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Rivera-Lugo R, Deng D, Anaya-Sanchez A, Tejedor-Sanz S, Tang E, Reyes Ruiz VM, Smith HB, Titov DV, Sauer JD, Skaar EP, Ajo-Franklin CM, Portnoy DA, Light SH. Listeria monocytogenes requires cellular respiration for NAD + regeneration and pathogenesis. eLife 2022; 11:e75424. [PMID: 35380108 PMCID: PMC9094743 DOI: 10.7554/elife.75424] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
Cellular respiration is essential for multiple bacterial pathogens and a validated antibiotic target. In addition to driving oxidative phosphorylation, bacterial respiration has a variety of ancillary functions that obscure its contribution to pathogenesis. We find here that the intracellular pathogen Listeria monocytogenes encodes two respiratory pathways which are partially functionally redundant and indispensable for pathogenesis. Loss of respiration decreased NAD+ regeneration, but this could be specifically reversed by heterologous expression of a water-forming NADH oxidase (NOX). NOX expression fully rescued intracellular growth defects and increased L. monocytogenes loads >1000-fold in a mouse infection model. Consistent with NAD+ regeneration maintaining L. monocytogenes viability and enabling immune evasion, a respiration-deficient strain exhibited elevated bacteriolysis within the host cytosol and NOX expression rescued this phenotype. These studies show that NAD+ regeneration represents a major role of L. monocytogenes respiration and highlight the nuanced relationship between bacterial metabolism, physiology, and pathogenesis.
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Affiliation(s)
- Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - David Deng
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Andrea Anaya-Sanchez
- Graduate Group in Microbiology, University of California, BerkeleyBerkeleyUnited States
| | - Sara Tejedor-Sanz
- Department of Biosciences, Rice UniversityHoustonUnited States
- The Molecular Foundry, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Eugene Tang
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Valeria M Reyes Ruiz
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashvilleUnited States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical CenterNashvilleUnited States
| | - Hans B Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - Denis V Titov
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Nutritional Sciences and Toxicology, University of California, BerkeleyBerkeleyUnited States
- Center for Computational Biology, University of California, BerkeleyBerkeleyUnited States
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashvilleUnited States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical CenterNashvilleUnited States
| | - Caroline M Ajo-Franklin
- Department of Biosciences, Rice UniversityHoustonUnited States
- The Molecular Foundry, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Daniel A Portnoy
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Samuel H Light
- Department of Microbiology, University of ChicagoChicagoUnited States
- Duchossois Family Institute, University of ChicagoChicagoUnited States
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Woida PJ, Satchell KJF. Bacterial Toxin and Effector Regulation of Intestinal Immune Signaling. Front Cell Dev Biol 2022; 10:837691. [PMID: 35252199 PMCID: PMC8888934 DOI: 10.3389/fcell.2022.837691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
The host immune response is highly effective to detect and clear infecting bacterial pathogens. Given the elaborate surveillance systems of the host, it is evident that in order to productively infect a host, the bacteria often coordinate virulence factors to fine-tune the host response during infection. These coordinated events can include either suppressing or activating the signaling pathways that control the immune response and thereby promote bacterial colonization and infection. This review will cover the surveillance and signaling systems for detection of bacteria in the intestine and a sample of the toxins and effectors that have been characterized that cirumvent these signaling pathways. These factors that promote infection and disease progression have also been redirected as tools or therapeutics. Thus, these toxins are enemies deployed to enhance infection, but can also be redeployed as allies to enable research and protect against infection.
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Zhang W, Zhang X, Su Q, Tang M, Zheng H, Zhou X. Genomic features underlying the evolutionary transitions of Apibacter to honey bee gut symbionts. INSECT SCIENCE 2022; 29:259-275. [PMID: 33811731 DOI: 10.1111/1744-7917.12912] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/20/2021] [Accepted: 02/21/2021] [Indexed: 05/16/2023]
Abstract
The gut bacteria of honey bee recognized as a mutualistic partner with the insect host might have originated from a free-living or parasitic lifestyle. However, little is known about the genomic features underlying this lifestyle transition. Here we compared the genomes of bee gut bacteria Apibacter with their close relatives living in different lifestyles. We found that despite general reduction in the Apibacter genome, genes involved in amino acid synthesis and monosaccharide detoxification were retained, which is putatively beneficial to the host. Interestingly, the microaerobic Apibacter species specifically acquired genes encoding for the nitrate respiration (NAR). These together with nitrate transporter and enzymatic cofactor synthesis genes were found clustered in the genomes. The NAR system is also conserved in the cohabitating bee gut microbe Snodgrassella, although with a different structure. This convergence suggests a key role of respiratory nitrate reduction for microaerophilic microbiomes to colonize bee gut epithelium. Genes involved in lipid, histidine degradation were found partially or completely lost in Apibacter. Particularly, genes encoding for the conversion to the toxic intermediates in phenylacetate degradation, as well as other potential virulence factors, are specifically lost in Apibacter group. Antibiotic resistance genes are only sporadically distributed among Apibacter species, but are prevalent in their relatives, which may be related to the remotely living feature and less exposure to antibiotics of their bee hosts. Collectively, this study advanced our knowledge of genomic features specialized to bee gut symbionts.
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Affiliation(s)
- Wenjun Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Qinzhi Su
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Min Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
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Yuan X, Xue H, Xu X, Jiao X, Pan Z, Zhang Y. Closely related Salmonella Derby strains triggered distinct gut microbiota alteration. Gut Pathog 2022; 14:6. [PMID: 35078518 PMCID: PMC8787955 DOI: 10.1186/s13099-022-00480-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Salmonella Derby is one of the most predominant Salmonella serotypes that seriously threatens food safety. This bacterium can be further differentiated to sub-populations with different population sizes; however, whether and how the S. Derby–gut microbiota interactions affect epidemic patterns of S. Derby sub-populations remain largely unknown.
Results
We selected two representative strains, 14T and 14C, which represent rarely distributed and prevalent sub-populations of the S. Derby ST40 group, respectively, to address this question using a mouse model. Effects of oral administration of both strains was monitored for 14 days. Alpha diversity of gut microbiota at early stages of infection (4 h post infection) was higher in 14C-treated mice and lower in 14T-treated mice compared with controls. Strain 14T triggered stronger inflammation responses but with lower pathogen titer in spleen compared with strain 14C at 14 days post infection. Certain known probiotic bacteria that can hinder colonization of Salmonella, such as Bifidobacteriaceae and Akkermansiaceae, exhibited increased relative abundance in 14T-treated mice compared with 14C-treated mice. Our results also demonstrated that Ligilactobacillus strains isolated from gut microbiota showed stronger antagonistic activity against strain 14T compared with strain 14C.
Conclusions
We identified how S. Derby infection affected gut microbiota composition, and found that the 14T strain, which represented a rarely distributed S. Derby sub-population, triggered stronger host inflammation responses and gut microbiota disturbance compared with the 14C strain, which represented a prevalent S. Derby sub-population. This study provides novel insights on the impacts of gut microbiota on the epidemic patterns of Salmonella populations.
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Abstract
Environmental chemicals can alter gut microbial community composition, known as dysbiosis. However, the gut microbiota is a highly dynamic system and its functions are still largely underexplored. Likewise, it is unclear whether xenobiotic exposure affects host health through impairing host-microbiota interactions. Answers to this question not only can lead to a more precise understanding of the toxic effects of xenobiotics but also can provide new targets for the development of new therapeutic strategies. Here, we aim to identify the major challenges in the field of microbiota-exposure research and highlight the need to exam the health effects of xenobiotic-induced gut microbiota dysbiosis in host bodies. Although the changes of gut microbiota frequently co-occur with the xenobiotic exposure, the causal relationship of xenobiotic-induced microbiota dysbiosis and diseases is rarely established. The high dynamics of the gut microbiota and the complex interactions among exposure, microbiota, and host, are the major challenges to decipher the specific health effects of microbiota dysbiosis. The next stage of study needs to combine various technologies to precisely assess the xenobiotic-induced gut microbiota perturbation and the subsequent health effects in host bodies. The exposure, gut microbiota dysbiosis, and disease outcomes have to be causally linked. Many microbiota-host interactions are established by previous studies, including signaling metabolites and response pathways in the host, which may use as start points for future research to examine the mechanistic interactions of exposure, gut microbiota, and host health. In conclusion, to precisely understand the toxicity of xenobiotics and develop microbiota-based therapies, the causal and mechanistic links of exposure and microbiota dysbiosis have to be established in the next stage study.
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Affiliation(s)
- Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC, United States
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC, United States
| | - Hongyu Ru
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC, United States,CONTACT Kun Lu Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC27599, United States
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Bornet E, Westermann AJ. The ambivalent role of Bacteroides in enteric infections. Trends Microbiol 2021; 30:104-108. [PMID: 34893402 DOI: 10.1016/j.tim.2021.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/28/2023]
Abstract
Bacteroides spp. are increasingly used as model gut commensals in cocolonization studies with enteropathogens. The collective findings imply common themes of colonization resistance but also pathogen crossfeeding. We discuss how cutting-edge transcriptomics may help to disentangle the molecular basis of the divergent roles of Bacteroides in either protecting against or promoting infection.
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Affiliation(s)
- Elise Bornet
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany; Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.
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57
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El Mouali Y, Ponath F, Scharrer V, Wenner N, Hinton JCD, Vogel J. Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease. RNA (NEW YORK, N.Y.) 2021; 27:1512-1527. [PMID: 34497069 PMCID: PMC8594473 DOI: 10.1261/rna.078954.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 05/25/2023]
Abstract
The FinO-domain protein ProQ belongs to a widespread family of RNA-binding proteins (RBPs) involved in gene regulation in bacterial chromosomes and mobile elements. While the cellular RNA targets of ProQ have been established in diverse bacteria, the functionally crucial ProQ residues remain to be identified under physiological conditions. Following our discovery that ProQ deficiency alleviates growth suppression of Salmonella with succinate as the sole carbon source, an experimental evolution approach was devised to exploit this phenotype. By coupling mutational scanning with loss-of-function selection, we identified multiple ProQ residues in both the amino-terminal FinO domain and the variable carboxy-terminal region that are required for ProQ activity. Two carboxy-terminal mutations abrogated ProQ function and mildly impaired binding of a model RNA target. In contrast, several mutations in the FinO domain rendered ProQ both functionally inactive and unable to interact with target RNA in vivo. Alteration of the FinO domain stimulated the rapid turnover of ProQ by Lon-mediated proteolysis, suggesting a quality control mechanism that prevents the accumulation of nonfunctional ProQ molecules. We extend this observation to Hfq, the other major sRNA chaperone of enteric bacteria. The Hfq Y55A mutant protein, defective in RNA-binding and oligomerization, proved to be labile and susceptible to degradation by Lon. Taken together, our findings connect the major AAA+ family protease Lon with RNA-dependent quality control of Hfq and ProQ, the two major sRNA chaperones of Gram-negative bacteria.
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Affiliation(s)
- Youssef El Mouali
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Vinzent Scharrer
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L7 3EA Liverpool, United Kingdom
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L7 3EA Liverpool, United Kingdom
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
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Mirzaei R, Dehkhodaie E, Bouzari B, Rahimi M, Gholestani A, Hosseini-Fard SR, Keyvani H, Teimoori A, Karampoor S. Dual role of microbiota-derived short-chain fatty acids on host and pathogen. Biomed Pharmacother 2021; 145:112352. [PMID: 34840032 DOI: 10.1016/j.biopha.2021.112352] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
A growing body of documents shows microbiota produce metabolites such as short-chain fatty acids (SCFAs) as crucial executors of diet-based microbial influence the host and bacterial pathogens. The production of SCFAs depends on the metabolic activity of intestinal microflora and is also affected by dietary changes. SCFAs play important roles in maintaining colonic health as an energy source, as a regulator of gene expression and cell differentiation, and as an anti-inflammatory agent. Additionally, the regulated expression of virulence genes is critical for successful infection by an intestinal pathogen. Bacteria rely on sensing environmental signals to find preferable niches and reach the infectious state. This review will present data supporting the diverse functional roles of microbiota-derived butyrate, propionate, and acetate on host cellular activities such as immune modulation, energy metabolism, nervous system, inflammation, cellular differentiation, and anti-tumor effects, among others. On the other hand, we will discuss and summarize data about the role of these SCFAs on the virulence factor of bacterial pathogens. In this regard, receptors and signaling routes for SCFAs metabolites in host and pathogens will be introduced.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Elahe Dehkhodaie
- Department of Biology, Science and Research Branch, Islamic Azad University Tehran, Iran
| | - Behnaz Bouzari
- Department of Pathology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mandana Rahimi
- Department of Pathology, School of Medicine, Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Gholestani
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Ali Teimoori
- Department of Virology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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59
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Osbelt L, Wende M, Almási É, Derksen E, Muthukumarasamy U, Lesker TR, Galvez EJC, Pils MC, Schalk E, Chhatwal P, Färber J, Neumann-Schaal M, Fischer T, Schlüter D, Strowig T. Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition. Cell Host Microbe 2021; 29:1663-1679.e7. [PMID: 34610293 DOI: 10.1016/j.chom.2021.09.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/27/2021] [Accepted: 09/09/2021] [Indexed: 01/08/2023]
Abstract
Gut colonization with multidrug-resistant (MDR) bacteria enhances the risk of bloodstream infections in susceptible individuals. We demonstrate highly variable degrees of ex vivo colonization resistance against a carbapenem-resistant Klebsiella pneumoniae strain in human feces samples and subsequently isolate diverse K. oxytoca strains from protected donors. Several of these K. oxytoca strains reduce gut colonization of MDR K. pneumoniae strains in antibiotic-treated and gnotobiotic mouse models. Comparative analysis of K. oxytoca strains coupled with CRISPR-Cas9-mediated deletion of casA, a protein essential for utilization of selected beta-glucosides, identified competition for specific carbohydrates as key in promoting colonization resistance. In addition to direct competition between K. oxytoca and K. pneumoniae, cooperation with additional commensals is required to reestablish full colonization resistance and gut decolonization. Finally, humanized microbiota mice generated from K. pneumoniae-susceptible donors are protected by K. oxytoca administration, demonstrating the potential of commensal K. oxytoca strains as next-generation probiotics.
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Affiliation(s)
- Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-Von-Guericke University, Magdeburg, Germany
| | - Marie Wende
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-Von-Guericke University, Magdeburg, Germany
| | - Éva Almási
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Elisabeth Derksen
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Eric J C Galvez
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Marina C Pils
- Mouse-Pathology Platform, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Enrico Schalk
- Department of Hematology and Oncology, University Hospital Magdeburg, Magdeburg, Germany
| | - Patrick Chhatwal
- Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Jacqueline Färber
- Department of Medical Microbiology and Hospital Hygiene, University Hospital Magdeburg, Magdeburg, Germany
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas Fischer
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-Von-Guericke University, Magdeburg, Germany; Department of Hematology and Oncology, University Hospital Magdeburg, Magdeburg, Germany
| | - Dirk Schlüter
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-Von-Guericke University, Magdeburg, Germany; Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany; Center for Individualized Infection Medicine, Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany.
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60
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Mackie GM, Copland A, Takahashi M, Nakanishi Y, Everard I, Kato T, Oda H, Kanaya T, Ohno H, Maslowski KM. Bacterial cancer therapy in autochthonous colorectal cancer affects tumor growth and metabolic landscape. JCI Insight 2021; 6:e139900. [PMID: 34710062 PMCID: PMC8675204 DOI: 10.1172/jci.insight.139900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/27/2021] [Indexed: 12/21/2022] Open
Abstract
Bacterial cancer therapy (BCT) shows great promise for treatment of solid tumors, yet basic mechanisms of bacterial-induced tumor suppression remain undefined. Attenuated strains of Salmonella enterica serovar Typhimurium (STm) have commonly been used in mouse models of BCT in xenograft and orthotopic transplant cancer models. We aimed to better understand the tumor epithelium-targeted mechanisms of BCT by using autochthonous mouse models of intestinal cancer and tumor organoid cultures to assess the effectiveness and consequences of oral treatment with aromatase A-deficient STm (STmΔaroA). STmΔaroA delivered by oral gavage significantly reduced tumor burden and tumor load in both a colitis-associated colorectal cancer (CAC) model and in a spontaneous Apcmin/+ intestinal cancer model. STmΔaroA colonization of tumors caused alterations in transcription of mRNAs associated with tumor stemness, epithelial-mesenchymal transition, and cell cycle. Metabolomic analysis of tumors demonstrated alteration in the metabolic environment of STmΔaroA-treated tumors, suggesting that STmΔaroA imposes metabolic competition on the tumor. Use of tumor organoid cultures in vitro recapitulated effects seen on tumor stemness, mesenchymal markers, and altered metabolome. Furthermore, live STmΔaroA was required, demonstrating active mechanisms including metabolite usage. We have demonstrated that oral BCT is efficacious in autochthonous intestinal cancer models, that BCT imposes metabolic competition, and that BCT has direct effects on the tumor epithelium affecting tumor stem cells.
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Affiliation(s)
- Gillian M. Mackie
- University of Birmingham, Institute of Immunology and Immunotherapy and Institute of Metabolism and Systems Research, Birmingham, United Kingdom
| | - Alastair Copland
- University of Birmingham, Institute of Immunology and Immunotherapy and Institute of Metabolism and Systems Research, Birmingham, United Kingdom
| | - Masumi Takahashi
- Laboratory for Intestinal Ecosystem, RIKEN Institute for Integrative Medical Science, Yokohama, Japan
| | - Yumiko Nakanishi
- Laboratory for Intestinal Ecosystem, RIKEN Institute for Integrative Medical Science, Yokohama, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Immunobiology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Isabel Everard
- University of Birmingham, Institute of Immunology and Immunotherapy and Institute of Metabolism and Systems Research, Birmingham, United Kingdom
| | - Tamotsu Kato
- Laboratory for Intestinal Ecosystem, RIKEN Institute for Integrative Medical Science, Yokohama, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Immunobiology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hirotsugu Oda
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Inflammatory Disease Section, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Takashi Kanaya
- Laboratory for Intestinal Ecosystem, RIKEN Institute for Integrative Medical Science, Yokohama, Japan
- Immunobiology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Institute for Integrative Medical Science, Yokohama, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Immunobiology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kendle M. Maslowski
- University of Birmingham, Institute of Immunology and Immunotherapy and Institute of Metabolism and Systems Research, Birmingham, United Kingdom
- Laboratory for Intestinal Ecosystem, RIKEN Institute for Integrative Medical Science, Yokohama, Japan
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61
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Shealy NG, Yoo W, Byndloss MX. Colonization resistance: metabolic warfare as a strategy against pathogenic Enterobacteriaceae. Curr Opin Microbiol 2021; 64:82-90. [PMID: 34688039 DOI: 10.1016/j.mib.2021.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022]
Abstract
The intestine is home to a large and complex bacterial ecosystem (microbiota), which performs multiple beneficial functions for the host, including immune education, nutrition, and protection against invasion by enteric pathogens (colonization resistance). The host and microbiome symbiotic interactions occur in part through metabolic crosstalk. Thus, microbiota members have evolved highly diverse metabolic pathways to inhibit pathogen colonization via activation of protective immune responses and nutrient acquisition and utilization. Conversely, pathogenic Enterobacteriaceae actively induce an inflammation-dependent disruption of the gut microbial ecosystem (dysbiosis) to gain a competitive metabolic advantage against the resident microbiota. This review discusses the recent findings on the crucial role of microbiota metabolites in colonization resistance regulation. Additionally, we summarize metabolic mechanisms used by pathogenic Enterobacteriaceae to outcompete commensal microbes and cause disease.
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Affiliation(s)
- Nicolas G Shealy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Woongjae Yoo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mariana X Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
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Chen D, Burford WB, Pham G, Zhang L, Alto LT, Ertelt JM, Winter MG, Winter SE, Way SS, Alto NM. Systematic reconstruction of an effector-gene network reveals determinants of Salmonella cellular and tissue tropism. Cell Host Microbe 2021; 29:1531-1544.e9. [PMID: 34536347 DOI: 10.1016/j.chom.2021.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/24/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
The minimal genetic requirements for microbes to survive within multiorganism communities, including host-pathogen interactions, remain poorly understood. Here, we combined targeted gene mutagenesis with phenotype-guided genetic reassembly to identify a cooperative network of SPI-2 T3SS effector genes that are sufficient for Salmonella Typhimurium (STm) to cause disease in a natural host organism. Five SPI-2 effector genes support pathogen survival within the host cell cytoplasm by coordinating bacterial replication with Salmonella-containing vacuole (SCV) division. Unexpectedly, this minimal genetic repertoire does not support STm systemic infection of mice. In vivo screening revealed a second effector-gene network, encoded by the spv operon, that expands the life cycle of STm from growth in cells to deep-tissue colonization in a murine model of typhoid fever. Comparison between Salmonella infection models suggests how cooperation between effector genes drives tissue tropism in a pathogen group.
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Affiliation(s)
- Didi Chen
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wesley B Burford
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Giang Pham
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Lishu Zhang
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Laura T Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James M Ertelt
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sing Sing Way
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Neal M Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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63
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Sibinelli-Sousa S, de Araújo-Silva AL, Hespanhol JT, Bayer-Santos E. Revisiting the steps of Salmonella gut infection with a focus on antagonistic interbacterial interactions. FEBS J 2021; 289:4192-4211. [PMID: 34546626 DOI: 10.1111/febs.16211] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
A commensal microbial community is established in the mammalian gut during its development, and these organisms protect the host against pathogenic invaders. The hallmark of noninvasive Salmonella gut infection is the induction of inflammation via effector proteins secreted by the type III secretion system, which modulate host responses to create a new niche in which the pathogen can overcome the colonization resistance imposed by the microbiota. Several studies have shown that endogenous microbes are important to control Salmonella infection by competing for resources. However, there is limited information about antimicrobial mechanisms used by commensals and pathogens during these in vivo disputes for niche control. This review aims to revisit the steps that Salmonella needs to overcome during gut colonization-before and after the induction of inflammation-to achieve an effective infection. We focus on a series of reported and hypothetical antagonistic interbacterial interactions in which both contact-independent and contact-dependent mechanisms might define the outcome of the infection.
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Affiliation(s)
| | | | - Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
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64
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Fujiwara H. Crosstalk Between Intestinal Microbiota Derived Metabolites and Tissues in Allogeneic Hematopoietic Cell Transplantation. Front Immunol 2021; 12:703298. [PMID: 34512627 PMCID: PMC8429959 DOI: 10.3389/fimmu.2021.703298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an evidence based- cellular immunotherapy for hematological malignancies. Immune reactions not only promote graft-versus-tumor effects that kill hematological malignant cells but also graft-versus-host disease (GVHD) that is the primary complication characterized by systemic organ damages consisting of T-cells and antigen presenting cells (APCs) activation. GVHD has long been recognized as an immunological reaction that requires an immunosuppressive treatment targeting immune cells. However immune suppression cannot always prevent GVHD or effectively treat it once it has developed. Recent studies using high-throughput sequencing technology investigated the impact of microbial flora on GVHD and provided profound insights of the mechanism of GVHD other than immune cells. Allo-HSCT affects the intestinal microbiota and microbiome-metabolome axis that can alter intestinal homeostasis and the severity of experimental GVHD. This axis can potentially be manipulated via dietary intervention or metabolites produced by intestinal bacteria affected post-allo-HSCT. In this review, we discuss the mechanism of experimental GVHD regulation by the complex microbial community-metabolites-host tissue axis. Furthermore, we summarize the major findings of microbiome-based immunotherapeutic approaches that protect tissues from experimental GVHD. Understanding the complex relationships between gut microbiota-metabolites-host tissues axis provides crucial insight into the pathogenesis of GVHD and advances the development of new therapeutic approaches.
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Affiliation(s)
- Hideaki Fujiwara
- Department of Hematology and Oncology, Okayama University Hospital, Okayama, Japan
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65
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Sauvaitre T, Etienne-Mesmin L, Sivignon A, Mosoni P, Courtin CM, Van de Wiele T, Blanquet-Diot S. Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections. FEMS Microbiol Rev 2021; 45:5918835. [PMID: 33026073 DOI: 10.1093/femsre/fuaa052] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively referred as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonise the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely, the gut microbiota, under health and disease situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.
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Affiliation(s)
- Thomas Sauvaitre
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France.,Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
| | - Adeline Sivignon
- Université Clermont Auvergne, UMR 1071 Inserm, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Pascale Mosoni
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
| | - Christophe M Courtin
- KU Leuven, Faculty of Bioscience Engineering, Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium
| | - Tom Van de Wiele
- Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
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66
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Miller BM, Liou MJ, Zhang LF, Nguyen H, Litvak Y, Schorr EM, Jang KK, Tiffany CR, Butler BP, Bäumler AJ. Anaerobic Respiration of NOX1-Derived Hydrogen Peroxide Licenses Bacterial Growth at the Colonic Surface. Cell Host Microbe 2021; 28:789-797.e5. [PMID: 33301718 DOI: 10.1016/j.chom.2020.10.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/14/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022]
Abstract
The colonic microbiota exhibits cross-sectional heterogeneity, but the mechanisms that govern its spatial organization remain incompletely understood. Here we used Citrobacter rodentium, a pathogen that colonizes the colonic surface, to identify microbial traits that license growth and survival in this spatial niche. Previous work showed that during colonic crypt hyperplasia, type III secretion system (T3SS)-mediated intimate epithelial attachment provides C. rodentium with oxygen for aerobic respiration. However, we find that prior to the development of colonic crypt hyperplasia, T3SS-mediated intimate attachment is not required for aerobic respiration but for hydrogen peroxide (H2O2) respiration using cytochrome c peroxidase (Ccp). The epithelial NADPH oxidase NOX1 is the primary source of luminal H2O2 early after C. rodentium infection and is required for Ccp-dependent growth. Our results suggest that NOX1-derived H2O2 is a resource that governs bacterial growth and survival in close proximity to the mucosal surface during gut homeostasis.
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Affiliation(s)
- Brittany M Miller
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Megan J Liou
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Lillian F Zhang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA; Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem 9190401, Israel
| | - Eva-Magdalena Schorr
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kyung Ku Jang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA; Present address: Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA
| | - Brian P Butler
- Department of Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616, USA.
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67
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Pérez-Morales D, Bustamante VH. Cross-kingdom metabolic manipulation promotes Salmonella replication inside macrophages. Nat Commun 2021; 12:1862. [PMID: 33767154 PMCID: PMC7994845 DOI: 10.1038/s41467-021-22198-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Deyanira Pérez-Morales
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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68
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Establishing causality in Salmonella-microbiota-host interaction: The use of gnotobiotic mouse models and synthetic microbial communities. Int J Med Microbiol 2021; 311:151484. [PMID: 33756190 DOI: 10.1016/j.ijmm.2021.151484] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/07/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Colonization resistance (CR), the ability to block infections by potentially harmful microbes, is a fundamental function of host-associated microbial communities and highly conserved between animals and humans. Environmental factors such as antibiotics and diet can disturb microbial community composition and thereby predispose to opportunistic infections. The most prominent is Clostridioides difficile, the causative agent of diarrhea and pseudomembranous colitis. In addition, the risk to succumb to infections with genuine human enteric pathogens like nontyphoidal Salmonella (NTS) is also increased by a low-diverse, diet or antibiotic-disrupted microbiota. Despite extensive microbial community profiling efforts, only a limited set of microorganisms have been causally linked with protection against enteric pathogens. Furthermore, it remains a challenge to predict colonization resistance from complex microbiome signatures due to context-dependent action of microorganisms. In the past decade, the study of NTS infection has led to the description of several fundamental principles of microbiota-host-pathogen interaction. In this review, I will give an overview on the current state of knowledge in this field and outline experimental approaches to gain functional insight to the role of specific microbes, functions and metabolites in Salmonella-microbiota-host interaction. In particular, I will highlight the value of mouse infection models, which, in combination with culture collections, synthetic communities and gnotobiotic models have become essential tools to screen for protective members of the microbiota and establishing causal relationship and mechanisms in infection research.
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69
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Affiliation(s)
- Jason P Lynch
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Cammie F Lesser
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
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70
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Rosenberg G, Yehezkel D, Hoffman D, Mattioli CC, Fremder M, Ben-Arosh H, Vainman L, Nissani N, Hen-Avivi S, Brenner S, Itkin M, Malitsky S, Ohana E, Ben-Moshe NB, Avraham R. Host succinate is an activation signal for
Salmonella
virulence during intracellular infection. Science 2021; 371:400-405. [DOI: 10.1126/science.aba8026] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 08/06/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Gili Rosenberg
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dror Yehezkel
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dotan Hoffman
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | | | - Moran Fremder
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Hadar Ben-Arosh
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Leia Vainman
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Noa Nissani
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shelly Hen-Avivi
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shirley Brenner
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ehud Ohana
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Noa Bossel Ben-Moshe
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
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71
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Abstract
A balanced gut microbiota contributes to health, but the mechanisms maintaining homeostasis remain elusive. Microbiota assembly during infancy is governed by competition between species and by environmental factors, termed habitat filters, that determine the range of successful traits within the microbial community. These habitat filters include the diet, host-derived resources, and microbiota-derived metabolites, such as short-chain fatty acids. Once the microbiota has matured, competition and habitat filtering prevent engraftment of new microbes, thereby providing protection against opportunistic infections. Competition with endogenous Enterobacterales, habitat filtering by short-chain fatty acids, and a host-derived habitat filter, epithelial hypoxia, also contribute to colonization resistance against Salmonella serovars. However, at a high challenge dose, these frank pathogens can overcome colonization resistance by using their virulence factors to trigger intestinal inflammation. In turn, inflammation increases the luminal availability of host-derived resources, such as oxygen, nitrate, tetrathionate, and lactate, thereby creating a state of abnormal habitat filtering that enables the pathogen to overcome growth inhibition by short-chain fatty acids. Thus, studying the process of ecosystem invasion by Salmonella serovars clarifies that colonization resistance can become weakened by disrupting host-mediated habitat filtering. This insight is relevant for understanding how inflammation triggers dysbiosis linked to noncommunicable diseases, conditions in which endogenous Enterobacterales expand in the fecal microbiota using some of the same growth-limiting resources required by Salmonella serovars for ecosystem invasion. In essence, ecosystem invasion by Salmonella serovars suggests that homeostasis and dysbiosis simply represent states where competition and habitat filtering are normal or abnormal, respectively.
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72
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Heinzinger LR, Johnson A, Wurster JI, Nilson R, Penumutchu S, Belenky P. Oxygen and Metabolism: Digesting Determinants of Antibiotic Susceptibility in the Gut. iScience 2020; 23:101875. [PMID: 33354661 PMCID: PMC7744946 DOI: 10.1016/j.isci.2020.101875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Microbial metabolism is a major determinant of antibiotic susceptibility. Environmental conditions that modify metabolism, notably oxygen availability and redox potential, can directly fine-tune susceptibility to antibiotics. Despite this, relatively few studies have discussed these modifications within the gastrointestinal tract and their implication on in vivo drug activity and the off-target effects of antibiotics in the gut. In this review, we discuss the environmental and biogeographical complexity of the gastrointestinal tract in regard to oxygen availability and redox potential, addressing how the heterogeneity of gut microhabitats may modify antibiotic activity in vivo. We contextualize the current literature surrounding oxygen availability and antibiotic efficacy and discuss empirical treatments. We end by discussing predicted patterns of antibiotic activity in prominent microbiome taxa, given gut heterogeneity, oxygen availability, and polymicrobial interactions. We also propose additional work required to fully elucidate the role of oxygen metabolism on antibiotic susceptibility in the context of the gut.
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Affiliation(s)
- Lauren R. Heinzinger
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
| | - Angus Johnson
- Department of Biological Science, Binghamton University, Binghamton, NY 13902, USA
| | - Jenna I. Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Rachael Nilson
- 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
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
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73
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Atypical immunometabolism and metabolic reprogramming in liver cancer: Deciphering the role of gut microbiome. Adv Cancer Res 2020; 149:171-255. [PMID: 33579424 DOI: 10.1016/bs.acr.2020.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related mortality worldwide. Much recent research has delved into understanding the underlying molecular mechanisms of HCC pathogenesis, which has revealed to be heterogenous and complex. Two major hallmarks of HCC include: (i) a hijacked immunometabolism and (ii) a reprogramming in metabolic processes. We posit that the gut microbiota is a third component in an entanglement triangle contributing to HCC progression. Besides metagenomic studies highlighting the diagnostic potential in the gut microbiota profile, recent research is pinpointing the gut microbiota as an instigator, not just a mere bystander, in HCC. In this chapter, we discuss mechanistic insights on atypical immunometabolism and metabolic reprogramming in HCC, including the examination of tumor-associated macrophages and neutrophils, tumor-infiltrating lymphocytes (e.g., T-cell exhaustion, regulatory T-cells, natural killer T-cells), the Warburg effect, rewiring of the tricarboxylic acid cycle, and glutamine addiction. We further discuss the potential involvement of the gut microbiota in these characteristics of hepatocarcinogenesis. An immediate highlight is that microbiota metabolites (e.g., short chain fatty acids, secondary bile acids) can impair anti-tumor responses, which aggravates HCC. Lastly, we describe the rising 'new era' of immunotherapies (e.g., immune checkpoint inhibitors, adoptive T-cell transfer) and discuss for the potential incorporation of gut microbiota targeted therapeutics (e.g., probiotics, fecal microbiota transplantation) to alleviate HCC. Altogether, this chapter invigorates for continuous research to decipher the role of gut microbiome in HCC from its influence on immunometabolism and metabolic reprogramming.
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74
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Abstract
There are 100 trillion diverse bacterial residents in the mammalian gut. Commensal bacterial species/strains cooperate and compete with each other to establish a well-balanced community, crucial for the maintenance of host health. Pathogenic bacteria hijack cooperative mechanisms or use strategies to evade competitive mechanisms to establish infection. Moreover, pathogenic bacteria cause marked environmental changes in the gut, such as the induction of inflammation, which fosters the selective growth of pathogens. In this review, we summarize the latest findings concerning the mechanisms by which commensal bacterial species/strains colonize the gut through cooperative or competitive behaviors. We also review the mechanisms by which pathogenic bacteria adapt to the inflamed gut and thrive at the expense of commensal bacteria. The understanding of bacterial adaptation to the healthy and the inflamed gut may provide new bacteria-targeted therapeutic approaches that selectively promote the expansion of beneficial commensal bacteria or limit the growth of pathogenic bacteria.
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Affiliation(s)
- Yijie Guo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA,Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Sho Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA,CONTACT Nobuhiko Kamada Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
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75
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Chanin RB, Winter MG, Spiga L, Hughes ER, Zhu W, Taylor SJ, Arenales A, Gillis CC, Büttner L, Jimenez AG, Smoot MP, Santos RL, Winter SE. Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation. Cell Host Microbe 2020; 28:780-788.e5. [PMID: 33053375 DOI: 10.1016/j.chom.2020.09.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/06/2020] [Accepted: 09/03/2020] [Indexed: 12/19/2022]
Abstract
The intestinal epithelium separates host tissue and gut-associated microbial communities. During inflammation, the host releases reactive oxygen and nitrogen species as an antimicrobial response. The impact of these radicals on gut microbes is incompletely understood. We discovered that the cryptic appBCX genes, predicted to encode a cytochrome bd-II oxidase, conferred a fitness advantage for E. coli in chemical and genetic models of non-infectious colitis. This fitness advantage was absent in mice that lacked epithelial NADPH oxidase 1 (NOX1) activity. In laboratory growth experiments, supplementation with exogenous hydrogen peroxide enhanced E. coli growth through AppBCX-mediated respiration in a catalase-dependent manner. We conclude that epithelial-derived reactive oxygen species are degraded in the gut lumen, which gives rise to molecular oxygen that supports the aerobic respiration of E. coli. This work illustrates how epithelial host responses intersect with gut microbial metabolism in the context of gut inflammation.
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Affiliation(s)
- Rachael B Chanin
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth R Hughes
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Savannah J Taylor
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alexandre Arenales
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270, Brazil
| | - Caroline C Gillis
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa Büttner
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Angel G Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Madeline P Smoot
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Renato L Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270, Brazil
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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76
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The Salmonella LysR Family Regulator RipR Activates the SPI-13-Encoded Itaconate Degradation Cluster. Infect Immun 2020; 88:IAI.00303-20. [PMID: 32719152 DOI: 10.1128/iai.00303-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/21/2020] [Indexed: 11/20/2022] Open
Abstract
Itaconate is a dicarboxylic acid that inhibits the isocitrate lyase enzyme of the bacterial glyoxylate shunt. Activated macrophages have been shown to produce itaconate, suggesting that these immune cells may employ this metabolite as a weapon against invading bacteria. Here, we demonstrate that in vitro, itaconate can exhibit bactericidal effects under acidic conditions similar to the pH of a macrophage phagosome. In parallel, successful pathogens, including Salmonella, have acquired a genetic operon encoding itaconate degradation proteins, which are induced heavily in macrophages. We characterized the regulation of this operon by the neighboring gene ripR in specific response to itaconate. Moreover, we developed an itaconate biosensor based on the operon promoter that can detect itaconate in a semiquantitative manner and, when combined with the ripR gene, is sufficient for itaconate-regulated expression in Escherichia coli Using this biosensor with fluorescence microscopy, we observed bacteria responding to itaconate in the phagosomes of macrophages and provide additional evidence that gamma interferon stimulates macrophage itaconate synthesis and that J774 mouse macrophages produce substantially more itaconate than the human THP-1 monocyte cell line. In summary, we examined the role of itaconate as an antibacterial metabolite in mouse and human macrophages, characterized the regulation of Salmonella's defense against it, and developed it as a convenient itaconate biosensor and inducible promoter system.
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Abstract
Vibrio cholerae remains a challenge in the developing world and incidence of the disease it causes, cholera, is anticipated to increase with rising global temperatures and with emergent, highly infectious strains. At present, the underlying metabolic processes that support V. cholerae growth during infection are less well understood than specific virulence traits, such as production of a toxin or pilus. In this study, we determined that oxidative metabolism of host substrates such as mucin contribute significantly to V. cholerae population expansion in vivo. Identifying metabolic pathways critical for growth can provide avenues for controlling V. cholerae infection and the knowledge may be translatable to other pathogens of the gastrointestinal tract. Vibrio cholerae replicates to high cell density in the human small intestine, leading to the diarrheal disease cholera. During infection, V. cholerae senses and responds to environmental signals that govern cellular responses. Spatial localization of V. cholerae within the intestine affects nutrient availability and metabolic pathways required for replicative success. Metabolic processes used by V. cholerae to reach such high cell densities are not fully known. We sought to better define the metabolic traits that contribute to high levels of V. cholerae during infection. By disrupting the pyruvate dehydrogenase (PDH) complex and pyruvate formate-lyase (PFL), we could differentiate aerobic and anaerobic metabolic pathway involvement in V. cholerae proliferation. We demonstrate that oxidative metabolism is a key contributor to the replicative success of V. choleraein vivo using an infant mouse model in which PDH mutants were attenuated 100-fold relative to the wild type for colonization. Additionally, metabolism of host substrates, including mucin, was determined to support V. cholerae growth in vitro as a sole carbon source, primarily under aerobic growth conditions. Mucin likely contributes to population expansion during human infection as it is a ubiquitous source of carbohydrates. These data highlight oxidative metabolism as important in the intestinal environment and warrant further investigation of how oxygen and other host substrates shape the intestinal landscape that ultimately influences bacterial disease. We conclude from our results that oxidative metabolism of host substrates is a key driver of V. cholerae proliferation during infection, leading to the substantial bacterial burden exhibited in cholera patients.
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Blueberry malvidin-3-galactoside modulated gut microbial dysbiosis and microbial TCA cycle KEGG pathway disrupted in a liver cancer model induced by HepG2 cells. FOOD SCIENCE AND HUMAN WELLNESS 2020. [DOI: 10.1016/j.fshw.2020.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Kin LX, Butler CA, Slakeski N, Hoffmann B, Dashper SG, Reynolds EC. Metabolic cooperativity between Porphyromonas gingivalis and Treponema denticola. J Oral Microbiol 2020; 12:1808750. [PMID: 32944158 PMCID: PMC7482830 DOI: 10.1080/20002297.2020.1808750] [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: 01/01/2023] Open
Abstract
Background Porphyromonas gingivalis and Treponema denticola are proteolytic periodontopathogens that co-localize in polymicrobial subgingival plaque biofilms, display in vitro growth symbiosis and synergistic virulence in animal models of disease. These symbioses are underpinned by a range of metabolic interactions including cooperative hydrolysis of glycine-containing peptides to produce free glycine, which T. denticola uses as a major energy and carbon source. Objective To characterize the P. gingivalis gene products essential for these interactions. Methods: The P. gingivalis transcriptome exposed to cell-free T. denticola conditioned medium was determined using RNA-seq. P. gingivalis proteases potentially involved in hydrolysis of glycine-containing peptides were identified using a bioinformatics approach. Results One hundred and thirty-twogenes displayed differential expression, with the pattern of gene expression consistent with succinate cross-feeding from T. denticola to P. gingivalis and metabolic shifts in the P. gingivalis folate-mediated one carbon superpathway. Interestingly, no P. gingivalis proteases were significantly up-regulated. Three P. gingivalis proteases were identified as candidates and inactivated to determine their role in the release of free glycine. P. gingivalis PG0753 and PG1788 but not PG1605 are involved in the hydrolysis of glycine-containing peptides, making free glycine available for T. denticola utilization. Conclusion Collectively these metabolic interactions help to partition resources and engage synergistic interactions between these two species.
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Affiliation(s)
- Lin Xin Kin
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Catherine A Butler
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Nada Slakeski
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Brigitte Hoffmann
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Stuart G Dashper
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
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Affiliation(s)
- Mariana X Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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Le Bastard Q, Chapelet G, Birgand G, Hillmann BM, Javaudin F, Hayatgheib N, Bourigault C, Bemer P, De Decker L, Batard E, Lepelletier D, Montassier E. Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases. Antimicrob Resist Infect Control 2020; 9:107. [PMID: 32665016 PMCID: PMC7359458 DOI: 10.1186/s13756-020-00773-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/03/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The prevalence of extended beta-lactamase producing Enterobacteriaceae (ESBL-E) has been constantly increasing over the last few decades. These microorganisms that have acquired broad antibiotic resistance are now common human pathogens. Changes in the gut microbiome, induced by antibiotics or other drugs, enable expansion of these microorganisms, but the mechanisms are not yet fully understood. OBJECTIVES The main objective was to identify specific bacteria and functional pathways and genes characterizing the gut microbiome of nursing home residents carrying ESBL-E, using metagenomics. SUBJECTS AND METHODS We included 144 residents living in two different nursing homes. All fecal samples were screened for ESBL-E and gut microbiome was characterized using shallow shotgun metagenomic DNA sequencing. RESULTS Ten nursing home residents were colonized by ESBL-E, namely Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae species, and were compared to non-carriers. We found that ESBL-E carriers had an alteration in within-sample diversity. Using a bootstrap algorithm, we found that the gut microbiome of ESBL-E carriers was depleted in butyrate-producing species, enriched in succinate-producing species and enriched in pathways involved in intracellular pH homeostasis compared to non-carriers individuals. Several energy metabolism pathways were overrepresented in ESBL-E carriers suggesting a greater ability to metabolize multiple microbiota and mucus layer-derived nutrients. CONCLUSIONS The gut microbiome of ESBL-E carriers in nursing homes harbors specific taxonomic and functional characteristics, conferring an environment that enables Enterobacteriaceae expansion. Here we describe new functional features associated with ESBL-E carriage that could help us to elucidate the complex interactions leading to colonization persistence in the human gut microbiota.
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Affiliation(s)
- Quentin Le Bastard
- MiHAR lab, Université de Nantes, 44000, Nantes, France.
- Department of Emergency Medicine, CHU Nantes, Nantes University Hospital, 44000, Nantes, France.
| | - Guillaume Chapelet
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Pole de gérontologie clinique, Nantes University Hospital, 44000, Nantes, France
| | - Gabriel Birgand
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Regional Infection Control Centre, Pays de la Loire, Nantes, France
| | - Benjamin M Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - François Javaudin
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Department of Emergency Medicine, CHU Nantes, Nantes University Hospital, 44000, Nantes, France
| | | | - Céline Bourigault
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Bacteriology and Infection Control Department, Nantes University Hospital, Nantes, France
| | - Pascale Bemer
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Bacteriology and Infection Control Department, Nantes University Hospital, Nantes, France
| | - Laure De Decker
- Pole de gérontologie clinique, Nantes University Hospital, 44000, Nantes, France
| | - Eric Batard
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Department of Emergency Medicine, CHU Nantes, Nantes University Hospital, 44000, Nantes, France
| | - Didier Lepelletier
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Bacteriology and Infection Control Department, Nantes University Hospital, Nantes, France
| | - Emmanuel Montassier
- MiHAR lab, Université de Nantes, 44000, Nantes, France.
- Department of Emergency Medicine, CHU Nantes, Nantes University Hospital, 44000, Nantes, France.
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Shelton CD, Byndloss MX. Gut Epithelial Metabolism as a Key Driver of Intestinal Dysbiosis Associated with Noncommunicable Diseases. Infect Immun 2020; 88:e00939-19. [PMID: 32122941 PMCID: PMC7309626 DOI: 10.1128/iai.00939-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In high-income countries, the leading causes of death are noncommunicable diseases (NCDs), such as obesity, cancer, and cardiovascular disease. An important feature of most NCDs is inflammation-induced gut dysbiosis characterized by a shift in the microbial community structure from obligate to facultative anaerobes such as Proteobacteria This microbial imbalance can contribute to disease pathogenesis by either a depletion in or the production of microbiota-derived metabolites. However, little is known about the mechanism by which inflammation-mediated changes in host physiology disrupt the microbial ecosystem in our large intestine leading to disease. Recent work by our group suggests that during gut homeostasis, epithelial hypoxia derived from peroxisome proliferator-activated receptor γ (PPAR-γ)-dependent β-oxidation of microbiota-derived short-chain fatty acids limits oxygen availability in the colon, thereby maintaining a balanced microbial community. During inflammation, disruption in gut anaerobiosis drives expansion of facultative anaerobic Enterobacteriaceae, regardless of their pathogenic potential. Therefore, our research group is currently exploring the concept that dysbiosis-associated expansion of Enterobacteriaceae can be viewed as a microbial signature of epithelial dysfunction and may play a greater role in different models of NCDs, including diet-induced obesity, atherosclerosis, and inflammation-associated colorectal cancer.
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Affiliation(s)
- Catherine D Shelton
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mariana X Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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83
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Taylor SJ, Winter SE. Salmonella finds a way: Metabolic versatility of Salmonella enterica serovar Typhimurium in diverse host environments. PLoS Pathog 2020; 16:e1008540. [PMID: 32525928 PMCID: PMC7289338 DOI: 10.1371/journal.ppat.1008540] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Savannah J. Taylor
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (SEW); (SJT)
| | - Sebastian E. Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (SEW); (SJT)
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Nguyen BD, Cuenca V M, Hartl J, Gül E, Bauer R, Meile S, Rüthi J, Margot C, Heeb L, Besser F, Escriva PP, Fetz C, Furter M, Laganenka L, Keller P, Fuchs L, Christen M, Porwollik S, McClelland M, Vorholt JA, Sauer U, Sunagawa S, Christen B, Hardt WD. Import of Aspartate and Malate by DcuABC Drives H 2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice. Cell Host Microbe 2020; 27:922-936.e6. [PMID: 32416061 PMCID: PMC7292772 DOI: 10.1016/j.chom.2020.04.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
Initial enteropathogen growth in the microbiota-colonized gut is poorly understood. Salmonella Typhimurium is metabolically adaptable and can harvest energy by anaerobic respiration using microbiota-derived hydrogen (H2) as an electron donor and fumarate as an electron acceptor. As fumarate is scarce in the gut, the source of this electron acceptor is unclear. Here, transposon sequencing analysis along the colonization trajectory of S. Typhimurium implicates the C4-dicarboxylate antiporter DcuABC in early murine gut colonization. In competitive colonization assays, DcuABC and enzymes that convert the C4-dicarboxylates aspartate and malate into fumarate (AspA, FumABC), are required for fumarate/H2-dependent initial growth. Thus, S. Typhimurium obtains fumarate by DcuABC-mediated import and conversion of L-malate and L-aspartate. Fumarate reduction yields succinate, which is exported by DcuABC in exchange for L-aspartate and L-malate. This cycle allows S. Typhimurium to harvest energy by H2/fumarate respiration in the microbiota-colonized gut. This strategy may also be relevant for commensal E. coli diminishing the S. Typhimurium infection.
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Affiliation(s)
- Bidong D Nguyen
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Johannes Hartl
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Ersin Gül
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Rebekka Bauer
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Susanne Meile
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Joel Rüthi
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Céline Margot
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Laura Heeb
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Franziska Besser
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Pau Pérez Escriva
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Céline Fetz
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Markus Furter
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Philipp Keller
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Lea Fuchs
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthias Christen
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Julia A Vorholt
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Shinichi Sunagawa
- Institute of Microbiology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland.
| | - Beat Christen
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland.
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Campylobacter jejuni BumSR directs a response to butyrate via sensor phosphatase activity to impact transcription and colonization. Proc Natl Acad Sci U S A 2020; 117:11715-11726. [PMID: 32398371 DOI: 10.1073/pnas.1922719117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Campylobacter jejuni monitors intestinal metabolites produced by the host and microbiota to initiate intestinal colonization of avian and animal hosts for commensalism and infection of humans for diarrheal disease. We previously discovered that C. jejuni has the capacity to spatially discern different intestinal regions by sensing lactate and the short-chain fatty acids acetate and butyrate and then alter transcription of colonization factors appropriately for in vivo growth. In this study, we identified the C. jejuni butyrate-modulated regulon and discovered that the BumSR two-component signal transduction system (TCS) directs a response to butyrate by identifying mutants in a genetic screen defective for butyrate-modulated transcription. The BumSR TCS, which is important for infection of humans and optimal colonization of avian hosts, senses butyrate likely by indirect means to alter transcription of genes encoding important colonization determinants. Unlike many canonical TCSs, the predicted cytoplasmic sensor kinase BumS lacked in vitro autokinase activity, which would normally lead to phosphorylation of the cognate BumR response regulator. Instead, BumS has likely evolved mutations to naturally function as a phosphatase whose activity is influenced by exogenous butyrate to control the level of endogenous phosphorylation of BumR and its ability to alter transcription of target genes. To our knowledge, the BumSR TCS is the only bacterial signal transduction system identified so far that mediates responses to the microbiota-generated intestinal metabolite butyrate, an important factor for host intestinal health and homeostasis. Our findings suggest that butyrate sensing by this system is vital for C. jejuni colonization of multiple hosts.
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86
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Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production. PLoS Pathog 2020; 16:e1008448. [PMID: 32208465 PMCID: PMC7141690 DOI: 10.1371/journal.ppat.1008448] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 04/08/2020] [Accepted: 03/01/2020] [Indexed: 01/08/2023] Open
Abstract
The composition of the intestinal microbiota influences the outcome of enteric infections in human and mice. However, the role of specific members and their metabolites contributing to disease severity is largely unknown. Using isogenic mouse lines harboring distinct microbiota communities, we observed highly variable disease kinetics of enteric Citrobacter rodentium colonization after infection. Transfer of communities from susceptible and resistant mice into germ-free mice verified that the varying susceptibilities are determined by microbiota composition. The strongest differences in colonization were observed in the cecum and could be maintained in vitro by coculturing cecal bacteria with C. rodentium. Cohousing of animals as well as the transfer of cultivable bacteria from resistant to susceptible mice led to variable outcomes in the recipient mice. Microbiome analysis revealed that a higher abundance of butyrate-producing bacteria was associated with the resistant phenotype. Quantification of short-chain fatty acid (SCFA) levels before and after infection revealed increased concentrations of acetate, butyrate and propionate in mice with delayed colonization. Addition of physiological concentrations of butyrate, but not of acetate and/or propionate strongly impaired growth of C. rodentium in vitro. In vivo supplementation of susceptible, antibiotic-treated and germ-free mice with butyrate led to the same level of protection, notably only when cecal butyrate concentration reached a concentration higher than 50 nmol/mg indicating a critical threshold for protection. In the recent years, commensal-derived primary and secondary bacterial metabolites emerged as potent modulators of hosts susceptibility to infection. Our results provide evidence that variations in SCFA production in mice fed fibre-rich chow-based diets modulate susceptibility to colonization with Enterobacteriaceae not only in antibiotic-disturbed ecosystems but even in undisturbed microbial communities. These findings emphasise the need for microbiota normalization across laboratory mouse lines for infection experiments with the model-pathogen C. rodentium independent of investigations of diet and antibiotic usage. The distinct composition of the gut microbiota in each individual results in variable metabolic activity and output of these communities, which influences the host, including resistance to enteric pathogens. Lack of reproducibility in biomedical research is nowadays frequently attributed to the microbiota, but little is known about which specific members and metabolites contribute to disease severity. Here, we use genetically identical mouse lines with variable microbiota compositions on a standardized diet and observed highly variable colonization with the enteric pathogen Citrobacter rodentium without antibiotics intervention. We found the same differences in formerly germ-free animals harbouring the respective donors microbiota and also in vitro by coculturing cecal bacteria from resistant and susceptible animals with C. rodentium showing that the phenotype is fully dependent on differences in the microbiota. We analysed the microbiome composition and found a higher abundance of butyrate-producing bacteria as well as increased levels of butyrate in resistant mice. By supplementation of susceptible and germ-free animals with butyrate, we could significantly lower the levels of colonization highlighting that commensal-derived primary and secondary bacterial metabolites are highly variable between laboratory animals from different vendors and are potent modulators of hosts susceptibility to infection with C. rodentium.
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87
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Rosas‐Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF. Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment. Protein Sci 2020; 29:711-722. [PMID: 31811683 PMCID: PMC7021002 DOI: 10.1002/pro.3796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/24/2019] [Accepted: 12/04/2019] [Indexed: 11/06/2022]
Abstract
Galactarate dehydratase (GarD) is the first enzyme in the galactarate/glucarate pathway and catalyzes the dehydration of galactarate to 3-keto-5-dehydroxygalactarate. This protein is known to increase colonization fitness of intestinal pathogens in antibiotic-treated mice and to promote bacterial survival during stress. The galactarate/glucarate pathway is widespread in bacteria, but not in humans, and thus could be a target to develop new inhibitors for use in combination therapy to combat antibiotic resistance. The structure of almost all the enzymes of the galactarate/glucarate pathway were solved previously, except for GarD, for which only the structure of the N-terminal domain was determined previously. Herein, we report the first crystal structure of full-length GarD solved using a seleno-methoionine derivative revealing a new protein fold. The protein consists of three domains, each presenting a novel twist as compared to their distant homologs. GarD in the crystal structure forms dimers and each monomer consists of three domains. The N-terminal domain is comprised of a β-clip fold, connected to the second domain by a long unstructured linker. The second domain serves as a dimerization interface between two monomers. The C-terminal domain forms an unusual variant of a Rossmann fold with a crossover and is built around a seven-stranded parallel β-sheet supported by nine α-helices. A metal binding site in the C-terminal domain is occupied by Ca2+ . The activity of GarD was corroborated by the production of 5-keto-4-deoxy-D-glucarate under reducing conditions and in the presence of iron. Thus, GarD is an unusual enolase with a novel protein fold never previously seen in this class of enzymes.
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Affiliation(s)
- Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Ludmilla Shuvalova
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center–LS‐CATNorthwestern UniversityArgonneIllinois
| | - Olga Kiryukhina
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Nathan Mih
- Department of BioengineeringUniversity of California San DiegoLa JollaCalifornia
| | - Lukasz Jaroszewski
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Department of Biomedical SciencesUniversity of California at RiversideRiversideCalifornia
| | - Bernhard Palsson
- Department of BioengineeringUniversity of California San DiegoLa JollaCalifornia
- Systems Biology Center for Antibiotic ResistanceUniversity of California San DiegoLa JollaCalifornia
| | - Adam Godzik
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Department of Biomedical SciencesUniversity of California at RiversideRiversideCalifornia
| | - Karla J. F. Satchell
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
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Zhu W, Winter MG, Spiga L, Hughes ER, Chanin R, Mulgaonkar A, Pennington J, Maas M, Behrendt CL, Kim J, Sun X, Beiting DP, Hooper LV, Winter SE. Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis. Cell Host Microbe 2020; 27:376-388.e8. [PMID: 32075741 DOI: 10.1016/j.chom.2020.01.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/02/2019] [Accepted: 01/16/2020] [Indexed: 02/06/2023]
Abstract
During short-lived perturbations, such as inflammation, the gut microbiota exhibits resilience and reverts to its original configuration. Although microbial access to the micronutrient iron is decreased during colitis, pathogens can scavenge iron by using siderophores. How commensal bacteria acquire iron during gut inflammation is incompletely understood. Curiously, the human commensal Bacteroides thetaiotaomicron does not produce siderophores but grows under iron-limiting conditions using enterobacterial siderophores. Using RNA-seq, we identify B. thetaiotaomicron genes that were upregulated during Salmonella-induced gut inflammation and were predicted to be involved in iron uptake. Mutants in the xusABC locus (BT2063-2065) were defective for xenosiderophore-mediated iron uptake in vitro. In the normal mouse gut, the XusABC system was dispensable, while a xusA mutant colonized poorly during colitis. This work identifies xenosiderophore utilization as a critical mechanism for B. thetaiotaomicron to sustain colonization during inflammation and suggests a mechanism of how interphylum iron metabolism contributes to gut microbiota resilience.
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Affiliation(s)
- Wenhan Zhu
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria G Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luisella Spiga
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth R Hughes
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rachael Chanin
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aditi Mulgaonkar
- Radiology and Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jenelle Pennington
- Radiology and Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michelle Maas
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cassie L Behrendt
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiankai Sun
- Radiology and Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lora V Hooper
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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89
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Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly. mSystems 2020; 5:5/1/e00620-19. [PMID: 32019832 PMCID: PMC7002114 DOI: 10.1128/msystems.00620-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious levels. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota culture collection comprising 1,590 isolates belonging to 102 species. This culture collection represents 34.57% of the taxonomic diversity and 70% functional capacity, as estimated by metagenomic sequencing of the fecal samples used for culture. Using whole-genome sequencing, we characterized species representatives from this collection and predicted their phenotypic traits, further characterizing isolates by defining nutrient utilization profiles and short-chain fatty acid production. When screened with a coculture assay, 66 species in our culture collection inhibited Clostridioides difficile Several phenotypes, particularly, growth rate, production of SCFAs, and the utilization of mannitol, sorbitol, or succinate, correlated with C. difficile inhibition. We used a combinatorial community assembly approach to formulate defined bacterial mixes inhibitory to C. difficile We tested 256 combinations and found that both species composition and blend size were important in inhibition. Our results show that the interaction of bacteria with one another in a mix and with other members of gut commensals must be investigated to design defined bacterial mixes for inhibiting C. difficile in vivo IMPORTANCE Antibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, thus allowing pathogens such as Clostridioides difficile to colonize and causing recurrent infection and mortality. Although fecal microbiome transplantation has been shown to be an effective treatment for C. difficile infection (CDI), a more desirable approach would be the use of a defined mix of inhibitory gut bacteria. The C. difficile-inhibiting species and bacterial combinations identified herein improve the understanding of the ecological interactions controlling colonization resistance against C. difficile and could aid in the design of defined bacteriotherapy as a nonantibiotic alternative against CDI.
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90
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Chijiiwa R, Hosokawa M, Kogawa M, Nishikawa Y, Ide K, Sakanashi C, Takahashi K, Takeyama H. Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota. MICROBIOME 2020; 8:5. [PMID: 31969191 PMCID: PMC6977353 DOI: 10.1186/s40168-019-0779-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/23/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND The gut microbiota can have dramatic effects on host metabolism; however, current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabolic changes in the microbiota. In this study, we describe a novel single-cell genomic sequencing technique that can identify metabolic responders at the species level without the need for reference genomes, and apply this method to identify bacterial responders to an inulin-based diet in the mouse gut microbiota. RESULTS Inulin-feeding changed the mouse fecal microbiome composition to increase Bacteroides spp., resulting in the production of abundant succinate in the mouse intestine. Using our massively parallel single-cell genome sequencing technique, named SAG-gel platform, we obtained 346 single-amplified genomes (SAGs) from mouse gut microbes before and after dietary inulin supplementation. After quality control, the SAGs were classified as 267 bacteria, spanning 2 phyla, 4 classes, 7 orders, and 14 families, and 31 different strains of SAGs were graded as high- and medium-quality draft genomes. From these, we have successfully obtained the genomes of the dominant inulin-responders, Bacteroides spp., and identified their polysaccharide utilization loci and their specific metabolic pathways for succinate production. CONCLUSIONS Our single-cell genomics approach generated a massive amount of SAGs, enabling a functional analysis of uncultured bacteria in the intestinal microbiome. This enabled us to estimate metabolic lineages involved in the bacterial fermentation of dietary fiber and metabolic outcomes such as short-chain fatty acid production in the intestinal environment based on the fibers ingested. The technique allows the in-depth isolation and characterization of uncultured bacteria with specific functions in the microbiota and could be exploited to improve human and animal health. Video abstract.
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Affiliation(s)
- Rieka Chijiiwa
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masahito Hosokawa
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- PRESTO, Japan Science and Technology Agency (JST), 5-3 Yonban-cho, Chiyoda-ku, Tokyo, 102-0075, Japan.
| | - Masato Kogawa
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Yohei Nishikawa
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Keigo Ide
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Chikako Sakanashi
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Kai Takahashi
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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91
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Abstract
There is now a wealth of evidence showing that communication between microbiota and the host is critical to sustain the vital functions of the healthy host, and disruptions of this homeostatic coexistence are known to be associated with a range of diseases including obesity and type 2 diabetes. Microbiota-derived metabolites act both as nutrients and as messenger molecules and can signal to distant organs in the body to shape host pathophysiology. In this review, we provide a new perspective on succinate as a gut microbiota-derived metabolite with a key role governing intestinal homeostasis and energy metabolism. Thus, succinate is not merely a major intermediary of the TCA traditionally considered as an extracellular danger signal in the host, but also a by-product of some bacteria and a primary cross-feeding metabolite between gut resident microbes. In addition to maintain a healthy microbiome, specific functions of microbiota-derived succinate in peripheral tissues regulating host nutrient metabolism should not be rule out. Indeed, recent research point to some probiotic interventions directed to modulate succinate levels in the intestinal lumen, as a new microbiota-based therapies to treat obesity and related co-morbidities. While further research is essential, a large body of evidence point to succinate as a new strategic mediator in the microbiota-host cross-talk, which might provide the basis for new therapeutically approaches in a near future.
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Affiliation(s)
- Sonia Fernández-Veledo
- Departament of Endocrinology and Nutrition and Research Unit, University Hospital of Tarragona Joan XXIII-Institut d'Investigació Sanitària Pere Virgili (IISPV), c/ Dr. Mallafré Guasch, 4, 43007, Tarragona, Spain.
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain.
| | - Joan Vendrell
- Departament of Endocrinology and Nutrition and Research Unit, University Hospital of Tarragona Joan XXIII-Institut d'Investigació Sanitària Pere Virgili (IISPV), c/ Dr. Mallafré Guasch, 4, 43007, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Rovira i Virgili University, Tarragona, Spain
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92
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Vila Nova M, Durimel K, La K, Felten A, Bessières P, Mistou MY, Mariadassou M, Radomski N. Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. BMC Genomics 2019; 20:814. [PMID: 31694533 PMCID: PMC6836353 DOI: 10.1186/s12864-019-6188-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv). RESULTS Based on a genome dataset including Salmonella serovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively. CONCLUSIONS Our results suggest that the genetic and metabolic determinants of Salmonella adaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.
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Affiliation(s)
- Meryl Vila Nova
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Kévin Durimel
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Kévin La
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Arnaud Felten
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Philippe Bessières
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Michel-Yves Mistou
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Mahendra Mariadassou
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nicolas Radomski
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France.
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93
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Regulation of Gut Microbiota and Metabolic Endotoxemia with Dietary Factors. Nutrients 2019; 11:nu11102277. [PMID: 31547555 PMCID: PMC6835897 DOI: 10.3390/nu11102277] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 02/08/2023] Open
Abstract
Metabolic endotoxemia is a condition in which blood lipopolysaccharide (LPS) levels are elevated, regardless of the presence of obvious infection. It has been suggested to lead to chronic inflammation-related diseases such as obesity, type 2 diabetes mellitus, non-alcoholic fatty liver disease (NAFLD), pancreatitis, amyotrophic lateral sclerosis, and Alzheimer’s disease. In addition, it has attracted attention as a target for the prevention and treatment of these chronic diseases. As metabolic endotoxemia was first reported in mice that were fed a high-fat diet, research regarding its relationship with diets has been actively conducted in humans and animals. In this review, we summarize the relationship between fat intake and induction of metabolic endotoxemia, focusing on gut dysbiosis and the influx, kinetics, and metabolism of LPS. We also summarize the recent findings about dietary factors that attenuate metabolic endotoxemia, focusing on the regulation of gut microbiota. We hope that in the future, control of metabolic endotoxemia using dietary factors will help maintain human health.
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94
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Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB, Kuijper EJ. Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection. Microbiol Mol Biol Rev 2019; 83:e00007-19. [PMID: 31167904 PMCID: PMC6710460 DOI: 10.1128/mmbr.00007-19] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gut microbiome is critical in providing resistance against colonization by exogenous microorganisms. The mechanisms via which the gut microbiota provide colonization resistance (CR) have not been fully elucidated, but they include secretion of antimicrobial products, nutrient competition, support of gut barrier integrity, and bacteriophage deployment. However, bacterial enteric infections are an important cause of disease globally, indicating that microbiota-mediated CR can be disturbed and become ineffective. Changes in microbiota composition, and potential subsequent disruption of CR, can be caused by various drugs, such as antibiotics, proton pump inhibitors, antidiabetics, and antipsychotics, thereby providing opportunities for exogenous pathogens to colonize the gut and ultimately cause infection. In addition, the most prevalent bacterial enteropathogens, including Clostridioides difficile, Salmonella enterica serovar Typhimurium, enterohemorrhagic Escherichia coli, Shigella flexneri, Campylobacter jejuni, Vibrio cholerae, Yersinia enterocolitica, and Listeria monocytogenes, can employ a wide array of mechanisms to overcome colonization resistance. This review aims to summarize current knowledge on how the gut microbiota can mediate colonization resistance against bacterial enteric infection and on how bacterial enteropathogens can overcome this resistance.
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Affiliation(s)
- Q R Ducarmon
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - R D Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - B V H Hornung
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - W van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - V B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - E J Kuijper
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- Netherlands Donor Feces Bank, Leiden, Netherlands
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95
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Ziesack M, Gibson T, Oliver JKW, Shumaker AM, Hsu BB, Riglar DT, Giessen TW, DiBenedetto NV, Bry L, Way JC, Silver PA, Gerber GK. Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium. mSystems 2019; 4:e00352-19. [PMID: 31409662 PMCID: PMC6697442 DOI: 10.1128/msystems.00352-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/23/2019] [Indexed: 01/15/2023] Open
Abstract
In nature, microbes interact antagonistically, neutrally, or beneficially. To shed light on the effects of positive interactions in microbial consortia, we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wild-type consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments, including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments.IMPORTANCE Microbial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment, and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortium function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us in deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.
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Affiliation(s)
- Marika Ziesack
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Travis Gibson
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John K W Oliver
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew M Shumaker
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Bryan B Hsu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - David T Riglar
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas V DiBenedetto
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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96
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Nilsson OR, Kari L, Steele-Mortimer O. Foodborne infection of mice with Salmonella Typhimurium. PLoS One 2019; 14:e0215190. [PMID: 31393874 PMCID: PMC6687127 DOI: 10.1371/journal.pone.0215190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/28/2019] [Indexed: 01/08/2023] Open
Abstract
The bacterial pathogen Salmonella enterica serovar Typhimurium is one of the most common causes of foodborne disease in humans and is also an important model system for bacterial pathogenesis. Oral inoculation of C57Bl/6 mice, which are genetically susceptible to Salmonella, results in systemic infection but the murine intestine is not efficiently colonized unless the intestinal microbiota is disrupted. Pretreatment of C57Bl/6 mice with streptomycin, followed by oral inoculation with Salmonella Typhimurium results in colitis resembling human intestinal Salmonellosis. The predominant method of delivery of bacteria is oral gavage, during which organisms are deposited directly into the stomach via a feeding needle. Although convenient, this method can be stressful for mice, and may lead to unwanted tracheal or systemic introduction of bacteria. Here, we developed a method for oral infection of mice by voluntary consumption of regular mouse chow inoculated with bacteria. Mice readily ate chow fragments containing up to 108 CFU Salmonella, allowing for a wide range of infectious doses. In mice pretreated with streptomycin, infection with inoculated chow resulted in reproducible infections with doses as low as 103 CFU. Mice not treated with streptomycin, as well as resistant Nramp1 reconstituted C57Bl/6J mice, were also readily infected using this method. In summary, voluntary consumption of chow inoculated with Salmonella represents a natural route of infection for foodborne salmonellosis and a viable alternative to oral gavage.
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Affiliation(s)
- Olof R. Nilsson
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Laszlo Kari
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Olivia Steele-Mortimer
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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97
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Maslowski KM. Metabolism at the centre of the host-microbe relationship. Clin Exp Immunol 2019; 197:193-204. [PMID: 31107965 PMCID: PMC6642865 DOI: 10.1111/cei.13329] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2019] [Indexed: 12/13/2022] Open
Abstract
Maintaining homoeostatic host–microbe interactions is vital for host immune function. The gut microbiota shapes the host immune system and the immune system reciprocally shapes and modifies the gut microbiota. However, our understanding of how these microbes are tolerated and how individual, or communities of, gut microbes influence host function is limited. This review will focus on metabolites as key mediators of this complex host–microbe relationship. It will look at the central role of epithelial metabolism in shaping the gut microbiota, how microbial metabolites influence the epithelium and the mucosal and peripheral immune system, and how the immune system shapes microbial composition and metabolism. Finally, this review will look at how metabolites are involved in cross‐talk between different members of the microbiota and their role during infections.
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Affiliation(s)
- K M Maslowski
- Institute of Immunology and Immunotherapy and Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
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98
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Velazquez EM, Nguyen H, Heasley KT, Saechao CH, Gil LM, Rogers AWL, Miller BM, Rolston MR, Lopez CA, Litvak Y, Liou MJ, Faber F, Bronner DN, Tiffany CR, Byndloss MX, Byndloss AJ, Bäumler AJ. Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection. Nat Microbiol 2019; 4:1057-1064. [PMID: 30911125 PMCID: PMC6533147 DOI: 10.1038/s41564-019-0407-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 02/11/2019] [Indexed: 12/16/2022]
Abstract
Lack of reproducibility is a prominent problem in biomedical research. An important source of variation in animal experiments is the microbiome, but little is known about specific changes in the microbiota composition that cause phenotypic differences. Here we show that genetically similar laboratory mice obtained from four different commercial vendors exhibited marked phenotypic variation in their susceptibility to Salmonella infection. Fecal microbiota transplantation into germ-free mice replicated donor susceptibility, revealing that variability was due to changes in the gut microbiota composition. Co-housing of mice only partially transferred protection against Salmonella infection, suggesting that minority species within the gut microbiota might confer this trait. Consistent with this idea, we identified endogenous Enterobacteriaceae, a low abundance taxon, as keystone species responsible for variation in the susceptibility to Salmonella infection. Protection conferred by endogenous Enterobacteriaceae could be modeled by inoculating mice with probiotic Escherichia coli, which conferred resistance by using its aerobic metabolism to compete with Salmonella for resources. We conclude that a mechanistic understanding of phenotypic variation can accelerate development of strategies for enhancing the reproducibility of animal experiments.
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Affiliation(s)
- Eric M Velazquez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Keaton T Heasley
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Cheng H Saechao
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Lindsey M Gil
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andrew W L Rogers
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Brittany M Miller
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Matthew R Rolston
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Megan J Liou
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Franziska Faber
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Denise N Bronner
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Austin J Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.
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Host-Derived Metabolites Modulate Transcription of Salmonella Genes Involved in l-Lactate Utilization during Gut Colonization. Infect Immun 2019; 87:IAI.00773-18. [PMID: 30617205 DOI: 10.1128/iai.00773-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/02/2019] [Indexed: 12/14/2022] Open
Abstract
During Salmonella enterica serovar Typhimurium infection, host inflammation alters the metabolic environment of the gut lumen to favor the outgrowth of the pathogen at the expense of the microbiota. Inflammation-driven changes in host cell metabolism lead to the release of l-lactate and molecular oxygen from the tissue into the gut lumen. Salmonella utilizes lactate as an electron donor in conjunction with oxygen as the terminal electron acceptor to support gut colonization. Here, we investigated transcriptional regulation of the respiratory l-lactate dehydrogenase LldD in vitro and in mouse models of Salmonella infection. The two-component system ArcAB repressed transcription of l-lactate utilization genes under anaerobic conditions in vitro The ArcAB-mediated repression of lldD transcription was relieved under microaerobic conditions. Transcription of lldD was induced by l-lactate but not d-lactate. A mutant lacking the regulatory protein LldR failed to induce lldD transcription in response to l-lactate. Furthermore, the lldR mutant exhibited reduced transcription of l-lactate utilization genes and impaired fitness in murine models of infection. These data provide evidence that the host-derived metabolites oxygen and l-lactate serve as cues for Salmonella to regulate lactate oxidation metabolism on a transcriptional level.
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