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Price CTD, Hanford HE, Al-Quadan T, Santic M, Shin CJ, Da'as MSJ, Abu Kwaik Y. Amoebae as training grounds for microbial pathogens. mBio 2024; 15:e0082724. [PMID: 38975782 PMCID: PMC11323580 DOI: 10.1128/mbio.00827-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.
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Affiliation(s)
- Christopher T. D. Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Hannah E. Hanford
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Tasneem Al-Quadan
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | | | - Cheon J. Shin
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Manal S. J. Da'as
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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2
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Parmar D, Rosado-Rosa JM, Shrout JD, Sweedler JV. Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms. Methods 2024; 224:21-34. [PMID: 38295894 PMCID: PMC11149699 DOI: 10.1016/j.ymeth.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/17/2023] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.
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Affiliation(s)
- Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joenisse M Rosado-Rosa
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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3
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Vanderpool EJ, Rumbaugh KP. Host-microbe interactions in chronic rhinosinusitis biofilms and models for investigation. Biofilm 2023; 6:100160. [PMID: 37928619 PMCID: PMC10622848 DOI: 10.1016/j.bioflm.2023.100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a debilitating condition characterized by long-lasting inflammation of the paranasal sinuses. It affects a significant portion of the population, causing a considerable burden on individuals and healthcare systems. The pathogenesis of CRS is multifactorial, with bacterial infections playing a crucial role in CRS development and persistence. In recent years, the presence of biofilms has emerged as a key contributor to the chronicity of sinusitis, further complicating treatment and exacerbating symptoms. This review aims to explore the role of biofilms in CRS, focusing on the involvement of the bacterial species Staphylococcus aureus and Pseudomonas aeruginosa, their interactions in chronic infections, and model systems for studying biofilms in CRS. These species serve as an example of how microbial interplay can influence disease progression and exemplify the need for continued investigation and innovation in CRS research.
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Affiliation(s)
- Emily J. Vanderpool
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kendra P. Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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Lewin GR, Kapur A, Cornforth DM, Duncan RP, Diggle FL, Moustafa DA, Harrison SA, Skaar EP, Chazin WJ, Goldberg JB, Bomberger JM, Whiteley M. Application of a quantitative framework to improve the accuracy of a bacterial infection model. Proc Natl Acad Sci U S A 2023; 120:e2221542120. [PMID: 37126703 PMCID: PMC10175807 DOI: 10.1073/pnas.2221542120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/07/2023] [Indexed: 05/03/2023] Open
Abstract
Laboratory models are critical to basic and translational microbiology research. Models serve multiple purposes, from providing tractable systems to study cell biology to allowing the investigation of inaccessible clinical and environmental ecosystems. Although there is a recognized need for improved model systems, there is a gap in rational approaches to accomplish this goal. We recently developed a framework for assessing the accuracy of microbial models by quantifying how closely each gene is expressed in the natural environment and in various models. The accuracy of the model is defined as the percentage of genes that are similarly expressed in the natural environment and the model. Here, we leverage this framework to develop and validate two generalizable approaches for improving model accuracy, and as proof of concept, we apply these approaches to improve models of Pseudomonas aeruginosa infecting the cystic fibrosis (CF) lung. First, we identify two models, an in vitro synthetic CF sputum medium model (SCFM2) and an epithelial cell model, that accurately recapitulate different gene sets. By combining these models, we developed the epithelial cell-SCFM2 model which improves the accuracy of over 500 genes. Second, to improve the accuracy of specific genes, we mined publicly available transcriptome data, which identified zinc limitation as a cue present in the CF lung and absent in SCFM2. Induction of zinc limitation in SCFM2 resulted in accurate expression of 90% of P. aeruginosa genes. These approaches provide generalizable, quantitative frameworks for microbiological model improvement that can be applied to any system of interest.
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Affiliation(s)
- Gina R. Lewin
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30332
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30332
| | - Ananya Kapur
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA15219
| | - Daniel M. Cornforth
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30332
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30332
| | - Rebecca P. Duncan
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30332
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA30322
| | - Frances L. Diggle
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30332
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30332
| | - Dina A. Moustafa
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30332
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA30322
| | - Simone A. Harrison
- Department of Biochemistry, Vanderbilt University, Nashville, TN37232
- Department of Chemistry, Vanderbilt University, Nashville, TN37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN37232
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Walter J. Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN37232
- Department of Chemistry, Vanderbilt University, Nashville, TN37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN37232
| | - Joanna B. Goldberg
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30332
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA30322
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA15219
| | - Marvin Whiteley
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30332
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30332
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Mariani F, Juarez GE, Barberis C, Veiga F, Vay C, Galvan EM. Interspecies interactions in mixed-species biofilms formed by Enterococcus faecalis and gram-negative bacteria isolated from polymicrobial diabetic foot ulcers. BIOFOULING 2023; 39:579-590. [PMID: 37482939 DOI: 10.1080/08927014.2023.2236949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023]
Abstract
Diabetic foot ulcers (DFU) are exacerbated by bacterial colonisation. Here, a high prevalence of Enterococcus faecalis was observed in DFU patients from an Argentinean hospital. E. faecalis was frequently co-isolated with Escherichia coli, Morganella morganii, and Pseudomonas aeruginosa. The effect of interspecies interactions on bacterial growth was investigated in mixed-species macrocolony biofilms developed in Lubbock-Glc-agar. Similar cell counts were found for E. faecalis and M. morganii growing in mixed and single-species biofilms. An E. faecalis strain showed 1 Log higher cell counts in mixed biofilms with E. coli. Remarkably, E. faecalis strains showed 2 to 4 Log higher cell counts in mixed biofilms with P. aeruginosa. This effect was not observed in planktonic growth or biofilms developed in tryptic soy agar. The present findings reveal bacterial interactions that benefit E. faecalis in mixed-species biofilms, mainly with P. aeruginosa, in a medium that partially mimics the nutrients found in DFU.
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Affiliation(s)
- Florencia Mariani
- Laboratorio de Patogénesis Bacteriana, Departamento de Investigaciones Bioquímicas y Farmacéuticas, Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Guillermo E Juarez
- Laboratorio de Patogénesis Bacteriana, Departamento de Investigaciones Bioquímicas y Farmacéuticas, Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Claudia Barberis
- Cátedra de Microbiología Clínica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Fisiopatología y Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Florencia Veiga
- Cátedra de Microbiología Clínica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Fisiopatología y Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carlos Vay
- Cátedra de Microbiología Clínica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Fisiopatología y Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Estela M Galvan
- Laboratorio de Patogénesis Bacteriana, Departamento de Investigaciones Bioquímicas y Farmacéuticas, Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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Kilic T, Bali EB. Biofilm control strategies in the light of biofilm-forming microorganisms. World J Microbiol Biotechnol 2023; 39:131. [PMID: 36959476 DOI: 10.1007/s11274-023-03584-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
Biofilm is a complex consortium of microorganisms attached to biotic or abiotic surfaces and live in self-produced or acquired extracellular polymeric substances (EPSs). EPSs are mainly formed by lipids, polysaccharides, proteins, and extracellular DNAs. The adherence to the surface of microbial communities is seen in food, medical, dental, industrial, and environmental fields. Biofilm development in food processing areas challenges food hygiene, and human health. In addition, bacterial attachment and biofilm formation on medical implants inside human tissue can cause multiple critical chronic infections. More than 30 years of international research on the mechanisms of biofilm formation have been underway to address concerns about bacterial biofilm infections. Antibiofilm strategies contain cold atmospheric plasma, nanotechnological, phage-based, antimicrobial peptides, and quorum sensing inhibition. In the last years, the studies on environmentally-friendly techniques such as essential oils and bacteriophages have been intensified to reduce microbial growth. However, the mechanisms of the biofilm matrix formation are still unclear. This review aims to discuss the latest antibiofilm therapeutic strategies against biofilm-forming bacteria.
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Affiliation(s)
- Tugba Kilic
- Department of Medical Services and Techniques, Program of Medical Laboratory Techniques, Vocational School of Health Services, Gazi University, Ankara, 06830, Turkey.
| | - Elif Burcu Bali
- Department of Medical Services and Techniques, Program of Medical Laboratory Techniques, Vocational School of Health Services, Gazi University, Ankara, 06830, Turkey
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7
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Wu H, Zhang Y, Chen H, Liu J, Xiu L, Huang J. Preparation, antioxidant and antibacterial activities of cryptate copper(II)/sulfonate chitosan complexes. Int J Biol Macromol 2023; 231:123200. [PMID: 36634801 DOI: 10.1016/j.ijbiomac.2023.123200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
In this work, we synthesized cryptate copper(II) followed by complexed with sulfonate chitosan (SCS). After characterization, the evaluation of the antioxidant properties of resulting complexes were carried out by 1,1-Diphenyl-2-picrylhydrazyl radical (DPPH•), hydroxyl radical (•OH), and 2,2'-Azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS•+), while the antibacterial and biofilm inhibitory activity against Pseudomonas aeruginosa PAO1 (P. aeruginosa PAO1) were also investigated. According to the results, cryptate copper(II) exhibited the best antioxidant activity followed by cryptate copper(II)/SCS complexes, and SCS. Significant antibacterial activity of cryptate copper(II) against P. aeruginosa PAO1 was observed with the minimum inhibitory concentration of MIC value 12.50 μg/mL and minimum bactericidal concentration of MBC value 100.00 μg/mL, followed by cryptate copper(II)/SCS complexes and SCS. Cryptate copper(II) and cryptate copper(II)/SCS exhibited antibacterial activity which copper ions might enter the interior of cells, and the intracellular ions made the killed bacteria serve as an antibacterial agent showing a zombie effect. The copper ions complexed with cryptate and SCS rendering potential unlimited biological activities, might become one of the most popular research areas because of their unique coordination chemistry and their long-term biological activities.
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Affiliation(s)
- Huixiang Wu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, PR China
| | - Yujun Zhang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, PR China
| | - Hao Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, PR China
| | - Jing Liu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, PR China
| | - Lili Xiu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, PR China
| | - Jianying Huang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, PR China.
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