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Green HD, Van Horn GT, Williams T, Eberly A, Morales GH, Mann R, Hauter IM, Hadjifrangiskou M, Schmitz JE. Intra-strain colony biofilm heterogeneity in uropathogenic Escherichia coli and the effect of the NlpI lipoprotein. Biofilm 2024; 8:100214. [PMID: 39184815 PMCID: PMC11344014 DOI: 10.1016/j.bioflm.2024.100214] [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: 03/19/2024] [Revised: 06/25/2024] [Accepted: 07/09/2024] [Indexed: 08/27/2024] Open
Abstract
Biofilm growth facilitates the interaction of uropathogenic Escherichia coli (UPEC) with the host environment. The extracellular polymeric substances (EPS) of UPEC biofilms are composed prominently of curli amyloid fiber and cellulose polysaccharide. When the organism is propagated as a colony biofilm on agar media, these macromolecules can generate pronounced macroscopic structures. Moreover, curli/cellulose associate tightly with Congo red, generating a characteristic pink-to-red staining pattern when the media is supplemented with this dye. Among different clinical isolates of UPEC, changes in the abundance of curli/cellulose can lead to diverse colony biofilm phenotypes on a strain-by-strain basis. Nevertheless, for any given isolate, these phenotypes are classically homogenous throughout the colony biofilm. Here, we report that a subset of clinical UPEC isolates display heterogenous 'peppermint' colony biofilms, with distinct pale and red subpopulations. Through isolation of these subpopulations and whole genome sequencing, we demonstrate various emergent mutations associated with the phenomenon, including within the gene encoding the outer membrane lipoprotein nlpI. Deletion of nlpI within independent strain-backgrounds increased biofilm rugosity, while its overexpression induced the peppermint phenotype. Upregulation of EPS-associated proteins and transcripts was likewise observed in the absence of nlpI. Overall, these results demonstrate that EPS elaboration in UPEC is impacted by nlpI. More broadly, this phenomenon of intra-strain colony biofilm heterogeneity may be leveraged as a tool to identify additional members within the broad collection of genes that regulate or otherwise affect biofilm formation.
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Affiliation(s)
- Hamilton D. Green
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Gerald T. Van Horn
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy Williams
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Allison Eberly
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Grace H. Morales
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Robert Mann
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Indiana M. Hauter
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Maria Hadjifrangiskou
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Institute for Infection, Immunology & Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan E. Schmitz
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Institute for Infection, Immunology & Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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Köksaldı İÇ, Avcı E, Köse S, Özkul G, Kehribar EŞ, Şafak Şeker UÖ. Genetically engineered bacterial biofilm materials enhances portable whole cell sensing. Biosens Bioelectron 2024; 264:116644. [PMID: 39137519 DOI: 10.1016/j.bios.2024.116644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 07/16/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
In recent years, whole-cell biosensors (WCBs) have emerged as a potent approach for environmental monitoring and on-site analyte detection. These biosensors harness the biological apparatus of microorganisms to identify specific analytes, offering advantages in sensitivity, specificity, and real-time monitoring capabilities. A critical hurdle in biosensor development lies in ensuring the robust attachment of cells to surfaces, a crucial step for practical utility. In this study, we present a comprehensive approach to tackle this challenge via engineering Escherichia coli cells for immobilization on paper through the Curli biofilm pathway. Furthermore, incorporating a cellulose-binding peptide domain to the CsgA biofilm protein enhances cell adhesion to paper surfaces, consequently boosting biosensor efficacy. To demonstrate the versatility of this platform, we developed a WCB for copper, optimized to exhibit a discernible response, even with the naked eye. To confirm its suitability for practical field use, we characterized our copper sensor under various environmental conditions-temperature, salinity, and pH-to mimic real-world scenarios. The biosensor-equipped paper discs can be freeze-dried for deployment in on-site applications, providing a practical method for long-term storage without loss of sensitivity paper discs demonstrate sustained functionality and viability even after months of storage with 5 μM limit of detection for copper with visible-to-naked-eye signal levels. Biofilm-mediated surface attachment and analyte sensing can be independently engineered, allowing for flexible utilization of this platform as required. With the implementation of copper sensing as a proof-of-concept study, we underscore the potential of WCBs as a promising avenue for the on-site detection of a multitude of analytes.
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Affiliation(s)
- İlkay Çisil Köksaldı
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Ece Avcı
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Sıla Köse
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Gökçe Özkul
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Ebru Şahin Kehribar
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey.
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3
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Yu G, Ge X, Li W, Ji L, Yang S. Interspecific cross-talk: The catalyst driving microbial biosynthesis of secondary metabolites. Biotechnol Adv 2024; 76:108420. [PMID: 39128577 DOI: 10.1016/j.biotechadv.2024.108420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/07/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Microorganisms co-exist and co-evolve in nature, forming intricate ecological communities. The interspecies cross-talk within these communities creates and sustains their great biosynthetic potential, making them an important source of natural medicines and high-value-added chemicals. However, conventional investigations into microbial metabolites are typically carried out in pure cultures, resulting in the absence of specific activating factors and consequently causing a substantial number of biosynthetic gene clusters to remain silent. This, in turn, hampers the in-depth exploration of microbial biosynthetic potential and frequently presents researchers with the challenge of rediscovering compounds. In response to this challenge, the coculture strategy has emerged to explore microbial biosynthetic capabilities and has shed light on the study of cross-talk mechanisms. These elucidated mechanisms will contribute to a better understanding of complex biosynthetic regulations and offer valuable insights to guide the mining of secondary metabolites. This review summarizes the research advances in microbial cross-talk mechanisms, with a particular focus on the mechanisms that activate the biosynthesis of secondary metabolites. Additionally, the instructive value of these mechanisms for developing strategies to activate biosynthetic pathways is discussed. Moreover, challenges and recommendations for conducting in-depth studies on the cross-talk mechanisms are presented.
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Affiliation(s)
- Guihong Yu
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China.
| | - Xiaoxuan Ge
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Wanting Li
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Linwei Ji
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China.
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4
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Peroutka-Bigus N, Nielsen DW, Trachsel J, Mou KT, Sharma VK, Kudva IT, Loving CL. Phenotypic and genomic comparison of three human outbreak and one cattle-associated Shiga toxin-producing Escherichia coli O157:H7. Microbiol Spectr 2024; 12:e0414023. [PMID: 39254337 PMCID: PMC11451603 DOI: 10.1128/spectrum.04140-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 08/02/2024] [Indexed: 09/11/2024] Open
Abstract
Escherichia coli O157:H7-adulterated food products are associated with disease outbreaks in humans. Although cattle feces are a source for E. coli O157:H7 contamination, it is unclear if human-associated outbreak isolates differentially colonize and shed in the feces of cattle from that of non-outbreak isolates. It is also unclear if phenotypes, such as biofilm formation, cell attachment, or toxin production, differentiate environmental E. coli O157:H7 isolates from those associated with human illness. The objective of this study was to compare the genotypes and phenotypes of a diverse set of E. coli O157:H7 isolates, with the intent of identifying differences that could inform cattle colonization and fecal shedding, along with virulence potential in humans. Isolates differed in attachment phenotypes on human Caco-2 cells and bovine-derived recto-anal junction squamous epithelial cells, with curli having a strong impact on attachment to the human-derived cell line. The prototypical E. coli O157 isolate EDL933 had the greatest expression of the adhesin gene iha, yet it had decreased expression of the virulence genes stx2, eae, and ehxA compared the lineage I/II isolates RM6067W and/or FRIK1989. Strong or weak biofilm production was not associated with significant differences in cattle colonization or shedding, suggesting biofilms may not play a major role in cattle colonization. No significant differences in cattle colonization and fecal shedding were detected, despite genomic and in vitro phenotypic differences. The outbreak isolate associated with the greatest incidence of hemolytic uremic syndrome, RM6067W, induced the greatest Vero cell cytotoxicity and had the greatest stx2 gene expression. IMPORTANCE Foodborne illness has major impacts on global health and imposes financial hardships on food industries. Escherichia coli serotype O157:H7 is associated with foodborne illness. Cattle feces are a source of E. coli O157:H7, and routine surveillance has led to an abundance of E. coli O157:H7 genomic data. The relationship between E. coli O157:H7 genome and phenotype is not clearly discerned for cattle colonization/shedding and improved understanding could lead to additional strategies to limit E. coli O157:H7 in the food chain. The goal of the research was to evaluate genomic and phenotypic attributes of E. coli O157:H7 associated with cattle colonization and shedding, environmental persistence, and human illness. Our results indicate variations in biofilm formation and in vitro cellular adherence was not associated with differences in cattle colonization or shedding. Overall, processes involved in cattle colonization and various phenotypes in relation to genotype are complex and remain not well understood.
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Affiliation(s)
- Nathan Peroutka-Bigus
- Food Safety and
Enteric Pathogens Research Unit, National Animal Disease Center,
Agricultural Research Service, USDA,
Ames, Iowa, USA
- Oak Ridge Institute
for Science and Education, Agricultural Research Service Participation
Program, Oak Ridge,
Tennessee, USA
| | - Daniel W. Nielsen
- Food Safety and
Enteric Pathogens Research Unit, National Animal Disease Center,
Agricultural Research Service, USDA,
Ames, Iowa, USA
- Oak Ridge Institute
for Science and Education, Agricultural Research Service Participation
Program, Oak Ridge,
Tennessee, USA
| | - Julian Trachsel
- Food Safety and
Enteric Pathogens Research Unit, National Animal Disease Center,
Agricultural Research Service, USDA,
Ames, Iowa, USA
| | - Kathy T. Mou
- Food Safety and
Enteric Pathogens Research Unit, National Animal Disease Center,
Agricultural Research Service, USDA,
Ames, Iowa, USA
- Oak Ridge Institute
for Science and Education, Agricultural Research Service Participation
Program, Oak Ridge,
Tennessee, USA
| | - Vijay K. Sharma
- Food Safety and
Enteric Pathogens Research Unit, National Animal Disease Center,
Agricultural Research Service, USDA,
Ames, Iowa, USA
| | - Indira T. Kudva
- Food Safety and
Enteric Pathogens Research Unit, National Animal Disease Center,
Agricultural Research Service, USDA,
Ames, Iowa, USA
| | - Crystal L. Loving
- Food Safety and
Enteric Pathogens Research Unit, National Animal Disease Center,
Agricultural Research Service, USDA,
Ames, Iowa, USA
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5
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Olsen WP, Courtade G, Peña‐Díaz S, Nagaraj M, Sønderby TV, Mulder FAA, Malle MG, Otzen DE. CsgA gatekeeper residues control nucleation but not stability of functional amyloid. Protein Sci 2024; 33:e5178. [PMID: 39302107 PMCID: PMC11414021 DOI: 10.1002/pro.5178] [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: 05/07/2024] [Revised: 08/16/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024]
Abstract
Functional amyloids, beneficial to the organism producing them, are found throughout life, from bacteria to humans. While disease-related amyloids form by uncontrolled aggregation, the fibrillation of functional amyloid is regulated by complex cellular machinery and optimized sequences, including so-called gatekeeper residues such as Asp. However, the molecular basis for this regulation remains unclear. Here we investigate how the introduction of additional gatekeeper residues affects fibril formation and stability in the functional amyloid CsgA from E. coli. Step-wise introduction of additional Asp gatekeepers gradually eliminated fibrillation unless preformed fibrils were added, illustrating that gatekeepers mainly affect nucleus formation. Once formed, the mutant CsgA fibrils were just as stable as wild-type CsgA. HSQC NMR spectra confirmed that CsgA is intrinsically disordered, and that the introduction of gatekeeper residues does not alter this ensemble. NMR-based Dark-state Exchange Saturation Transfer (DEST) experiments on the different CsgA variants, however, show a decrease in transient interactions between monomeric states and the fibrils, highlighting a critical role for these interactions in the fibrillation process. We conclude that gatekeeper residues affect fibrillation kinetics without compromising structural integrity, making them useful and selective modulators of fibril properties.
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Affiliation(s)
- William P. Olsen
- Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityAarhus CDenmark
- Sino‐Danish College (SDC)University of Chinese Academy of SciencesBeijingChina
| | - Gaston Courtade
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food ScienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Samuel Peña‐Díaz
- Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityAarhus CDenmark
| | - Madhu Nagaraj
- Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityAarhus CDenmark
| | | | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityAarhus CDenmark
- Institute of BiochemistryJohannes Kepler UniversityLinzAustria
- Department of ChemistryAarhus UniversityAarhus CDenmark
| | - Mette G. Malle
- Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityAarhus CDenmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityAarhus CDenmark
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6
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Bamford NC, Morris RJ, Prescott A, Murphy P, Erskine E, MacPhee CE, Stanley-Wall NR. TasA Fibre Interactions Are Necessary for Bacillus subtilis Biofilm Structure. Mol Microbiol 2024. [PMID: 39344640 DOI: 10.1111/mmi.15315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 10/01/2024]
Abstract
The extracellular matrix of biofilms provides crucial structural support to the community and protection from environmental perturbations. TasA, a key Bacillus subtilis biofilm matrix protein, forms both amyloid and non-amyloid fibrils. Non-amyloid TasA fibrils are formed via a strand-exchange mechanism, whereas the amyloid-like form involves non-specific self-assembly. We performed mutagenesis of the N-terminus to assess the role of non-amyloid fibrils in biofilm development. We find that the N-terminal tail is essential for the formation of structured biofilms, providing evidence that the strand-exchange fibrils are the active form in the biofilm matrix. Furthermore, we demonstrate that fibre formation alone is not sufficient to give structure to the biofilm. We build an interactome of TasA with other extracellular protein components, and identify important interaction sites. Our results provide insight into how protein-matrix interactions modulate biofilm development.
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Affiliation(s)
- Natalie C Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ryan J Morris
- National Biofilms Innovation Centre, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Alan Prescott
- Centre for Advanced Scientific Technologies, School of Life Sciences, University of Dundee, Dundee, UK
| | - Paul Murphy
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Elliot Erskine
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Cait E MacPhee
- National Biofilms Innovation Centre, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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7
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Hantus CE, Moppel IJ, Frizzell JK, Francis AE, Nagashima K, Ryno LM. L-Rhamnose Globally Changes the Transcriptome of Planktonic and Biofilm Escherichia coli Cells and Modulates Biofilm Growth. Microorganisms 2024; 12:1911. [PMID: 39338585 PMCID: PMC11434101 DOI: 10.3390/microorganisms12091911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 09/16/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
L-rhamnose, a naturally abundant sugar, plays diverse biological roles in bacteria, influencing biofilm formation and pathogenesis. This study investigates the global impact of L-rhamnose on the transcriptome and biofilm formation of PHL628 E. coli under various experimental conditions. We compared growth in planktonic and biofilm states in rich (LB) and minimal (M9) media at 28 °C and 37 °C, with varying concentrations of L-rhamnose or D-glucose as a control. Our results reveal that L-rhamnose significantly affects growth kinetics and biofilm formation, particularly reducing biofilm growth in rich media at 37 °C. Transcriptomic analysis through RNA-seq showed that L-rhamnose modulates gene expression differently depending on the temperature and media conditions, promoting a planktonic state by upregulating genes involved in rhamnose transport and metabolism and downregulating genes related to adhesion and biofilm formation. These findings highlight the nuanced role of L-rhamnose in bacterial adaptation and survival, providing insight into potential applications in controlling biofilm-associated infections and industrial biofilm management.
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Affiliation(s)
| | | | | | | | | | - Lisa M. Ryno
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA
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8
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Golpasand T, Keshvari M, Behzadi P. Distribution of chaperone-usher fimbriae and curli fimbriae among uropathogenic Escherichia coli. BMC Microbiol 2024; 24:344. [PMID: 39271999 PMCID: PMC11401301 DOI: 10.1186/s12866-024-03472-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND In the present study, we aimed to determine the frequency of the csgA, fimH, mrkD, foc, papaGI, papGII and papGIII genes, to provide and to design fimbrial adhesin gene (FAG) patterns and profiles for the isolated uropathogenic Escherichia coli (UPEC) strains. METHODS The enrollment of 108 positive urine samples was performed during seven months, between January 2022 and July 2022. The UPEC strains were confirmed through the standard microbiological and biochemical tests. The antimicrobial susceptibility test was performed through the Kirby-Bauer disc diffusion method. Molecular screening of FAGs was done through the polymerase chain reaction technology. The statistical analyses including chi square and Fisher's exact tests were performed to interpret the obtained results in the present study. RESULTS As the main results, the antimicrobial resistance (AMR) patterns, multi- (MDR) and extensively drug-resistance (XDR) patterns and FAG patterns were designed and provided. fimH (93.3%), csgA (90.4%) and papG (37.5%) (papGII (30.8%)) genes were recognized as the top three FAGs, respectively. Moreover, the frequency of csgA-fimH gene profile was identified as the top FAG pattern (46.2%) among the others. The isolates bearing csgA-fimH gene profile were armed with a versatile of phenotypic AMR patterns. In the current study, 27.8%, 69.4% and 1.9% of the UPEC isolates were detected as extended-spectrum ß-lactamases (ESBLs) producers, MDR and XDR strains, respectively. CONCLUSIONS In conclusion, detection, providing and designing of patterns and profiles in association with FAGs, AMR feature in UPEC strains give us an effective option to have a successful and influential prevention for both of UTIs initiation and AMR feature.
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Affiliation(s)
- Taha Golpasand
- Department of Microbiology, Shahr-E-Qods Branch, Islamic Azad University, Tehran, 37541-374, Iran
| | - Mohammad Keshvari
- Department of Microbiology, Shahr-E-Qods Branch, Islamic Azad University, Tehran, 37541-374, Iran
| | - Payam Behzadi
- Department of Microbiology, Shahr-E-Qods Branch, Islamic Azad University, Tehran, 37541-374, Iran.
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9
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Carter MQ, Carychao D, Lindsey RL. Conditional expression of flagellar motility, curli fimbriae, and biofilms in Shiga toxin- producing Escherichia albertii. Front Microbiol 2024; 15:1456637. [PMID: 39318426 PMCID: PMC11420993 DOI: 10.3389/fmicb.2024.1456637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/14/2024] [Indexed: 09/26/2024] Open
Abstract
Escherichia albertii is an emerging foodborne pathogen. We previously reported that some avian Shiga toxin-producing E. albertii strains exhibited higher or comparable cytotoxicity in Vero-d2EGFP cells with several enterohemorrhagic E. coli (EHEC) outbreak strains. To better understand the environmental persistence of this pathogen, comparative genomics and phenotypic assays were applied to assess adhesion capability, motility, and biofilm formation in E. albertii. Among the 108 adherence-related genes, those involved in biogenesis of curli fimbriae, hemorrhagic E. coli pilus, type 1 fimbriae, and Sfm fimbriae were conserved in E. albertii. All 20 E. albertii strains carried a complete set of primary flagellar genes that were organized into four gene clusters, while five strains possessed genes related to the secondary flagella, also known as lateral flagella. Compared to EHEC strain EDL933, the eight chemotaxis genes located within the primary flagellar gene clusters were deleted in E. albertii. Additional deletion of motility genes flhABCD and motBC was identified in several E. albertii strains. Swimming motility was detected in three strains when grown in LB medium, however, when grown in 5% TSB or in the pond water-supplemented with 10% pigeon droppings, an additional four strains became motile. Although all E. albertii strains carried curli genes, curli fimbriae were detected only in four, eight, and nine strains following 24, 48, and 120 h incubation, respectively. Type 1 fimbriae were undetectable in any of the strains grown at 37°C or 28°C. Strong biofilms were detected in strains that produced curli fimbriae and in a chicken isolate that was curli fimbriae negative but carried genes encoding adhesive fimbriae K88, a signature of enterotoxigenic E. coli strains causing neonatal diarrhea in piglets. In all phenotypic traits examined, no correlation was revealed between the strains isolated from different sources, or between the strains with and without Shiga toxin genes. The phenotypic variations could not be explained solely by the genetic diversity or the difference in adherence genes repertoire, implying complex regulation in expression of various adhesins. Strains that exhibited a high level of cytotoxicity and were also proficient in biofilm production, may have potential to emerge into high-risk pathogens.
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Affiliation(s)
- Michelle Qiu Carter
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Diana Carychao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Rebecca L Lindsey
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
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10
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Calzas C, Alkie TN, Suderman M, Embury-Hyatt C, Khatri V, Le Goffic R, Berhane Y, Bourgault S, Archambault D, Chevalier C. M2e nanovaccines supplemented with recombinant hemagglutinin protect chickens against heterologous HPAI H5N1 challenge. NPJ Vaccines 2024; 9:161. [PMID: 39237609 PMCID: PMC11377767 DOI: 10.1038/s41541-024-00944-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/07/2024] [Indexed: 09/07/2024] Open
Abstract
Current poultry vaccines against influenza A viruses target the globular head region of the hemagglutinin (HA1), providing limited protection against antigenically divergent strains. Experimental subunit vaccines based on the conserved ectodomain of the matrix protein 2 (M2e) induce cross-reactive antibody responses, but fail to fully prevent virus shedding after low pathogenic avian influenza (LPAI) virus challenge, and are ineffective against highly pathogenic avian influenza (HPAI) viruses. This study assessed the benefits of combining nanoparticles bearing three tandem M2e repeats (NR-3M2e nanorings or NF-3M2e nanofilaments) with an HA1 subunit vaccine in protecting chickens against a heterologous HPAI H5N1 virus challenge. Chickens vaccinated with the combined formulations developed M2e and HA1-specific antibodies, were fully protected from clinical disease and mortality, and showed no histopathological lesions or virus shedding, unlike those given only HA1, NR-3M2e, or NF-3M2e. Thus, the combined vaccine formulations provided complete cross-protection against HPAI H5N1 virus, and prevented environmental virus shedding, crucial for controlling avian influenza outbreaks.
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Affiliation(s)
- Cynthia Calzas
- INRAE, UVSQ, UMR892 VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Tamiru N Alkie
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Matthew Suderman
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Carissa Embury-Hyatt
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Vinay Khatri
- Chemistry Department, Université du Québec à Montréal, Montréal, QC, Canada
- Department of Biological Sciences, Université du Québec à Montréal, Montréal, QC, Canada
| | - Ronan Le Goffic
- INRAE, UVSQ, UMR892 VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, Canada
| | - Steve Bourgault
- Chemistry Department, Université du Québec à Montréal, Montréal, QC, Canada
| | - Denis Archambault
- Department of Biological Sciences, Université du Québec à Montréal, Montréal, QC, Canada.
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11
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Jotta VFM, García GJY, Fonseca PLC, de Mello Ferreira A, Azevedo V, Brenig B, Góes-Neto A, Badotti F. Taxonomic and functional characterization of biofilms from a photovoltaic panel reveals high genetic and metabolic complexity of the communities. J Appl Microbiol 2024; 135:lxae231. [PMID: 39257028 DOI: 10.1093/jambio/lxae231] [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: 07/05/2024] [Revised: 08/19/2024] [Accepted: 09/08/2024] [Indexed: 09/12/2024]
Abstract
AIMS Biofilms are complex microbial cell aggregates that attach to different surfaces in nature, industrial environments, or hospital settings. In photovoltaic panels (PVs), biofilms are related to significant energy conversion losses. In this study, our aim was to characterize the communities of microorganisms and the genes involved in biofilm formation. METHODS AND RESULTS In this study, biofilm samples collected from a PV system installed in southeastern Brazil were analyzed through shotgun metagenomics, and the microbial communities and genes involved in biofilm formation were investigated. A total of 2030 different genera were identified in the samples, many of which were classified as extremophiles or producers of exopolysaccharides. Bacteria prevailed in the samples (89%), mainly the genera Mucilaginibacter, Microbacterium, Pedobacter, Massilia, and Hymenobacter. The functional annotation revealed >12 000 genes related to biofilm formation and stress response. Genes involved in the iron transport and synthesis of c-di-GMP and c-AMP second messengers were abundant in the samples. The pathways related to these components play a crucial role in biofilm formation and could be promising targets for preventing biofilm formation in the PV. In addition, Raman spectroscopy analysis indicated the presence of hematite, goethite, and ferrite, consistent with the mineralogical composition of the regional soil and metal-resistant bacteria. CONCLUSIONS Taken together, our findings reveal that PV biofilms are a promising source of microorganisms of industrial interest and genes of central importance in regulating biofilm formation and persistence.
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Affiliation(s)
- Viviane Faria Morais Jotta
- Programa de Pós-Graduação em Tecnologia de Produtos e Processos, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), 30510-000, Belo Horizonte, MG, Brazil
| | - Glen Jasper Yupanqui García
- Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), 31270-901, Belo Horizonte, MG, Brazil
| | - Paula Luize Camargos Fonseca
- Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), 31270-901, Belo Horizonte, MG, Brazil
| | - Angela de Mello Ferreira
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), 30421-169, Belo Horizonte, MG, Brazil
| | - Vasco Azevedo
- Department of Genetics, Evolution and Ecology, Institute of Biological Science, Universidade Federal de Minas Gerais (UFMG), 31270-901, Belo Horizonte, MG, Brazil
| | - Bertram Brenig
- Georg-August-University Goettingen, Institute of Veterinary Medicine, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), 31270-901, Belo Horizonte, MG, Brazil
| | - Fernanda Badotti
- Programa de Pós-Graduação em Tecnologia de Produtos e Processos, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), 30510-000, Belo Horizonte, MG, Brazil
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), 30421-169, Belo Horizonte, MG, Brazil
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12
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Aqeel H, Brei E, Allen DG, Liss SN. Distribution of extracellular adhesins in environmental biofilms and flocs: Reimagining the microbial structure. CHEMOSPHERE 2024; 363:142928. [PMID: 39048048 DOI: 10.1016/j.chemosphere.2024.142928] [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: 05/21/2024] [Revised: 07/20/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
Extracellular cellular adhesins facilitate microbial aggregation; however, most of the information about extracellular adhesins is based on pure culture studies. In this study, we characterized the hydrophobic characteristics and distribution of the extracellular adhesins in environmental biofilms and flocs. The hydrophobic characteristics of the extracellular adhesins were studied by sonicating the microbial aggregates to disperse the cells and by fractionating them using the microbial adhesion to the hydrocarbon method. Furthermore, we probed environmental biofilms and flocs using immunohistochemistry coupled with confocal laser scanning microscopy for reimaging the microbial aggregates based on extracellular adhesins. Small flocs have a relatively dispersed distribution of extracellular adhesins (flagella, fimbriae, pili, and amyloid adhesins). The stratified distribution of extracellular adhesins was observed in environmental biofilms. It was observed that the pili and amyloid adhesins were predominantly present in the core of biofilms, whereas flagella and fimbriae were present in the outer layer of the microbial aggregates. The dispersion of microbial aggregates is one of the limiting factors that challenge the sustainable application of wastewater treatment processes. Greater attention to the components of extracellular protein (such as the adhesins) is required to understand the aggregation of dispersible environmental microbial aggregates.
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Affiliation(s)
- Hussain Aqeel
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Elena Brei
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - D Grant Allen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Steven N Liss
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada; School of Environmental Studies, Queen's University, Kingston, Canada; Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa.
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13
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Dear AJ, Meisl G, Taylor CG, Palmiero UC, Stubbe SN, Liu Q, Arosio P, Linse S, Knowles TPJ, Andreasen M. Surface effects on functional amyloid formation. NANOSCALE 2024; 16:16172-16182. [PMID: 39135495 DOI: 10.1039/d4nr01496k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Functional amyloids formed by the protein FapC in Pseudomonas bacteria are key structural components of Pseudomonas biofilms, which mediate chronic infections and also contribute to antimicrobial resistance. Here, we combine kinetic experiments with mechanistic modelling to probe the role of surfaces in FapC functional amyloid formation. We find that nucleation of new fibrils is predominantly heterogeneous in vitro, being catalysed by reaction vessel walls but not by the air/water interface. Removal of such interfaces by using microdroplets greatly slows heterogeneous nucleation and reveals a hitherto undetected fibril surface-catalysed "secondary nucleation" reaction step. We tune the degree of catalysis by varying the interface chemistry of the reaction vessel and by adding nanoparticles with tailored surface properties that catalyse fibril nucleation. In so doing, we discover that the rate of nucleation is controlled predominantly by the strength with which FapC binds to the catalytic sites on the interface, and by its surface area. Surprisingly, neither primary nucleation rate nor catalytic site binding strength appear closely correlated to the charge and hydrophilicity of the interface. This indicates the importance of considering experimental design in terms of surface chemistry of the reaction container while also highlighting the notion that fibril nucleation during protein aggregation is a heterogeneous process.
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Affiliation(s)
- Alexander J Dear
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Biochemistry and Structural Biology, Lund University, SE-221 00 Lund, Sweden
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Christopher G Taylor
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Umberto Capasso Palmiero
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Susanne Nordby Stubbe
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Aarhus DK-8000, Denmark.
| | - Qian Liu
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Aarhus DK-8000, Denmark.
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, SE-221 00 Lund, Sweden
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Aarhus DK-8000, Denmark.
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14
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Fleeman R, Beckman R, Cella E, Azarian T, Rendueles O. Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae. RESEARCH SQUARE 2024:rs.3.rs-4630973. [PMID: 39149462 PMCID: PMC11326372 DOI: 10.21203/rs.3.rs-4630973/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Klebsiella pneumoniae infections have become a growing threat for human health. The lack of understanding of the relationship between antibiotic resistance, mucoviscosity, and biofilm formation in clinical isolates impedes our abilities to effectively predict K. pneumoniae infection outcomes. These traits are also associated with fitness in natural populations and more specifically within a host. The Multidrug-Resistant Organism Repository and Surveillance Network offers a unique opportunity into the genetic and phenotypic variabilities in the K. pneumoniae isolates encountered in the clinics today. To this end, we compared the genetic profiles of these isolates with the phenotypic biofilm formation abilities, percent mucoviscosity, and growth rates. We found most isolates formed limited biofilm, although a select group of isolates could form extremely robust biofilms. Variation in biofilm formation could not be explained by difference in growth rate, suggesting specific genetic and physical determinants. Interestingly, the most mucoid strains in the populations were lacking the genetic element regulating the mucoid phenotype and three of these isolates were able to form robust biofilms. There was a significant phenotype-genotype correlation with decreased biofilm formation and an insertion sequence in the transcriptional activator of the type III fimbrial system. Finally, confocal microscopy highlighted the structural and spatial heterogeneity of biofilm among the most robust biofilm formers not detected by traditional methods. The combination of phenotypic, genomic and image analyses allowed us to reveal an unexpected phenotypic diversity and an intricate relation between growth, mucoviscosity and specific virulence-associated genetic determinants.
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15
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Ghosh N, Sinha K, Sil PC. Pesticides and the Gut Microbiota: Implications for Parkinson's Disease. Chem Res Toxicol 2024; 37:1071-1085. [PMID: 38958636 DOI: 10.1021/acs.chemrestox.4c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Parkinson's disease (PD) affects more people worldwide than just aging alone can explain. This is likely due to environmental influences, genetic makeup, and changes in daily habits. The disease develops in a complex way, with movement problems caused by Lewy bodies and the loss of dopamine-producing neurons. Some research suggests Lewy bodies might start in the gut, hinting at a connection between these structures and gut health in PD patients. These patients often have different gut bacteria and metabolites. Pesticides are known to increase the risk of PD, with evidence showing they harm more than just dopamine neurons. Long-term exposure to pesticides in food might affect the gut barrier, gut bacteria, and the blood-brain barrier, but the exact link is still unknown. This review looks at how pesticides and gut bacteria separately influence PD development and progression, highlighting the harmful effects of pesticides and changes in gut bacteria. We have examined the interaction between pesticides and gut bacteria in PD patients, summarizing how pesticides cause imbalances in gut bacteria, the resulting changes, and their overall effects on the PD prognosis.
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Affiliation(s)
- Nabanita Ghosh
- Assistant Professor in Zoology, Maulana Azad College, Kolkata 700013, India
| | - Krishnendu Sinha
- Assistant Professor in Zoology, Jhargram Raj College, Jhargram 721507 India
| | - Parames C Sil
- Professor, Division of Molecular Medicine, Bose Institute, Kolkata 700054 India
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16
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Jones TB, Chu P, Wilkey B, Lynch L, Jentarra G. Regional Differences in Microbial Infiltration of Brain Tissue from Alzheimer's Disease Patients and Control Individuals. Brain Sci 2024; 14:677. [PMID: 39061418 PMCID: PMC11274863 DOI: 10.3390/brainsci14070677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by cognitive decline and neuropathology including amyloid beta (Aβ) plaques and neurofibrillary tangles (tau). Factors initiating or driving these pathologies remain unclear, though microbes have been increasingly implicated. Our data and others' findings indicate that microbes may be common constituents of the brain. It is notable that Aβ and tau have antimicrobial properties, suggesting a response to microbes in the brain. We used 16S rRNA sequencing to compare major bacterial phyla in post-mortem tissues from individuals exhibiting a range of neuropathology and cognitive status in two brain regions variably affected in AD. Our data indicate that strong regional differences exist, driven in part by the varied presence of Proteobacteria and Firmicutes. We confirmed our data using ELISA of bacterial lipopolysaccharide (LPS) and lipoteichoic acid in the same brain tissue. We identified a potential association between the composition of phyla and the presence of neuropathology but not cognitive status. Declining cognition and increasing pathology correlated closely with serum LPS, but not brain levels of LPS, although brain LPS showed a strong negative correlation with cerebral amyloid angiopathy. Collectively, our data suggest a region-specific heterogeneity of microbial populations in brain tissue potentially associated with neurodegenerative pathology.
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Affiliation(s)
- T. Bucky Jones
- College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA; (T.B.J.); (P.C.); (L.L.)
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ 85308, USA;
| | - Ping Chu
- College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA; (T.B.J.); (P.C.); (L.L.)
| | - Brooke Wilkey
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ 85308, USA;
- School of Medicine, Creighton University, Phoenix, AZ 85012, USA
| | - Leigha Lynch
- College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA; (T.B.J.); (P.C.); (L.L.)
| | - Garilyn Jentarra
- College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA; (T.B.J.); (P.C.); (L.L.)
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ 85308, USA;
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17
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Riegelman E, Xue KS, Wang JS, Tang L. Gut-Brain Axis in Focus: Polyphenols, Microbiota, and Their Influence on α-Synuclein in Parkinson's Disease. Nutrients 2024; 16:2041. [PMID: 38999791 PMCID: PMC11243524 DOI: 10.3390/nu16132041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
With the recognition of the importance of the gut-brain axis in Parkinson's disease (PD) etiology, there is increased interest in developing therapeutic strategies that target α-synuclein, the hallmark abhorrent protein of PD pathogenesis, which may originate in the gut. Research has demonstrated that inhibiting the aggregation, oligomerization, and fibrillation of α-synuclein are key strategies for disease modification. Polyphenols, which are rich in fruits and vegetables, are drawing attention for their potential role in this context. In this paper, we reviewed how polyphenols influence the composition and functional capabilities of the gut microbiota and how the resulting microbial metabolites of polyphenols may potentially enhance the modulation of α-synuclein aggregation. Understanding the interaction between polyphenols and gut microbiota and identifying which specific microbes may enhance the efficacy of polyphenols is crucial for developing therapeutic strategies and precision nutrition based on the microbiome.
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Affiliation(s)
| | | | | | - Lili Tang
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA; (E.R.); (K.S.X.); (J.-S.W.)
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18
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Li Z, Zhang M, Lei G, Lu X, Yang X, Kan B. A Single Base Change in the csgD Promoter Resulted in Enhanced Biofilm in Swine-Derived Salmonella Typhimurium. Microorganisms 2024; 12:1258. [PMID: 39065026 PMCID: PMC11278976 DOI: 10.3390/microorganisms12071258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/08/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
Pathogenic Salmonella strains causing gastroenteritis typically can colonize and proliferate in the intestines of multiple host species. They retain the ability to form red dry and rough (rdar) biofilms, as seen in Salmonella enterica serovar Typhimurium. Conversely, Salmonella serovar like Typhi, which can cause systemic infections and exhibit host restriction, are rdar-negative. In this study, duck-derived strains and swine-derived strains of S. Typhimurium locate on independent phylogenetic clades and display relative genomic specificity. The duck isolates appear more closely related to human blood isolates and invasive non-typhoidal Salmonella (iNTS), whereas the swine isolates were more distinct. Phenotypically, compared to duck isolates, swine isolates exhibited enhanced biofilm formation that was unaffected by the temperature. The transcriptomic analysis revealed the upregulation of csgDEFG transcription as the direct cause. This upregulation may be mainly attributed to the enhanced promoter activity caused by the G-to-T substitution at position -44 of the csgD promoter. Swine isolates have created biofilm polymorphisms by altering a conserved base present in Salmonella Typhi, iNTS, and most Salmonella Typhimurium (such as duck isolates). This provides a genomic characteristics perspective for understanding Salmonella transmission cycles and evolution.
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Affiliation(s)
- Zhe Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.L.)
| | - Mengke Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.L.)
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Gaopeng Lei
- Center for Disease Control and Prevention of Sichuan Province, Chengdu 610041, China
| | - Xin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.L.)
| | - Xiaorong Yang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu 610041, China
| | - Biao Kan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Z.L.)
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19
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Jonblat S, As-Sadi F, Zibara K, Sabban ME, Dermesrobian V, Khoury AE, Kallassy M, Chokr A. Staphylococcus epidermidis biofilm assembly and self-dispersion: bacteria and matrix dynamics. Int Microbiol 2024; 27:831-844. [PMID: 37824024 DOI: 10.1007/s10123-023-00433-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Staphylococcus epidermidis, despite being a commensal of human skin and mucosa, is a major nosocomial pathogen implicated in device-associated infections. The dissemination of infection to other body sites is related to biofilm dispersal. This study focused on the dispersion stage of S. epidermidis CIP 444 biofilm, with the assessment of biofilm matrix composition in a time-dependent experiment (7 days extended) with 3 independent repetitions, using confocal laser scanning microcopy (CLSM) in association with ZEN 3.4 blue edition, COMSTAT, and ImageJ software. SYTO-9, propidium iodide (PI), DID'OIL, FITC, and calcofluor white M2R (CFW) were used to stain biofilm components. The results indicated that the biomass of dead cells increased from 15.18 ± 1.81 µm3/µm2 (day 3) to 23.15 ± 6.075 µm3/µm2 (day 4), along with a decrease in alive cells' biomass from 22.75 ± 2.968 µm3/µm2 (day 3) to 18.95 ± 5.713 µm3/µm2 (day 4). When the intensities were measured after marking the biofilm components, in a 24-h-old biofilm, polysaccharide made up the majority of the investigated components (52%), followed by protein (18.9%). Lipids make up just 11.6% of the mature biofilm. Protein makes up the largest portion (48%) of a 4-day-old biofilm, followed by polysaccharides (37.8%) and lipids (7.27%). According to our findings, S. epidermidis CIP 444 dispersion occurred on day 4 of incubation, and new establishment of the biofilm occurred on day 7. Remarkable changes in biofilm composition will pave the way for a new approach to understanding bacterial strategies inside biofilms and finding solutions to their impacts in the medical field.
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Affiliation(s)
- Suzanne Jonblat
- Research Laboratory of Microbiology (RLM), Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat Campus, Beirut, Lebanon
- Platform of Research and Analysis in Environmental Sciences (PRASE), Doctoral School of Sciences and Technologies, Lebanese University, Hadat Campus, Beirut, Lebanon
- Functional Genomics and Proteomic Laboratory, Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus Des Sciences Et Technologies, Mar Roukos, Matn, Lebanon
- Centre d'Analyses Et de Recherche (CAR), Unité de Recherche Technologies Et Valorisation Agro-Alimentaire (UR-TVA), Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus Des Sciences Et Technologies, Mar Roukos, Matn, Lebanon
| | - Falah As-Sadi
- Research Laboratory of Microbiology (RLM), Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat Campus, Beirut, Lebanon
- Department of Plant Production, Faculty of Agriculture and Veterinary Medicine, Lebanese University, Beirut, 999095, Lebanon
| | - Kazem Zibara
- ER045, Laboratory of Stem Cells, DSST, Biology Department, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Marwan El Sabban
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Bliss Street, Beirut, 1107, Lebanon
| | - Vera Dermesrobian
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Bliss Street, Beirut, 1107, Lebanon
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Louvain, Belgium
| | - André El Khoury
- Centre d'Analyses Et de Recherche (CAR), Unité de Recherche Technologies Et Valorisation Agro-Alimentaire (UR-TVA), Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus Des Sciences Et Technologies, Mar Roukos, Matn, Lebanon
| | - Mireille Kallassy
- Functional Genomics and Proteomic Laboratory, Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus Des Sciences Et Technologies, Mar Roukos, Matn, Lebanon
| | - Ali Chokr
- Research Laboratory of Microbiology (RLM), Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat Campus, Beirut, Lebanon.
- Platform of Research and Analysis in Environmental Sciences (PRASE), Doctoral School of Sciences and Technologies, Lebanese University, Hadat Campus, Beirut, Lebanon.
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20
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Guragain M, Schmidt JW, Bagi LK, Paoli GC, Kalchayanand N, Bosilevac JM. Antibiotic Resistance and Disinfectant Resistance Among Escherichia coli Isolated During Red Meat Production. J Food Prot 2024; 87:100288. [PMID: 38697484 DOI: 10.1016/j.jfp.2024.100288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024]
Abstract
Escherichia coli commonly found in the gastrointestinal tracts of food animals include Shiga toxin-producing E. coli (STEC, stx+, eae-), Enterohemorrhagic E. coli (EHEC, stx+, eae+), Enteropathogenic E. coli (EPEC, stx-, eae+), and "nondiarrheagenic" E. coli (NDEC, stx-, eae-). EHEC, EPEC, and STEC are associated with foodborne disease outbreaks. During meat processing, disinfectants are employed to control various bacteria, including human pathogens. Concerns exist that E. coli resistant to antibiotics are less susceptible to disinfectants used during meat processing. Since EHEC, EPEC, and STEC with reduced susceptibility to disinfectants are potential public health risks, the goal of this study was to evaluate the association of antibiotic resistant (ABR) E. coli with increased tolerance to 4% lactic acid (LA) and 150 ppm quaternary ammonium compounds (QACs). A pool of 3,367 E. coli isolated from beef cattle, veal calves, swine, and sheep at various processing stages was screened to identify ABR E. coli. Resistance to ≥1 of the six antibiotics examined was identified in 27.9%, 36.1%, 54.5%, and 28.7% among the NDEC (n = 579), EHEC (n = 693), EPEC (n = 787), and STEC (n = 1308) isolates evaluated, respectively. Disinfectant tolerance did not differ (P > 0.05) between ABR and antibiotic susceptible EHEC isolates. Comparable frequencies (P > 0.05) of biofilm formation or congo red binding were observed between ABR and antibiotic susceptible strains of E. coli. Understanding the frequencies of ABR and disinfectant tolerance among E. coli present in food-animal is a critically important component of meat safety.
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Affiliation(s)
- Manita Guragain
- Characterization and Interventions for Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA.
| | - John W Schmidt
- Meat Safety and Quality Research Unit, Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE, USA
| | - Lori K Bagi
- Characterization and Interventions for Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - George C Paoli
- Characterization and Interventions for Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - Norasak Kalchayanand
- Meat Safety and Quality Research Unit, Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE, USA
| | - Joseph M Bosilevac
- Meat Safety and Quality Research Unit, Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE, USA
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21
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Bu F, Dee DR, Liu B. Structural insight into Escherichia coli CsgA amyloid fibril assembly. mBio 2024; 15:e0041924. [PMID: 38501920 PMCID: PMC11005368 DOI: 10.1128/mbio.00419-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
The discovery of functional amyloids in bacteria dates back several decades, and our understanding of the Escherichia coli curli biogenesis system has gradually expanded over time. However, due to its high aggregation propensity and intrinsically disordered nature, CsgA, the main structural component of curli fibrils, has eluded comprehensive structural characterization. Recent advancements in cryo-electron microscopy (cryo-EM) offer a promising tool to achieve high-resolution structural insights into E. coli CsgA fibrils. In this study, we outline an approach to addressing the colloidal instability challenges associated with CsgA, achieved through engineering and electrostatic repulsion. Then, we present the cryo-EM structure of CsgA fibrils at 3.62 Å resolution. This structure provides new insights into the cross-β structure of E. coli CsgA. Additionally, our study identifies two distinct spatial arrangements within several CsgA fibrils, a 2-CsgA-fibril pair and a 3-CsgA-fibril bundle, shedding light on the intricate hierarchy of the biofilm extracellular matrix and laying the foundation for precise manipulation of CsgA-derived biomaterials.IMPORTANCEThe visualization of the architecture of Escherichia coli CsgA amyloid fibril has been a longstanding research question, for which a high-resolution structure is still unavailable. CsgA serves as a major subunit of curli, the primary component of the extracellular matrix generated by bacteria. The support provided by this extracellular matrix enables bacterial biofilms to resist antibiotic treatment, significantly impacting human health. CsgA has been identified in members of Enterobacteriaceae, with pathogenic E. coli being the most well-known model system. Our novel insights into the structure of E. coli CsgA protofilaments form the basis for drug design targeting diseases associated with biofilms. Additionally, CsgA is widely researched in biomaterials due to its self-assembly characteristics. The resolved spatial arrangements of CsgA amyloids revealed in our study will further enhance the precision design of functional biomaterials. Therefore, our study uniquely contributes to the understanding of CsgA amyloids for both microbiology and material science.
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Affiliation(s)
- Fan Bu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Derek R. Dee
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bin Liu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
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22
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Corcionivoschi N, Balta I, McCleery D, Bundurus I, Pet I, Calaway T, Nichita I, Stef L, Morariu S. Mechanisms of Pathogenic Escherichia coli Attachment to Meat. Foodborne Pathog Dis 2024. [PMID: 38593459 DOI: 10.1089/fpd.2023.0164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Escherichia coli are present in the human and animal microbiome as facultative anaerobes and are viewed as an integral part of the whole gastrointestinal environment. In certain circumstances, some species can also become opportunistic pathogens responsible for severe infections in humans. These infections are caused by the enterotoxinogenic E. coli, enteroinvasive E. coli, enteropathogenic E. coli and the enterohemorrhagic E. coli species, frequently present in food products and on food matrices. Severe human infections can be caused by consumption of meat contaminated upon exposure to animal feces, and as such, farm animals are considered to be a natural reservoir. The mechanisms by which these four major species of E. coli adhere and persist in meat postslaughter are of major interest to public health and food processors given their frequent involvement in foodborne outbreaks. This review aims to structure and provide an update on the mechanistic roles of environmental factors, curli, type I and type IV pili on E. coli adherence/interaction with meat postslaughter. Furthermore, we emphasize on the importance of bacterial surface structures, which can be used in designing interventions to enhance food safety and protect public health by reducing the burden of foodborne illnesses.
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Affiliation(s)
- Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, Timisoara, Romania
- Academy of Romanian Scientists, Bucharest, Romania
| | - Igori Balta
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, Timisoara, Romania
| | - David McCleery
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Iulia Bundurus
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, Timisoara, Romania
| | - Ioan Pet
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, Timisoara, Romania
| | - Todd Calaway
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA
| | - Ileana Nichita
- Faculty of Veterinary Medicine, University of Life Sciences King Mihai I from Timisoara, Timisoara, Romania
| | - Lavinia Stef
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, Timisoara, Romania
| | - Sorin Morariu
- Faculty of Veterinary Medicine, University of Life Sciences King Mihai I from Timisoara, Timisoara, Romania
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Saini P, Bandsode V, Singh A, Mendem SK, Semmler T, Alam M, Ahmed N. Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment. mBio 2024; 15:e0354523. [PMID: 38376265 PMCID: PMC10936179 DOI: 10.1128/mbio.03545-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations. IMPORTANCE Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.
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Affiliation(s)
- Poorvi Saini
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Viraj Bandsode
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Anuradha Singh
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Suresh Kumar Mendem
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Munirul Alam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Niyaz Ahmed
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
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24
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Li Y, Sun Z. Phenotypic and genomic insights into the pathogenicity and antimicrobial resistance of an Enterobacter roggenkampii strain isolated from diseased silver arowana (Osteoglossum bicirrhosum). JOURNAL OF FISH DISEASES 2024; 47:e13898. [PMID: 38014710 DOI: 10.1111/jfd.13898] [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: 08/30/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Enterobacter roggenkampii is an opportunistic pathogen that causes infections in a wide range of hosts. A bacterial strain named EOBSR_19 was isolated from diseased silver arowana, Osteoglossum bicirrhosum. This bacterium was identified as E. roggenkampii based on the phenotypic characteristics and sequence analysis of the16S rDNA and gyrB genes. Average nucleotide identity and phylogenetic analysis based on the whole genome sequence further confirmed the bacterial taxonomy of EOBSR_19. Artificial experimental infection indicated that EOBSR_19 was pathogenic to fish. Antimicrobial susceptibility test showed it was multi-drug resistant. The EOBSR_19 was found to be resistant to 18 antibiotics belonging to quinolones, macrolides, sulfonamides, aminoglycosides, and β-lactams classes. The whole genome sequencing analysis showed that EOBSR_19 carried 730 virulence genes that were annotated for different functional modules, such as adhesion and invasion, secretion system, siderophore transport system and bacterial toxin. Among them, the virulence genes related to adhesion and invasion were the most abundant. In addition, drug resistance genes involved in multiple mechanisms of antimicrobial resistance were identified in its genomics, including multidrug resistance efflux pumps, antibiotic inactivating enzymes, and antibiotic binding site mutations. Its genomic analysis via whole-genome sequencing provided insights into the pathogenicity and antimicrobial resistance.
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Affiliation(s)
- Yuerui Li
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Zhongshi Sun
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
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25
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Ren J, Wang M, Zhou W, Liu Z. Efflux pumps as potential targets for biofilm inhibition. Front Microbiol 2024; 15:1315238. [PMID: 38596384 PMCID: PMC11002903 DOI: 10.3389/fmicb.2024.1315238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/26/2024] [Indexed: 04/11/2024] Open
Abstract
Biofilms account for a great deal of infectious diseases and contribute significantly to antimicrobial resistance. Efflux pumps confer antimicrobial resistance to microorganisms and involve multiple processes of biofilm formation. Efflux pump inhibitors (EPIs) are attracting considerable attention as a biofilm inhibition strategy. The regulatory functions of efflux pumps in biofilm formation such as mediating adherence, quorum sensing (QS) systems, and the expression of biofilm-associated genes have been increasingly identified. The versatile properties confer efflux pumps both positive and negative effects on biofilm formation. Furthermore, the expression and function of efflux pumps in biofilm formation are species-specific. Therefore, this review aims to detail the double-edged sword role of efflux pumps in biofilm formation to provide potential inhibition targets and give an overview of the effects of EPIs on biofilm formation.
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Affiliation(s)
| | | | - Wenjuan Zhou
- Department of Implantology, Yantai Stomatological Hospital Affiliated to Binzhou Medical University, Yantai, China
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26
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Fung BL, Esin JJ, Visick KL. Vibrio fischeri: a model for host-associated biofilm formation. J Bacteriol 2024; 206:e0037023. [PMID: 38270381 PMCID: PMC10882983 DOI: 10.1128/jb.00370-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
Multicellular communities of adherent bacteria known as biofilms are often detrimental in the context of a human host, making it important to study their formation and dispersal, especially in animal models. One such model is the symbiosis between the squid Euprymna scolopes and the bacterium Vibrio fischeri. Juvenile squid hatch aposymbiotically and selectively acquire their symbiont from natural seawater containing diverse environmental microbes. Successful pairing is facilitated by ciliary movements that direct bacteria to quiet zones on the surface of the squid's symbiotic light organ where V. fischeri forms a small aggregate or biofilm. Subsequently, the bacteria disperse from that aggregate to enter the organ, ultimately reaching and colonizing deep crypt spaces. Although transient, aggregate formation is critical for optimal colonization and is tightly controlled. In vitro studies have identified a variety of polysaccharides and proteins that comprise the extracellular matrix. Some of the most well-characterized matrix factors include the symbiosis polysaccharide (SYP), cellulose polysaccharide, and LapV adhesin. In this review, we discuss these components, their regulation, and other less understood V. fischeri biofilm contributors. We also highlight what is currently known about dispersal from these aggregates and host cues that may promote it. Finally, we briefly describe discoveries gleaned from the study of other V. fischeri isolates. By unraveling the complexities involved in V. fischeri's control over matrix components, we may begin to understand how the host environment triggers transient biofilm formation and dispersal to promote this unique symbiotic relationship.
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Affiliation(s)
- Brittany L. Fung
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Jeremy J. Esin
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Karen L. Visick
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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27
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Böhning J, Tarafder AK, Bharat TA. The role of filamentous matrix molecules in shaping the architecture and emergent properties of bacterial biofilms. Biochem J 2024; 481:245-263. [PMID: 38358118 PMCID: PMC10903470 DOI: 10.1042/bcj20210301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Numerous bacteria naturally occur within spatially organised, multicellular communities called biofilms. Moreover, most bacterial infections proceed with biofilm formation, posing major challenges to human health. Within biofilms, bacterial cells are embedded in a primarily self-produced extracellular matrix, which is a defining feature of all biofilms. The biofilm matrix is a complex, viscous mixture primarily composed of polymeric substances such as polysaccharides, filamentous protein fibres, and extracellular DNA. The structured arrangement of the matrix bestows bacteria with beneficial emergent properties that are not displayed by planktonic cells, conferring protection against physical and chemical stresses, including antibiotic treatment. However, a lack of multi-scale information at the molecular level has prevented a better understanding of this matrix and its properties. Here, we review recent progress on the molecular characterisation of filamentous biofilm matrix components and their three-dimensional spatial organisation within biofilms.
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Affiliation(s)
- Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Abul K. Tarafder
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
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28
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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29
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Siri M, Mangiarotti A, Vázquez-Dávila M, Bidan CM. Curli Amyloid Fibers in Escherichia coli Biofilms: The Influence of Water Availability on their Structure and Functional Properties. Macromol Biosci 2024; 24:e2300234. [PMID: 37776075 DOI: 10.1002/mabi.202300234] [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: 05/24/2023] [Revised: 09/22/2023] [Indexed: 10/01/2023]
Abstract
Escherichia coli biofilms consist of bacteria embedded in a self-produced matrix mainly made of protein fibers and polysaccharides. The curli amyloid fibers found in the biofilm matrix are promising versatile building blocks to design sustainable bio-sourced materials. To exploit this potential, it is crucial to understand i) how environmental cues during biofilm growth influence the molecular structure of these amyloid fibers, and ii) how this translates at higher length scales. To explore these questions, the effect of water availability during biofilm growth on the conformation and functions of curli is studied. Microscopy and spectroscopy are used to characterize the amyloid fibers purified from biofilms grown on nutritive substrates with different water contents, and micro-indentation to measure the rigidity of the respective biofilms. The purified curli amyloid fibers present differences in the yield, structure, and functional properties upon biofilm growth conditions. Fiber packing and β-sheets content correlate with their hydrophobicity and chemical stability, and with the rigidity of the biofilms. This study highlights how E. coli biofilm growth conditions impact curli structure and functions contributing to macroscopic materials properties. These fundamental findings infer an alternative strategy to tune curli structure, which will ultimately benefit engineering hierarchical and functional curli-based materials.
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Affiliation(s)
- Macarena Siri
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Agustín Mangiarotti
- Max Planck Institute of Colloids and Interfaces, Department of Sustainable and Bio-inspired Materials, 14476, Potsdam, Germany
| | - Mónica Vázquez-Dávila
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Cécile M Bidan
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
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30
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Thomas GA, Paradell Gil T, Müller CT, Rogers HJ, Berger CN. From field to plate: How do bacterial enteric pathogens interact with ready-to-eat fruit and vegetables, causing disease outbreaks? Food Microbiol 2024; 117:104389. [PMID: 37919001 DOI: 10.1016/j.fm.2023.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023]
Abstract
Ready-to-eat fruit and vegetables are a convenient source of nutrients and fibre for consumers, and are generally safe to eat, but are vulnerable to contamination with human enteric bacterial pathogens. Over the last decade, Salmonella spp., pathogenic Escherichia coli, and Listeria monocytogenes have been linked to most of the bacterial outbreaks of foodborne illness associated with fresh produce. The origins of these outbreaks have been traced to multiple sources of contamination from pre-harvest (soil, seeds, irrigation water, domestic and wild animal faecal matter) or post-harvest operations (storage, preparation and packaging). These pathogens have developed multiple processes for successful attachment, survival and colonization conferring them the ability to adapt to multiple environments. However, these processes differ across bacterial strains from the same species, and across different plant species or cultivars. In a competitive environment, additional risk factors are the plant microbiome phyllosphere and the plant responses; both factors directly modulate the survival of the pathogens on the leaf's surface. Understanding the mechanisms involved in bacterial attachment to, colonization of, and proliferation, on fresh produce and the role of the plant in resisting bacterial contamination is therefore crucial to reducing future outbreaks.
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Affiliation(s)
- Gareth A Thomas
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Teresa Paradell Gil
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Carsten T Müller
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Cedric N Berger
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
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31
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Yang X, Narvaez-Bravo C, Zhang P. Driving forces shaping the microbial ecology in meat packing plants. Front Microbiol 2024; 14:1333696. [PMID: 38322759 PMCID: PMC10844536 DOI: 10.3389/fmicb.2023.1333696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/22/2023] [Indexed: 02/08/2024] Open
Abstract
Meat production is a complex system, continually receiving animals, water, air, and workers, all of which serve as carriers of bacteria. Selective pressures involved in different meat processing stages such as antimicrobial interventions and low temperatures, may promote the accumulation of certain residential microbiota in meat cutting facilities. Bacteria including human pathogens from all these sources can contaminate meat surfaces. While significant advancements have been made in enhancing hygienic standards and pathogen control measures in meat plants, resulting in a notable reduction in STEC recalls and clinical cases, STEC still stands as a predominant contributor to foodborne illnesses associated with beef and occasionally with pork. The second-and third-generation sequencing technology has become popular in microbiota related studies and provided a better image of the microbial community in the meat processing environments. In this article, we reviewed the potential factors influencing the microbial ecology in commercial meat processing facilities and conducted a meta-analysis on the microbiota data published in the last 10 years. In addition, the mechanisms by which bacteria persist in meat production environments have been discussed with a focus on the significant human pathogen E. coli O157:H7 and generic E. coli, an indicator often used for the hygienic condition in food production.
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Affiliation(s)
- Xianqin Yang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | | | - Peipei Zhang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
- Department of Animal Sciences, Center for Meat Safety and Quality, Colorado State University, Fort Collins, CO, United States
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32
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Boya BR, Lee JH, Lee J. Antimicrobial and antibiofilm activities of chromone derivatives against uropathogenic Escherichia coli. Microbiol Res 2024; 278:127537. [PMID: 37922697 DOI: 10.1016/j.micres.2023.127537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
Uropathogenic Escherichia coli (UPEC) is a urinary tract pathogen responsible for most nosocomial urinary tract infections and can cause severe conditions like acute cystitis of the bladder or pyelonephritis. UPEC harbors a host of virulence factors like curli, hemolysin, siderophore, and motility factors and can form biofilm-like communities and quiescent reservoirs that aid its survival. This study was performed to investigate the antibiofilm, antimicrobial, and antivirulence potentials of three chromone derivatives, namely, 6-bromo 3-formylchromone, 6-chloro 3-formylchromone, and 3-formyl 6-isopropylchromone. These chromones had MICs against UPEC of 20, 20, and 50 µg/ml, respectively, inhibited biofilm formation by 72-96% at 20 µg/ml, and inhibited UPEC-associated virulence factors, that is, hemolysis, motility, curli, siderophore production, indole production, quiescent colony formation, and cell surface hydrophobicity. Gene expression analysis indicated these three derivatives downregulated virulence genes associated with toxins, biofilm production, and stress regulation and suggested they might target two-component UvrY response regulator. 3D-QSAR analysis showed that substitutions at the third and sixth positions of the chromone scaffold favor antimicrobial activity against UPEC. Furthermore, ADME profiles and C. elegans cytotoxicity assays indicated that these chromone derivatives are potent, safe drug candidates.
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Affiliation(s)
- Bharath Reddy Boya
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Republic of Korea
| | - Jin-Hyung Lee
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Republic of Korea
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Republic of Korea.
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Asensio‐Calavia A, Ceballos‐Munuera Á, Méndez‐Pérez A, Álvarez B, Fernández LÁ. A tuneable genetic switch for tight control of tac promoters in Escherichia coli boosts expression of synthetic injectisomes. Microb Biotechnol 2024; 17:e14328. [PMID: 37608576 PMCID: PMC10832536 DOI: 10.1111/1751-7915.14328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
Biosafety of engineered bacteria as living therapeutics requires a tight regulation to control the specific delivery of protein effectors, maintaining minimum leakiness in the uninduced (OFF) state and efficient expression in the induced (ON) state. Here, we report a three repressors (3R) genetic circuit that tightly regulates the expression of multiple tac promoters (Ptac) integrated in the chromosome of E. coli and drives the expression of a complex type III secretion system injectisome for therapeutic protein delivery. The 3R genetic switch is based on the tetracycline repressor (TetR), the non-inducible lambda repressor cI (ind-) and a mutant lac repressor (LacIW220F ) with higher activity. The 3R switch was optimized with different protein translation and degradation signals that control the levels of LacIW220F . We demonstrate the ability of an optimized switch to fully repress the strong leakiness of the Ptac promoters in the OFF state while triggering their efficient activation in the ON state with anhydrotetracycline (aTc), an inducer suitable for in vivo use. The implementation of the optimized 3R switch in the engineered synthetic injector E. coli (SIEC) strain boosts expression of injectisomes upon aTc induction, while maintaining a silent OFF state that preserves normal growth in the absence of the inducer. Since Ptac is a commonly used promoter, the 3R switch may have multiple applications for tight control of protein expression in E. coli. In addition, the modularity of the 3R switch may enable its tuning for the control of Ptac promoters with different inducers.
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Affiliation(s)
- Alejandro Asensio‐Calavia
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Álvaro Ceballos‐Munuera
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
- Programa de Doctorado en Biociencias MolecularesUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Almudena Méndez‐Pérez
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
- Programa de Doctorado en Biociencias MolecularesUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
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Chowdhury S, Sarkar N. Exploring the potential of amyloids in biomedical applications: A review. Biotechnol Bioeng 2024; 121:26-38. [PMID: 37822225 DOI: 10.1002/bit.28569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/31/2023] [Accepted: 09/24/2023] [Indexed: 10/13/2023]
Abstract
Amyloid is defined as a fibrous quaternary structure formed by assembling protein or peptide monomers into intermolecularly hydrogen linked β-sheets. There is a prevalent issue with protein aggregation and the buildup of amyloid molecules, which results in human neurological illnesses including Alzheimer's and Parkinson's. But it is now evident that many organisms, like bacteria, fungi as well as humans, use the same fibrillar structure to carry out a variety of biological functions, such as structure and protection supporting interface transitions and cell-cell recognition, protein control and storage, epigenetic inheritance, and memory. Recent discoveries of self-assembling amyloidogenic peptides and proteins, based on the amyloid core structure, give rise to interesting biomaterials with potential uses in numerous industries. These functions dramatically diverge from the initial conception of amyloid fibrils as intrinsically diseased entities. Apart from the natural ability of amyloids to spontaneously arrange themselves and their exceptional material characteristics, this aspect has prompted extensive research into engineering artificial amyloids for generating various nanostructures, molecular substances, and combined materials. Here, we discuss significant developments in the artificial design of useful amyloids as well as how amyloid materials serve as examples of how function emerges from protein self-assembly at various length scales.
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Affiliation(s)
- Srijita Chowdhury
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India
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Carneiro DG, Pereira Aguilar A, Mantovani HC, Mendes TADO, Vanetti MCD. The quorum sensing molecule C12-HSL promotes biofilm formation and increases adrA expression in Salmonella Enteritidis under anaerobic conditions. BIOFOULING 2024; 40:14-25. [PMID: 38254292 DOI: 10.1080/08927014.2024.2305385] [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: 05/09/2023] [Accepted: 01/07/2024] [Indexed: 01/24/2024]
Abstract
Acyl-homoserine lactones (AHLs) are quorum-sensing signaling molecules in Gram-negative bacteria and positively regulate biofilm formation in Salmonella under specific conditions. In this study, biofilm formation in Salmonella enterica was evaluated at 28 and 37 °C, under aerobic and anaerobic conditions. Additionally, the influence of the N-dodecanoyl-DL-homoserine lactone (C12-HSL) on biofilm formation and the expression of genes related to the synthesis of structural components, regulation, and quorum sensing was assessed under anaerobiosis at 28 and 37 °C. Biofilm formation was found not to be influenced by the atmospheric conditions at 28 °C. However, it was reduced at 37 °C under anaerobiosis. C12-HSL enhanced biofilm formation at 37 °C under anaerobiosis and increased the expression of the adrA and luxS genes, suggesting an increase in c-di-GMP, a second messenger that controls essential physiological functions in bacteria. These results provide new insights into the regulation of biofilm formation in Salmonella under anaerobic conditions.
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Affiliation(s)
| | - Ananda Pereira Aguilar
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa (UFV), Viçosa, Brazil
| | - Hilário Cuquetto Mantovani
- Department of Microbiology, Universidade Federal de Viçosa (UFV), Viçosa, Brazil
- Department of Animal and Dairy Sciences, University of WI, Madison, USA
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36
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Charron R, Lemée P, Huguet A, Minlong O, Boulanger M, Houée P, Soumet C, Briandet R, Bridier A. Polyhexamethylene biguanide promotes adaptive cross-resistance to gentamicin in Escherichia coli biofilms. Front Cell Infect Microbiol 2023; 13:1324991. [PMID: 38149014 PMCID: PMC10750414 DOI: 10.3389/fcimb.2023.1324991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 12/28/2023] Open
Abstract
Antimicrobial resistance is a critical public health issue that requires a thorough understanding of the factors that influence the selection and spread of antibiotic-resistant bacteria. Biocides, which are widely used in cleaning and disinfection procedures in a variety of settings, may contribute to this resistance by inducing similar defense mechanisms in bacteria against both biocides and antibiotics. However, the strategies used by bacteria to adapt and develop cross-resistance remain poorly understood, particularly within biofilms -a widespread bacterial habitat that significantly influences bacterial tolerance and adaptive strategies. Using a combination of adaptive laboratory evolution experiments, genomic and RT-qPCR analyses, and biofilm structural characterization using confocal microscopy, we investigated in this study how Escherichia coli biofilms adapted after 28 days of exposure to three biocidal active substances and the effects on cross-resistance to antibiotics. Interestingly, polyhexamethylene biguanide (PHMB) exposure led to an increase of gentamicin resistance (GenR) phenotypes in biofilms formed by most of the seven E. coli strains tested. Nevertheless, most variants that emerged under biocidal conditions did not retain the GenR phenotype after removal of antimicrobial stress, suggesting a transient adaptation (adaptive resistance). The whole genome sequencing of variants with stable GenR phenotypes revealed recurrent mutations in genes associated with cellular respiration, including cytochrome oxidase (cydA, cyoC) and ATP synthase (atpG). RT-qPCR analysis revealed an induction of gene expression associated with biofilm matrix production (especially curli synthesis), stress responses, active and passive transport and cell respiration during PHMB exposure, providing insight into potential physiological responses associated with adaptive crossresistance. In addition, confocal laser scanning microscopy (CLSM) observations demonstrated a global effect of PHMB on biofilm architectures and compositions formed by most E. coli strains, with the appearance of dense cellular clusters after a 24h-exposure. In conclusion, our results showed that the PHMB exposure stimulated the emergence of an adaptive cross-resistance to gentamicin in biofilms, likely induced through the activation of physiological responses and biofilm structural modulations altering gradients and microenvironmental conditions in the biological edifice.
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Affiliation(s)
- Raphaël Charron
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
- Université Paris-Saclay, National Research Institute for Agriculture, Food and the Environment (INRAE), AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Lemée
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Antoine Huguet
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Ornella Minlong
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Marine Boulanger
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Paméla Houée
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Christophe Soumet
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Romain Briandet
- Université Paris-Saclay, National Research Institute for Agriculture, Food and the Environment (INRAE), AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
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37
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Tao F, Han Q, Yang P. Interface-mediated protein aggregation. Chem Commun (Camb) 2023; 59:14093-14109. [PMID: 37955330 DOI: 10.1039/d3cc04311h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The aggregation of proteins at interfaces has significant roles and can also lead to dysfunction of different physiological processes. The interfacial effects on the assembly and aggregation of biopolymers are not only crucial for a comprehensive understanding of protein biological functions, but also hold great potential for advancing the state-of-the-art applications of biopolymer materials. Recently, there has been remarkable progress in a collaborative context, as we strive to gain control over complex interfacial assembly structures of biopolymers. These biopolymer structures range from the nanoscale to mesoscale and even macroscale, and are attained through the rational design of interactions between biological building blocks and surfaces/interfaces. This review spotlights the recent advancements in interface-mediated assembly and properties of biopolymer materials. Initially, we introduce the solid-liquid interface (SIL)-mediated biopolymer assembly that includes the inorganic crystalline template effect and protein self-adoptive deposition through phase transition. Next, we display the advancement of biopolymer assembly instigated by the air-water interface (AWI) that acts as an energy conversion station. Lastly, we discuss succinctly the assembly of biopolymers at the liquid-liquid interface (LLI) along with their applications. It is our hope that this overview will stimulate the integration and progression of the science of interfacial assembled biopolymer materials and surfaces/interfaces.
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Affiliation(s)
- Fei Tao
- Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, school of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Qian Han
- Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, school of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Peng Yang
- Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, school of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
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Khatri V, Jafari M, Gaudreault R, Beauregard M, Siaj M, Archambault D, Loranger É, Bourgault S. Bionanocomposites with Enhanced Physical Properties from Curli Amyloid Assemblies and Cellulose Nanofibrils. Biomacromolecules 2023; 24:5290-5302. [PMID: 37831506 DOI: 10.1021/acs.biomac.3c00786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Proteinaceous amyloid fibrils are one of the stiffest biopolymers due to their extensive cross-β-sheet quaternary structure, whereas cellulose nanofibrils (CNFs) exhibit interesting properties associated with their nanoscale size, morphology, large surface area, and biodegradability. Herein, CNFs were supplemented with amyloid fibrils assembled from the Curli-specific gene A (CsgA) protein, the main component of bacterial biofilms. The resulting composites showed superior mechanical properties, up to a 7-fold increase compared to unmodified CNF films. Wettability and thermogravimetric analyses demonstrated high surface hydrophobicity and robust thermal tolerance. Bulk spectroscopic characterization of CNF-CsgA films revealed key insights into the molecular organization within the bionanocomposites. Atomic force microscopy and photoinduced force microscopy revealed the high-resolution location of curli assemblies into the CNF films. This novel sustainable and cost-effective CNF-based bionanocomposites supplemented with intertwined bacterial amyloid fibrils opens novel directions for environmentally friendly applications demanding high mechanical, water-repelling properties, and thermal resistance.
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Affiliation(s)
- Vinay Khatri
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
- Department of Biological Sciences, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
- Québec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, Quebec H3C 3P8, Canada
| | - Maziar Jafari
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
| | - Roger Gaudreault
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
| | - Marc Beauregard
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 Des Forges, Trois-Rivières, Quebec G8Z 4M3, Canada
- Innovations Institute in Ecomatériaux, Ecoproduits et Ecoenergies (I2E3), Université du Québec à Trois-Rivières, 3351 Des Forges, Trois-Rivières, Québec G8Z 4M3, Canada
| | - Mohamed Siaj
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
| | - Denis Archambault
- Department of Biological Sciences, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
| | - Éric Loranger
- Innovations Institute in Ecomatériaux, Ecoproduits et Ecoenergies (I2E3), Université du Québec à Trois-Rivières, 3351 Des Forges, Trois-Rivières, Québec G8Z 4M3, Canada
- Department of Mechanical Engineering, Université du Québec à Trois-Rivières, 3351 Des Forges, Trois-Rivières, Quebec G8Z 4M3, Canada
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
- Québec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, Quebec H3C 3P8, Canada
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Walker A, Czyz DM. Oh my gut! Is the microbial origin of neurodegenerative diseases real? Infect Immun 2023; 91:e0043722. [PMID: 37750713 PMCID: PMC10580905 DOI: 10.1128/iai.00437-22] [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: 09/27/2023] Open
Abstract
There is no cure or effective treatment for neurodegenerative protein conformational diseases (PCDs), such as Alzheimer's or Parkinson's diseases, mainly because the etiology of these diseases remains elusive. Recent data suggest that unique changes in the gut microbial composition are associated with these ailments; however, our current understanding of the bacterial role in the pathogenesis of PCDs is hindered by the complexity of the microbial communities associated with specific microbiomes, such as the gut, oral, or vaginal microbiota. The composition of these specific microbiomes is regarded as a unique fingerprint affected by factors such as infections, diet, lifestyle, and antibiotics. All of these factors also affect the severity of neurodegenerative diseases. The majority of studies that reveal microbial contribution are correlational, and various models, including worm, fly, and mouse, are being utilized to decipher the role of individual microbes that may affect disease onset and progression. Recent evidence from across model organisms and humans shows a positive correlation between the presence of gram-negative enteropathogenic bacteria and the pathogenesis of PCDs. While these correlational studies do not provide a mechanistic explanation, they do reveal contributing bacterial species and provide an important basis for further investigation. One of the lurking concerns related to the microbial contribution to PCDs is the increasing prevalence of antibiotic resistance and poor antibiotic stewardship, which ultimately select for proteotoxic bacteria, especially the gram-negative species that are known for intrinsic resistance. In this review, we summarize what is known about individual microbial contribution to PCDs and the potential impact of increasing antimicrobial resistance.
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Affiliation(s)
- Alyssa Walker
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Daniel M. Czyz
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
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40
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Zanditenas E, Trebicz-Geffen M, Kolli D, Domínguez-García L, Farhi E, Linde L, Romero D, Chapman M, Kolodkin-Gal I, Ankri S. Digestive exophagy of biofilms by intestinal amoeba and its impact on stress tolerance and cytotoxicity. NPJ Biofilms Microbiomes 2023; 9:77. [PMID: 37813896 PMCID: PMC10562373 DOI: 10.1038/s41522-023-00444-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites colonize the large intestine, primarily feeding on bacteria. However, in the gastrointestinal tract, bacterial cells form aggregates or structured communities called biofilms too large for phagocytosis. Remarkably, trophozoites are still able to invade and degrade established biofilms, utilizing a mechanism that mimics digestive exophagy. Digestive exophagy refers to the secretion of digestive enzymes that promote the digestion of objects too large for direct phagocytosis by phagocytes. E. histolytica cysteine proteinases (CPs) play a crucial role in the degradation process of Bacillus subtilis biofilm. These proteinases target TasA, a major component of the B. subtilis biofilm matrix, also contributing to the adhesion of the parasite to the biofilm. In addition, they are also involved in the degradation of biofilms formed by Gram-negative and Gram-positive enteric pathogens. Furthermore, biofilms also play an important role in protecting trophozoites against oxidative stress. This specific mechanism suggests that the amoeba has adapted to prey on biofilms, potentially serving as an untapped reservoir for novel therapeutic approaches to treat biofilms. Consistently, products derived from the amoeba have been shown to restore antibiotic sensitivity to biofilm cells. In addition, our findings reveal that probiotic biofilms can act as a protective shield for mammalian cells, hindering the progression of the parasite towards them.
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Affiliation(s)
- Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Meirav Trebicz-Geffen
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Divya Kolli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Einan Farhi
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Liat Linde
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Matthew Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
- Scojen Institute for Synthetic Biology, Reichman University, Herzliya, Israel.
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel.
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41
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Zhang H, Zhai Y, Chen K, Shi H. Adhesion of Escherichia coli O157:H7 during sublethal injury and resuscitation: Importance of pili and surface properties. Food Microbiol 2023; 115:104329. [PMID: 37567635 DOI: 10.1016/j.fm.2023.104329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 08/13/2023]
Abstract
Escherichia coli O157:H7 can recover from sublethally injured (SI) state, which causes threat of foodborne illness. Adhesion plays a key role in the carriage of pathogens in food. In this study, we investigated the adhesion ability of SI and recovered E. coli O157:H7 wildtype and its three pili-deficient mutants (curli, type 1 fimbriae, and type IV pili) on six food-related surfaces. Plate counting was used to determine adhesion population after washing and oscillating the surfaces. Spinach exhibited the stronger adhesion population of E. coli O157:H7 than the other fresh produces (p < 0.05). In addition, at least one key pili dominated adhesion on these surfaces, and curli was always included. The adhesion population and contribution of different types of pili were jointly affected by surface and physiological state. This can be attributed to high hydrophobicity and positive charge density on surface and different expression levels of csgB, fimA, fimC and ppdD in SI and recovered cells. Among glucose, mannose, maltose, fructose, lactose, and sucrose, addition of 0.5% mannose could reduce adhesion of cells at all physiological states on stainless steel. Overall, this research will provide support for controlling adhesion of SI and recovered E. coli O157:H7.
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Affiliation(s)
- Hongchen Zhang
- College of Food Science, Southwest University, Chongqing, China
| | - Yujun Zhai
- College of Food Science, Southwest University, Chongqing, China
| | - Kewei Chen
- College of Food Science, Southwest University, Chongqing, China
| | - Hui Shi
- College of Food Science, Southwest University, Chongqing, China.
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42
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Schmit KJ, Garcia P, Sciortino A, Aho VTE, Pardo Rodriguez B, Thomas MH, Gérardy JJ, Bastero Acha I, Halder R, Cialini C, Heurtaux T, Ostahi I, Busi SB, Grandmougin L, Lowndes T, Singh Y, Martens EC, Mittelbronn M, Buttini M, Wilmes P. Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson's disease. Cell Rep 2023; 42:113071. [PMID: 37676767 PMCID: PMC10548091 DOI: 10.1016/j.celrep.2023.113071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/01/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Parkinson's disease (PD) is a neurological disorder characterized by motor dysfunction, dopaminergic neuron loss, and alpha-synuclein (αSyn) inclusions. Many PD risk factors are known, but those affecting disease progression are not. Lifestyle and microbial dysbiosis are candidates in this context. Diet-driven gut dysbiosis and reduced barrier function may increase exposure of enteric neurons to toxins. Here, we study whether fiber deprivation and exposure to bacterial curli, a protein cross-seeding with αSyn, individually or together, exacerbate disease in the enteric and central nervous systems of a transgenic PD mouse model. We analyze the gut microbiome, motor behavior, and gastrointestinal and brain pathologies. We find that diet and bacterial curli alter the microbiome and exacerbate motor performance, as well as intestinal and brain pathologies, but to different extents. Our results shed important insights on how diet and microbiome-borne insults modulate PD progression via the gut-brain axis and have implications for lifestyle management of PD.
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Affiliation(s)
- Kristopher J Schmit
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Institute for Medical Genetics and Applied Genomics, Hospital University Tubingen, 72076 Tubingen, Germany; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg.
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Alessia Sciortino
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Velma T E Aho
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Beatriz Pardo Rodriguez
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Mélanie H Thomas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Jean-Jacques Gérardy
- Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg; National Center of Pathology, Laboratoire National de Santé, 3555 Dudelange, Luxembourg
| | - Irati Bastero Acha
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Camille Cialini
- Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg; Department of Cancer Research, Luxembourg Institute of Health, 1526 Luxembourg, Luxembourg
| | - Tony Heurtaux
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg; Department of Life Sciences and Medicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Irina Ostahi
- National Center of Pathology, Laboratoire National de Santé, 3555 Dudelange, Luxembourg
| | - Susheel B Busi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Léa Grandmougin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Tuesday Lowndes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Yogesh Singh
- Institute for Medical Genetics and Applied Genomics, Hospital University Tubingen, 72076 Tubingen, Germany
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg; National Center of Pathology, Laboratoire National de Santé, 3555 Dudelange, Luxembourg; Department of Cancer Research, Luxembourg Institute of Health, 1526 Luxembourg, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg.
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43
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Visser JA, Yager D, Chambers SA, Lim JY, Cao X, Cegelski L. Nordihydroguaiaretic Acid (NDGA) Inhibits CsgA Polymerization, Bacterial Amyloid Biogenesis, and Biofilm Formation. Chembiochem 2023; 24:e202300266. [PMID: 37195016 DOI: 10.1002/cbic.202300266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/18/2023]
Abstract
Escherichia coli and other Enterobacteriaceae thrive in robust biofilm communities through the coproduction of curli amyloid fibers and phosphoethanolamine cellulose. Curli promote adhesion to abiotic surfaces and plant and human host tissues and are associated with pathogenesis in urinary tract infection and food-borne illness. The production of curli in the host has also been implicated in the pathogenesis of neurodegenerative diseases. We report that the natural product nordihydroguaiaretic acid (NDGA) is effective as a curlicide in E. coli. NDGA prevents CsgA polymerization in vitro in a dose-dependent manner. NDGA selectively inhibits cell-associated curli assembly and inhibits uropathogenic E. coli biofilm formation. More broadly, this work emphasizes the ability to evaluate and identify bioactive amyloid assembly inhibitors by using the powerful gene-directed amyloid biogenesis machinery in E. coli.
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Affiliation(s)
- Joshua A Visser
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Deborah Yager
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Schuyler A Chambers
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Ji Youn Lim
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Xujun Cao
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
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44
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Ou C, Dozois CM, Daigle F. Differential regulatory control of curli (csg) gene expression in Salmonella enterica serovar Typhi requires more than a functional CsgD regulator. Sci Rep 2023; 13:14905. [PMID: 37689734 PMCID: PMC10492818 DOI: 10.1038/s41598-023-42027-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/04/2023] [Indexed: 09/11/2023] Open
Abstract
The human-specific Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever, a systemic disease with no known reservoir. Curli fimbriae are major components of biofilm produced by Salmonella and are encoded by the csg gene cluster (csgBAC and csgDEFG). The role of curli in S. Typhi is unknown, although detection of anti-curli antibodies suggests they are produced during host infection. In this study, we investigated curli gene expression in S. Typhi. We demonstrated that the CsgD regulatory protein binds weakly to the csgB promoter. Yet, replacing S. Typhi csgD with the csgD allele from S. Typhimurium did not modify the curli negative phenotype on Congo Red medium suggesting that differential regulation of curli gene expression in S. Typhi is not dependent on modification of the CsgD regulator. The entire csg gene cluster from S. Typhimurium was also cloned into S. Typhi, but again, despite introduction of a fully functional csg gene cluster from S. Typhimurium, curli were still not detected in S. Typhi. Thus, in addition to intrinsic genomic differences in the csg gene cluster that have resulted in production of a modified CsgD protein, S. Typhi has likely undergone other changes independent of the csg gene cluster that have led to distinctive regulation of csg genes compared to other Salmonella serovars.
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Affiliation(s)
- Camille Ou
- Department of Microbiology, Infectiology and Immunology, University of Montréal, 2900 Bd Édouard-Montpetit, Montreal, QC, H3T 1J4, Canada
- CRIPA, Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, 3200 Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada
| | - Charles M Dozois
- CRIPA, Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, 3200 Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut Nationale de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC, H7V 1B7, Canada
| | - France Daigle
- Department of Microbiology, Infectiology and Immunology, University of Montréal, 2900 Bd Édouard-Montpetit, Montreal, QC, H3T 1J4, Canada.
- CRIPA, Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, 3200 Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada.
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45
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Buchmann D, Schwabe M, Weiss R, Kuss AW, Schaufler K, Schlüter R, Rödiger S, Guenther S, Schultze N. Natural phenolic compounds as biofilm inhibitors of multidrug-resistant Escherichia coli - the role of similar biological processes despite structural diversity. Front Microbiol 2023; 14:1232039. [PMID: 37731930 PMCID: PMC10507321 DOI: 10.3389/fmicb.2023.1232039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 09/22/2023] Open
Abstract
Multidrug-resistant gram-negative pathogens such as Escherichia coli have become increasingly difficult to treat and therefore alternative treatment options are needed. Targeting virulence factors like biofilm formation could be one such option. Inhibition of biofilm-related structures like curli and cellulose formation in E. coli has been shown for different phenolic natural compounds like epigallocatechin gallate. This study demonstrates this effect for other structurally unrelated phenolics, namely octyl gallate, scutellarein and wedelolactone. To verify whether these structurally different compounds influence identical pathways of biofilm formation in E. coli a broad comparative RNA-sequencing approach was chosen with additional RT-qPCR to gain initial insights into the pathways affected at the transcriptomic level. Bioinformatical analysis of the RNA-Seq data was performed using DESeq2, BioCyc and KEGG Mapper. The comparative bioinformatics analysis on the pathways revealed that, irrespective of their structure, all compounds mainly influenced similar biological processes. These pathways included bacterial motility, chemotaxis, biofilm formation as well as metabolic processes like arginine biosynthesis and tricarboxylic acid cycle. Overall, this work provides the first insights into the potential mechanisms of action of novel phenolic biofilm inhibitors and highlights the complex regulatory processes of biofilm formation in E. coli.
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Affiliation(s)
- David Buchmann
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Michael Schwabe
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Romano Weiss
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Andreas W. Kuss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Sebastian Guenther
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Nadin Schultze
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
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46
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Nowakowska AW, Wojciechowski JW, Szulc N, Kotulska M. The role of tandem repeats in bacterial functional amyloids. J Struct Biol 2023; 215:108002. [PMID: 37482232 DOI: 10.1016/j.jsb.2023.108002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Repetitivity and modularity of proteins are two related notions incorporated into multiple evolutionary concepts. We discuss whether they may also be essential for functional amyloids. Amyloids are proteins that create very regular and usually highly insoluble fibrils, which are often associated with neurodegeneration. However, recent discoveries showed that amyloid structure of a protein could also be beneficial and desired, e.g., to promote cell adhesion. Functional amyloids are proteins which differ in their characteristics from pathological amyloids, so that the fibril formation could be more under control of an organism. We propose that repeats in the sequence could regulate the aggregation propensity of these proteins. The inclusion of multiple symmetric interactions, due to the presence of the repeats, could be supporting and strengthening the desirable structural properties of functional amyloids. Our results show that tandem repeats in bacterial functional amyloids have a distinct characteristic. The pattern of repeats supports the appropriate level of fibril formation and better controllability of fibril stability. The repeats tend to be more imperfect, which attenuates excessive aggregation propensity. Their desired structure and function are also reinforced by their amino acid profile. Although in the study we focused on bacterial functional amyloids, due to their importance in biofilm formation, we propose that similar mechanisms could be employed in other functional amyloids which are designed by evolution to aggregate in a desirable manner, but not necessarily in pathological amyloids.
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Affiliation(s)
- Alicja W Nowakowska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
| | - Jakub W Wojciechowski
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland
| | - Natalia Szulc
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland; Wrocław University of Environmental and Life Sciences, Department of Physics and Biophysics, Poland; LPCT, CNRS, Universite de Lorraine, F-54000 Nancy, France
| | - Malgorzata Kotulska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
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47
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Bhopatkar AA, Kayed R. Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity. J Biol Chem 2023; 299:105122. [PMID: 37536631 PMCID: PMC10482755 DOI: 10.1016/j.jbc.2023.105122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/10/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
The β-sheet-rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins amyloid-β, α-synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.
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Affiliation(s)
- Anukool A Bhopatkar
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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48
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Liu X, Jiang Z, Liu Z, Li D, Liu Z, Dong X, Yan S, Zhu L, Cui D, Chen L, Wang J. Biofilm-forming ability of Salmonella enterica strains of different serotypes isolated from multiple sources in China. Microb Pathog 2023; 182:106275. [PMID: 37516211 DOI: 10.1016/j.micpath.2023.106275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Salmonella is an important zoonotic and foodborne pathogen that can infect humans and animals, causing severe concerns about food safety and a heavy financial burden worldwide. The pathogen can adhere to living and abiotic surfaces by forming biofilms, which increases the risk of transmission and infection. In this study, we investigated the biofilm-forming ability of 243 Salmonella strains of 36 serotypes from different sources in China using microplate crystal violet staining method. The results showed that 99.6% tested strains, with the exception of one strain of S. Thompson, were capable of forming biofilms. The strains with the biofilm-forming ability of strong, medium and weak accounted for 2.88%, 24.28% and 72.43%, respectively. The strains of S. Havana and S. Hvittingfoss had the strongest biofilm-forming ability, with the OD570 of 0.81 ± 0.02 and 0.81 ± 0.38, respectively, while the strains of S. Agona and S. Bovismorbificans had the weakest biofilm-forming ability, with the OD570 of 0.16 ± 0.02 and 0.15 ± 0.00, respectively. Furthermore, statistical analysis results demonstrated that isolation of source had no effect on the biofilm formation ability, while the detection rates of pefABCD and ddhC were positively correlated with the biofilm formation ability of Salmonella. In particular, the detection rate of ddhC gene was more than 60% in the biofilm forming strains. These findings have important guiding significance for the investigation of pathogenesis, as well as the prevention and control of salmonellosis.
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Affiliation(s)
- Xu Liu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zhaoxu Jiang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zijun Liu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Donghui Li
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zhenhai Liu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Xiaorui Dong
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Shigan Yan
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Liping Zhu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Daoshi Cui
- Qilu Animal Health Products Co., Ltd, Jinan, 250100, China
| | - Leilei Chen
- Institute of Agro-Food Sciences and Technology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Junwei Wang
- Laboratory of Pathogenic Microorganism Inspection, China Animal Health and Epidemiology Center, Qingdao, 266032, China
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49
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Sengupta S, Singh N, Paul A, Datta D, Chatterjee D, Mukherjee S, Gadhe L, Devi J, Mahesh Y, Jolly MK, Maji SK. p53 amyloid pathology is correlated with higher cancer grade irrespective of the mutant or wild-type form. J Cell Sci 2023; 136:jcs261017. [PMID: 37622400 PMCID: PMC7615089 DOI: 10.1242/jcs.261017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
p53 (also known as TP53) mutation and amyloid formation are long associated with cancer pathogenesis; however, the direct demonstration of the link between p53 amyloid load and cancer progression is lacking. Using multi-disciplinary techniques and 59 tissues (53 oral and stomach cancer tumor tissue samples from Indian individuals with cancer and six non-cancer oral and stomach tissue samples), we showed that p53 amyloid load and cancer grades are highly correlated. Furthermore, next-generation sequencing (NGS) data suggest that not only mutant p53 (e.g. single-nucleotide variants, deletions, and insertions) but wild-type p53 also formed amyloids either in the nucleus (50%) and/or in the cytoplasm in most cancer tissues. Interestingly, in all these cancer tissues, p53 displays a loss of DNA-binding and transcriptional activities, suggesting that the level of amyloid load correlates with the degree of loss and an increase in cancer grades. The p53 amyloids also sequester higher amounts of the related p63 and p73 (also known as TP63 and TP73, respectively) protein in higher-grade tumor tissues. The data suggest p53 misfolding and/or aggregation, and subsequent amyloid formation, lead to loss of the tumor-suppressive function and the gain of oncogenic function, aggravation of which might determine the cancer grade.
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Affiliation(s)
- Shinjinee Sengupta
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Noida, Uttar Pradesh, 201303, India
| | - Namrata Singh
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ajoy Paul
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Debalina Datta
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Debdeep Chatterjee
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Semanti Mukherjee
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Laxmikant Gadhe
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Jyoti Devi
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Yeshwanth Mahesh
- Centre for BioSystems Science and Engineering, Indian Institute of Science Bengaluru, Bengaluru, Karnataka 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science Bengaluru, Bengaluru, Karnataka 560012, India
| | - Samir K. Maji
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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50
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Perry EK, Tan MW. Bacterial biofilms in the human body: prevalence and impacts on health and disease. Front Cell Infect Microbiol 2023; 13:1237164. [PMID: 37712058 PMCID: PMC10499362 DOI: 10.3389/fcimb.2023.1237164] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
Bacterial biofilms can be found in most environments on our planet, and the human body is no exception. Consisting of microbial cells encased in a matrix of extracellular polymers, biofilms enable bacteria to sequester themselves in favorable niches, while also increasing their ability to resist numerous stresses and survive under hostile circumstances. In recent decades, biofilms have increasingly been recognized as a major contributor to the pathogenesis of chronic infections. However, biofilms also occur in or on certain tissues in healthy individuals, and their constituent species are not restricted to canonical pathogens. In this review, we discuss the evidence for where, when, and what types of biofilms occur in the human body, as well as the diverse ways in which they can impact host health under homeostatic and dysbiotic states.
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Affiliation(s)
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech, South San Francisco, CA, United States
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