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Ellermann M. Designing microbial communities to starve out invading pathogens. Cell Host Microbe 2024; 32:145-146. [PMID: 38359793 DOI: 10.1016/j.chom.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/17/2024]
Abstract
Identifying key features required for specific community-level functions can be challenging, especially considering the complexity of the gut microbiome. In a recent study in Science, Spragge et al. present a high-throughput experimental framework to rationally design microbial communities that can resist invasion by specific bacterial pathogens.
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Affiliation(s)
- Melissa Ellermann
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
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2
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Ellermann M. Emerging mechanisms by which endocannabinoids and their derivatives modulate bacterial populations within the gut microbiome. Adv Drug Alcohol Res 2023; 3:11359. [PMID: 38389811 PMCID: PMC10880783 DOI: 10.3389/adar.2023.11359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/28/2023] [Indexed: 02/24/2024]
Abstract
Bioactive lipids such as endocannabinoids serve as important modulators of host health and disease through their effects on various host functions including central metabolism, gut physiology, and immunity. Furthermore, changes to the gut microbiome caused by external factors such as diet or by disease development have been associated with altered endocannabinoid tone and disease outcomes. These observations suggest the existence of reciprocal relationships between host lipid signaling networks and bacterial populations that reside within the gut. Indeed, endocannabinoids and their congeners such as N-acylethanolamides have been recently shown to alter bacterial growth, functions, physiology, and behaviors, therefore introducing putative mechanisms by which these bioactive lipids directly modulate the gut microbiome. Moreover, these potential interactions add another layer of complexity to the regulation of host health and disease pathogenesis that may be mediated by endocannabinoids and their derivatives. This mini review will summarize recent literature that exemplifies how N-acylethanolamides and monoacylglycerols including endocannabinoids can impact bacterial populations in vitro and within the gut microbiome. We also highlight exciting preclinical studies that have engineered gut bacteria to synthesize host N-acylethanolamides or their precursors as potential strategies to treat diseases that are in part driven by aberrant lipid signaling, including obesity and inflammatory bowel diseases.
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Affiliation(s)
- Melissa Ellermann
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
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3
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Older EA, Zhang J, Ferris ZE, Xue D, Zhong Z, Mitchell MK, Madden M, Wang Y, Chen H, Nagarkatti P, Nagarkatti M, Fan D, Ellermann M, Li YX, Li J. Biosynthetic Enzyme-guided Disease Correlation Connects Gut Microbial Metabolites Sulfonolipids to Inflammatory Bowel Disease Involving TLR4 Signaling. bioRxiv 2023:2023.03.16.533047. [PMID: 36993324 PMCID: PMC10055157 DOI: 10.1101/2023.03.16.533047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The trillions of microorganisms inhabiting the human gut are intricately linked to human health. At the species abundance level, correlational studies have connected specific bacterial taxa to various diseases. While the abundances of these bacteria in the gut serve as good indicators for disease progression, understanding the functional metabolites they produce is critical to decipher how these microbes influence human health. Here, we report a unique biosynthetic enzyme-guided disease correlation approach to uncover microbial functional metabolites as potential molecular mechanisms in human health. We directly connect the expression of gut microbial sulfonolipid (SoL) biosynthetic enzymes to inflammatory bowel disease (IBD) in patients, revealing a negative correlation. This correlation is then corroborated by targeted metabolomics, identifying that SoLs abundance is significantly decreased in IBD patient samples. We experimentally validate our analysis in a mouse model of IBD, showing that SoLs production is indeed decreased while inflammatory markers are increased in diseased mice. In support of this connection, we apply bioactive molecular networking to show that SoLs consistently contribute to the immunoregulatory activity of SoL-producing human microbes. We further reveal that sulfobacins A and B, two representative SoLs, primarily target Toll-like receptor 4 (TLR4) to mediate immunomodulatory activity through blocking TLR4's natural ligand lipopolysaccharide (LPS) binding to myeloid differentiation factor 2, leading to significant suppression of LPS-induced inflammation and macrophage M1 polarization. Together, these results suggest that SoLs mediate a protective effect against IBD through TLR4 signaling and showcase a widely applicable biosynthetic enzyme-guided disease correlation approach to directly link the biosynthesis of gut microbial functional metabolites to human health.
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4
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Viladomiu M, Khounlotham M, Dogan B, Lima SF, Elsaadi A, Cardakli E, Castellanos JG, Ng C, Herzog J, Schoenborn AA, Ellermann M, Liu B, Zhang S, Gulati AS, Sartor RB, Simpson KW, Lipkin SM, Longman RS. Agr2-associated ER stress promotes adherent-invasive E. coli dysbiosis and triggers CD103 + dendritic cell IL-23-dependent ileocolitis. Cell Rep 2022; 41:111637. [PMID: 36384110 PMCID: PMC9805753 DOI: 10.1016/j.celrep.2022.111637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Endoplasmic reticulum (ER) stress is associated with Crohn's disease (CD), but its impact on host-microbe interaction in disease pathogenesis is not well defined. Functional deficiency in the protein disulfide isomerase anterior gradient 2 (AGR2) has been linked with CD and leads to epithelial cell ER stress and ileocolitis in mice and humans. Here, we show that ileal expression of AGR2 correlates with mucosal Enterobactericeae abundance in human inflammatory bowel disease (IBD) and that Agr2 deletion leads to ER-stress-dependent expansion of mucosal-associated adherent-invasive Escherichia coli (AIEC), which drives Th17 cell ileocolitis in mice. Mechanistically, our data reveal that AIEC-induced epithelial cell ER stress triggers CD103+ dendritic cell production of interleukin-23 (IL-23) and that IL-23R is required for ileocolitis in Agr2-/- mice. Overall, these data reveal a specific and reciprocal interaction of the expansion of the CD pathobiont AIEC with ER-stress-associated ileocolitis and highlight a distinct cellular mechanism for IL-23-dependent ileocolitis.
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Affiliation(s)
- Monica Viladomiu
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Manirath Khounlotham
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Belgin Dogan
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Svetlana F. Lima
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ahmed Elsaadi
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Emre Cardakli
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jim G. Castellanos
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Charles Ng
- Department of Pathology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeremy Herzog
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexi A. Schoenborn
- Department of Pediatrics, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa Ellermann
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Present address: Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Bo Liu
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shiying Zhang
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ajay S. Gulati
- Department of Pediatrics, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - R. Balfour Sartor
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth W. Simpson
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Steven M. Lipkin
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,Correspondence: (S.M.L.), (R.S.L.)
| | - Randy S. Longman
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,Jill Roberts Center for IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA,Lead contact,Correspondence: (S.M.L.), (R.S.L.)
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5
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Mitchell MK, Ellermann M. Long Chain Fatty Acids and Virulence Repression in Intestinal Bacterial Pathogens. Front Cell Infect Microbiol 2022; 12:928503. [PMID: 35782143 PMCID: PMC9247172 DOI: 10.3389/fcimb.2022.928503] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
When bacterial pathogens enter the gut, they encounter a complex milieu of signaling molecules and metabolites produced by host and microbial cells or derived from external sources such as the diet. This metabolomic landscape varies throughout the gut, thus establishing a biogeographical gradient of signals that may be sensed by pathogens and resident bacteria alike. Enteric bacterial pathogens have evolved elaborate mechanisms to appropriately regulate their virulence programs, which involves sensing and responding to many of these gut metabolites to facilitate successful gut colonization. Long chain fatty acids (LCFAs) represent major constituents of the gut metabolome that can impact bacterial functions. LCFAs serve as important nutrient sources for all cellular organisms and can function as signaling molecules that regulate bacterial metabolism, physiology, and behaviors. Moreover, in several enteric pathogens, including Salmonella enterica, Listeria monocytogenes, Vibrio cholerae, and enterohemorrhagic Escherichia coli, LCFA sensing results in the transcriptional repression of virulence through two general mechanisms. First, some LCFAs function as allosteric inhibitors that decrease the DNA binding affinities of transcriptional activators of virulence genes. Second, some LCFAs also modulate the activation of histidine kinase receptors, which alters downstream intracellular signaling networks to repress virulence. This mini-review will summarize recent studies that have investigated the molecular mechanisms by which different LCFA derivatives modulate the virulence of enteric pathogens, while also highlighting important gaps in the field regarding the roles of LCFAs as determinants of infection and disease.
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6
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Ellermann M, Pacheco AR, Jimenez AG, Russell RM, Cuesta S, Kumar A, Zhu W, Vale G, Martin SA, Raj P, McDonald JG, Winter SE, Sperandio V. Endocannabinoids Inhibit the Induction of Virulence in Enteric Pathogens. Cell 2020; 183:650-665.e15. [PMID: 33031742 DOI: 10.1016/j.cell.2020.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 06/30/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Abstract
Endocannabinoids are host-derived lipid hormones that fundamentally impact gastrointestinal (GI) biology. The use of cannabis and other exocannabinoids as anecdotal treatments for various GI disorders inspired the search for mechanisms by which these compounds mediate their effects, which led to the discovery of the mammalian endocannabinoid system. Dysregulated endocannabinoid signaling was linked to inflammation and the gut microbiota. However, the effects of endocannabinoids on host susceptibility to infection has not been explored. Here, we show that mice with elevated levels of the endocannabinoid 2-arachidonoyl glycerol (2-AG) are protected from enteric infection by Enterobacteriaceae pathogens. 2-AG directly modulates pathogen function by inhibiting virulence programs essential for successful infection. Furthermore, 2-AG antagonizes the bacterial receptor QseC, a histidine kinase encoded within the core Enterobacteriaceae genome that promotes the activation of pathogen-associated type three secretion systems. Taken together, our findings establish that endocannabinoids are directly sensed by bacteria and can modulate bacterial function.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alline R Pacheco
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Angel G Jimenez
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Regan M Russell
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Santiago Cuesta
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aman Kumar
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenhan Zhu
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gonçalo Vale
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sarah A Martin
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prithvi Raj
- Microbiome Research Lab, Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeffrey G McDonald
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vanessa Sperandio
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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7
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Abstract
Antibiotics profoundly reduced worldwide mortality. However, the emergence of resistance to the growth inhibiting effects of these drugs occurred. New approaches to treat infectious disease that reduce the likelihood for resistance are needed. In bacterial pathogens, complex signaling networks regulate virulence. Anti-virulence therapies aim to disrupt these networks to attenuate virulence without affecting growth. Quorum-sensing, a cell-to-cell communication system, represents an attractive anti-virulence target because it often activates virulence. The challenge is to identify druggable targets that inhibit virulence, while also minimizing the likelihood of mutations promoting resistance. Moreover, given the ubiquity of quorum-sensing systems in commensals, any potential effects of anti-virulence therapies on microbiome function should also be considered. Here we highlight the efficacy and drawbacks of anti-virulence approaches.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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8
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Jimenez AG, Ellermann M, Abbott W, Sperandio V. Diet-derived galacturonic acid regulates virulence and intestinal colonization in enterohaemorrhagic Escherichia coli and Citrobacter rodentium. Nat Microbiol 2019; 5:368-378. [PMID: 31873206 PMCID: PMC6992478 DOI: 10.1038/s41564-019-0641-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022]
Abstract
Enteric pathogens sense the complex chemistry within the gastrointestinal (GI) tract to efficiently compete with the resident microbiota and establish a colonization niche. Here we show that enterohemorrhagic E. coli (EHEC), and its surrogate murine infection model Citrobacter rodentium, sense galacturonic-acid to initiate a multi-layered program towards successful mammalian infection. Galacturonic-acid utilization as a carbon source aids the initial pathogen expansion. The main source of galacturonic-acid is dietary pectin, which is broken into galacturonic-acid by the prominent member of the microbiota, Bacteroides thetaiotamicron (Bt). This regulation occurs through the ExuR transcription factor. However, galacturonic-acid is also sensed as a signal through ExuR to modulate the expression of the genes encoding a molecular syringe known as a type three secretion system (T3SS) leading to infectious colitis and inflammation. Galacturonic-acid moonlights as a nutrient and a signal directing the exquisite microbiota-pathogen relationships within the GI tract. Importantly, this work highlights that differential dietary sugar availability impacts the relationship between the microbiota and enteric pathogens, as well as disease outcomes.
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Affiliation(s)
- Angel G Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Melissa Ellermann
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Abstract
The overuse of antibiotics has led to the evolution of drug-resistant bacteria that are becoming increasingly dangerous to human health. According to the Centers for Disease Control and Prevention, antibiotic-resistant bacteria cause at least 2 million illnesses and 23,000 deaths in the United States annually. Traditionally, antibiotics are bactericidal or bacteriostatic agents that place selective pressure on bacteria, leading to the expansion of antibiotic-resistant strains. In addition, antibiotics that are effective against some pathogens can also exacerbate their pathogenesis and may lead to severe progression of the disease. Therefore, alternative strategies are needed to treat antibiotic-resistant bacterial infections. One novel approach is to target bacterial virulence to prevent or limit pathogen colonization, while also minimizing tissue damage and disease comorbidities in the host. This review focuses on the interactions between enteric pathogens and naturally occurring small molecules in the human gut as potential therapeutic targets for antivirulence strategies. Individual small molecules in the intestines modulate enteric pathogen virulence and subsequent intestinal fitness and colonization. Targeted interruption of pathogen sensing of these small molecules could therefore attenuate their virulence. This review highlights the paths of discovery for new classes of antimicrobials that could potentially mitigate the urgent problem of antibiotic resistance.
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Affiliation(s)
- Aman Kumar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Melissa Ellermann
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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10
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Ellermann M, Gharaibeh RZ, Maharshak N, Peréz-Chanona E, Jobin C, Carroll IM, Arthur JC, Plevy SE, Fodor AA, Brouwer CR, Sartor RB. Dietary iron variably modulates assembly of the intestinal microbiota in colitis-resistant and colitis-susceptible mice. Gut Microbes 2019; 11:32-50. [PMID: 31179826 PMCID: PMC6973310 DOI: 10.1080/19490976.2019.1599794] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Iron deficiency, a common comorbidity of gastrointestinal inflammatory disorders such as inflammatory bowel diseases (IBD), is often treated with oral iron supplementation. However, the safety of oral iron supplementation remains controversial because of its association with exacerbated disease activity in a subset of IBD patients. Because iron modulates bacterial growth and function, one possible mechanism by which iron may exacerbate inflammation in susceptible hosts is by modulating the intestinal microbiota. We, therefore, investigated the impact of dietary iron on the intestinal microbiota, utilizing the conventionalization of germ-free mice as a model of a microbial community in compositional flux to recapitulate the instability of the IBD-associated intestinal microbiota. Our findings demonstrate that altering intestinal iron availability during community assembly modulated the microbiota in non-inflamed wild type (WT) and colitis-susceptible interleukin-10-deficient (Il10-/-) mice. Depletion of luminal iron availability promoted luminal compositional changes associated with dysbiotic states irrespective of host genotype, including an expansion of Enterobacteriaceae such as Escherichia coli. Mechanistic in vitro growth competitions confirmed that high-affinity iron acquisition systems in E. coli enhance its abundance over other bacteria in iron-restricted conditions, thereby enabling pathobiont iron scavenging during dietary iron restriction. In contrast, distinct luminal community assembly was observed with dietary iron supplementation in WT versus Il10-/- mice, suggesting that the effects of increased iron on the microbiota differ with host inflammation status. Taken together, shifts in dietary iron intake during community assembly modulate the ecological structure of the intestinal microbiota and is dependent on host genotype and inflammation status.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Raad Z. Gharaibeh
- Bioinformatics Services Division, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC, USA,Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Nitsan Maharshak
- Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel, USA
| | - Ernesto Peréz-Chanona
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA,Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL, USA
| | - Ian M. Carroll
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA,Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA,Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Scott E Plevy
- Immunology Research and Development, Janssen Pharmaceuticals, Spring House, PA, USA
| | - Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Cory R. Brouwer
- Bioinformatics Services Division, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC, USA,Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - R. Balfour Sartor
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA,Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA,CONTACT R. Balfour Sartor Department of Microbiology and Immunology, University of North Carolina, Room 7309A Biomolecular Building, CB# 7032, Chapel Hill, NC 27599-7032, USA
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11
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Ellermann M, Sartor RB. Intestinal bacterial biofilms modulate mucosal immune responses. J Immunol Sci 2018; 2:13-18. [PMID: 30393787 PMCID: PMC6214460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Host-associated microbial communities modulate numerous aspects of host physiology at the epithelial interface within mucosal environments. Perturbations to this symbiotic relationship between host and microbiota has been linked to numerous microbial-driven pathological states, including Crohn's disease (CD). This is in part driven by the outgrowth of aggressive resident bacterial strains such as adherent and invasive Escherichia coli (AIEC) and changes in bacterial physiology and function that promote enhanced mucosal association of pathobionts and aberrant stimulation of mucosal immunity. Endogenous bacteria from host-associated microbial communities can adopt a sessile lifestyle and form multicellular structures known as biofilms that are generated through the expression of extracellular adhesion factors that include curli amyloid fibrils, cellulose and type 1 pili. In addition to enabling bacterial attachment to mucosal surfaces, biofilm components also stimulate immune responses and can therefore instigate or perpetuate microbial-driven inflammatory diseases such as CD. These host-bacterial interactions provide pharmacological targets that can potentially be exploited to limit mucosal adherence of aggressive enteric bacteria, inappropriate stimulation of inflammatory immune responses and consequent development of chronic intestinal inflammation.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - R. Balfour Sartor
- Departments of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
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12
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Affiliation(s)
- Laura E. Fulbright
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Melissa Ellermann
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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13
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Abstract
Iron is an essential micronutrient for most life forms including the majority of resident bacteria of the microbiota and their mammalian hosts. Bacteria have evolved numerous mechanisms to competitively acquire iron within host environments, such as the secretion of small molecules known as siderophores that can solubilize iron for bacterial use. However, siderophore biosynthesis and acquisition is not a capability equally harbored by all resident bacteria. Moreover, the structural diversity of siderophores creates variability in the susceptibility to host mechanisms that serve to counteract siderophore-mediated iron acquisition and limit bacterial growth. As a result, the differential capabilities to acquire iron among members of a complex microbial community carry important implications for the growth and function of resident bacteria. Siderophores can also directly influence host function by modulating cellular iron homeostasis, further providing a mechanism by which resident bacteria may influence their local environment at the host-microbial interface. This review will explore the putative mechanisms by which siderophore production by resident bacteria in the intestines may influence microbial community dynamics and host-bacterial interactions with important implications for pathogen- and microbiota-driven diseases including infection, inflammatory bowel diseases and colorectal cancer.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Janelle C Arthur
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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14
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Packey CD, Shanahan MT, Manick S, Bower MA, Ellermann M, Tonkonogy SL, Carroll IM, Sartor RB. Molecular detection of bacterial contamination in gnotobiotic rodent units. Gut Microbes 2013; 4:361-70. [PMID: 23887190 PMCID: PMC3839980 DOI: 10.4161/gmic.25824] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Gnotobiotic rodents provide an important technique to study the functional roles of commensal bacteria in host physiology and pathophysiology. To ensure sterility, these animals must be screened frequently for contamination. The traditional screening approaches of culturing and Gram staining feces have inherent limitations, as many bacteria are uncultivable and fecal Gram stains are difficult to interpret. Thus, we developed and validated molecular methods to definitively detect and identify contamination in germ-free (GF) and selectively colonized animals. Fresh fecal pellets were collected from rodents housed in GF isolators, spontaneously contaminated ex-GF isolators, selectively colonized isolators and specific pathogen-free (SPF) conditions. DNA isolated from mouse and rat fecal samples was amplified by polymerase chain reaction (PCR) and subjected to quantitative PCR (qPCR) using universal primers that amplify the 16S rRNA gene from all bacterial groups. PCR products were sequenced to identify contaminating bacterial species. Random amplification of polymorphic DNA (RAPD) PCR profiles verified bacterial inoculation of selectively colonized animals. These PCR techniques more accurately detected and identified GF isolator contamination than current standard approaches. These molecular techniques can be utilized to more definitively screen GF and selectively colonized animals for bacterial contamination when Gram stain and/or culture results are un-interpretable or inconsistent.
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Affiliation(s)
- Christopher D Packey
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Michael T Shanahan
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Sayeed Manick
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Maureen A Bower
- The National Gnotobiotic Rodent Resource Center; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Melissa Ellermann
- Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Susan L Tonkonogy
- Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,College of Veterinary Medicine, North Carolina State University; Raleigh, NC USA
| | - Ian M Carroll
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - R Balfour Sartor
- Department of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Center for Gastrointestinal Biology and Diseases; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,The National Gnotobiotic Rodent Resource Center; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Correspondence to: R Balfour Sartor,
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15
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Maharshak N, Packey CD, Ellermann M, Manick S, Siddle JP, Huh EY, Plevy S, Sartor RB, Carroll IM. Altered enteric microbiota ecology in interleukin 10-deficient mice during development and progression of intestinal inflammation. Gut Microbes 2013; 4:316-24. [PMID: 23822920 PMCID: PMC3744516 DOI: 10.4161/gmic.25486] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Inflammatory bowel diseases (IBD) result from dysregulated immune responses toward microbial and perhaps other luminal antigens in a genetically susceptible host, and are associated with altered composition and diversity of the intestinal microbiota. The interleukin 10-deficient (IL-10 (-/-) ) mouse has been widely used to model human IBD; however the specific alterations that occur in the intestinal microbiota of this mouse model during the onset of colonic inflammation have not yet been defined. The aim of our study was to define the changes in diversity and composition that occur in the intestinal microbiota of IL-10 (-/-) mice during the onset and progression of colonic inflammation. We used high throughput sequencing of the 16S rRNA gene to characterize the diversity and composition of formerly germ-free, wild-type and IL-10 (-/-) mice associated with the same intestinal microbiota over time. Following two weeks of colonization with a specific pathogen-free (SPF) microbiota we observed a significant increase in the diversity and richness of the intestinal microbiota of wild-type mice. In contrast, a progressive decrease in diversity and richness was observed at three and four weeks in IL-10 (-/-) mice. This decrease in diversity and richness was mirrored by an increase in Proteobacteria and Escherichia coli in IL-10 (-/-) mice. An increase in E. coli was also observed in conventionally raised IL-10 (-/-) mice at the point of colonic inflammation. Our data reports the sequential changes in diversity and composition of the intestinal microbiota in an immune-mediated mouse model that may help provide insights into the primary vs. secondary role of dysbiosis in human IBD patients.
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Affiliation(s)
- Nitsan Maharshak
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Gastroenterology and Liver diseases; Tel Aviv Sourasky Medical Center; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Christopher D. Packey
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Melissa Ellermann
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Sayeed Manick
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Jennica P. Siddle
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Eun Young Huh
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Scott Plevy
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - R. Balfour Sartor
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Department of Microbiology and Immunology; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Ian M. Carroll
- Division of Gastroenterology and Hepatology; Center for Gastrointestinal Biology and Disease; University of North Carolina at Chapel Hill; Chapel Hill, NC USA,Correspondence to: Ian M. Carroll,
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