly adaptable pathogen, requiring only 10 to 100 CFUs to cause infection. This ability was achieved partially by acquiring mobile genetic elements, such as genomic islands, that promote overall fitness. Mannose is an intestinal mucus-derived sugar that stimulates virulence and is preferentially used by EHEC during infection. Here, we characterize the OI167 genomic island of EHEC, which encodes a novel two-component signaling system (TCS) and transporters and metabolic enzymes (EDL5429-5434) involved in mannose utilization. The TCS directly upregulates EDL5429-5434 and genes encoding the type III secretion system in the presence of mannose. Moreover, the TCS contributes greatly to EHEC virulence ex vivo and in vivo. Our data demonstrate an elegant example in which EHEC strains evolve by acquiring genetic elements horizontally to recognize the host metabolic landscape and regulate virulence expression accordingly, leading to successful infections.
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22
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Tutukina MN, Dakhnovets AI, Kaznadzey AD, Gelfand MS, Ozoline ON. Sense and antisense RNA products of the uxuR gene can affect motility and chemotaxis acting independent of the UxuR protein. Front Mol Biosci 2023; 10:1121376. [PMID: 36936992 PMCID: PMC10016265 DOI: 10.3389/fmolb.2023.1121376] [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: 12/11/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Small non-coding and antisense RNAs are widespread in all kingdoms of life, however, the diversity of their functions in bacteria is largely unknown. Here, we study RNAs synthesised from divergent promoters located in the 3'-end of the uxuR gene, encoding transcription factor regulating hexuronate metabolism in Escherichia coli. These overlapping promoters were predicted in silico with rather high scores, effectively bound RNA polymerase in vitro and in vivo and were capable of initiating transcription in sense and antisense directions. The genome-wide correlation between in silico promoter scores and RNA polymerase binding in vitro and in vivo was higher for promoters located on the antisense strands of the genes, however, sense promoters within the uxuR gene were more active. Both regulatory RNAs synthesised from the divergent promoters inhibited expression of genes associated with the E. coli motility and chemotaxis independent of a carbon source on which bacteria had been grown. Direct effects of these RNAs were confirmed for the fliA gene encoding σ28 subunit of RNA polymerase. In addition to intracellular sRNAs, promoters located within the uxuR gene could initiate synthesis of transcripts found in the fraction of RNAs secreted in the extracellular medium. Their profile was also carbon-independent suggesting that intragenic uxuR transcripts have a specific regulatory role not directly related to the function of the protein in which gene they are encoded.
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Affiliation(s)
- Maria N. Tutukina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
| | - Artemiy I. Dakhnovets
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biotechnology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna D. Kaznadzey
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Mikhail S. Gelfand
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Olga N. Ozoline
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
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23
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Ferrara E, Pecoraro MT, Cice D, Piccolella S, Formato M, Esposito A, Petriccione M, Pacifico S. A Joint Approach of Morphological and UHPLC-HRMS Analyses to Throw Light on the Autochthonous 'Verdole' Chestnut for Nutraceutical Innovation of Its Waste. Molecules 2022; 27:molecules27248924. [PMID: 36558057 PMCID: PMC9785621 DOI: 10.3390/molecules27248924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Nowadays, chestnut by-products are gaining a lot of interest as a low-cost raw material, exploitable for developing added-value products. This is in line with suitable chestnut by-products' management, aimed at reducing the environmental impact, thus improving the chestnut industry's competitiveness and economic sustainability. In this context, with the aim of valorizing local cultivars of European chestnuts (Castanea sativa Mill.), our attention focused on the Verdole cultivar, which has been characterized by using the UPOV guidelines for its distinctness, homogeneity, and stability. After harvesting, Verdole chestnuts were properly dissected to collect the outer and inner shells, and episperm. Each chestnut part, previously crushed, shredded, and passed through diverse sieves, underwent ultrasound-assisted extraction. The extracts obtained were evaluated for their total phenolic, flavonoid, and tannin content. The antiradical capacity by DPPH and ABTS assays, and the Fe(III) reducing power, were also evaluated. Although all the samples showed dose-dependent antioxidant efficacy, plant matrix size strongly impacted on extraction efficiency. LC-HRMS-based metabolic profiling highlighted the occurrence of different polyphenol subclasses, whose quantitative ratio varied among the chestnut parts investigated. The outer shell was more chemically rich than inner shell and episperm, according to its pronounced antioxidant activity. The polyphenol diversity of Verdole by-products is a resource not intended for disposal, appliable in the nutraceutical sector, thus realizing a new scenario in processing chestnut waste.
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Affiliation(s)
- Elvira Ferrara
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy
- CREA-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura, Via Torrino 3, 81100 Caserta, Italy
| | - Maria Tommasina Pecoraro
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy
- CREA-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura, Via Torrino 3, 81100 Caserta, Italy
| | - Danilo Cice
- CREA-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura, Via Torrino 3, 81100 Caserta, Italy
| | - Simona Piccolella
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy
| | - Marialuisa Formato
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy
| | - Assunta Esposito
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy
| | - Milena Petriccione
- CREA-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura, Via Torrino 3, 81100 Caserta, Italy
- Correspondence:
| | - Severina Pacifico
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy
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24
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Escherichia coli O157:H7 senses microbiota-produced riboflavin to increase its virulence in the gut. Proc Natl Acad Sci U S A 2022; 119:e2212436119. [PMID: 36409903 PMCID: PMC9860305 DOI: 10.1073/pnas.2212436119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Riboflavin is produced by most commensal bacteria in the human colon, where enterohemorrhagic Escherichia coli (EHEC) colonizes and causes diseases. Sensing environmental signals to site-specifically express the type-III secretion system (T3SS), which injects effectors into host cells leading to intestinal colonization and disease, is key to the pathogenesis of EHEC. Here, we reveal that EHEC O157:H7, a dominant EHEC serotype frequently associated with severe diseases, acquired a previously uncharacterized two-component regulatory system rbfSR, which senses microbiota-produced riboflavin to directly activate the expression of LEE genes encoding the T3SS in the colon. rbfSR is present in O157:H7 and O145:H28 but absent from other EHEC serotypes. The binding site of RbfR through which it regulates LEE gene expression was identified and is conserved in all EHEC serotypes and Citrobacter rodentium, a surrogate for EHEC in mice. Introducing rbfSR into C. rodentium enabled bacteria to sense microbiota-produced riboflavin in the mouse colon to increase the expression of LEE genes, causing increased disease severity in mice. Phylogenic analysis showed that the O55:H7 ancestor of O157:H7 obtained rbfSR which has been kept in O157:H7 since then. Thus, acquiring rbfSR represents an essential step in the evolution of the highly pathogenic O157:H7. The expression of LEE genes and cell attachment ability of other EHEC serotypes in the presence of riboflavin significantly increased when rbfSR was introduced into them, indicating that those serotypes are ready to use RbfSR to increase their pathogenicity. This may present a potential public health issue as horizontal gene transfer is frequent in enteric bacteria.
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25
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Bessonova TA, Fando MS, Kostareva OS, Tutukina MN, Ozoline ON, Gelfand MS, Nikulin AD, Tishchenko SV. Differential Impact of Hexuronate Regulators ExuR and UxuR on the Escherichia coli Proteome. Int J Mol Sci 2022; 23:ijms23158379. [PMID: 35955512 PMCID: PMC9369180 DOI: 10.3390/ijms23158379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to a uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in strongly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and in a reduced amount of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins. Consequently, the physiological roles of proteins predicted as homologs seem to be far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate, activation of both was not so prominent. During the growth with glucose, maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests, thus suggesting the involvement of UxuR in the regulation of bacterial motility and biofilm formation.
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Affiliation(s)
- Tatiana A. Bessonova
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
| | - Maria S. Fando
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Olga S. Kostareva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Maria N. Tutukina
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30 Build 1, Moscow 121205, Russia;
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per 19 Build 1, Moscow 127051, Russia
- Correspondence:
| | - Olga N. Ozoline
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30 Build 1, Moscow 121205, Russia;
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per 19 Build 1, Moscow 127051, Russia
| | - Alexey D. Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Svetlana V. Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
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26
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Zhang H, Jiang F, Zhang J, Wang W, Li L, Yan J. Modulatory effects of polysaccharides from plants, marine algae and edible mushrooms on gut microbiota and related health benefits: A review. Int J Biol Macromol 2022; 204:169-192. [PMID: 35122806 DOI: 10.1016/j.ijbiomac.2022.01.166] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/21/2022] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
Naturally occurring carbohydrate polymers containing non-starch polysaccharides (NPs) are a class of biomacromolecules isolated from plants, marine algae, and edible mushrooms, and their biological activities has shown potential uses in the prevention and treatment of human diseases. Importantly, NPs serve as prebiotics to provide health benefits to the host through stimulating the proliferation of beneficial gut microbiota (GM) and enhancing the production of short-chain fatty acids (SCFAs). The composition and diversity of GM play a critical role in regulating host health and have been extensively studied in recent years. In this review, the extraction, isolation, purification, and structural characterization of NPs derived from plants, marine algae, and edible mushrooms are outlined. Importantly, the degradation and metabolism of these NPs in the intestinal tract, the effects of NPs on the microbial community and SCFAs generation, and the beneficial effects of NPs on host health by modulating GM are systematically highlighted. Overall, we hope that this review can provide some theoretical references and a new perspective for applications of NPs as prebiotics in functional food and drug development.
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Affiliation(s)
- Henan Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, China.
| | - Fuchun Jiang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, China
| | - Jinsong Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, China
| | - Wenhan Wang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, China
| | - Lin Li
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan 523808, China.
| | - Jingkun Yan
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan 523808, China.
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27
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Beukema M, Akkerman R, Jermendi É, Koster T, Laskewitz A, Kong C, Schols HA, Faas MM, de Vos P. Pectins that Structurally Differ in the Distribution of Methyl-Esters Attenuate Citrobacter rodentium-Induced Colitis. Mol Nutr Food Res 2021; 65:e2100346. [PMID: 34369649 PMCID: PMC9285458 DOI: 10.1002/mnfr.202100346] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/29/2021] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Pectins have anti-inflammatory properties on intestinal immunity through direct interactions on Toll-like receptors (TLRs) in the small intestine or via stimulating microbiota-dependent effects in the large intestine. Both the degree of methyl-esterification (DM) and the distribution of methyl-esters (degree of blockiness; DB) of pectins contribute to this influence on immunity, but whether and how the DB impacts immunity through microbiota-dependent effects in the large intestine is unknown. Therefore, this study tests pectins that structurally differ in DB in a mouse model with Citrobacter rodentium induced colitis and studies the impact on the intestinal microbiota composition and associated attenuation of inflammation. METHODS AND RESULTS Both low and high DB pectins induce a more rich and diverse microbiota composition. These pectins also lower the bacterial load of C. rodentium in cecal digesta. Through these effects, both low and high DB pectins attenuate C. rodentium induced colitis resulting in reduced intestinal damage, reduced numbers of Th1-cells, which are increased in case of C. rodentium induced colitis, and reduced levels of GATA3+ Tregs, which are related to tissue inflammation. CONCLUSION Pectins prevent C. rodentium induced colonic inflammation by lowering the C. rodentium load in the caecum independently of the DB.
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Affiliation(s)
- Martin Beukema
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity Medical Center GroningenGroningenThe Netherlands
| | - Renate Akkerman
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity Medical Center GroningenGroningenThe Netherlands
| | - Éva Jermendi
- Laboratory of Food ChemistryWageningen University and ResearchWageningenThe Netherlands
| | - Taco Koster
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity Medical Center GroningenGroningenThe Netherlands
| | - Anne Laskewitz
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity Medical Center GroningenGroningenThe Netherlands
| | - Chunli Kong
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity Medical Center GroningenGroningenThe Netherlands
| | - Henk A. Schols
- Laboratory of Food ChemistryWageningen University and ResearchWageningenThe Netherlands
| | - Marijke M. Faas
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity Medical Center GroningenGroningenThe Netherlands
| | - Paul de Vos
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity Medical Center GroningenGroningenThe Netherlands
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28
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Caballero-Flores G, Pickard JM, Núñez G. Regulation of Citrobacter rodentium colonization: virulence, immune response and microbiota interactions. Curr Opin Microbiol 2021; 63:142-149. [PMID: 34352594 DOI: 10.1016/j.mib.2021.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 01/07/2023]
Abstract
Citrobacter rodentium is a mouse-specific pathogen commonly used to model infection by human Enteropathogenic Escherichia coli, an important cause of infant diarrhea and mortality worldwide. In the early phase of infection, C. rodentium overcomes competition by the gut microbiota for successful replication. Then, the pathogen uses a type three secretion system (T3SS) to inject effector proteins into intestinal epithelial cells and induce metabolic and inflammatory conditions that promote colonization of the intestinal epithelium. C. rodentium also elicits highly coordinated innate and adaptive immune responses in the gut that regulate pathogen colonization and eradication. In this review, we highlight recent work on the regulation and function of the C. rodentium T3SS, the mechanisms employed by the pathogen to evade competition by the microbiota, and the function of the host immune response against infection.
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Affiliation(s)
- Gustavo Caballero-Flores
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Joseph M Pickard
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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29
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Liang Q, Vallance BA. What's for dinner? How Citrobacter rodentium's metabolism helps it thrive in the competitive gut. Curr Opin Microbiol 2021; 63:76-82. [PMID: 34243134 DOI: 10.1016/j.mib.2021.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 01/04/2023]
Abstract
Enteric bacterial infections impose a significant and global health burden on society, and their threat is increasing in concert with a rise in antibiotic resistance. There is thus a great need to quickly develop new antimicrobial treatments and interest is growing in targeting pathogen nutrition and metabolism. In this review, we highlight recent research on the metabolism of Citrobacter rodentium, a murine-specific relative of enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC). We focus on the mechanisms by which C. rodentium acquires nutrients as well as the distinct metabolic strategies that C. rodentium employs in varying spatiotemporal niches. We propose that identifying and targeting nutrients found essential for bacterial pathogenesis is an attractive anti-microbial approach in the new post-antibiotic era.
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Affiliation(s)
- Qiaochu Liang
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, BC Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce A Vallance
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, BC Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada.
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30
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Wale KR, Cottam C, Connolly JP, Roe AJ. Transcriptional and metabolic regulation of EHEC and Citrobacter rodentium pathogenesis. Curr Opin Microbiol 2021; 63:70-75. [PMID: 34224961 DOI: 10.1016/j.mib.2021.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/04/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022]
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) is a gastrointestinal pathogen that colonizes the colonic epithelium of humans and ruminants using a Type Three Secretion System (T3SS). This system is indispensable for disease and is regulated in response to a plethora of host and microbiota derived signals. The murine pathogen, Citrobacter rodentium, has become an instrumental tool in studying EHEC infection mechanisms in vivo, given its natural ability to infect mice and reliance on the same colonisation machinery. Here, we provide a review of the most recent advancements in EHEC infection biology, focusing on transcriptional regulation of the T3SS in response to physiologically relevant signals and how colonisation impacts on the metabolic micro-environment of the host niche. We pay particular attention to studies that have employed the C. rodentium model for elucidation of such mechanisms in vivo.
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Affiliation(s)
- Kabo R Wale
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Curtis Cottam
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - James Pr Connolly
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Andrew J Roe
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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31
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Chengxiao Y, Dongmei W, Kai Z, Hou L, Xiao H, Ding T, Liu D, Ye X, Linhardt RJ, Chen S. Challenges of pectic polysaccharides as a prebiotic from the perspective of fermentation characteristics and anti-colitis activity. Carbohydr Polym 2021; 270:118377. [PMID: 34364621 DOI: 10.1016/j.carbpol.2021.118377] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/26/2022]
Abstract
Several studies are described that contribute to the systematic exploration of new aspects of digestion, fermentation, and biological activities of pectic polysaccharides (PPS) leading to a better understanding of prebiotics. Inflammatory bowel disease (IBD) is thought to be associated with the dysbacteriosis induced by different environmental agents in genetically susceptible persons. PPS are considered as an indispensable gut-microbiota-accessible carbohydrate that play a dominant role in maintaining gut microbiota balance and show a better effect in ameliorating IBD than some traditional prebiotics. The aim of this review is to summarize the fermentation characteristics of PPS, highlight its role in improving IBD, and propose a view that PPS may be a new and effective prebiotic.
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Affiliation(s)
- Yu Chengxiao
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China
| | - Wu Dongmei
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China
| | - Zhu Kai
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China
| | - Lijuan Hou
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China
| | - Hang Xiao
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China
| | - Tian Ding
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China
| | - Donghong Liu
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China
| | - Xingqian Ye
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Shiguo Chen
- College of Biosystems, Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Ningbo Research Institute, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou, China.
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Kimizuka T, Seki N, Yamaguchi G, Akiyama M, Higashi S, Hase K, Kim YG. Amino Acid-Based Diet Prevents Lethal Infectious Diarrhea by Maintaining Body Water Balance in a Murine Citrobacter rodentium Infection Model. Nutrients 2021; 13:nu13061896. [PMID: 34072947 PMCID: PMC8227537 DOI: 10.3390/nu13061896] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 01/02/2023] Open
Abstract
Infectious diarrhea is one of the most important health problems worldwide. Although nutritional status influences the clinical manifestation of various enteric pathogen infections, the effect of diet on enteric infectious diseases remains unclear. Using a fatal infectious diarrheal model, we found that an amino acid-based diet (AD) protected susceptible mice infected with the enteric pathogen Citrobacter rodentium. While the mice fed other diets, including a regular diet, were highly susceptible to C. rodentium infection, AD-fed mice had an increased survival rate. An AD did not suppress C. rodentium colonization or intestinal damage; instead, it prevented diarrhea-induced dehydration by increasing water intake. An AD altered the plasma and fecal amino acid levels and changed the gut microbiota composition. Treatment with glutamate, whose level was increased in the plasma and feces of AD-fed mice, promoted water intake and improved the survival of C. rodentium-infected mice. Thus, an AD changes the systemic amino acid balance and protects against lethal infectious diarrhea by maintaining total body water content.
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Affiliation(s)
- Tatsuki Kimizuka
- Research Center for Drug Discovery, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; (T.K.); (N.S.); (G.Y.); (M.A.)
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan;
| | - Natsumi Seki
- Research Center for Drug Discovery, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; (T.K.); (N.S.); (G.Y.); (M.A.)
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan;
| | - Genki Yamaguchi
- Research Center for Drug Discovery, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; (T.K.); (N.S.); (G.Y.); (M.A.)
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan;
| | - Masahiro Akiyama
- Research Center for Drug Discovery, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; (T.K.); (N.S.); (G.Y.); (M.A.)
| | - Seiichiro Higashi
- Co-Creation Center, Meiji Holdings Co., Ltd., Tokyo 192-0919, Japan;
| | - Koji Hase
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan;
| | - Yun-Gi Kim
- Research Center for Drug Discovery, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; (T.K.); (N.S.); (G.Y.); (M.A.)
- Correspondence:
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33
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Collard JM, Sansonetti P, Papon N. Taurine Makes Our Microbiota Stronger. Trends Endocrinol Metab 2021; 32:259-261. [PMID: 33707094 DOI: 10.1016/j.tem.2021.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
Our gut microbiota is known as an efficient barrier for infection; however, the physiological processes involved are poorly understood. Stacy et al. recently shed light on the key contribution of taurine to the trainable resistance of the gut microbiota to infection. This represents a groundbreaking advance for future microbiota-based therapeutics.
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Affiliation(s)
- Jean-Marc Collard
- Experimental Bacteriology Laboratory, Institut Pasteur of Shanghai/Chinese Academy of Sciences, Shanghai, China.
| | - Philippe Sansonetti
- Center for Microbes, Development and Health, Institut Pasteur of Shanghai/Chinese Academy of Sciences, Shanghai, China.
| | - Nicolas Papon
- Host-Pathogen Interaction Study Group (GEIHP, EA 3142), University of Angers, University of Brest, Angers, France; Federative Structure of Research 'Cellular Interactions and Therapeutic Applications', SFR 4208 ICAT, University of Angers, Angers, France
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34
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Pan Q, Li Z, Ju X, Hou C, Xiao Y, Shi R, Fu C, Danchin A, You C. Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations. Microb Biotechnol 2021; 14:1084-1106. [PMID: 33650807 PMCID: PMC8085971 DOI: 10.1111/1751-7915.13776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 01/20/2023] Open
Abstract
How bacteria adjust gene expression to cope with variable environments remains open to question. Here, we investigated the way global gene expression changes in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways. Coarse-grained analysis of gene co-expression identified a novel regulation pattern: we established that the gene expression trend following immediately the reduction of growth rate (GR) was correlated to its initial expression level. Subsequent fine-grained analysis of co-expression demonstrated that the Crp regulator, coupled with a change in GR, governed the response of most GR-dependent genes. By contrast, the Cra, Mlc and Fur regulators governed the expression of genes responding to non-glycolytic substrates, glycolytic substrates or phosphotransferase system transported sugars following an idiosyncratic way. This work allowed us to expand additional genes in the panel of gene complement regulated by each regulator and to elucidate the regulatory functions of each regulator comprehensively. Interestingly, the bulk of genes controlled by Cra and Mlc were, respectively, co-regulated by Crp- or GR-related effect and our quantitative analysis showed that each factor took turns to work as the primary one or contributed equally depending on the conditions.
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Affiliation(s)
- Qing Pan
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao, ShandongChina
| | - Zongjin Li
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Xian Ju
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Chaofan Hou
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Yunzhu Xiao
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Ruoping Shi
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao, ShandongChina
| | - Antoine Danchin
- Kodikos Labs/Stellate TherapeuticsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
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35
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Wu D, Ye X, Linhardt RJ, Liu X, Zhu K, Yu C, Ding T, Liu D, He Q, Chen S. Dietary pectic substances enhance gut health by its polycomponent: A review. Compr Rev Food Sci Food Saf 2021; 20:2015-2039. [PMID: 33594822 DOI: 10.1111/1541-4337.12723] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
Pectic substances, one of the cell wall polysaccharides, exist widespread in vegetables and fruits. A surge of recent research has revealed that pectic substances can inhibit gut inflammation and relieve inflammatory bowel disease symptoms. However, physiological functions of pectins are strongly structure dependent. Pectic substances are essentially heteropolysaccharides composed of homogalacturonan and rhamnogalacturonan backbones substituted by various neutral sugar sidechains. Subtle changes in the architecture of pectic substances may remarkably influence the nutritional function of gut microbiota and the host homeostasis of immune system. In this context, developing a structure-function understanding of how pectic substances have an impact on an inflammatory bowel is of primary importance for diet therapy and new drugs. Therefore, the present review has summarized the polycomponent nature of pectic substances, the activities of different pectic polymers, the effects of molecular characteristics and the underlying mechanisms of pectic substances. The immunomodulated property of pectic substances depends on not only the chemical composition but also the physical structure characteristics, such as molecular weight (Mw ) and chain conformation. The potential mechanisms by which pectic substances exert their protective effects are mainly reversing the disordered gut microbiota, regulating immune cells, enhancing barrier function, and inhibiting pathogen adhesion. The manipulation of pectic substances on gut health is sophisticated, and the link between structural specificity of pectins and selective regulation needs further exploration.
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Affiliation(s)
- Dongmei Wu
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Xingqian Ye
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China.,Fuli Institute of Food Science, Zhejiang University, Hangzhou, China.,Ningbo Research Institute, Zhejiang University, Hangzhou, China
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Xuwei Liu
- UMR408, Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), INRAE, Avignon, France
| | - Kai Zhu
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Chengxiao Yu
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Tian Ding
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Donghong Liu
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shiguo Chen
- National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China.,Fuli Institute of Food Science, Zhejiang University, Hangzhou, China.,Ningbo Research Institute, Zhejiang University, Hangzhou, China
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36
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The Canonical Long-Chain Fatty Acid Sensing Machinery Processes Arachidonic Acid To Inhibit Virulence in Enterohemorrhagic Escherichia coli. mBio 2021; 12:mBio.03247-20. [PMID: 33468701 PMCID: PMC7845647 DOI: 10.1128/mbio.03247-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Polyunsaturated fatty acids (PUFAs) play important roles in host immunity. Manipulation of lipid content in host tissues through diet or pharmacological interventions is associated with altered severity of various inflammatory diseases. The mammalian gastrointestinal tract is a complex biochemical organ that generates a diverse milieu of host- and microbe-derived metabolites. In this environment, bacterial pathogens sense and respond to specific stimuli, which are integrated into the regulation of their virulence programs. Previously, we identified the transcription factor FadR, a long-chain fatty acid (LCFA) acyl coenzyme A (acyl-CoA) sensor, as a novel virulence regulator in the human foodborne pathogen enterohemorrhagic Escherichia coli (EHEC). Here, we demonstrate that exogenous LCFAs directly inhibit the locus of enterocyte effacement (LEE) pathogenicity island in EHEC through sensing by FadR. Moreover, in addition to LCFAs that are 18 carbons in length or shorter, we introduce host-derived arachidonic acid (C20:4) as an additional LCFA that is recognized by the FadR system in EHEC. We show that arachidonic acid is processed by the acyl-CoA synthetase FadD, which permits binding to FadR and decreases FadR affinity for its target DNA sequences. This interaction enables the transcriptional regulation of FadR-responsive operons by arachidonic acid in EHEC, including the LEE. Finally, we show that arachidonic acid inhibits hallmarks of EHEC disease in a FadR-dependent manner, including EHEC attachment to epithelial cells and the formation of attaching and effacing lesions. Together, our findings delineate a molecular mechanism demonstrating how LCFAs can directly inhibit the virulence of an enteric bacterial pathogen. More broadly, our findings expand the repertoire of ligands sensed by the canonical LFCA sensing machinery in EHEC to include arachidonic acid, an important bioactive lipid that is ubiquitous within host environments.
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37
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Cao Y, Liu J, Zhu W, Qin N, Ren X, Zhu B, Xia X. Impact of dietary components on enteric infectious disease. Crit Rev Food Sci Nutr 2021; 62:4010-4035. [PMID: 33455435 DOI: 10.1080/10408398.2021.1871587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Diets impact host health in multiple ways and an unbalanced diet could contribute to the initiation or progression of a variety of diseases. Although a wealth of information exists on the connections between diet and chronic metabolic diseases such as cardiovascular disease, diabetes mellitus, etc., how diet influences enteric infectious disease still remain underexplored. The review summarizes the current findings on the link between various dietary components and diverse enteric infectious diseases. Dietary ingredients discussed include macronutrients (carbohydrates, lipids, proteins), micronutrients (vitamins, minerals), and other dietary ingredients (phytonutrients and probiotic supplements). We first describe the importance of enteric infectious diseases and the direct and indirect relationship between diet and enteric infectious diseases. Then we discuss the effects of different dietary components on the susceptibility to or progression of enteric infectious disease. Finally, we delineate current knowledge gap and highlighted future research directions. The literature review revealed that different dietary components affect host resistance to enteric infections through a variety of mechanisms. Dietary components may directly inhibit or bind to enteric pathogens, or indirectly influence enteric infections through modulating immune function and gut microbiota. Elucidating the unique repercussions of different diets on enteric infections in this review may help provide dietary guidelines or design dietary interventions to prevent or alleviate enteric infectious diseases.
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Affiliation(s)
- Yu Cao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Jiaxiu Liu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Wenxiu Zhu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Ningbo Qin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Xiaomeng Ren
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Beiwei Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Xiaodong Xia
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
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38
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Glowacki RWP, Martens EC. If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria. J Bacteriol 2020; 203:JB.00481-20. [PMID: 33168637 PMCID: PMC8092160 DOI: 10.1128/jb.00481-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to persist, successful bacterial inhabitants of the human gut need to adapt to changing nutrient conditions, which are influenced by host diet and a variety of other factors. For members of the Bacteroidetes and several other phyla, this has resulted in diversification of a variety of enzyme-based systems that equip them to sense and utilize carbohydrate-based nutrients from host, diet, and bacterial origin. In this review, we focus first on human gut Bacteroides and describe recent findings regarding polysaccharide utilization loci (PULs) and the mechanisms of the multi-protein systems they encode, including their regulation and the expanding diversity of substrates that they target. Next, we highlight previously understudied substrates such as monosaccharides, nucleosides, and Maillard reaction products that can also affect the gut microbiota by feeding symbionts that possess specific systems for their metabolism. Since some pathogens preferentially utilize these nutrients, they may represent nutrient niches competed for by commensals and pathogens. Finally, we address recent work to describe nutrient acquisition mechanisms in other important gut species such as those belonging to the Gram-positive anaerobic phyla Actinobacteria and Firmicutes, as well as the Proteobacteria Because gut bacteria contribute to many aspects of health and disease, we showcase advances in the field of synthetic biology, which seeks to engineer novel, diet-controlled nutrient utilization pathways within gut symbionts to create rationally designed live therapeutics.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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39
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Arya G, Pal M, Sharma M, Singh B, Singh S, Agrawal V, Chaba R. Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli. Mol Microbiol 2020; 115:591-609. [PMID: 33068046 DOI: 10.1111/mmi.14625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 01/23/2023]
Abstract
Several GntR/FadR transcriptional regulators govern sugar acid metabolism in bacteria. Although effectors have been identified for a few sugar acid regulators, the mode of effector binding is unknown. Even in the overall FadR subfamily, there are limited details on effector-regulator interactions. Here, we identified the effector-binding cavity in Escherichia coli DgoR, a FadR subfamily transcriptional repressor of D-galactonate metabolism that employs D-galactonate as its effector. Using a genetic screen, we isolated several dgoR superrepressor alleles. Blind docking suggested eight amino acids corresponding to these alleles to form a part of the effector-binding cavity. In vivo and in vitro assays showed that these mutations compromise the inducibility of DgoR without affecting its oligomeric status or affinity for target DNA. Taking Bacillus subtilis GntR as a representative, we demonstrated that the effector-binding cavity is similar among FadR subfamily sugar acid regulators. Finally, a comparison of sugar acid regulators with other FadR members suggested conserved features of effector-regulator recognition within the FadR subfamily. Sugar acid metabolism is widely implicated in bacterial colonization and virulence. The present study sets the basis to investigate the influence of natural genetic variations in FadR subfamily regulators on their sensitivity to sugar acids and ultimately on host-bacterial interactions.
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Affiliation(s)
- Garima Arya
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Mohinder Pal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Vishal Agrawal
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
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40
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Ellermann M, Pacheco AR, Jimenez AG, Russell RM, Cuesta S, Kumar A, Zhu W, Vale G, Martin SA, Raj P, McDonald JG, Winter SE, Sperandio V. Endocannabinoids Inhibit the Induction of Virulence in Enteric Pathogens. Cell 2020; 183:650-665.e15. [PMID: 33031742 DOI: 10.1016/j.cell.2020.09.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 06/30/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Abstract
Endocannabinoids are host-derived lipid hormones that fundamentally impact gastrointestinal (GI) biology. The use of cannabis and other exocannabinoids as anecdotal treatments for various GI disorders inspired the search for mechanisms by which these compounds mediate their effects, which led to the discovery of the mammalian endocannabinoid system. Dysregulated endocannabinoid signaling was linked to inflammation and the gut microbiota. However, the effects of endocannabinoids on host susceptibility to infection has not been explored. Here, we show that mice with elevated levels of the endocannabinoid 2-arachidonoyl glycerol (2-AG) are protected from enteric infection by Enterobacteriaceae pathogens. 2-AG directly modulates pathogen function by inhibiting virulence programs essential for successful infection. Furthermore, 2-AG antagonizes the bacterial receptor QseC, a histidine kinase encoded within the core Enterobacteriaceae genome that promotes the activation of pathogen-associated type three secretion systems. Taken together, our findings establish that endocannabinoids are directly sensed by bacteria and can modulate bacterial function.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alline R Pacheco
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Angel G Jimenez
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Regan M Russell
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Santiago Cuesta
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aman Kumar
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenhan Zhu
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gonçalo Vale
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sarah A Martin
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prithvi Raj
- Microbiome Research Lab, Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeffrey G McDonald
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vanessa Sperandio
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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41
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Kreuzer M, Hardt WD. How Food Affects Colonization Resistance Against Enteropathogenic Bacteria. Annu Rev Microbiol 2020; 74:787-813. [DOI: 10.1146/annurev-micro-020420-013457] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Salmonella Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on colonization resistance, host defenses, and the infection process as well as the merits and limitations of mouse models and experimental foods, which are available to decipher the underlying mechanisms.
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Affiliation(s)
- Markus Kreuzer
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
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Genomic plasticity of pathogenic Escherichia coli mediates d-serine tolerance via multiple adaptive mechanisms. Proc Natl Acad Sci U S A 2020; 117:22484-22493. [PMID: 32848072 PMCID: PMC7486766 DOI: 10.1073/pnas.2004977117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pathogens ensure infection of favored sites in the body by responding to chemical signals. One chemical abundant in urine, the amino acid d-Ser, is toxic to EHEC and reduces expression of the machinery used for host cell attachment, making the bladder an unfavorable environment. We observed that under d-Ser stress, EHEC acquires genetic changes that lead to blocking d-Ser uptake into the cell or activating a silent enzyme for degrading d-Ser. This prevents growth inhibition and, critically, inhibits the repression of attachment machinery normally caused by d-Ser. These findings highlight the importance of pathogen evolution in determining how host molecules regulate colonization. These interactions underpin a process known as niche restriction that is important for pathogen success within the host. The molecular environment of the host can have profound effects on the behavior of resident bacterial species. We recently established how the sensing and response of enterohemorrhagic Escherichia coli (EHEC) to d-serine (d-Ser) resulted in down-regulation of type 3 secretion system-dependent colonization, thereby avoiding unfavorable environments abundant in this toxic metabolite. However, this model ignores a key determinant of the success of bacterial pathogens, adaptive evolution. In this study, we have explored the adaptation of EHEC to d-Ser and its consequences for pathogenesis. We rapidly isolated multiple, independent, EHEC mutants whose growth was no longer compromised in the presence of d-Ser. Through a combination of whole-genome sequencing and transcriptomics, we showed that tolerance could be attributed to disruption of one of two d-Ser transporters and/or activation of a previously nonfunctional d-Ser deaminase. While the implication of cytoplasmic transport in d-Ser toxicity was unsurprising, disruption of a single transporter, CycA, was sufficient to completely overcome the repression of type 3 secretion system activity normally associated with exposure to d-Ser. Despite the fact that this reveals a mechanism by which evolution could drive a pathogen to colonize new niches, interrogation of sequenced E. coli O157:H7 genomes showed a high level of CycA conservation, highlighting a strong selective pressure for functionality. Collectively, these data show that CycA is a critically important conduit for d-Ser uptake that is central to the niche restriction of EHEC.
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