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Chen YT, Lohia GK, Chen S, Riquelme SA. Immunometabolic Regulation of Bacterial Infection, Biofilms, and Antibiotic Susceptibility. J Innate Immun 2024; 16:143-158. [PMID: 38310854 PMCID: PMC10914382 DOI: 10.1159/000536649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/01/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Upon infection, mucosal tissues activate a brisk inflammatory response to clear the pathogen, i.e., resistance to disease. Resistance to disease is orchestrated by tissue-resident macrophages, which undergo profound metabolic reprogramming after sensing the pathogen. These metabolically activated macrophages release many inflammatory factors, which promote their bactericidal function. However, in immunocompetent individuals, pathogens like Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella evade this type of immunity, generating communities that thrive for the long term. SUMMARY These organisms develop features that render them less susceptible to eradication, such as biofilms and increased tolerance to antibiotics. Furthermore, after antibiotic therapy withdrawal, "persister" cells rapidly upsurge, triggering inflammatory relapses that worsen host health. How these pathogens persisted in inflamed tissues replete with activated macrophages remains poorly understood. KEY MESSAGES In this review, we discuss recent findings indicating that the ability of P. aeruginosa, S. aureus, and Salmonella to evolve biofilms and antibiotic tolerance is promoted by the similar metabolic routes that regulate macrophage metabolic reprogramming.
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Affiliation(s)
- Ying-Tsun Chen
- Department of Pediatrics, Division of Infectious Diseases, Columbia University, New York, New York, USA
| | - Gaurav Kumar Lohia
- Department of Pediatrics, Division of Infectious Diseases, Columbia University, New York, New York, USA
| | - Samantha Chen
- Department of Pediatrics, Division of Infectious Diseases, Columbia University, New York, New York, USA
| | - Sebastián A Riquelme
- Department of Pediatrics, Division of Infectious Diseases, Columbia University, New York, New York, USA
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2
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Vohra M, Kour A, Kalia NP, Kumar M, Sharma S, Jaglan S, Kamath N, Sharma S. A comprehensive review of genomics, transcriptomics, proteomics, and metabolomic insights into the differentiation of Pseudomonas aeruginosa from the planktonic to biofilm state: A multi-omics approach. Int J Biol Macromol 2024; 257:128563. [PMID: 38070800 DOI: 10.1016/j.ijbiomac.2023.128563] [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: 07/20/2023] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
Biofilm formation by Pseudomonas aeruginosa is primarily responsible for chronic wound and lung infections in humans. These infections are persistent owing to the biofilm's high tolerance to antimicrobials and constantly changing environmental factors. Understanding the mechanism governing biofilm formation can help to develop therapeutics explicitly directed against the molecular markers responsible for this process. After numerous years of research, many genes responsible for both in vitro and in vivo biofilm development remain unidentified. However, there is no "all in one" complete in vivo or in vitro biofilm model. Recent findings imply that the shift from planktonic bacteria to biofilms is a complicated and interrelated differentiation process. Research on the applications of omics technologies in P. aeruginosa biofilm development is ongoing, and these approaches hold great promise for expanding our knowledge of the mechanisms of biofilm formation. This review discusses the different factors that affect biofilm formation and compares P. aeruginosa biofilm formation using the omics approaches targeting essential biological macromolecules, such as DNA, RNA, Protein, and metabolome. Furthermore, we have outlined the application of currently available omics tools, such as genomics, proteomics, metabolomics, transcriptomics, and integrated multi-omics methodologies, to understand the differential gene expression (biofilm vs. planktonic bacteria) of P. aeruginosa biofilms.
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Affiliation(s)
- Mustafa Vohra
- Department of Medical Laboratory Science, Lovely Professional University, Punjab 144411, India; Department of Microbiology, Shri Vinoba Bhave Civil Hospital, Silvassa 396230, India
| | - Avleen Kour
- Department of Medical Laboratory Science, Lovely Professional University, Punjab 144411, India
| | - Nitin Pal Kalia
- Department of Biological Sciences (Pharmacology & Toxicology), National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Manoj Kumar
- Maternal and Child Health Program, Research Department, Sidra Medicine, Doha 122104, Qatar
| | - Sarika Sharma
- Department of Sponsored Research, Division of Research & Development, Lovely Professional University, India
| | - Sundeep Jaglan
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180016, J&K, India
| | - Narayan Kamath
- Department of Microbiology, Shri Vinoba Bhave Civil Hospital, Silvassa 396230, India; Department of Microbiology, NAMO Medical Education and Research Institute, Silvassa 396230, India
| | - Sandeep Sharma
- Department of Medical Laboratory Science, Lovely Professional University, Punjab 144411, India.
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Thirumoorthy G, Balasubramanian B, George JA, Nizam A, Nagella P, Srinatha N, Pappuswamy M, Alanazi AM, Meyyazhagan A, Rengasamy KRR, Veerappa Lakshmaiah V. Phytofabricated bimetallic synthesis of silver-copper nanoparticles using Aerva lanata extract to evaluate their potential cytotoxic and antimicrobial activities. Sci Rep 2024; 14:1270. [PMID: 38218918 PMCID: PMC10787839 DOI: 10.1038/s41598-024-51647-x] [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: 06/16/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024] Open
Abstract
In this study, we demonstrate the green synthesis of bimetallic silver-copper nanoparticles (Ag-Cu NPs) using Aerva lanata plant extract. These NPs possess diverse biological properties, including in vitro antioxidant, antibiofilm, and cytotoxic activities. The synthesis involves the reduction of silver nitrate and copper oxide salts mediated by the plant extract, resulting in the formation of crystalline Ag-Cu NPs with a face-centered cubic structure. Characterization techniques confirm the presence of functional groups from the plant extract, acting as stabilizing and reducing agents. The synthesized NPs exhibit uniform-sized spherical morphology ranging from 7 to 12 nm. They demonstrate significant antibacterial activity against Staphylococcus aureus and Pseudomonas aeruginosa, inhibiting extracellular polysaccharide secretion in a dose-dependent manner. The Ag-Cu NPs also exhibit potent cytotoxic activity against cancerous HeLa cell lines, with an inhibitory concentration (IC50) of 17.63 µg mL-1. Additionally, they demonstrate strong antioxidant potential, including reducing capability and H2O2 radical scavenging activity, particularly at high concentrations (240 µg mL-1). Overall, these results emphasize the potential of A. lanata plant metabolite-driven NPs as effective agents against infectious diseases and cancer.
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Affiliation(s)
- Gopishankar Thirumoorthy
- Department of Life Sciences, CHRIST (Deemed to be University), Hosur Rd, Bengaluru, Karnataka, 560029, India
| | | | - Jincy A George
- Department of Life Sciences, CHRIST (Deemed to be University), Hosur Rd, Bengaluru, Karnataka, 560029, India
| | - Aatika Nizam
- Department of Chemistry, CHRIST (Deemed to be University), Hosur Rd, Bengaluru, Karnataka, 560029, India
| | - Praveen Nagella
- Department of Life Sciences, CHRIST (Deemed to be University), Hosur Rd, Bengaluru, Karnataka, 560029, India
| | - N Srinatha
- Department of Physics, RV Institute of Technology and Management, Bengaluru, 560 076, India
| | - Manikantan Pappuswamy
- Department of Life Sciences, CHRIST (Deemed to be University), Hosur Rd, Bengaluru, Karnataka, 560029, India
| | - Amer M Alanazi
- Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Arun Meyyazhagan
- Department of Life Sciences, CHRIST (Deemed to be University), Hosur Rd, Bengaluru, Karnataka, 560029, India
| | - Kannan R R Rengasamy
- Laboratory of Natural Products and Medicinal Chemistry (LNPMC), Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602105, India.
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, 2520, South Africa.
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4
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Choi E, Murray B, Choi S. Biofilm and Cancer: Interactions and Future Directions for Cancer Therapy. Int J Mol Sci 2023; 24:12836. [PMID: 37629016 PMCID: PMC10454087 DOI: 10.3390/ijms241612836] [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: 07/31/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
There is a growing body of evidence supporting the significant role of bacterial biofilms in the pathogenesis of various human diseases, including cancer. Biofilms are polymicrobial communities enclosed within an extracellular matrix composed of polysaccharides, proteins, extracellular DNA, and lipids. This complex matrix provides protection against antibiotics and host immune responses, enabling the microorganisms to establish persistent infections. Moreover, biofilms induce anti-inflammatory responses and metabolic changes in the host, further facilitating their survival. Many of these changes are comparable to those observed in cancer cells. This review will cover recent research on the role of bacterial biofilms in carcinogenesis, especially in colorectal (CRC) and gastric cancers, emphasizing the shared physical and chemical characteristics of biofilms and cancer. This review will also discuss the interactions between bacteria and the tumor microenvironment, which can facilitate oncogene expression and cancer progression. This information will provide insight into developing new therapies to identify and treat biofilm-associated cancers, such as utilizing bacteria as delivery vectors, using bacteria to upregulate immune function, or more selectively targeting biofilms and cancer for their shared traits.
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Affiliation(s)
- Euna Choi
- Department of Biology, Union University, Jackson, TN 38305, USA; (E.C.); (B.M.)
| | - Ben Murray
- Department of Biology, Union University, Jackson, TN 38305, USA; (E.C.); (B.M.)
| | - Sunga Choi
- Department of Bioinformatics and Biosystems, Seongnam Campus of Korea Polytechnics, Seongnam-si 13122, Republic of Korea
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5
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Sugianto W, Altin-Yavuzarslan G, Tickman BI, Kiattisewee C, Yuan SF, Brooks SM, Wong J, Alper HS, Nelson A, Carothers JM. Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction. Mater Today Bio 2023; 20:100677. [PMID: 37273790 PMCID: PMC10239009 DOI: 10.1016/j.mtbio.2023.100677] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023] Open
Abstract
Engineered living materials (ELMs) fabricated by encapsulating microbes in hydrogels have great potential as bioreactors for sustained bioproduction. While long-term metabolic activity has been demonstrated in these systems, the capacity and dynamics of gene expression over time is not well understood. Thus, we investigate the long-term gene expression dynamics in microbial ELMs constructed using different microbes and hydrogel matrices. Through direct gene expression measurements of engineered E. coli in F127-bisurethane methacrylate (F127-BUM) hydrogels, we show that inducible, input-responsive genetic programs in ELMs can be activated multiple times and maintained for multiple weeks. Interestingly, the encapsulated bacteria sustain inducible gene expression almost 10 times longer than free-floating, planktonic cells. These ELMs exhibit dynamic responsiveness to repeated induction cycles, with up to 97% of the initial gene expression capacity retained following a subsequent induction event. We demonstrate multi-week bioproduction cycling by implementing inducible CRISPR transcriptional activation (CRISPRa) programs that regulate the expression of enzymes in a pteridine biosynthesis pathway. ELMs fabricated from engineered S. cerevisiae in bovine serum albumin (BSA) - polyethylene glycol diacrylate (PEGDA) hydrogels were programmed to express two different proteins, each under the control of a different chemical inducer. We observed scheduled bioproduction switching between betaxanthin pigment molecules and proteinase A in S. cerevisiae ELMs over the course of 27 days under continuous cultivation. Overall, these results suggest that the capacity for long-term genetic expression may be a general property of microbial ELMs. This work establishes approaches for implementing dynamic, input-responsive genetic programs to tailor ELM functions for a wide range of advanced applications.
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Affiliation(s)
- Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Gokce Altin-Yavuzarslan
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - Benjamin I. Tickman
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Cholpisit Kiattisewee
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
| | - Shuo-Fu Yuan
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, United States
| | - Sierra M. Brooks
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Jitkanya Wong
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - Hal S. Alper
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, United States
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Alshakim Nelson
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - James M. Carothers
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States
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6
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Young BD, Rosales SM, Enochs IC, Kolodziej G, Formel N, Moura A, D'Alonso GL, Traylor-Knowles N. Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata. PLoS One 2023; 18:e0286293. [PMID: 37228141 DOI: 10.1371/journal.pone.0286293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.
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Affiliation(s)
- Benjamin D Young
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, United States of America
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Miami, Florida, United States of America
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Stephanie M Rosales
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Miami, Florida, United States of America
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Ian C Enochs
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Graham Kolodziej
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Miami, Florida, United States of America
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Nathan Formel
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Amelia Moura
- Coral Restoration Foundation, Tavernier, Florida, United States of America
| | | | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, United States of America
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7
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Blanco-Romero E, Durán D, Garrido-Sanz D, Redondo-Nieto M, Martín M, Rivilla R. Adaption of Pseudomonas ogarae F113 to the Rhizosphere Environment-The AmrZ-FleQ Hub. Microorganisms 2023; 11:microorganisms11041037. [PMID: 37110460 PMCID: PMC10146422 DOI: 10.3390/microorganisms11041037] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Motility and biofilm formation are two crucial traits in the process of rhizosphere colonization by pseudomonads. The regulation of both traits requires a complex signaling network that is coordinated by the AmrZ-FleQ hub. In this review, we describe the role of this hub in the adaption to the rhizosphere. The study of the direct regulon of AmrZ and the phenotypic analyses of an amrZ mutant in Pseudomonas ogarae F113 has shown that this protein plays a crucial role in the regulation of several cellular functions, including motility, biofilm formation, iron homeostasis, and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) turnover, controlling the synthesis of extracellular matrix components. On the other hand, FleQ is the master regulator of flagellar synthesis in P. ogarae F113 and other pseudomonads, but its implication in the regulation of multiple traits related with environmental adaption has been shown. Genomic scale studies (ChIP-Seq and RNA-Seq) have shown that in P. ogarae F113, AmrZ and FleQ are general transcription factors that regulate multiple traits. It has also been shown that there is a common regulon shared by the two transcription factors. Moreover, these studies have shown that AmrZ and FleQ form a regulatory hub that inversely regulate traits such as motility, extracellular matrix component production, and iron homeostasis. The messenger molecule c-di-GMP plays an essential role in this hub since its production is regulated by AmrZ and it is sensed by FleQ and required for its regulatory role. This regulatory hub is functional both in culture and in the rhizosphere, indicating that the AmrZ-FleQ hub is a main player of P. ogarae F113 adaption to the rhizosphere environment.
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Affiliation(s)
- Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
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8
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Inorganic Carbon Assimilation and Electrosynthesis of Platform Chemicals in Bioelectrochemical Systems (BESs) Inoculated with Clostridium saccharoperbutylacetonicum N1-H4. Microorganisms 2023; 11:microorganisms11030735. [PMID: 36985308 PMCID: PMC10051846 DOI: 10.3390/microorganisms11030735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023] Open
Abstract
The need for greener processes to satisfy the demand of platform chemicals together with the possibility of reusing CO2 from human activities has recently encouraged research on the set-up, optimization, and development of bioelectrochemical systems (BESs) for the electrosynthesis of organic compounds from inorganic carbon (CO2, HCO3−). In the present study, we tested the ability of Clostridium saccharoperbutylacetonicum N1-4 (DSMZ 14923) to produce acetate and D-3-hydroxybutyrate from inorganic carbon present in a CO2:N2 gas mix. At the same time, we tested the ability of a Shewanella oneidensis MR1 and Pseudomonas aeruginosa PA1430/CO1 consortium to provide reducing power to sustain carbon assimilation at the cathode. We tested the performance of three different systems with the same layouts, inocula, and media, but with the application of 1.5 V external voltage, of a 1000 Ω external load, and without any connection between the electrodes or external devices (open circuit voltage, OCV). We compared both CO2 assimilation rate and production of metabolites (formate, acetate 3-D-hydroxybutyrate) in our BESs with the values obtained in non-electrogenic control cultures and estimated the energy used by our BESs to assimilate 1 mol of CO2. Our results showed that C. saccharoperbutylacetonicum NT-1 achieved the maximum CO2 assimilation (95.5%) when the microbial fuel cells (MFCs) were connected to the 1000 Ω external resistor, with the Shewanella/Pseudomonas consortium as the only source of electrons. Furthermore, we detected a shift in the metabolism of C. saccharoperbutylacetonicum NT-1 because of its prolonged activity in BESs. Our results open new perspectives for the utilization of BESs in carbon capture and electrosynthesis of platform chemicals.
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Liu X, Jia M, Wang J, Cheng H, Cai Z, Yu Z, Liu Y, Ma LZ, Zhang L, Zhang Y, Yang L. Cell division factor ZapE regulates Pseudomonas aeruginosa biofilm formation by impacting the pqs quorum sensing system. MLIFE 2023; 2:28-42. [PMID: 38818333 PMCID: PMC10989928 DOI: 10.1002/mlf2.12059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 06/01/2024]
Abstract
Pseudomonas aeruginosa is one of the leading nosocomial pathogens that causes both severe acute and chronic infections. The strong capacity of P. aeruginosa to form biofilms can dramatically increase its antibiotic resistance and lead to treatment failure. The biofilm resident bacterial cells display distinct gene expression profiles and phenotypes compared to their free-living counterparts. Elucidating the genetic determinants of biofilm formation is crucial for the development of antibiofilm drugs. In this study, a high-throughput transposon-insertion site sequencing (Tn-seq) approach was employed to identify novel P. aeruginosa biofilm genetic determinants. When analyzing the novel biofilm regulatory genes, we found that the cell division factor ZapE (PA4438) controls the P. aeruginosa pqs quorum sensing system. The ∆zapE mutant lost fitness against the wild-type PAO1 strain in biofilms and its production of 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) had been reduced. Further biochemical analysis showed that ZapE interacts with PqsH, which encodes the synthase that converts 2-heptyl-4-quinolone (HHQ) to PQS. In addition, site-directed mutagenesis of the ATPase active site of ZapE (K72A) abolished the positive regulation of ZapE on PQS signaling. As ZapE is highly conserved among the Pseudomonas group, our study suggests that it is a potential drug target for the control of Pseudomonas infections.
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Affiliation(s)
- Xi Liu
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Key University Laboratory of Metabolism and Health of Guangdong, School of MedicineSouthern University of Science and TechnologyShenzhenChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Minlu Jia
- Key University Laboratory of Metabolism and Health of Guangdong, School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Jing Wang
- Key University Laboratory of Metabolism and Health of Guangdong, School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Hang Cheng
- Key University Laboratory of Metabolism and Health of Guangdong, School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Zhao Cai
- Key University Laboratory of Metabolism and Health of Guangdong, School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Zhaoxiao Yu
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yang Liu
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
| | - Luyan Z. Ma
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Yingdan Zhang
- Key University Laboratory of Metabolism and Health of Guangdong, School of MedicineSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Third People's Hospital, National Clinical Research Center for Infectious DiseaseThe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhenChina
| | - Liang Yang
- Key University Laboratory of Metabolism and Health of Guangdong, School of MedicineSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Third People's Hospital, National Clinical Research Center for Infectious DiseaseThe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhenChina
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10
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Sánchez-Lozano I, Muñoz-Cruz LC, Hellio C, Band-Schmidt CJ, Cruz-Narváez Y, Becerra-Martínez E, Hernández-Guerrero CJ. Metabolomic Insights of Biosurfactant Activity from Bacillus niabensis against Planktonic Cells and Biofilm of Pseudomonas stutzeri Involved in Marine Biofouling. Int J Mol Sci 2023; 24:ijms24044249. [PMID: 36835662 PMCID: PMC9965525 DOI: 10.3390/ijms24044249] [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: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm, biosurfactants (BS) produced by the genus Bacillus have demonstrated considerable potential. To elucidate the changes that BS from B. niabensis promote in growth inhibition and biofilm formation, this research performed a nuclear magnetic resonance (NMR) metabolomic profile analysis to compare the metabolic differences between planktonic cells and biofilms of Pseudomonas stutzeri, a pioneer fouling bacteria. The multivariate analysis showed a clear separation between groups with a higher concentration of metabolites in the biofilm than in planktonic cells of P. stutzeri. When planktonic and biofilm stages were treated with BS, some differences were found among them. In planktonic cells, the addition of BS had a minor effect on growth inhibition, but at a metabolic level, NADP+, trehalose, acetone, glucose, and betaine were up-regulated in response to osmotic stress. When the biofilm was treated with the BS, a clear inhibition was observed and metabolites such as glucose, acetic acid, histidine, lactic acid, phenylalanine, uracil, and NADP+ were also up-regulated, while trehalose and histamine were down-regulated in response to the antibacterial effect of the BS.
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Affiliation(s)
- Ilse Sánchez-Lozano
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Luz Clarita Muñoz-Cruz
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Claire Hellio
- CNRS, IRD, Ifremer, LEMAR, Univ. Brest, Institut Universitaire Européen de la Mer, F-29280 Plouzané, France
| | - Christine J. Band-Schmidt
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Yair Cruz-Narváez
- Laboratorio de Posgrado de Operaciones Unitarias, Instituto Politécnico Nacional-ESIQIE-UPALM, Unidad Profesional Adolfo López Mateos, Edificio 7, 1.er Piso, Sección A, Av. Luis Enrique Erro S/N, Zacatenco, Delegación Gustavo A. Madero, Mexico City 07738, Mexico
| | - Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Unidad Profesional Adolfo López Mateos, Av. Luis Enrique Erro S/N, Zacatenco, Delegación Gustavo A. Madero, Mexico City 07738, Mexico
- Correspondence: (E.B.-M.); (C.J.H.-G.)
| | - Claudia J. Hernández-Guerrero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
- Correspondence: (E.B.-M.); (C.J.H.-G.)
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11
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Khalid A, Cookson AR, Whitworth DE, Beeton ML, Robins LI, Maddocks SE. A Synthetic Polymicrobial Community Biofilm Model Demonstrates Spatial Partitioning, Tolerance to Antimicrobial Treatment, Reduced Metabolism, and Small Colony Variants Typical of Chronic Wound Biofilms. Pathogens 2023; 12:pathogens12010118. [PMID: 36678466 PMCID: PMC9862141 DOI: 10.3390/pathogens12010118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Understanding chronic wound infection is key for successful treatment and requires accurate laboratory models. We describe a modified biofilm flow device that effectively mimics the chronic wound environment, including simulated wound fluid, a collagen-based 3D biofilm matrix, and a five-species mixture of clinically relevant bacteria (Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Enterococcus faecalis, and Citrobacter freundii). Mixed biofilms were cultured for between 3 and 14 days with consistent numbers of bacteria that exhibited reduced metabolic activity, which increased with a high dose of glucose. S. aureus was recovered from biofilms as a small colony variant, but as a normal colony variant if P. aeruginosa was excluded from the system. Bacteria within the biofilm did not co-aggregate but formed discrete, species-specific clusters. Biofilms demonstrated differential tolerance to the topical antimicrobials Neosporin and HOCl, consistent with protection due to the biofilm lifestyle. The characteristics exhibited within this model match those of real-world wound biofilms, reflecting the clinical scenario and yielding a powerful in vitro tool that is versatile, inexpensive, and pivotal for understanding chronic wound infection.
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Affiliation(s)
- Ammara Khalid
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff CF5 2YB, UK
| | - Alan R. Cookson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DD, UK
| | - David E. Whitworth
- Department of Life Sciences, Aberystwyth University, Aberystwyth SY23 3DD, UK
| | - Michael L. Beeton
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff CF5 2YB, UK
| | - Lori I. Robins
- Department of Physical Sciences, University of Washington, Bothell, WA 98011-8246, USA
| | - Sarah E. Maddocks
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff CF5 2YB, UK
- Correspondence:
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12
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Doolan JA, Williams GT, Hilton KLF, Chaudhari R, Fossey JS, Goult BT, Hiscock JR. Advancements in antimicrobial nanoscale materials and self-assembling systems. Chem Soc Rev 2022; 51:8696-8755. [PMID: 36190355 PMCID: PMC9575517 DOI: 10.1039/d1cs00915j] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Antimicrobial resistance is directly responsible for more deaths per year than either HIV/AIDS or malaria and is predicted to incur a cumulative societal financial burden of at least $100 trillion between 2014 and 2050. Already heralded as one of the greatest threats to human health, the onset of the coronavirus pandemic has accelerated the prevalence of antimicrobial resistant bacterial infections due to factors including increased global antibiotic/antimicrobial use. Thus an urgent need for novel therapeutics to combat what some have termed the 'silent pandemic' is evident. This review acts as a repository of research and an overview of the novel therapeutic strategies being developed to overcome antimicrobial resistance, with a focus on self-assembling systems and nanoscale materials. The fundamental mechanisms of action, as well as the key advantages and disadvantages of each system are discussed, and attention is drawn to key examples within each field. As a result, this review provides a guide to the further design and development of antimicrobial systems, and outlines the interdisciplinary techniques required to translate this fundamental research towards the clinic.
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Affiliation(s)
- Jack A Doolan
- School of Chemistry and Forensic Science, University of Kent, Canterbury, Kent CT2 7NH, UK.
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - George T Williams
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Kira L F Hilton
- School of Chemistry and Forensic Science, University of Kent, Canterbury, Kent CT2 7NH, UK.
| | - Rajas Chaudhari
- School of Chemistry and Forensic Science, University of Kent, Canterbury, Kent CT2 7NH, UK.
| | - John S Fossey
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Benjamin T Goult
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Jennifer R Hiscock
- School of Chemistry and Forensic Science, University of Kent, Canterbury, Kent CT2 7NH, UK.
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13
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Ch'ng JH, Muthu M, Chong KKL, Wong JJ, Tan CAZ, Koh ZJS, Lopez D, Matysik A, Nair ZJ, Barkham T, Wang Y, Kline KA. Heme cross-feeding can augment Staphylococcus aureus and Enterococcus faecalis dual species biofilms. THE ISME JOURNAL 2022; 16:2015-2026. [PMID: 35589966 PMCID: PMC9296619 DOI: 10.1038/s41396-022-01248-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 04/18/2022] [Accepted: 04/29/2022] [Indexed: 12/17/2022]
Abstract
The contribution of biofilms to virulence and as a barrier to treatment is well-established for Staphylococcus aureus and Enterococcus faecalis, both nosocomial pathogens frequently isolated from biofilm-associated infections. Despite frequent co-isolation, their interactions in biofilms have not been well-characterized. We report that in combination, these two species can give rise to augmented biofilms biomass that is dependent on the activation of E. faecalis aerobic respiration. In E. faecalis, respiration requires both exogenous heme to activate the cydAB-encoded heme-dependent cytochrome bd, and the availability of O2. We determined that the ABC transporter encoded by cydDC contributes to heme import. In dual species biofilms, S. aureus provides the heme to activate E. faecalis respiration. S. aureus mutants deficient in heme biosynthesis were unable to augment biofilms whereas heme alone is sufficient to augment E. faecalis mono-species biofilms. Our results demonstrate that S. aureus-derived heme, likely in the form of released hemoproteins, promotes E. faecalis biofilm formation, and that E. faecalis gelatinase activity facilitates heme extraction from hemoproteins. This interspecies interaction and metabolic cross-feeding may explain the frequent co-occurrence of these microbes in biofilm-associated infections.
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Affiliation(s)
- Jun-Hong Ch'ng
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore. .,Department of Surgery Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Infectious Disease Translational Research Program, National University Health System, Singapore, Singapore. .,Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
| | - Mugil Muthu
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Kelvin K L Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Nanyang Technological University Institute for Health Technologies, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Jun Jie Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, Singapore, Singapore
| | - Casandra A Z Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, Singapore, Singapore
| | - Zachary J S Koh
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
| | - Daniel Lopez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Artur Matysik
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Zeus J Nair
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Timothy Barkham
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Nanyang, Singapore
| | - Kimberly A Kline
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore. .,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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14
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Identification of metabolite extraction method for targeted exploration of antimicrobial resistance associated metabolites of Klebsiella pneumoniae. Sci Rep 2022; 12:8939. [PMID: 35624184 PMCID: PMC9142494 DOI: 10.1038/s41598-022-12153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/22/2022] [Indexed: 11/08/2022] Open
Abstract
Antimicrobial resistant Klebsiella pneumoniae (K. pneumoniae), as being a pathogen of critical clinical concern, urgently demands effective therapeutic options. However, the discovery of novel antibiotics over the last three decades has declined drastically and necessitates exploring novel strategies. Metabolomic modulation has been the promising approach for the development of effective therapeutics to deal with AMR; however, only limited efforts have been made to-date, possibly due to the unavailability of suitable metabolites extraction protocols. Therefore, in order to establish a detailed metabolome of K. pneumoniae and identify a method for targeted exploration of metabolites that are involved in the regulation of AMR associated processes, metabolites were extracted using multiple methods of metabolites extraction (freeze-thaw cycle (FTC) and sonication cycle (SC) method alone or in combination (FTC followed by SC; FTC + SC)) from K. pneumoniae cells and then identified using an orbitrap mass analyzer (ESI-LC-MS/MS). A total of 151 metabolites were identified by using FTC, 132 metabolites by using FTC+SC, 103 metabolites by using SC and 69 metabolites common among all the methods used which altogether enabled the identification of 199 unique metabolites. Of these 199, 70 metabolites were known to have an association with AMR phenotype and among these, the FTC + SC method yielded better (identified 55 metabolites), quantitatively and qualitatively compared to FTC and SC alone (identified 51 and 41 metabolites respectively). Each method of metabolite extraction showed a definite degree of biasness and specificity towards chemical classes of metabolites and jointly contributed to the development of a detailed metabolome of the pathogen. FTC method was observed to give higher metabolomic coverage as compared to SC alone and FTC + SC. However, FTC + SC resulted in the identification of a higher number of AMR associated metabolites of K. pneumoniae compared to FTC and SC alone.
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15
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Wylie MR, Windham IH, Blum FC, Wu H, Merrell DS. In vitro antibacterial activity of nimbolide against Helicobacter pylori. JOURNAL OF ETHNOPHARMACOLOGY 2022; 285:114828. [PMID: 34763046 PMCID: PMC8714693 DOI: 10.1016/j.jep.2021.114828] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/27/2021] [Accepted: 11/05/2021] [Indexed: 05/02/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Nimbolide is one of hundreds of phytochemicals that have been identified within the neem tree (Azadirachta indica A. Juss). As an evergreen tree native to the Indian subcontinent, components of the neem tree have been used for millennia in traditional medicine to treat dental, gastrointestinal, urinary tract, and blood-related ailments, ulcers, headaches, heartburn, and diabetes. In modern times, natural oils and extracts from the neem tree have been found to have activities against a variety of microorganisms, including human pathogens. AIM OF THE STUDY Helicobacter pylori, a prevalent gastric pathogen, shows increasing levels of antibiotic resistance. Thus, there is an increasing demand for novel therapeutics to treat chronic infections. The in vitro activity of neem oil extract against H. pylori was previously characterized and found to be bactericidal. Given the numerous phytochemicals found in neem oil extract, the present study was designed to define and characterize specific compounds showing bactericidal activity against H. pylori. MATERIALS AND METHODS Azadirachtin, gedunin, and nimbolide, which are all common in neem extracts, were tested for antimicrobial activity; the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined for nine strains of H. pylori. The specific properties of nimbolide were further characterized against H. pylori strain G27. Bactericidal kinetics, reversibility, effectiveness at low pH, and activity under bacteriostatic conditions were examined. The hemolytic activity of nimbolide was also measured. Finally, neem oil extract and nimbolide effectiveness against H. pylori biofilms were examined in comparison to common antibiotics used to treat H. pylori infection. RESULTS Nimbolide, but not azadirachtin or gedunin, was effective against H. pylori; MICs and MBCs against the nine tested strains ranged between 1.25-5 μg/mL and 2.5-10 μg/mL, respectively. Additionally, neem oil extract and nimbolide were both effective against H. pylori biofilms. Nimbolide exhibited no significant hemolytic activity at biologically relevant concentrations. The bactericidal activity of nimbolide was time- and dose-dependent, independent of active H. pylori growth, and synergistic with low pH. Furthermore, nimbolide-mediated H. pylori cell death was irreversible after exposure to high nimbolide concentrations (80 μg/mL, after 2 h of exposure time and 40 μg/mL after 8 h of exposure). CONCLUSIONS Nimbolide has significant bactericidal activity against H. pylori, killing both free living bacterial cells as well as cells within a biofilm. Furthermore, the lack of hemolytic activity, synergistic activity at low pH and bactericidal properties even against bacteria in a state of growth arrest are all ideal pharmacological and biologically relevant properties for a potential new agent. This study underscores the potential of neem oil extract or nimbolide to be used as a future treatment for H. pylori infection.
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Affiliation(s)
- Marina R Wylie
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, United States
| | - Ian H Windham
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, United States
| | - Faith C Blum
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, United States
| | - Hannah Wu
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, United States
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, United States.
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16
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Heald R, Salyer S, Ham K, Wilgus TA, Subramaniam VV, Prakash S. Electroceutical treatment of infected chronic wounds in a dog and a cat. Vet Surg 2022; 51:520-527. [PMID: 34994470 DOI: 10.1111/vsu.13758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 09/27/2021] [Accepted: 12/10/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVES To describe the use of an innovative printed electroceutical dressing (PED) to treat non-healing, infected chronic wounds in one dog and one cat and report outcomes. ANIMALS A 4-year-old female spayed Mastiff and a 1-year-old female spayed domestic shorthair cat. STUDY DESIGN Short case series. METHODS Both cases had chronic wounds (duration: approximately 1 year for the dog and 6 3/4 months for the cat) that remained open and infected despite various wound management strategies. Both animals were treated with the PED. Observations from the records regarding wound size, antimicrobial susceptibility, and the time to healing were recorded. RESULTS After 10 days of PED treatment in the dog and 17 days of PED treatment in the cat, the wounds had decreased in size by approximately 4.2 times in the dog and 2.5 times in the cat. Culture of punch biopsies yielded negative results. Wounds were clinically healed at 67 days in the dog and 47 days in the cat. No further treatment of the wounds was required beyond that point. CONCLUSION Application of a PED led to closure of two chronic wounds and resolution of their persistent infection. CLINICAL SIGNIFICANCE PEDs may provide a new treatment modality to mitigate infection and promote healing of chronic wounds.
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Affiliation(s)
- Rachel Heald
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Salyer
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen Ham
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA.,Department of Small Animal Clinical Sciences, University of Florida, Gainesville, Florida, USA
| | - Traci A Wilgus
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Vish V Subramaniam
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Shaurya Prakash
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio, USA
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17
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Abstract
Formation of microbial biofilms has long been implicated in the occurrence of periprosthetic joint infections (PJIs). Despite the widespread acknowledgment of the severity of these infections, much is still unknown regarding the underlying mechanisms of biofilm establishment and proliferation in the joint space. The presence of these resilient, complex communities poses many clinical challenges with respect to prevention, diagnosis, and treatment practices. Mature biofilms are known to be highly recalcitrant to antibiotic therapeutics as well as host immune system mediated clearance. A comprehensive understanding of biofilms in the unique joint environment at the molecular level will provide clinicians valuable insight into how best to combat them. As each stage in the process of biofilm establishment has the potential for clinical intervention, this review will provide a sequential analysis of the existing literature, following each step in the formation cycle. New insights into bacterial survival mechanisms from antimicrobial challenge and host immune defenses will be discussed. These new observations in the field may shed light on the early protection conferred upon entry into the joint space ultimately leading to the establishment of a mature biofilm. Additionally, standards of clinical diagnosis as well as current measures of prevention and treatment will be briefly discussed.
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Affiliation(s)
- Amelia Staats
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Daniel Li
- Department of Orthopaedics, The Ohio State University, Columbus, Ohio, USA
| | - Anne C Sullivan
- Department of Orthopaedics, The Ohio State University, Columbus, Ohio, USA
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA.,Department of Orthopaedics, The Ohio State University, Columbus, Ohio, USA.,National Centre for Advanced Tribology at Southampton and National Biofilm Innovation Centre, Mechanical Engineering, University of Southampton, Southampton, UK
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18
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Žiemytė M, Carda-Diéguez M, Rodríguez-Díaz JC, Ventero MP, Mira A, Ferrer MD. Real-time monitoring of Pseudomonas aeruginosa biofilm growth dynamics and persister cells' eradication. Emerg Microbes Infect 2021; 10:2062-2075. [PMID: 34663186 PMCID: PMC8583918 DOI: 10.1080/22221751.2021.1994355] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 01/11/2023]
Abstract
Biofilm formation and the appearance of persister cells with low metabolic rates are key factors affecting conventional treatment failure and antibiotic resistance. Using impedance-based measurements, crystal violet staining and traditional culture we have studied the biofilm growth dynamics of 13 Pseudomonas aeruginosa strains under the effect of seven conventional antibiotics. Real-time growth quantifications revealed that the exposure of established P. aeruginosa biofilms to certain concentrations of ciprofloxacin, ceftazidime and tobramycin induced the emergence of persister cells, that showed different morphology and pigmentation, as well increased antibiotic resistance. Whole-genome sequencing of wildtype and persister cells identified several SNPs, a genomic inversion and a genomic duplication in one of the strains. However, these mutations were not uniquely associated with persisters, suggesting that the persistent phenotype may be related to metabolic and transcriptional changes. Given that mannitol has been proposed to activate bacterial metabolism, the synergistic combination of mannitol and ciprofloxacin was evaluated on clinical 48 h P. aeruginosa biofilms. When administered at doses ≥320 mg/L, mannitol was capable of preventing persister cell formation by efficiently activating dormant bacteria and making them susceptible to the antibiotic. These results were confirmed using viable colony counting. As the tested ciprofloxacin-mannitol combination appeared to fully eradicate mature biofilms, we conclude that impedance-based biofilm diagnostics, which permits antibiotic susceptibility testing and the identification of persister cells, is of great potential for the clinical practice and could aid in establishing treatment breakpoints for emerging biofilm-related infections.
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Affiliation(s)
- Miglė Žiemytė
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
| | | | - Juan C. Rodríguez-Díaz
- Servicio de Microbiología, Hospital General Universitario de Alicante, ISABIAL, Alicante, Spain
| | - Maria P. Ventero
- Servicio de Microbiología, Hospital General Universitario de Alicante, ISABIAL, Alicante, Spain
| | - Alex Mira
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
| | - María D. Ferrer
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
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19
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Integrating transcriptomics and metabolomics analysis on kojic acid combating Acinetobacter baumannii biofilm and its potential roles. Microbiol Res 2021; 254:126911. [PMID: 34763140 DOI: 10.1016/j.micres.2021.126911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022]
Abstract
As a major secondary metabolite derived from a dominant marine filamentous fungus A7, kojic acid might confer the strain a competitive advantage in natural colonization. The bioactivities of kojic acid against bacterial growth and biofilm formation were investigated against Acinetobacter baumannii (A. baumannii) ATCC 19606. Then, transcriptomics and metabolomics were integrated to characterize the underlying mechanisms. It turned out that kojic acid exhibited a significantly suppressive impact against biofilm but a weak bacteriostatic activity. Meanwhile, a variety of transcriptional and metabolomic profiles were altered within biofilm formation as a result of kojic acid exposure. The alterations highlighted the mechanisms underlying biofilm formation, comprising of quorum sensing, fimbria assembly, bacterial virulence and metabolic plasticity, which could somewhat be hampered by kojic acid. The present study comprehensively elucidated multifactorial schemes for kojic acid combating biofilm formation of A. baumannii, which might provide mechanistic insights into the development of therapeutic strategies against this notorious pathogen. Meanwhile, our observations might shed new light on the ecological roles of kojic acid, e.g., serving as chemical deterrents for host adaptation to marine niches, which, however, awaits further validation.
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20
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Characterizations of the viability and gene expression of dispersal cells from Pseudomonas aeruginosa biofilms released by alginate lyase and tobramycin. PLoS One 2021; 16:e0258950. [PMID: 34695148 PMCID: PMC8544826 DOI: 10.1371/journal.pone.0258950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 10/08/2021] [Indexed: 11/19/2022] Open
Abstract
Biofilm infections are hard to manage using conventional antibiotic treatment regimens because biofilm structures discourage antibiotics from reaching the entire bacterial community and allow pathogen cells to persistently colonize and develop a plethora of tolerance mechanisms towards antibiotics. Moreover, the dispersed cells from biofilms can cause further complications by colonizing different sites and establishing new cycles of biofilms. Previously, we showed that alginate lyase enzyme (AlyP1400), purified from a marine Pseudoalteromonas bacterium, reduced Pseudomonas aeruginosa biofilm biomass and boosted bactericidal activity of tobramycin by degrading alginate within the biofilm extracellular polymeric substances matrix. In this work, we used a flow cytometry-based assay to analyze collected dispersal cells and demonstrated the synergy between tobramycin with AlyP1400 in enhancing the release of both live and dead biofilm cells from a mucoid P. aeruginosa strain CF27, which is a clinical isolate from cystic fibrosis (CF) patients. Interestingly, this enhanced dispersal was only observed when AlyP1400 was combined with tobramycin and administered simultaneously but not when AlyP1400 was added in advance of tobramycin in a sequential manner. Moreover, neither the combined nor sequential treatment altered the dispersal of the biofilms from a non-mucoid P. aeruginosa laboratory strain PAK. We then carried out the gene expression and tobramycin survival analyses to further characterize the impacts of the combined treatment on the CF27 dispersal cells. Gene expression analysis indicated that CF27 dispersal cells had increased expression in virulence- and antibiotic resistance-related genes, including algR, bdlA, lasB, mexF, mexY, and ndvB. In the CF27 dispersal cell population, the combinational treatment of AlyP1400 with tobramycin further induced bdlA, mexF, mexY, and ndvB genes more than non-treated and tobramycin-treated dispersal cells, suggesting an exacerbated bacterial stress response to the combinational treatment. Simultaneous to the gene expression analysis, the survival ability of the same batch of biofilm dispersal cells to a subsequent tobramycin challenge displayed a significantly higher tobramycin tolerant fraction of cells (~60%) upon the combinational treatment of AlyP1400 and tobramycin than non-treated and tobramycin-treated dispersal cells, as well as the planktonic cells (all below 10%). These results generate new knowledge about the gene expression and antibiotic resistance profiles of dispersed cells from biofilm. This information can guide the design of safer and more efficient therapeutic strategies for the combinational use of alginate lyase and tobramycin to treat P. aeruginosa biofilm-related infections in CF lungs.
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21
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Kriem LS, Wright K, Ccahuana-Vasquez RA, Rupp S. Mapping of a Subgingival Dual-Species Biofilm Model Using Confocal Raman Microscopy. Front Microbiol 2021; 12:729720. [PMID: 34675902 PMCID: PMC8525910 DOI: 10.3389/fmicb.2021.729720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/13/2021] [Indexed: 12/14/2022] Open
Abstract
Techniques for continuously monitoring the formation of subgingival biofilm, in relation to the determination of species and their accumulation over time in gingivitis and periodontitis, are limited. In recent years, advancements in the field of optical spectroscopic techniques have provided an alternative for analyzing three-dimensional microbiological structures, replacing the traditional destructive or biofilm staining techniques. In this work, we have demonstrated that the use of confocal Raman spectroscopy coupled with multivariate analysis provides an approach to spatially differentiate bacteria in an in vitro model simulating a subgingival dual-species biofilm. The present study establishes a workflow to evaluate and differentiate bacterial species in a dual-species in vitro biofilm model, using confocal Raman microscopy (CRM). Biofilm models of Actinomyces denticolens and Streptococcus oralis were cultured using the “Zürich in vitro model” and were analyzed using CRM. Cluster analysis was used to spatially differentiate and map the biofilm model over a specified area. To confirm the clustering of species in the cultured biofilm, confocal laser scanning microscopy (CLSM) was coupled with fluorescent in vitro hybridization (FISH). Additionally, dense bacteria interface area (DBIA) samples, as an imitation of the clusters in a biofilm, were used to test the developed multivariate differentiation model. This confirmed model was successfully used to differentiate species in a dual-species biofilm and is comparable to morphology. The results show that the developed workflow was able to identify main clusters of bacteria based on spectral “fingerprint region” information from CRM. Using this workflow, we have demonstrated that CRM can spatially analyze two-species in vitro biofilms, therefore providing an alternative technique to map oral multi-species biofilm models.
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Affiliation(s)
- Lukas Simon Kriem
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | | | | | - Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
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22
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Stolarek P, Bernat P, Szczerbiec D, Różalski A. Phospholipids and Fatty Acids Affect the Colonization of Urological Catheters by Proteus mirabilis. Int J Mol Sci 2021; 22:ijms22168452. [PMID: 34445157 PMCID: PMC8395112 DOI: 10.3390/ijms22168452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
Proteus mirabilis-mediated CAUTIs are usually initiated by the adherence of bacteria to a urinary catheter surface. In this paper, three isolates of different origin and exhibiting different adhesion abilities were investigated in search of any changes in lipidome components which might contribute to P. mirabilis adhesion to catheters. Using GC-MS and LC-MS/MS techniques, 21 fatty acids and 27 phospholipids were identified in the examined cells. The comparison of the profiles of phospholipids and fatty acids obtained for catheter-attached cells and planktonic cells of the pathogens indicated C11:0 and PE 37:2 levels as values which could be related to P. mirabilis adhesion to a catheter, as well as cis C16:1, PE 32:0, PE 33:0, PE 38:2, PG 33:1, PG 34:0, PE 30:1, PE 32:1 and PG 30:2 levels as values which could be associated with cell hydrophobicity. Based on DiBAC4 (3) fluorescence intensity and an affinity to p-xylene, it was found that the inner membrane depolarization, as well as strong cell-surface hydrophobicity, were important for P. mirabilis adhesion to a silicone catheter. A generalized polarization of Laurdan showed lower values for P. mirabilis cells attached to the catheter surface than for planktonic cells, suggesting lower packing density of membrane components of the adherent cells compared with tightly packed, stiffened membranes of the planktonic cells. Taken together, these data indicate that high surface hydrophobicity, fluidization and depolarization of P. mirabilis cell membranes enable colonization of a silicone urinary catheter surface.
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Affiliation(s)
- Paulina Stolarek
- Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (D.S.); (A.R.)
- Correspondence: ; Tel.: +48-42-635-43-24; Fax: +48-42-665-58-18
| | - Przemysław Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
| | - Dominika Szczerbiec
- Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (D.S.); (A.R.)
| | - Antoni Różalski
- Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (D.S.); (A.R.)
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23
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Hollmann B, Perkins M, Chauhan VM, Aylott JW, Hardie KR. Fluorescent nanosensors reveal dynamic pH gradients during biofilm formation. NPJ Biofilms Microbiomes 2021; 7:50. [PMID: 34140515 PMCID: PMC8211749 DOI: 10.1038/s41522-021-00221-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the dynamic environmental microniches of biofilms will permit us to detect, manage and exploit these communities. The components and architecture of biofilms have been interrogated in depth; however, little is known about the environmental microniches present. This is primarily because of the absence of tools with the required measurement sensitivity and resolution to detect these changes. We describe the application of ratiometric fluorescent pH-sensitive nanosensors, as a tool, to observe physiological pH changes in biofilms in real time. Nanosensors comprised two pH-sensitive fluorophores covalently encapsulated with a reference pH-insensitive fluorophore in an inert polyacrylamide nanoparticle matrix. The nanosensors were used to analyse the real-time three-dimensional pH variation for two model biofilm formers: (i) opportunistic pathogen Pseudomonas aeruginosa and (ii) oral pathogen Streptococcus mutans. The detection of sugar metabolism in real time by nanosensors provides a potential application to identify therapeutic solutions to improve oral health.
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Affiliation(s)
- Birte Hollmann
- Biodiscovery Institute, School of Life Sciences, University Park, University of Nottingham, Nottingham, UK
- Advanced Materials & Healthcare Technologies, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Mark Perkins
- Biodiscovery Institute, School of Life Sciences, University Park, University of Nottingham, Nottingham, UK
- Advanced Materials & Healthcare Technologies, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Veeren M Chauhan
- Advanced Materials & Healthcare Technologies, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Jonathan W Aylott
- Advanced Materials & Healthcare Technologies, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Kim R Hardie
- Biodiscovery Institute, School of Life Sciences, University Park, University of Nottingham, Nottingham, UK.
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24
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Motta JP, Wallace JL, Buret AG, Deraison C, Vergnolle N. Gastrointestinal biofilms in health and disease. Nat Rev Gastroenterol Hepatol 2021; 18:314-334. [PMID: 33510461 DOI: 10.1038/s41575-020-00397-y] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 01/30/2023]
Abstract
Microorganisms colonize various ecological niches in the human habitat, as they do in nature. Predominant forms of multicellular communities called biofilms colonize human tissue surfaces. The gastrointestinal tract is home to a profusion of microorganisms with intertwined, but not identical, lifestyles: as isolated planktonic cells, as biofilms and in biofilm-dispersed form. It is therefore of major importance in understanding homeostatic and altered host-microorganism interactions to consider not only the planktonic lifestyle, but also biofilms and biofilm-dispersed forms. In this Review, we discuss the natural organization of microorganisms at gastrointestinal surfaces, stratification of microbiota taxonomy, biogeographical localization and trans-kingdom interactions occurring within the biofilm habitat. We also discuss existing models used to study biofilms. We assess the contribution of the host-mucosa biofilm relationship to gut homeostasis and to diseases. In addition, we describe how host factors can shape the organization, structure and composition of mucosal biofilms, and how biofilms themselves are implicated in a variety of homeostatic and pathological processes in the gut. Future studies characterizing biofilm nature, physical properties, composition and intrinsic communication could shed new light on gut physiology and lead to potential novel therapeutic options for gastrointestinal diseases.
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Affiliation(s)
- Jean-Paul Motta
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France.
| | - John L Wallace
- Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Antibe Therapeutics Inc., Toronto, ON, Canada
| | - André G Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Céline Deraison
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France
| | - Nathalie Vergnolle
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France. .,Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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25
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Suskind DL, Lee D, Kim YM, Wahbeh G, Singh N, Braly K, Nuding M, Nicora CD, Purvine SO, Lipton MS, Jansson JK, Nelson WC. The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn's Disease: A Randomized Diet Controlled Trial. Nutrients 2020; 12:nu12123749. [PMID: 33291229 PMCID: PMC7762109 DOI: 10.3390/nu12123749] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Crohn’s disease (CD) is a chronic inflammatory intestinal disorder associated with intestinal dysbiosis. Diet modulates the intestinal microbiome and therefore has a therapeutic potential. The aim of this study is to determine the potential efficacy of three versions of the specific carbohydrate diet (SCD) in active Crohn’s Disease. Methods: 18 patients with mild/moderate CD (PCDAI 15–45) aged 7 to 18 years were enrolled. Patients were randomized to either SCD, modified SCD(MSCD) or whole foods (WF) diet. Patients were evaluated at baseline, 2, 4, 8 and 12 weeks. PCDAI, inflammatory labs and multi-omics evaluations were assessed. Results: Mean age was 14.3 ± 2.9 years. At week 12, all participants (n = 10) who completed the study achieved clinical remission. The C-reactive protein decreased from 1.3 ± 0.7 at enrollment to 0.9 ± 0.5 at 12 weeks in the SCD group. In the MSCD group, the CRP decreased from 1.6 ± 1.1 at enrollment to 0.7 ± 0.1 at 12 weeks. In the WF group, the CRP decreased from 3.9 ± 4.3 at enrollment to 1.6 ± 1.3 at 12 weeks. In addition, the microbiome composition shifted in all patients across the study period. While the nature of the changes was largely patient specific, the predicted metabolic mode of the organisms increasing and decreasing in activity was consistent across patients. Conclusions: This study emphasizes the impact of diet in CD. Each diet had a positive effect on symptoms and inflammatory burden; the more exclusionary diets were associated with a better resolution of inflammation.
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Affiliation(s)
- David L. Suskind
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
- Correspondence: ; Tel.: +1-206-987-2521; Fax: +1-206-987-2721
| | - Dale Lee
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-M.K.); (C.D.N.); (J.K.J.); (W.C.N.)
| | - Ghassan Wahbeh
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Namita Singh
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Kimberly Braly
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Mason Nuding
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-M.K.); (C.D.N.); (J.K.J.); (W.C.N.)
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (S.O.P.); (M.S.L.)
| | - Mary S. Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (S.O.P.); (M.S.L.)
| | - Janet K. Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-M.K.); (C.D.N.); (J.K.J.); (W.C.N.)
| | - William C. Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-M.K.); (C.D.N.); (J.K.J.); (W.C.N.)
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26
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Seneviratne CJ, Suriyanarayanan T, Widyarman AS, Lee LS, Lau M, Ching J, Delaney C, Ramage G. Multi-omics tools for studying microbial biofilms: current perspectives and future directions. Crit Rev Microbiol 2020; 46:759-778. [PMID: 33030973 DOI: 10.1080/1040841x.2020.1828817] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The advent of omics technologies has greatly improved our understanding of microbial biology, particularly in the last two decades. The field of microbial biofilms is, however, relatively new, consolidated in the 1980s. The morphogenic switching by microbes from planktonic to biofilm phenotype confers numerous survival advantages such as resistance to desiccation, antibiotics, biocides, ultraviolet radiation, and host immune responses, thereby complicating treatment strategies for pathogenic microorganisms. Hence, understanding the mechanisms governing the biofilm phenotype can result in efficient treatment strategies directed specifically against molecular markers mediating this process. The application of omics technologies for studying microbial biofilms is relatively less explored and holds great promise in furthering our understanding of biofilm biology. In this review, we provide an overview of the application of omics tools such as transcriptomics, proteomics, and metabolomics as well as multi-omics approaches for studying microbial biofilms in the current literature. We also highlight how the use of omics tools directed at various stages of the biological information flow, from genes to metabolites, can be integrated via multi-omics platforms to provide a holistic view of biofilm biology. Following this, we propose a future artificial intelligence-based multi-omics platform that can predict the pathways associated with different biofilm phenotypes.
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Affiliation(s)
- Chaminda J Seneviratne
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore.,Duke NUS Medical School, Singapore, Singapore
| | - Tanujaa Suriyanarayanan
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore.,Duke NUS Medical School, Singapore, Singapore
| | - Armelia Sari Widyarman
- Department of Microbiology, Faculty of Dentistry, Trisakti University, Grogol, West Jakarta, Indonesia
| | - Lye Siang Lee
- Duke-NUS Medical School, Metabolomics Lab, Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Matthew Lau
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore
| | - Jianhong Ching
- Duke-NUS Medical School, Metabolomics Lab, Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Christopher Delaney
- School of Medicine, Dentistry & Nursing, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, UK
| | - Gordon Ramage
- School of Medicine, Dentistry & Nursing, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, UK
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Caniglia G, Kranz C. Scanning electrochemical microscopy and its potential for studying biofilms and antimicrobial coatings. Anal Bioanal Chem 2020; 412:6133-6148. [PMID: 32691088 PMCID: PMC7442582 DOI: 10.1007/s00216-020-02782-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/08/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023]
Abstract
Biofilms are known to be well-organized microbial communities embedded in an extracellular polymeric matrix, which supplies bacterial protection against external stressors. Biofilms are widespread and diverse, and despite the considerable large number of publications and efforts reported regarding composition, structure and cell-to-cell communication within biofilms in the last decades, the mechanisms of biofilm formation, the interaction and communication between bacteria are still not fully understood. This knowledge is required to understand why biofilms form and how we can combat them or how we can take advantage of these sessile communities, e.g. in biofuel cells. Therefore, in situ and real-time monitoring of nutrients, metabolites and quorum sensing molecules is of high importance, which may help to fill that knowledge gap. This review focuses on the potential of scanning electrochemical microscopy (SECM) as a versatile method for in situ studies providing temporal and lateral resolution in order to elucidate cell-to-cell communication, microbial metabolism and antimicrobial impact, e.g. of antimicrobial coatings through the study of electrochemical active molecules. Given the complexity and diversity of biofilms, challenges and limitations will be also discussed.
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Affiliation(s)
- Giada Caniglia
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee, 11, 89081, Ulm, Germany
| | - Christine Kranz
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee, 11, 89081, Ulm, Germany.
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28
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Hueso-Gil Á, Calles B, de Lorenzo V. The Wsp intermembrane complex mediates metabolic control of the swim-attach decision of Pseudomonas putida. Environ Microbiol 2020; 22:3535-3547. [PMID: 32519402 DOI: 10.1111/1462-2920.15126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 11/29/2022]
Abstract
Pseudomonas putida is a microorganism of biotechnological interest that-similar to many other environmental bacteria-adheres to surfaces and forms biofilms. Although various mechanisms contributing to the swim-attach decision have been studied in this species, the role of a 7-gene operon homologous to the wsp cluster of Pseudomonas aeruginosa-which regulates cyclic di-GMP (cdGMP) levels upon surface contact-remained to be investigated. In this work, the function of the wsp operon of P. putida KT2440 has been characterized through inspection of single and multiple wsp deletion variants, complementation with Pseudomonas aeruginosa's homologues, combined with mutations of regulatory genes fleQ and fleN and removal of the flagellar regulator fglZ. The ability of the resulting strains to form biofilms at 6 and 24 h under three different carbon regimes (citrate, glucose and fructose) revealed that the Wsp complex delivers a similar function to both Pseudomonas species. In P. putida, the key components include WspR, a protein that harbours the domain for producing cdGMP, and WspF, which controls its activity. These results not only contribute to a deeper understanding of the network that regulates the sessile-planktonic decision of P. putida but also suggest strategies to exogenously control such a lifestyle switch.
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Affiliation(s)
- Ángeles Hueso-Gil
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
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29
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Brescia F, Marchetti-Deschmann M, Musetti R, Perazzolli M, Pertot I, Puopolo G. The rhizosphere signature on the cell motility, biofilm formation and secondary metabolite production of a plant-associated Lysobacter strain. Microbiol Res 2020; 234:126424. [PMID: 32036275 DOI: 10.1016/j.micres.2020.126424] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/10/2020] [Accepted: 01/26/2020] [Indexed: 12/15/2022]
Abstract
Lysobacter spp. are common bacterial inhabitants of the rhizosphere of diverse plant species. However, the impact of the rhizosphere conditions on their physiology is still relatively understudied. To provide clues on the behaviour of Lysobacter spp. in this ecological niche, we investigated the physiology of L. capsici AZ78 (AZ78), a biocontrol strain isolated from tobacco rhizosphere, on a common synthetic growth medium (LBA) and on a growth medium containing components of the plant rhizosphere (RMA). The presence of a halo surrounding the AZ78 colony on RMA was a first visible effect related to differences in growth medium composition and it corresponded to the formation of a large outer ring. The lower quantity of nutrients available in RMA as compared with LBA was associated to a higher expression of a gene encoding cAMP-receptor-like protein (Clp), responsible for cell motility and biofilm formation regulation. AZ78 cells on RMA were motile, equipped with cell surface appendages and organised in small groups embedded in a dense layer of fibrils. Metabolic profiling by mass spectrometry imaging revealed increased diversity of analytes produced by AZ78 on RMA as compared with LBA. In particular, putative cyclic lipodepsipeptides, polycyclic tetramate macrolactams, cyclic macrolactams and other putative secondary metabolites with antibiotic activity were identified. Overall, the results obtained in this study shed a light on AZ78 potential to thrive in the rhizosphere by its ability to move, form biofilm and release secondary metabolites.
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Affiliation(s)
- Francesca Brescia
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; PhD school in Agricultural Science and Biotechnology, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Martina Marchetti-Deschmann
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Vienna, 1060, Austria
| | - Rita Musetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, 33100, Italy
| | - Michele Perazzolli
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Ilaria Pertot
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy.
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Matsuda F, Maeda K, Okahashi N. Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming. Sci Rep 2020; 10:286. [PMID: 31937835 PMCID: PMC6959353 DOI: 10.1038/s41598-019-57146-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022] Open
Abstract
Measurement of metabolic flux levels using stable isotope labeling has been successfully used to investigate metabolic redirection and reprogramming in living cells or tissues. The metabolic flux ratio between two reactions can be estimated from the 13C-labeling patterns of a few metabolites combined with the knowledge of atom mapping in the complicated metabolic network. However, it remains unclear whether an observed change in the labeling pattern of the metabolites is sufficient evidence of a shift in flux ratio between two metabolic states. In this study, a data analysis method was developed for the quantitative assessment of metabolic reprogramming. The Metropolis-Hastings algorithm was used with an in silico metabolic model to generate a probability distribution of metabolic flux levels under a condition in which the 13C-labeling pattern was observed. Reanalysis of literature data demonstrated that the developed method enables analysis of metabolic redirection using whole 13C-labeling pattern data. Quantitative assessment by Cohen’s effect size (d) enables a more detailed read-out of metabolic reprogramming information. The developed method will enable future applications of the metabolic isotopomer analysis to various targets, including cultured cells, whole tissues, and organs.
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Affiliation(s)
- Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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Xu Y, Dhaouadi Y, Stoodley P, Ren D. Sensing the unreachable: challenges and opportunities in biofilm detection. Curr Opin Biotechnol 2019; 64:79-84. [PMID: 31766008 DOI: 10.1016/j.copbio.2019.10.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022]
Abstract
Bacteria can attach to essentially all materials and form multicellular biofilms with high-level tolerance to antimicrobials. Detrimental biofilms are responsible for a variety of problems ranging from food and water contamination, bio-corrosion, to drug resistant infections. Besides the challenges in control, biofilms are also difficult to detect due to the lack of biofilm-specific biomarkers and methods for non-destructive imaging. In this article, we present a concise review of recent advancements in this field, with a focus on medical device-associated infections. We also discuss the technologies that have potential for non-destructive detection of bacterial biofilms.
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Affiliation(s)
- Yikang Xu
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, United States; Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, United States
| | - Yousr Dhaouadi
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, United States; Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, United States
| | - Paul Stoodley
- Departments of Microbial Infection and Immunity and Orthopaedics and the Infectious Diseases Institute, Ohio State University, Columbus, OH 43210, United States; National Centre for Advanced Tribology at Southampton (nCATS), and National Biofilm Innovation Centre, Mechanical Engineering, University of Southampton, United Kingdom
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, United States; Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, United States; Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244, United States; Department of Biology, Syracuse University, Syracuse, NY 13244, United States.
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Wu C, Herold RA, Knoshaug EP, Wang B, Xiong W, Laurens LML. Fluxomic Analysis Reveals Central Carbon Metabolism Adaptation for Diazotroph Azotobacter vinelandii Ammonium Excretion. Sci Rep 2019; 9:13209. [PMID: 31520074 PMCID: PMC6744558 DOI: 10.1038/s41598-019-49717-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/30/2019] [Indexed: 11/09/2022] Open
Abstract
Diazotrophic bacteria are an attractive biological alternative to synthetic nitrogen fertilizers due to their remarkable capacity to fix atmospheric nitrogen gas to ammonium via nitrogenase enzymes. However, how diazotrophic bacteria tailor central carbon catabolism to accommodate the energy requirement for nitrogenase activity is largely unknown. In this study, we used Azotobacter vinelandii DJ and an ammonium excreting mutant, AV3 (ΔNifL), to investigate central carbon metabolism fluxes and central cell bioenergetics in response to ammonium availability and nitrogenase activity. Enabled by the powerful and reliable methodology of 13C-metabolic flux analysis, we show that the respiratory TCA cycle is upregulated in association with increased nitrogenase activity and causes a monotonic decrease in specific growth rate. Whereas the activity of the glycolytic Entner-Doudoroff pathway is positively correlated with the cell growth rate. These new observations are formulated into a 13C-metabolic flux model which further improves the understanding and interpretation of intracellular bioenergetics. This analysis leads to the conclusion that, under aerobic conditions, respiratory TCA metabolism is responsible for the supply of additional ATP and reducing equivalents required for elevated nitrogenase activity. This study provides a quantitative relationship between central carbon and nitrogen metabolism in an aerobic diazotroph for the first time.
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Affiliation(s)
- Chao Wu
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Ryan A Herold
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Bo Wang
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Wei Xiong
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA.
| | - Lieve M L Laurens
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA.
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Shimizu K, Matsuoka Y. Redox rebalance against genetic perturbations and modulation of central carbon metabolism by the oxidative stress regulation. Biotechnol Adv 2019; 37:107441. [PMID: 31472206 DOI: 10.1016/j.biotechadv.2019.107441] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/04/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022]
Abstract
The micro-aerophilic organisms and aerobes as well as yeast and higher organisms have evolved to gain energy through respiration (via oxidative phosphorylation), thereby enabling them to grow much faster than anaerobes. However, during respiration, reactive oxygen species (ROSs) are inherently (inevitably) generated, and threaten the cell's survival. Therefore, living organisms (or cells) must furnish the potent defense systems to keep such ROSs at harmless level, where the cofactor balance plays crucial roles. Namely, NADH is the source of energy generation (catabolism) in the respiratory chain reactions, through which ROSs are generated, while NADPH plays important roles not only for the cell synthesis (anabolism) but also for detoxifying ROSs. Therefore, the cell must rebalance the redox ratio by modulating the fluxes of the central carbon metabolism (CCM) by regulating the multi-level regulation machinery upon genetic perturbations and the change in the growth conditions. Here, we discuss about how aerobes accomplish such cofactor homeostasis against redox perturbations. In particular, we consider how single-gene mutants (including pgi, pfk, zwf, gnd and pyk mutants) modulate their metabolisms in relation to cofactor rebalance (and also by adaptive laboratory evolution). We also discuss about how the overproduction of NADPH (by the pathway gene mutation) can be utilized for the efficient production of useful value-added chemicals such as medicinal compounds, polyhydroxyalkanoates, and amino acids, all of which require NADPH in their synthetic pathways. We then discuss about the metabolic responses against oxidative stress, where αketoacids play important roles not only for the coordination between catabolism and anabolism, but also for detoxifying ROSs by non-enzymatic reactions, as well as for reducing the production of ROSs by repressing the activities of the TCA cycle and respiration (via carbon catabolite repression). Thus, we discuss about the mechanisms (basic strategies) that modulate the metabolism from respiration to respiro-fermentative metabolism causing overflow, based on the role of Pyk activity, affecting the NADPH production at the oxidative pentose phosphate (PP) pathway, and the roles of αketoacids for the change in the source of energy generation from the oxidative phosphorylation to the substrate level phosphorylation.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio university, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
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