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Rolli E, Ghitti E, Mapelli F, Borin S. Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity. FRONTIERS IN PLANT SCIENCE 2024; 15:1429096. [PMID: 39036359 PMCID: PMC11258928 DOI: 10.3389/fpls.2024.1429096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/13/2024] [Indexed: 07/23/2024]
Abstract
Introduction The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized. Methods Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms. Results Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation. Discussion These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.
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Affiliation(s)
| | | | | | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Kennelly C, Tran P, Prindle A. Environmental purines decrease Pseudomonas aeruginosa biofilm formation by disrupting c-di-GMP metabolism. Cell Rep 2024; 43:114154. [PMID: 38669142 PMCID: PMC11197132 DOI: 10.1016/j.celrep.2024.114154] [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: 11/06/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Cyclic di-guanosine monophosphate (c-di-GMP) is a bacterial second messenger that governs the lifestyle switch between planktonic and biofilm states. While substantial investigation has focused on the proteins that produce and degrade c-di-GMP, less attention has been paid to the potential for metabolic control of c-di-GMP signaling. Here, we show that micromolar levels of specific environmental purines unexpectedly decrease c-di-GMP and biofilm formation in Pseudomonas aeruginosa. Using a fluorescent genetic reporter, we show that adenosine and inosine decrease c-di-GMP even when competing purines are present. We confirm genetically that purine salvage is required for c-di-GMP decrease. Furthermore, we find that (p)ppGpp prevents xanthosine and guanosine from producing an opposing c-di-GMP increase, reinforcing a salvage hierarchy that favors c-di-GMP decrease even at the expense of growth. We propose that purines can act as a cue for bacteria to shift their lifestyle away from the recalcitrant biofilm state via upstream metabolic control of c-di-GMP signaling.
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Affiliation(s)
- Corey Kennelly
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Peter Tran
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Arthur Prindle
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
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Warsi OM, Upterworth LM, Breidenstein A, Lustig U, Mikkelsen K, Nagy T, Szatmari D, Ingmer H, Andersson DI. Staphylococcus aureus mutants resistant to the feed-additive monensin show increased virulence and altered purine metabolism. mBio 2024; 15:e0315523. [PMID: 38214510 PMCID: PMC10865815 DOI: 10.1128/mbio.03155-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024] Open
Abstract
Ionophores are antibacterial compounds that affect bacterial growth by changing intracellular concentrations of the essential cations, sodium and potassium. They are extensively used in animal husbandry to increase productivity and reduce infectious diseases, but our understanding of the potential for and effects of resistance development to ionophores is poorly known. Thus, given their widespread global usage, it is important to determine the potential negative consequences of ionophore use on human and animal health. In this study, we demonstrate that exposure to the ionophore monensin can select for resistant mutants in the human and animal pathogen Staphylococcus aureus, with a majority of the resistant mutants showing increased growth rates in vitro and/or in mice. Whole-genome sequencing and proteomic analysis of the resistant mutants show that the resistance phenotype is associated with de-repression of de novo purine synthesis, which could be achieved through mutations in different transcriptional regulators including mutations in the gene purR, the repressor of the purine de novo synthesis pathway. This study shows that mutants with reduced susceptibility to the ionophore monensin can be readily selected and highlights an unexplored link between ionophore resistance, purine metabolism, and fitness in pathogenic bacteria.IMPORTANCEThis study demonstrates a novel link between ionophore resistance, purine metabolism, and virulence/fitness in the key human and animal pathogen Staphylococcus aureus. The results show that mutants with reduced susceptibility to the commonly used ionophore monensin can be readily selected and that the reduced susceptibility observed is associated with an increased expression of the de novo purine synthesis pathway. This study increases our understanding of the impact of the use of animal feed additives on both human and veterinary medicine.
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Affiliation(s)
- Omar M. Warsi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lina M. Upterworth
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Annika Breidenstein
- Department of Medical Chemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Ulrika Lustig
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kasper Mikkelsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tamás Nagy
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Dávid Szatmari
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Ghitti E, Rolli E, Vergani L, Borin S. Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400. FRONTIERS IN PLANT SCIENCE 2024; 15:1325048. [PMID: 38371405 PMCID: PMC10869545 DOI: 10.3389/fpls.2024.1325048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Introduction Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress. Methods By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400. Results Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern. Discussions This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.
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Affiliation(s)
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Maisat W, Yuki K. Volatile anesthetic isoflurane exposure facilitates Enterococcus biofilm infection. FASEB J 2023; 37:e23186. [PMID: 37665578 PMCID: PMC10495085 DOI: 10.1096/fj.202301128r] [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: 06/06/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Enterococcus faecalis (E. faecalis) is one of the major pathogenic bacteria responsible for surgical site infections. Biofilm infections are major hospital-acquired infections. Previous studies suggested that ions could regulate biofilm formation in microbes. Volatile anesthetics, frequently administered in surgical setting, target ion channels. Here, we investigated the role of ion channels/transporters and volatile anesthetics in the biofilm formation by E. faecalis MMH594 strain and its ion transporter mutants. We found that a chloride transporter mutant significantly reduced biofilm formation compared to the parental strain. Downregulation of teichoic acid biosynthesis in the chloride transporter mutant impaired biofilm matrix formation and cellular adhesion, leading to mitigated biofilm formation. Among anesthetics, isoflurane exposure enhanced biofilm formation in vitro and in vivo. The upregulation of de novo purine biosynthesis pathway by isoflurane exposure potentially enhanced biofilm formation, an essential process for DNA, RNA, and ATP synthesis. We also demonstrated that isoflurane exposure to E. faecalis increased cyclic-di-AMP and extracellular DNA production, consistent with the increased purine biosynthesis. We further showed that isoflurane enhanced the enzymatic activity of phosphoribosyl pyrophosphate synthetase (PRPP-S). With the hypothesis that isoflurane directly bound to PRPP-S, we predicted isoflurane binding site on it using rigid docking. Our study provides a better understanding of the underlying mechanisms of E. faecalis biofilm formation and highlights the potential impact of an ion transporter and volatile anesthetic on this process. These findings may lead to the development of novel strategies for preventing E. faecalis biofilm formation and improving patient outcomes in clinical settings.
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Affiliation(s)
- Wiriya Maisat
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children’s Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Anesthesiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children’s Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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Xu T, Xiao Y, Wang H, Zhu J, Lu W, Chen W. Multiomics reveals the mechanism of B. longum in promoting the formation of mixed-species biofilms. Food Funct 2023; 14:8276-8290. [PMID: 37602484 DOI: 10.1039/d3fo01751f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
It has been found previously that Bifidobacterium longum, Bacteroides ovatus, Enterococcus faecalis, and Lactobacillus gasseri can form a biofilm better when co-cultured in vitro and B. longum is the core biofilm-formation-promoting strain in this community. B. longum is part of the core microbiota in the gut and is widely recognized as a probiotic. Therefore, it is necessary to explore its role in mixed-species biofilms through transcriptomics and metabolomics. Metabolomics showed that the increase in amino acid and purine content could promote biofilm formation. In transcriptomic analysis, many genes related to carbohydrate metabolism, amino acid metabolism, and environmental tolerance of B. longum were up-regulated. Combined with the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) analysis, the differentially expressed genes (DEGs) of B. longum in mixed-species biofilms were mainly correlated to "quorum sensing (QS)", "ABC transporters", "biosynthesis of amino acids", "microbial metabolism in different environments", "carbohydrate metabolism" and "two-component system". In addition, the rpl and rps gene families, which function in the metabolism of organic substances and the biosynthesis of amino acids, were the core DEGs according to the analysis of the protein-protein interaction (PPI) network. Finally, by combining metabolomics and quorum sensing mechanisms, it was found that the metabolism of autoinducer peptides (proliylglycine and glycylleucine), N-acyl homoserine lactone (N-(3-oxo hydroxy) homoserine lactone), and AI-2 can promote the formation of biofilms, both mono- and mixed-species biofilms composed of B. longum. Our research enabled us to understand the critical role of B. longum in mixed-species biofilms and the interactions between biofilm metabolism and gut health. In addition, the generated knowledge will be of great significance for us to develop biofilm products with beneficial functions in future.
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Affiliation(s)
- Tao Xu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yue Xiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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Pormohammad A, Firrincieli A, Salazar-Alemán DA, Mohammadi M, Hansen D, Cappelletti M, Zannoni D, Zarei M, Turner RJ. Insights into the Synergistic Antibacterial Activity of Silver Nitrate with Potassium Tellurite against Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0062823. [PMID: 37409940 PMCID: PMC10433965 DOI: 10.1128/spectrum.00628-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
The constant, ever-increasing antibiotic resistance crisis leads to the announcement of "urgent, novel antibiotics needed" by the World Health Organization. Our previous works showed a promising synergistic antibacterial activity of silver nitrate with potassium tellurite out of thousands of other metal/metalloid-based antibacterial combinations. The silver-tellurite combined treatment not only is more effective than common antibiotics but also prevents bacterial recovery, decreases the risk of future resistance chance, and decreases the effective concentrations. We demonstrate that the silver-tellurite combination is effective against clinical isolates. Further, this study was conducted to address knowledge gaps in the available data on the antibacterial mechanism of both silver and tellurite, as well as to give insight into how the mixture provides synergism as a combination. Here, we defined the differentially expressed gene profile of Pseudomonas aeruginosa under silver, tellurite, and silver-tellurite combination stress using an RNA sequencing approach to examine the global transcriptional changes in the challenged cultures grown in simulated wound fluid. The study was complemented with metabolomics and biochemistry assays. Both metal ions mainly affected four cellular processes, including sulfur homeostasis, reactive oxygen species response, energy pathways, and the bacterial cell membrane (for silver). Using a Caenorhabditis elegans animal model we showed silver-tellurite has reduced toxicity over individual metal/metalloid salts and provides increased antioxidant properties to the host. This work demonstrates that the addition of tellurite would improve the efficacy of silver in biomedical applications. IMPORTANCE Metals and/or metalloids could represent antimicrobial alternatives for industrial and clinical applications (e.g., surface coatings, livestock, and topical infection control) because of their great properties, such as good stability and long half-life. Silver is the most common antimicrobial metal, but resistance prevalence is high, and it can be toxic to the host above a certain concentration. We found that a silver-tellurite composition has antibacterial synergistic effect and that the combination is beneficial to the host. So, the efficacy and application of silver could increase by adding tellurite in the recommended concentration(s). We used different methods to evaluate the mechanism for how this combination can be so incredibly synergistic, leading to efficacy against antibiotic- and silver-resistant isolates. Our two main findings are that (i) both silver and tellurite mostly target the same pathways and (ii) the coapplication of silver with tellurite tends not to target new pathways but targets the same pathways with an amplified change.
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Affiliation(s)
- Ali Pormohammad
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
- CCrest Laboratories, Inc., Montreal, Quebec, Canada
| | - Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo, Italy
| | - Daniel A. Salazar-Alemán
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Mehdi Mohammadi
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Dave Hansen
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Mohammad Zarei
- Renal Division, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- John B. Little Center for Radiation Sciences, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Raymond J. Turner
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
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Wang TY, Guo R, Hu LL, Liu JJ, Lu HT. Mass Spectrometry-Based Targeted Metabolomics Revealed the Regulatory Roles of Magnesium on Biofilm Formation in Escherichia coli by Targeting Functional Metabolites. JOURNAL OF ANALYSIS AND TESTING 2022. [DOI: 10.1007/s41664-021-00208-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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The de novo Purine Biosynthesis Pathway Is the Only Commonly Regulated Cellular Pathway during Biofilm Formation in TSB-Based Medium in Staphylococcus aureus and Enterococcus faecalis. Microbiol Spectr 2021; 9:e0080421. [PMID: 34935415 PMCID: PMC8693917 DOI: 10.1128/spectrum.00804-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial biofilms are involved in chronic infections and confer 10 to 1,000 times more resistance to antibiotics compared with planktonic growth, leading to complications and treatment failure. When transitioning from a planktonic lifestyle to biofilms, some Gram-positive bacteria are likely to modulate several cellular pathways, including central carbon metabolism, biosynthesis pathways, and production of secondary metabolites. These metabolic adaptations might play a crucial role in biofilm formation by Gram-positive pathogens such as Staphylococcus aureus and Enterococcus faecalis. Here, we performed a transcriptomic approach to identify cellular pathways that might be similarly regulated during biofilm formation in these bacteria. Different strains and biofilm-inducing media were used to identify a set of regulated genes that are common and independent of the environment or accessory genomes analyzed. Our approach highlighted that the de novo purine biosynthesis pathway was upregulated in biofilms of both species when using a tryptone soy broth-based medium but not so when a brain heart infusion-based medium was used. We did not identify other pathways commonly regulated between both pathogens. Gene deletions and usage of a drug targeting a key enzyme showed the importance of this pathway in biofilm formation of S. aureus. The importance of the de novo purine biosynthesis pathway might reflect an important need for purine during biofilm establishment, and thus could constitute a promising drug target. IMPORTANCE Biofilms are often involved in nosocomial infections and can cause serious chronic infections if not treated properly. Current anti-biofilm strategies rely on antibiotic usage, but they have a limited impact because of the biofilm intrinsic tolerance to drugs. Metabolism remodeling likely plays a central role during biofilm formation. Using comparative transcriptomics of different strains of Staphylococcus aureus and Enterococcus faecalis, we determined that almost all cellular adaptations are not shared between strains and species. Interestingly, we observed that the de novo purine biosynthesis pathway was upregulated during biofilm formation by both species in a specific medium. The requirement for purine could constitute an interesting new anti-biofilm target with a wide spectrum that could also prevent resistance evolution. These results are also relevant to a better understanding of the physiology of biofilm formation.
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Gough EK, Edens TJ, Geum HM, Baharmand I, Gill SK, Robertson RC, Mutasa K, Ntozini R, Smith LE, Chasekwa B, Majo FD, Tavengwa NV, Mutasa B, Francis F, Carr L, Tome J, Stoltzfus RJ, Moulton LH, Prendergast AJ, Humphrey JH, Manges AR, Team SHINET. Maternal fecal microbiome predicts gestational age, birth weight and neonatal growth in rural Zimbabwe. EBioMedicine 2021; 68:103421. [PMID: 34139432 PMCID: PMC8217692 DOI: 10.1016/j.ebiom.2021.103421] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Preterm birth and low birth weight (LBW) affect one in ten and one in seven livebirths, respectively, primarily in low-income and middle-income countries (LMIC) and are major predictors of poor child health outcomes. However, both have been recalcitrant to public health intervention. The maternal intestinal microbiome may undergo substantial changes during pregnancy and may influence fetal and neonatal health in LMIC populations. METHODS Within a subgroup of 207 mothers and infants enrolled in the SHINE trial in rural Zimbabwe, we performed shotgun metagenomics on 351 fecal specimens provided during pregnancy and at 1-month post-partum to investigate the relationship between the pregnancy gut microbiome and infant gestational age, birth weight, 1-month length-, and weight-for-age z-scores using extreme gradient boosting machines. FINDINGS Pregnancy gut microbiome taxa and metabolic functions predicted birth weight and WAZ at 1 month more accurately than gestational age and LAZ. Blastoscystis sp, Brachyspira sp and Treponeme carriage were high compared to Western populations. Resistant starch-degraders were important predictors of birth outcomes. Microbiome capacity for environmental sensing, vitamin B metabolism, and signalling predicted increased infant birth weight and neonatal growth; while functions involved in biofilm formation in response to nutrient starvation predicted reduced birth weight and growth. INTERPRETATION The pregnancy gut microbiome in rural Zimbabwe is characterized by resistant starch-degraders and may be an important metabolic target to improve birth weight. FUNDING Bill and Melinda Gates Foundation, UK Department for International Development, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, and UNICEF.
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Affiliation(s)
- Ethan K. Gough
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thaddeus J. Edens
- Devil's Staircase Consulting, West Vancouver, British Columbia, Canada
| | - Hyun Min Geum
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Iman Baharmand
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Sandeep K. Gill
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | | | - Kuda Mutasa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Robert Ntozini
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Laura E Smith
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Department of Population Medicine and Diagnostics, Cornell University, Ithaca, NY, USA
| | - Bernard Chasekwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Florence D. Majo
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Naume V. Tavengwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Batsirai Mutasa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Freddy Francis
- Department of Experimental Medicine, University of British Columbia, Canada
| | - Lynnea Carr
- Department of Microbiology and Immunology, University of British Columbia, Canada
| | - Joice Tome
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | | | - Lawrence H. Moulton
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew J. Prendergast
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Blizard Institute, Queen Mary University of London, London, UK
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Jean H. Humphrey
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Blizard Institute, Queen Mary University of London, London, UK
| | - Amee R. Manges
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - SHINE Trial Team
- Members of the SHINE Trial team who are not named authors are listed in https://academic.oup.com/cid/article/61/suppl_7/S685/358186
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Interspecies Metabolic Complementation in Cystic Fibrosis Pathogens via Purine Exchange. Pathogens 2021; 10:pathogens10020146. [PMID: 33535659 PMCID: PMC7912780 DOI: 10.3390/pathogens10020146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 11/17/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease frequently associated with chronic lung infections caused by a consortium of pathogens. It is common for auxotrophy (the inability to biosynthesize certain essential metabolites) to develop in clinical isolates of the dominant CF pathogen Pseudomonas aeruginosa, indicating that the CF lung environment is replete in various nutrients. Many of these nutrients are likely to come from the host tissues, but some may come from the surrounding polymicrobial community within the lungs of CF patients as well. To assess the feasibility of nutrient exchange within the polymicrobial community of the CF lung, we selected P. aeruginosa and Staphylococcus aureus, two of the most prevalent species found in the CF lung environment. By comparing the polymicrobial culture of wild-type strains relative to their purine auxotrophic counterparts, we were able to observe metabolic complementation occurring in both P. aeruginosa and S. aureus when grown with a purine-producing cross-species pair. While our data indicate that some of this complementation is likely derived from extracellular DNA freed by lysis of S. aureus by the highly competitive P. aeruginosa, the partial complementation of S. aureus purine deficiency by P. aeruginosa demonstrates that bidirectional nutrient exchange between these classic competitors is possible.
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12
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Nan J, Zhang S, Zhan P, Jiang L. Evaluation of Bronopol and Disulfiram as Potential Candidatus Liberibacter asiaticus Inosine 5'-Monophosphate Dehydrogenase Inhibitors by Using Molecular Docking and Enzyme Kinetic. Molecules 2020; 25:E2313. [PMID: 32423116 PMCID: PMC7287799 DOI: 10.3390/molecules25102313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
Citrus huanglongbing (HLB) is a destructive disease that causes significant damage to many citrus producing areas worldwide. To date, no strategy against this disease has been established. Inosine 5'-monophosphate dehydrogenase (IMPDH) plays crucial roles in the de novo synthesis of guanine nucleotides. This enzyme is used as a potential target to treat bacterial infection. In this study, the crystal structure of a deletion mutant of CLas IMPDHΔ98-201 in the apo form was determined. Eight known bioactive compounds were used as ligands for molecular docking. The results showed that bronopol and disulfiram bound to CLas IMPDHΔ98-201 with high affinity. These compounds were tested for their inhibition against CLas IMPDHΔ98-201 activity. Bronopol and disulfiram showed high inhibition at nanomolar concentrations, and bronopol was found to be the most potent molecule (Ki = 234 nM). The Ki value of disulfiram was 616 nM. These results suggest that bronopol and disulfiram can be considered potential candidate agents for the development of CLas inhibitors.
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Affiliation(s)
- Jing Nan
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
| | - Shaoran Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ping Zhan
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
| | - Ling Jiang
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
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13
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Martinez S, Garcia JG, Williams R, Elmassry M, West A, Hamood A, Hurtado D, Gudenkauf B, Ventolini G, Schlabritz-Loutsevitch N. Lactobacilli spp.: real-time evaluation of biofilm growth. BMC Microbiol 2020; 20:64. [PMID: 32209050 PMCID: PMC7092459 DOI: 10.1186/s12866-020-01753-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Biofilm is a fundamental bacterial survival mode which proceeds through three main generalized phases: adhesion, maturation, and dispersion. Lactobacilli spp. (LB) are critical components of gut and reproductive health and are widely used probiotics. Evaluation of time-dependent mechanisms of biofilm formation is important for understanding of host-microbial interaction and development of therapeutic interventions. Time-dependent LB biofilm growth was studied in two systems: large biofilm output in continuous flow system (microfermenter (M), Institute Pasteur, France) and electrical impedance-based real time label-free cell analyzer (C) (xCELLigence, ACEA Bioscience Inc., San Diego, CA). L. plantarum biofilm growth in M system was video-recorded, followed by analyses using IMARIS software (Bitplane, Oxford Instrument Company, Concord, MA, USA). Additionally, whole genome expression and analyses of attached (A) and dispersed (D) biofilm phases at 24 and 48 h were performed. RESULTS The dynamic of biofilm growth of L. plantarum was similar in both systems except for D phases. Comparison of the transcriptome of A and D phases revealed, that 121 transcripts differ between two phases at 24 h. and 35 transcripts - at 48 h. of M growth. The main pathways, down-regulated in A compared to D phases after 24 h. were transcriptional regulation, purine nucleotide biosynthesis, and L-aspartate biosynthesis, and the upregulated pathways were fatty acid and phospholipid metabolism as well as ABC transporters and purine nucleotide biosynthesis. Four LB species differed in the duration and amplitude of attachment phases, while growth phases were similar. CONCLUSION LB spp. biofilm growth and propagation area dynamic, time-dependent processes with species-specific and time specific characteristics. The dynamic of LB biofilm growth agrees with published pathophysiological data and points out that real time evaluation is an important tool in understanding growth of microbial communities.
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Affiliation(s)
- Stacy Martinez
- Texas Tech University Health Sciences Center at the Permian Basin, 701 W. 5th Street, Odessa, TX, 79763, USA
| | - Jonathan Gomez Garcia
- Texas Tech University Health Sciences Center at the Permian Basin, 701 W. 5th Street, Odessa, TX, 79763, USA.,University of Texas at the Permian Basin, Odessa, TX, USA
| | - Roy Williams
- Texas Tech University Health Sciences Center at the Permian Basin, 701 W. 5th Street, Odessa, TX, 79763, USA.,University of Texas at the Permian Basin, Odessa, TX, USA
| | - Moamen Elmassry
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Andrew West
- Texas Tech University Health Sciences Center at the Permian Basin, 701 W. 5th Street, Odessa, TX, 79763, USA
| | - Abdul Hamood
- Department of Microbiology and Immunology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | | | - Brent Gudenkauf
- Texas Tech University Health Sciences Center at the Permian Basin, 701 W. 5th Street, Odessa, TX, 79763, USA
| | - Gary Ventolini
- Texas Tech University Health Sciences Center at the Permian Basin, 701 W. 5th Street, Odessa, TX, 79763, USA.
| | - Natalia Schlabritz-Loutsevitch
- Texas Tech University Health Sciences Center at the Permian Basin, 701 W. 5th Street, Odessa, TX, 79763, USA. .,Department of Neurobiology and Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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14
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Silva KCS, Silva LOS, Silva GAA, Borges CL, Novaes E, Paccez JD, Fontes W, Giambiagi-deMarval M, Soares CMDA, Parente-Rocha JA. Staphylococcus saprophyticus Proteomic Analyses Elucidate Differences in the Protein Repertories among Clinical Strains Related to Virulence and Persistence. Pathogens 2020; 9:pathogens9010069. [PMID: 31963821 PMCID: PMC7169411 DOI: 10.3390/pathogens9010069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus saprophyticus is a Gram-positive and coagulase negative cocci that composes the skin microbiota and can act as an opportunistic agent causing urinary tract infections, being more frequent in sexually active young women. The ability of a pathogen to cause infection in the host is associated to its ability to adhere to host cells and to survive host immune defenses. In this work, we presented the comparative proteomic profile of three S. saprophyticus strains. It was possible to characterize differences in the proteome content, specially related to expression of virulence factors. We compiled this data and previous data and we detected one strain (9325) possessing higher production and secretion of proteins related to virulence. Our results show that phenotypic, genotypic, and proteomic differences reflect in the ability to survive during interaction with host cells, since the 9325 strain presented a higher survival rate after macrophage interaction. In counterpart, the 7108 strain that possesses lower content of proteins related to virulence presented higher ability to form biofilm suggesting that this strain can be better adapted to persist in the host and in the environment. Our work describes, for the first time, proteomic flexibility among S. saprophyticus strains, reflecting in virulence and persistence.
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Affiliation(s)
- Karla Christina Sousa Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Lana O’Hara Souza Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Guilherme Algusto Alves Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Lavras 37200-900, Brazil;
| | - Juliano Domiraci Paccez
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Wagner Fontes
- Laboratório de Química de Proteínas, Instituto de Biologia, Universidade de Brasília, UnB-Brasilia 70910-900, Brazil;
| | - Marcia Giambiagi-deMarval
- Laboratório de Microbiologia Molecular, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro-RJ 21941-902, Brazil;
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
- Correspondence:
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15
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Bottagisio M, Soggiu A, Piras C, Bidossi A, Greco V, Pieroni L, Bonizzi L, Roncada P, Lovati AB. Proteomic Analysis Reveals a Biofilm-Like Behavior of Planktonic Aggregates of Staphylococcus epidermidis Grown Under Environmental Pressure/Stress. Front Microbiol 2019; 10:1909. [PMID: 31551940 PMCID: PMC6743020 DOI: 10.3389/fmicb.2019.01909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/05/2019] [Indexed: 01/14/2023] Open
Abstract
Prosthetic joint replacement failure has a huge impact on quality of life and hospitalization costs. A leading cause of prosthetic joint infection is bacteria-forming biofilm on the surface of orthopedic devices. Staphylococcus epidermidis is an emergent, low-virulence pathogen implicated in chronic infections, barely indistinguishable from aseptic loosening when embedded in a mature matrix. The literature on the behavior of quiescent S. epidermidis in mature biofilms is scarce. To fill this gap, we performed comparative analysis of the whole proteomic profiles of two methicillin-resistant S. epidermidis strains growing in planktonic and in sessile form to investigate the molecular mechanisms underlying biofilm stability. After 72-h culture of biofilm-forming S. epidermidis, overexpression of proteins involved in the synthesis of nucleoside triphosphate and polysaccharides was observed, whereas planktonic bacteria expressed proteins linked to stress and anaerobic growth. Cytological analysis was performed to determine why planktonic bacteria unexpectedly expressed proteins typical of sessile culture. Images evidenced that prolonged culture under vigorous agitation can create a stressful growing environment that triggers microorganism aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. The choice of a unique late time point provided an important clue for future investigations into the biofilm-like behavior of planktonic cells. Our preliminary results may inform comparative proteomic strategies in the study of mature bacterial biofilm. Finally, there is an increasing number of studies on the aggregation of free-floating bacteria embedded in an extracellular matrix, prompting the need to gain further insight into this mode of bacterial growth.
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Affiliation(s)
- Marta Bottagisio
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Alessio Soggiu
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Cristian Piras
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Alessandro Bidossi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Viviana Greco
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore Roma, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Luigi Bonizzi
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Paola Roncada
- Department of Health Sciences, Università degli Studi "Magna Græcia", Catanzaro, Italy
| | - Arianna B Lovati
- IRCCS Istituto Ortopedico Galeazzi, Cell and Tissue Engineering Laboratory, Milan, Italy
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16
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Doan T, Hinterwirth A, Worden L, Arzika AM, Maliki R, Abdou A, Kane S, Zhong L, Cummings ME, Sakar S, Chen C, Cook C, Lebas E, Chow ED, Nachamkin I, Porco TC, Keenan JD, Lietman TM. Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution. Nat Med 2019; 25:1370-1376. [PMID: 31406349 DOI: 10.1038/s41591-019-0533-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/25/2019] [Indexed: 01/25/2023]
Abstract
The MORDOR I trial1, conducted in Niger, Malawi and Tanzania, demonstrated that mass azithromycin distribution to preschool children reduced childhood mortality1. However, the large but simple trial design precluded determination of the mechanisms involved. Here we examined the gut microbiome of preschool children from 30 Nigerien communities randomized to either biannual azithromycin or placebo. Gut microbiome γ-diversity was not significantly altered (P = 0.08), but the relative abundances of two Campylobacter species, along with another 33 gut bacteria, were significantly reduced in children treated with azithromycin at the 24-month follow-up. Metagenomic analysis revealed functional differences in gut bacteria between treatment groups. Resistome analysis showed an increase in macrolide resistance gene expression in gut microbiota in communities treated with azithromycin (P = 0.004). These results suggest that prolonged mass azithromycin distribution to reduce childhood mortality reduces certain gut bacteria, including known pathogens, while selecting for antibiotic resistance.
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Affiliation(s)
- T Doan
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA.
- Department of Ophthalmology, University of California, San Francisco, CA, USA.
| | - A Hinterwirth
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - L Worden
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | | | - R Maliki
- The Carter Center, Niamey, Niger
| | - A Abdou
- Ministry of Public Health, Niamey, Niger
- Programme National de Soins Oculaires, Niamey, Niger
| | - S Kane
- The Carter Center, Niamey, Niger
| | - L Zhong
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - M E Cummings
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - S Sakar
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - C Chen
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - C Cook
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - E Lebas
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
| | - E D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - I Nachamkin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - T C Porco
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - J D Keenan
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - T M Lietman
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
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17
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Balasubramanian S, Skaf J, Holzgrabe U, Bharti R, Förstner KU, Ziebuhr W, Humeida UH, Abdelmohsen UR, Oelschlaeger TA. A New Bioactive Compound From the Marine Sponge-Derived Streptomyces sp. SBT348 Inhibits Staphylococcal Growth and Biofilm Formation. Front Microbiol 2018; 9:1473. [PMID: 30050506 PMCID: PMC6050364 DOI: 10.3389/fmicb.2018.01473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/13/2018] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus epidermidis, the common inhabitant of human skin and mucosal surfaces has emerged as an important pathogen in patients carrying surgical implants and medical devices. Entering the body via surgical sites and colonizing the medical devices through formation of multi-layered biofilms leads to refractory and persistent device-related infections (DRIs). Staphylococci organized in biofilms are more tolerant to antibiotics and immune responses, and thus are difficult-to-treat. The consequent morbidity and mortality, and economic losses in health care systems has strongly necessitated the need for development of new anti-bacterial and anti-biofilm-based therapeutics. In this study, we describe the biological activity of a marine sponge-derived Streptomyces sp. SBT348 extract in restraining staphylococcal growth and biofilm formation on polystyrene, glass, medically relevant titan metal, and silicone surfaces. A bioassay-guided fractionation was performed to isolate the active compound (SKC3) from the crude SBT348 extract. Our results demonstrated that SKC3 effectively inhibits the growth (MIC: 31.25 μg/ml) and biofilm formation (sub-MIC range: 1.95–<31.25 μg/ml) of S. epidermidis RP62A in vitro. Chemical characterization of SKC3 by heat and enzyme treatments, and mass spectrometry (HRMS) revealed its heat-stable and non-proteinaceous nature, and high molecular weight (1258.3 Da). Cytotoxicity profiling of SKC3 in vitro on mouse fibroblast (NIH/3T3) and macrophage (J774.1) cell lines, and in vivo on the greater wax moth larvae Galleria mellonella revealed its non-toxic nature at the effective dose. Transcriptome analysis of SKC3 treated S. epidermidis RP62A has further unmasked its negative effect on central metabolism such as carbon flux as well as, amino acid, lipid, and energy metabolism. Taken together, these findings suggest a potential of SKC3 as a putative drug to prevent staphylococcal DRIs.
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Affiliation(s)
| | - Joseph Skaf
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
| | - Richa Bharti
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Wilma Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Ute H Humeida
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Usama R Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Tobias A Oelschlaeger
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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18
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Wermser C, Lopez D. Identification of Staphylococcus aureus genes involved in the formation of structured macrocolonies. MICROBIOLOGY-SGM 2018; 164:801-815. [PMID: 29638209 DOI: 10.1099/mic.0.000660] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human pathogen Staphylococcus aureus causes difficult-to-eradicate biofilm-associated infections that generally become chronic. Understanding the genetic regulation of biofilm formation in S. aureus is central to a precise definition of the conditions and genes involved in development of chronic biofilm-associated infections. Biofilm-related genes have been detected by comparing mutants using the classical submerged biofilm formation assay, in which cells adhere to the bottom of a well containing culture medium. We recently developed an alternative biofilm formation model for S. aureus, based on macrocolony formation on agar plates, comparable to an assay used to study biofilm formation in a few other bacterial species. As organism features are the result of environmental conditions as well as of genes, we used a genome-wide collection of transposon-mapped mutants in this macrocolony assay to seek S. aureus developmental genes and pathways not identified by the classical biofilm formation assay. We identified routes related to glucose and purine metabolism and clarified their regulatory link to macrocolony formation. Our study demonstrates that formation of microbial communities must be correlated to specific growth conditions, and the role of metabolism must be considered in S. aureus biofilm formation and thus, in the development of chronic infections.
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Affiliation(s)
- Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany.,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany.,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany.,National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid 28049, Spain
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19
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Mesarich CH, Rees-George J, Gardner PP, Ghomi FA, Gerth ML, Andersen MT, Rikkerink EHA, Fineran PC, Templeton MD. Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae. PLoS One 2017; 12:e0172790. [PMID: 28249011 PMCID: PMC5332098 DOI: 10.1371/journal.pone.0172790] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/09/2017] [Indexed: 01/15/2023] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa), the causal agent of kiwifruit canker, is one of the most devastating plant diseases of recent times. We have generated two mini-Tn5-based random insertion libraries of Psa ICMP 18884. The first, a 'phenotype of interest' (POI) library, consists of 10,368 independent mutants gridded into 96-well plates. By replica plating onto selective media, the POI library was successfully screened for auxotrophic and motility mutants. Lipopolysaccharide (LPS) biosynthesis mutants with 'Fuzzy-Spreader'-like morphologies were also identified through a visual screen. The second, a 'mutant of interest' (MOI) library, comprises around 96,000 independent mutants, also stored in 96-well plates, with approximately 200 individuals per well. The MOI library was sequenced on the Illumina MiSeq platform using Transposon-Directed Insertion site Sequencing (TraDIS) to map insertion sites onto the Psa genome. A grid-based PCR method was developed to recover individual mutants, and using this strategy, the MOI library was successfully screened for a putative LPS mutant not identified in the visual screen. The Psa chromosome and plasmid had 24,031 and 1,236 independent insertion events respectively, giving insertion frequencies of 3.65 and 16.6 per kb respectively. These data suggest that the MOI library is near saturation, with the theoretical probability of finding an insert in any one chromosomal gene estimated to be 97.5%. However, only 47% of chromosomal genes had insertions. This surprisingly low rate cannot be solely explained by the lack of insertions in essential genes, which would be expected to be around 5%. Strikingly, many accessory genes, including most of those encoding type III effectors, lacked insertions. In contrast, 94% of genes on the Psa plasmid had insertions, including for example, the type III effector HopAU1. These results suggest that some chromosomal sites are rendered inaccessible to transposon insertion, either by DNA-binding proteins or by the architecture of the nucleoid.
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Affiliation(s)
- Carl H. Mesarich
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
- Laboratory of Molecular Plant Pathology, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, New Zealand
| | - Jonathan Rees-George
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Paul P. Gardner
- Bio-Protection Research Centre, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Fatemeh Ashari Ghomi
- Bio-Protection Research Centre, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Monica L. Gerth
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Mark T. Andersen
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Erik H. A. Rikkerink
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Peter C. Fineran
- Bio-Protection Research Centre, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Matthew D. Templeton
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
- Bio-Protection Research Centre, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Ertesvåg H, Sletta H, Senneset M, Sun YQ, Klinkenberg G, Konradsen TA, Ellingsen TE, Valla S. Identification of genes affecting alginate biosynthesis in Pseudomonas fluorescens by screening a transposon insertion library. BMC Genomics 2017; 18:11. [PMID: 28049432 PMCID: PMC5210274 DOI: 10.1186/s12864-016-3467-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/23/2016] [Indexed: 12/16/2022] Open
Abstract
Background Polysaccharides often are necessary components of bacterial biofilms and capsules. Production of these biopolymers constitutes a drain on key components in the central carbon metabolism, but so far little is known concerning if and how the cells divide their resources between cell growth and production of exopolysaccharides. Alginate is an industrially important linear polysaccharide synthesized from fructose 6-phosphate by several bacterial species. The aim of this study was to identify genes that are necessary for obtaining a normal level of alginate production in alginate-producing Pseudomonas fluorescens. Results Polysaccharide biosynthesis is costly, since it utilizes nucleotide sugars and sequesters carbon. Consequently, transcription of the genes necessary for polysaccharide biosynthesis is usually tightly regulated. In this study we used an engineered P. fluorescens SBW25 derivative where all genes encoding the proteins needed for biosynthesis of alginate from fructose 6-phosphate and export of the polymer are expressed from inducible Pm promoters. In this way we would avoid identification of genes merely involved in regulating the expression of the alginate biosynthetic genes. The engineered strain was subjected to random transposon mutagenesis and a library of about 11500 mutants was screened for strains with altered alginate production. Identified inactivated genes were mainly found to encode proteins involved in metabolic pathways related to uptake and utilization of carbon, nitrogen and phosphor sources, biosynthesis of purine and tryptophan and peptidoglycan recycling. Conclusions The majority of the identified mutants resulted in diminished alginate biosynthesis while cell yield in most cases were less affected. In some cases, however, a higher final cell yield were measured. The data indicate that when the supplies of fructose 6-phosphate or GTP are diminished, less alginate is produced. This should be taken into account when bacterial strains are designed for industrial polysaccharide production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3467-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helga Ertesvåg
- Department of Biotechnology, NTNU-Norwegian University of Science and Technology, Trondheim, Norway.
| | | | - Mona Senneset
- Department of Biotechnology, NTNU-Norwegian University of Science and Technology, Trondheim, Norway.,SINTEF Materials and Chemistry, Trondheim, Norway
| | - Yi-Qian Sun
- Department of Biotechnology, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | | | - Svein Valla
- Department of Biotechnology, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
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