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Maureira A, Zapata M, Olave J, Jeison D, Wong LS, Panico A, Hernández P, Cisternas LA, Rivas M. MICP mediated by indigenous bacteria isolated from tailings for biocementation for reduction of wind erosion. Front Bioeng Biotechnol 2024; 12:1393334. [PMID: 38938979 PMCID: PMC11208896 DOI: 10.3389/fbioe.2024.1393334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/23/2024] [Indexed: 06/29/2024] Open
Abstract
In this study, native ureolytic bacteria were isolated from copper tailings soils to perform microbial-induced carbonate precipitation (MICP) tests and evaluate their potential for biocement formation and their contribution to reduce the dispersion of particulate matter into the environment from tailings containing potentially toxic elements. It was possible to isolate a total of 46 bacteria; among them only three showed ureolytic activity: Priestia megaterium T130-1, Paenibacillus sp. T130-13 and Staphylococcus sp. T130-14. Biocement cores were made by mixing tailings with the isolated bacteria in presence of urea, resulting similar to those obtained with Sporosarcina pasteurii and Bacillus subtilis used as positive control. Indeed, XRD analysis conducted on biocement showed the presence of microcline (B. subtilis 17%; P. megaterium 11. 9%), clinochlore (S. pasteurii, 6.9%) and magnesiumhornblende (Paenibacillus sp. 17.8%; P. megaterium 14.6%); all these compounds were not initially present in the tailings soils. Moreover the presence of calcite (control 0.828%; Paenibacillus sp. 5.4%) and hematite (control 0.989%; B. subtilis 6.4%) was also significant unlike the untreated control. The development of biofilms containing abundant amount of Ca, C, and O on microscopic soil particles was evidenced by means of FE-SEM-EDX and XRD. Wind tunnel tests were carried out to investigate the resistance of biocement samples, accounted for a mass loss five holds lower than the control, i.e., the rate of wind erosion in the control corresponded to 82 g/m2h while for the biocement treated with Paenibacillus sp. it corresponded to only 16.371 g/m2h. Finally, in compression tests, the biocement samples prepared with P. megaterium (28.578 psi) and Paenibacillus sp. (28.404 psi) showed values similar to those obtained with S. pasteurii (27.102 psi), but significantly higher if compared to the control (15.427 psi), thus improving the compression resistance capacity of the samples by 85.2% and 84.1% with respect to the control. According to the results obtained, the biocement samples generated with the native strains showed improvements in the mechanical properties of the soil supporting them as potential candidates in applications for the stabilization of mining liabilities in open environments using bioaugmentation strategies with native strains isolated from the same mine tailing.
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Affiliation(s)
- Alejandro Maureira
- Laboratorio de Biotecnología Ambiental Aplicada BIOAL, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Manuel Zapata
- Laboratorio de Biotecnología Ambiental Aplicada BIOAL, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Jorge Olave
- Laboratorio de Biotecnología Ambiental Aplicada BIOAL, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - David Jeison
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Liey-Si Wong
- Centro Lithium I+D+i Universidad Católica del Norte, Antofagasta, Chile
| | - Antonio Panico
- Department of Engineering, University of Campania L. Vanvitelli, Aversa, Italy
| | - Pía Hernández
- Departamento de Ingeniería Química y Procesos de Minerales, Facultad de Ingeniería, Universidad de Antofagasta, Antofagasta, Chile
| | - Luis A. Cisternas
- Departamento de Ingeniería Química y Procesos de Minerales, Facultad de Ingeniería, Universidad de Antofagasta, Antofagasta, Chile
| | - Mariella Rivas
- Laboratorio de Biotecnología Ambiental Aplicada BIOAL, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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Huq MA, Nam K, Rahman MS, Rahman MM, Parvez MAK, Kang KK, Akter S. Nocardioides agri sp. nov., isolated from garden soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38888593 DOI: 10.1099/ijsem.0.006407] [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] [Indexed: 06/20/2024] Open
Abstract
A novel bacterial strain, designated as MAH-18T, was isolated from soil sampled in a flower garden. Cells of strain MAH-18T were Gram-stain-positive, aerobic, motile, and rod-shaped. The colonies were beige in colour, smooth, and spherical when grown on Reasoner's 2A agar medium. Strain MAH-18T grew at 20-40 °C, pH 6.0-8.0, and 0-1.0 % NaCl. Cells were able to hydrolyse aesculin, gelatin, and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was determined to be a member of the genus Nocardioides and most closely related to Nocardioides pyridinolyticus OS4T (97.9 %), Nocardioides hankookensis DS-30T (97.9 %), Nocardioides aquiterrae GW-9T (97.6 %), Nocardioides soli mbc-2T (97.5 %), Nocardioides conyzicola HWE 2-02T (97.4 %), and Nocardioides mangrovi GBK3QG-3T (96.3 %). Strain MAH-18T has a draft genome size of 4 788 325 bp (eight contigs), 4572 protein-coding genes, 46 tRNA, and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-18T and the closest type strains were 81.5-83.4 % and 24.4-25.8 %, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAH-18T. The G+C content of the genomic DNA of strain was 72.2 mol% and the predominant isoprenoid quinone was MK-8 (H4). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unknown phospholipids. The major cellular fatty acids were determined to be C16:0 iso and C17 : 1 ω6c. The DNA-DNA hybridization results and phenotypic, genotypic, and chemotaxonomic data demonstrated that strain MAH-18T represents a novel species, for which the name Nocardioides agri sp. nov. is proposed, with MAH-18T as the type strain (=KACC 19744T=CGMCC 1.13656T).
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Kihong Nam
- Department of Horticultural Life Science, Hankyong National University, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
| | | | - Kwon-Kyoo Kang
- Department of Horticultural Life Science, Hankyong National University, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
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Gutierrez-Gongora D, Woods M, Prosser RS, Geddes-McAlister J. Natural compounds from freshwater mussels disrupt fungal virulence determinants and influence fluconazole susceptibility in the presence of macrophages in Cryptococcus neoformans. Microbiol Spectr 2024; 12:e0284123. [PMID: 38329361 PMCID: PMC10913472 DOI: 10.1128/spectrum.02841-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Cryptococcus neoformans is a human fungal pathogen responsible for fatal infections, especially in patients with a depressed immune system. Overexposure to antifungal drugs due to prolonged treatment regimens and structure-similar applications in agriculture have weakened the efficacy of current antifungals in the clinic. The rapid evolution of antifungal resistance urges the discovery of new compounds that inhibit fungal virulence determinants, rather than directly killing the pathogen, as alternative strategies to overcome disease and reduce selective pressure toward resistance. Here, we evaluated the efficacy of freshwater mussel extracts (crude and clarified) against the production of well-defined virulence determinants (i.e., thermotolerance, melanin, capsule, and biofilm) and fluconazole resistance in C. neoformans. We demonstrated the extracts' influence on fungal thermotolerance, capsule production, and biofilm formation, as well as susceptibility to fluconazole in the presence of macrophages. Additionally, we measured the inhibitory activity of extracts against commercial peptidases (family representatives of cryptococcal orthologs) related to fungal virulence determinants and fluconazole resistance, and integrated these phenotypic findings with quantitative proteomics profiling. Our approach defined distinct signatures of each treatment and validated a new mechanism of anti-virulence action toward the polysaccharide capsule from a selected extract following fractionation. By understanding the mechanisms driving the antifungal activity of mussels, we may develop innovative treatment options to overcome fungal infections and promote susceptibility to fluconazole in resistant strains. IMPORTANCE As the prevalence and severity of global fungal infections rise, along with an increasing incidence of antifungal resistance, new strategies to combat fungal pathogens and overcome resistance are urgently needed. Critically, our current methods to overcome fungal infections are limited and drive the evolution of resistance forward; however, an anti-virulence approach to disarm virulence factors of the pathogen and promote host cell clearance is promising. Here, we explore the efficacy of natural compounds derived from freshwater mussels against classical fungal virulence determinants, including thermotolerance, capsule production, stress response, and biofilm formation. We integrate our phenotypic discoveries with state-of-the-art mass spectrometry-based proteomics to identify mechanistic drivers of these antifungal properties and propose innovative avenues to reduce infection and support the treatment of resistant strains.
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Affiliation(s)
| | - Michael Woods
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ryan S. Prosser
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
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Straková D, Sánchez-Porro C, de la Haba RR, Ventosa A. Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species. Microorganisms 2024; 12:334. [PMID: 38399738 PMCID: PMC10892550 DOI: 10.3390/microorganisms12020334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024] Open
Abstract
The genus Halomicroarcula, classified within the family Haloarculaceae, presently comprises eight haloarchaeal species isolated from diverse saline habitats, such as solar salterns, hypersaline soils, marine salt, and marine algae. Here, a detailed taxogenomic study and comparative genomic analysis of the genus Halomicroarcula was carried out. In addition, two strains, designated S1CR25-12T and S3CR25-11T, that were isolated from hypersaline soils located in the Odiel Saltmarshes in Huelva (Spain) were included in this study. The 16S rRNA and rpoB' gene sequence analyses affiliated the two strains to the genus Halomicroarcula. Typically, the species of the genus Halomicroarcula possess multiple heterogeneous copies of the 16S rRNA gene, which can lead to misclassification of the taxa and overestimation of the prokaryotic diversity. In contrast, the application of overall genome relatedness indexes (OGRIs) augments the capacity for the precise taxonomic classification and categorization of prokaryotic organisms. The relatedness indexes of the two new isolates, particularly digital DNA-DNA hybridization (dDDH), orthologous average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that strains S1CR25-12T (= CECT 30620T = CCM 9252T) and S3CR25-11T (= CECT 30621T = CCM 9254T) constitute two novel species of the genus Halomicroarcula. The names Halomicroarcula saliterrae sp. nov. and Halomicroarcula onubensis sp. nov. are proposed for S1CR25-12T and S3CR25-11T, respectively. Metagenomic fragment recruitment analysis, conducted using seven shotgun metagenomic datasets, revealed that the species belonging to the genus Halomicroarcula were predominantly recruited from hypersaline soils found in the Odiel Saltmarshes and the ponds of salterns with high salt concentrations. This reinforces the understanding of the extreme halophilic characteristics associated with the genus Halomicroarcula. Finally, comparing pan-genomes across the twenty Halomicroarcula and Haloarcula species allowed for the identification of commonalities and differences between the species of these two related genera.
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Affiliation(s)
| | | | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain; (D.S.); (C.S.-P.); (R.R.d.l.H.)
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Kujović A, Gostinčar C, Kavkler K, Govedić N, Gunde-Cimerman N, Zalar P. Degradation Potential of Xerophilic and Xerotolerant Fungi Contaminating Historic Canvas Paintings. J Fungi (Basel) 2024; 10:76. [PMID: 38248985 PMCID: PMC10817455 DOI: 10.3390/jof10010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Fungi are important contaminants of historic canvas paintings worldwide. They can grow on both sides of the canvas and decompose various components of the paintings. They excrete pigments and acids that change the visual appearance of the paintings and weaken their structure, leading to flaking and cracking. With the aim of recognizing the most dangerous fungal species to the integrity and stability of paintings, we studied 55 recently isolated and identified strains from historic paintings or depositories, including 46 species from 16 genera. The fungi were categorized as xero/halotolerant or xero/halophilic based on their preference for solutes (glycerol or NaCl) that lower the water activity (aw) of the medium. Accordingly, the aw value of all further test media had to be adjusted to allow the growth of xero/halophilic species. The isolates were tested for growth at 15, 24 °C and 37 °C. The biodeterioration potential of the fungi was evaluated by screening their acidification properties, their ability to excrete pigments and their enzymatic activities, which were selected based on the available nutrients in paintings on canvas. A DNase test was performed to determine whether the selected fungi could utilize DNA of dead microbial cells that may be covering surfaces of the painting. The sequestration of Fe, which is made available through the production of siderophores, was also tested. The ability to degrade aromatic and aliphatic substrates was investigated to consider the potential degradation of synthetic restoration materials. Xerotolerant and moderately xerophilic species showed a broader spectrum of enzymatic activities than obligate xerophilic species: urease, β-glucosidase, and esterase predominated, while obligate xerophiles mostly exhibited β-glucosidase, DNase, and urease activity. Xerotolerant and moderately xerophilic species with the highest degradation potential belong to the genus Penicillium, while Aspergillus penicillioides and A. salinicola represent obligately xerophilic species with the most diverse degradation potential in low aw environments.
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Affiliation(s)
- Amela Kujović
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (A.K.); (C.G.); (N.G.); (N.G.-C.)
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (A.K.); (C.G.); (N.G.); (N.G.-C.)
| | - Katja Kavkler
- Institute for the Protection of Cultural Heritage of Slovenia, Poljanska 40, SI-1000 Ljubljana, Slovenia;
| | - Natalija Govedić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (A.K.); (C.G.); (N.G.); (N.G.-C.)
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (A.K.); (C.G.); (N.G.); (N.G.-C.)
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (A.K.); (C.G.); (N.G.); (N.G.-C.)
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Peng M, Zhang C, Duan YY, Liu HB, Peng XY, Wei Q, Chen QY, Sang H, Kong QT. Antifungal activity of the repurposed drug disulfiram against Cryptococcus neoformans. Front Pharmacol 2024; 14:1268649. [PMID: 38273827 PMCID: PMC10808519 DOI: 10.3389/fphar.2023.1268649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Fungal infections have become clinically challenging owing to the emergence of drug resistance in invasive fungi and the rapid increase in the number of novel pathogens. The development of drug resistance further restricts the use of antifungal agents. Therefore, there is an urgent need to identify alternative treatments for Cryptococcus neoformans (C. neoformans). Disulfiram (DSF) has a good human safety profile and promising applications as an antiviral, antifungal, antiparasitic, and anticancer agent. However, the effect of DSF on Cryptococcus is yet to be thoroughly investigated. This study investigated the antifungal effects and the mechanism of action of DSF against C. neoformans to provide a new theoretical foundation for the treatment of Cryptococcal infections. In vitro studies demonstrated that DSF inhibited Cryptococcus growth at minimum inhibitory concentrations (MICs) ranging from 1.0 to 8.0 μg/mL. Combined antifungal effects have been observed for DSF with 5-fluorocytosine, amphotericin B, terbinafine, or ketoconazole. DSF exerts significant protective effects and synergistic effects combined with 5-FU for Galleria mellonella infected with C. neoformans. Mechanistic investigations showed that DSF dose-dependently inhibited melanin, urease, acetaldehyde dehydrogenase, capsule and biofilm viability of C. neoformans. Further studies indicated that DSF affected C. neoformans by interfering with multiple biological pathways, including replication, metabolism, membrane transport, and biological enzyme activity. Potentially essential targets of these pathways include acetaldehyde dehydrogenase, catalase, ATP-binding cassette transporter (ABC transporter), and iron-sulfur cluster transporter. These findings provide novel insights into the application of DSF and contribute to the understanding of its mechanisms of action in C. neoformans.
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Affiliation(s)
- Min Peng
- Department of Dermatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Chen Zhang
- Department of Dermatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yuan-Yuan Duan
- Affiliated Hospital for Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China
| | - Hai-Bo Liu
- Department of Dermatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xin-Yuan Peng
- Department of Dermatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | | | - Qi-Ying Chen
- Department of Dermatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Hong Sang
- Department of Dermatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Qing-Tao Kong
- Department of Dermatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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Koublová V, Sedlář K, Sedláček I, Musilová J, Staňková E, Králová S, Koudelková S, Krsek D, Švec P. Corynebacterium mendelii sp. nov., a novel bacterium isolated from Adélie penguin oral cavity. Int J Syst Evol Microbiol 2024; 74. [PMID: 38289223 DOI: 10.1099/ijsem.0.006244] [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] [Indexed: 02/01/2024] Open
Abstract
The taxonomic status of strain P5891T, isolated from an Adélie penguin beak swab, was investigated. Based on the 16S rRNA gene sequence, the strain was identified as a potentially novel Corynebacterium species, with the highest sequence similarities to Corynebacterium rouxii FRC0190T (96.7 %) and Corynebacterium epidermidicanis DSM 45586T (96.6 %). The average nucleotide identity values between strain P5891T and C. rouxii FRC0190T and C. epidermidicanis DSM 45586T were 68.2 and 69.2 %, respectively. The digital DNA-DNA hybridization values between strain P5891T and C. rouxii FRC0190T and C. epidermidicanis DSM 45586T were 23.7 and 21.4 %, respectively. Phylogenetic trees based on the 16S rRNA sequence placed strain P5891T in a separate branch with Corynebacterium canis 1170T and Corynebacterium freiburgense 1045T, while a phylogenomic tree based on the Corynebacterium species core genome placed the strain next to Corynebacterium choanae 200CHT. Extensive phenotyping and genomic analyses clearly confirmed that strain P5891T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium mendelii sp. nov. is proposed, with the type strain P5891T (=CCM 8862T=LMG 31627T).
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Affiliation(s)
- Vendula Koublová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 12, 616 00 Brno, Czech Republic
- Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333 Munich, Germany
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jana Musilová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 12, 616 00 Brno, Czech Republic
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sylva Koudelková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, The National Institute of Public Health, Šrobárova 49/48 100 00 Prague 10, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Yu CK, Stephenson CJ, Villamor TC, Dyba TG, Schulz BL, Fraser JA. SAGA Complex Subunit Hfi1 Is Important in the Stress Response and Pathogenesis of Cryptococcus neoformans. J Fungi (Basel) 2023; 9:1198. [PMID: 38132798 PMCID: PMC10744473 DOI: 10.3390/jof9121198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023] Open
Abstract
The Spt-Ada-Gcn Acetyltransferase (SAGA) complex is a highly conserved co-activator found across eukaryotes. It is composed of a number of modules which can vary between species, but all contain the core module. Hfi1 (known as TADA1 in Homo sapiens) is one of the proteins that forms the core module, and has been shown to play an important role in maintaining complex structural integrity in both brewer's yeast and humans. In this study we successfully identified the gene encoding this protein in the important fungal pathogen, Cryptococcus neoformans, and named it HFI1. The hfi1Δ mutant is highly pleiotropic in vitro, influencing phenotypes, ranging from temperature sensitivity and melanin production to caffeine resistance and titan cell morphogenesis. In the absence of Hfi1, the transcription of several other SAGA genes is impacted, as is the acetylation and deubiquination of several histone residues. Importantly, loss of the gene significantly impacts virulence in a murine inhalation model of cryptococcosis. In summary, we have established that Hfi1 modulates multiple pathways that directly affect virulence and survival in C. neoformans, and provided deeper insight into the importance of the non-enzymatic components of the SAGA complex.
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Affiliation(s)
| | | | | | | | | | - James A. Fraser
- School of Chemistry & Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia; (C.K.Y.); (C.J.S.); (T.C.V.); (T.G.D.); (B.L.S.)
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de Andrade IB, Alves V, Pereira L, Miranda B, Corrêa-Junior D, Galdino Figueiredo-Carvalho MH, Santos MV, Almeida-Paes R, Frases S. Effect of rapamycin on Cryptococcus neoformans: cellular organization, biophysics and virulence factors. Future Microbiol 2023; 18:1061-1075. [PMID: 37721517 DOI: 10.2217/fmb-2023-0097] [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] [Indexed: 09/19/2023] Open
Abstract
Background: Cryptococcus neoformans is an opportunistic fungal pathogen that causes infections mainly in immunosuppressed individuals, such as transplant recipients. Aims: This study investigated the effects of rapamycin, an immunosuppressant drug, on the cellular organization, biophysical characteristics, and main virulence factors of C. neoformans. Methods: Morphological, structural, physicochemical and biophysical analyses of cells and secreted polysaccharides of the reference H99 C. neoformans strain were investigated under the effect of subinhibitory concentrations of rapamycin. Results: Rapamycin at a minimum inhibitory concentration of 2.5 μM reduced C. neoformans cell viability by 53%, decreased capsule, increased cell size, chitin and lipid body formation, and changed peptidase and urease activity. Conclusion: Further studies are needed to assess how rapamycin affects the virulence factors and pathogenicity of C. neoformans.
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Affiliation(s)
- Iara Bastos de Andrade
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vinicius Alves
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiza Pereira
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruna Miranda
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dario Corrêa-Junior
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Marcos Vinicius Santos
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Rede Micologia - FAPERJ, Rio de Janeiro, Brazil
| | - Susana Frases
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Rede Micologia - FAPERJ, Rio de Janeiro, Brazil
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Straková D, Galisteo C, de la Haba RR, Ventosa A. Characterization of Haloarcula terrestris sp. nov. and reclassification of a Haloarcula species based on a taxogenomic approach. Int J Syst Evol Microbiol 2023; 73. [PMID: 37990990 DOI: 10.1099/ijsem.0.006157] [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] [Indexed: 11/23/2023] Open
Abstract
An extremely halophilic archaeon, strain S1AR25-5AT, was isolated from a hypersaline soil sampled in Odiel Saltmarshes Natural Area (Huelva, Spain). The cells were Gram-stain-negative, motile, pleomorphic rods. Cell growth was observed in the presence of 15-30 % (w/v) NaCl [optimum, 25 % (w/v) NaCl], at pH 6.0-9.0 (optimum, pH 6.5-7.5) and at 25-50 °C (optimum, 37 °C). Based on the 16S rRNA and rpoB' gene sequence comparisons, strain S1AR25-5AT was affiliated to the genus Haloarcula. Taxogenomic analysis, including comparison of the genomes and the phylogenomic tree based on the core-orthologous proteins, together with the genomic indices, i.e., orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, confirmed that strain S1AR25-5AT (=CCM 9249T=CECT 30619T) represents a new species of the genus Haloarcula, for which we propose the name Haloarcula terrestris sp. nov. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and an unidentified glycolipid, which correlated with the lipid profile of species of the genus Haloarcula. In addition, based on the modern approach in description of species in taxonomy of prokaryotes, the above mentioned genomic indexes indicated that the species Haloarcula tradensis should be considered as a heterotypic synonym of Haloarcula argentinensis.
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Affiliation(s)
- Dáša Straková
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Galisteo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Také A, Uojima H, Sakaguchi Y, Gotoh K, Satoh T, Hidaka H, Horio K, Mizokami M, Hayashi S, Kusano C. Impact of liver fibrosis on the relative abundance of a urease-positive Streptococcus salivarius group from saliva in patients with chronic liver disease. Hepatol Res 2023; 53:998-1007. [PMID: 37279155 DOI: 10.1111/hepr.13930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023]
Abstract
AIM We performed genomic analysis to study the relative abundance of a urease-positive Streptococcus salivarius group isolated from the saliva of patients with chronic liver disease. METHODS Male and female patients with chronic liver disease aged over 20 years were included. First, we assessed the frequency and type of the S. salivarius group isolated from oral saliva using molecular biology techniques based on 16S rRNA and dephospho-coenzyme A kinase gene sequencing. Next, we assessed the correlation between the urease positivity rate in the S. salivarius group isolated from oral saliva and liver fibrosis based on chronic liver disease. Urease-positive strains were identified by the urease test using urea broth (Difco, Franklin Lakes, NJ, USA). Liver fibrosis was evaluated by the liver stiffness measurement value based on magnetic resonance elastography. RESULTS A total of 45 patients identified using the multiplex polymerase chain reaction for the 16S rRNA gene were tested using the multiplex polymerase chain reaction for the dephospho-coenzyme A kinase gene. Confirming the strains detected in each of the 45 patients, urease-positive S. salivarius was detected in 28 patients (62%), urease-negative S. salivarius in 25 patients (56%), and urease-positive Streptococcus vestibularis in 12 patients (27%). There was no patient with urease-negative S. vestibularis. The urease-positive rate of the S. salivarius group in the cirrhosis and non-cirrhosis groups were 82.2% and 39.2%, respectively. The liver cirrhosis group had a higher urease positivity rate than the non-cirrhotic group (p < 0.001). CONCLUSIONS Liver fibrosis influences the frequency of a urease-positive S. salivarius group isolated from oral saliva.
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Affiliation(s)
- Akira Také
- Department of Microbiology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Haruki Uojima
- Department of Gastroenterology, Internal Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Department of Genome Medical Sciences Project, Research Institute, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Yoshihiko Sakaguchi
- Department of Microbiology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Kazuyoshi Gotoh
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, Japan
| | - Hisashi Hidaka
- Department of Gastroenterology, Internal Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kazue Horio
- Department of Gastroenterology, Internal Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Masashi Mizokami
- Department of Genome Medical Sciences Project, Research Institute, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Shunji Hayashi
- Department of Microbiology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Chika Kusano
- Department of Gastroenterology, Internal Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
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12
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Kohta M, Koyanagi H, Inagaki Y, Nishikawa K, Kobayashi N, Tamura S, Ishikawa M, Banno Y, Takekoshi K, Mano K, Sugama J. Selective detection of urease-producing bacteria on the genital skin surface in patients with incontinence-associated dermatitis. Int Wound J 2023; 20:3289-3297. [PMID: 37095598 PMCID: PMC10502248 DOI: 10.1111/iwj.14209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
We aimed to investigate the association between the presence of cutaneous urease-producing bacteria and the development of incontinence-associated dermatitis (IAD) using an original urea agar medium as a step toward developing advanced preventive measures. In previous clinical assessments, we developed an original urea agar medium to detect urease-producing bacteria via the medium's colour changes. In a cross-sectional study, specimens were collected via the swabbing technique at genital skin sites in 52 stroke patients hospitalised in a university hospital. The primary objective was to compare the presence of urease-producing bacteria between the IAD and no-IAD groups. Determining the bacterial count was the secondary objective. The prevalence of IAD was 48%. A significantly higher detection rate of urease-producing bacteria was observed in the IAD group than in the no-IAD group (P = .002) despite the total number of bacteria being equivalent between them. In conclusion, we discovered that there was a significant association between the presence of urease-producing bacteria and IAD development in hospitalised stroke patients.
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Affiliation(s)
- Masushi Kohta
- Research Center for Implementation Nursing Science InitiativeFujita Health UniversityToyoakeJapan
| | - Hiroe Koyanagi
- Research Center for Implementation Nursing Science InitiativeFujita Health UniversityToyoakeJapan
| | | | - Keiji Nishikawa
- Department of NursingFujita Health University Nanakuri Memorial HospitalTsuJapan
| | - Nanako Kobayashi
- Department of NursingFujita Health University HospitalToyoakeJapan
| | - Shigeru Tamura
- Department of NursingFujita Health University HospitalToyoakeJapan
| | - Miyuki Ishikawa
- Department of NursingFujita Health University HospitalToyoakeJapan
| | - Yumi Banno
- Department of NursingFujita Health University HospitalToyoakeJapan
| | - Kanako Takekoshi
- Department of NursingFujita Health University HospitalToyoakeJapan
| | - Keiko Mano
- Department of NursingFujita Health University HospitalToyoakeJapan
| | - Junko Sugama
- Research Center for Implementation Nursing Science InitiativeFujita Health UniversityToyoakeJapan
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13
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Katsande PM, Nguyen VD, Nguyen TLP, Nguyen TKC, Mills G, Bailey DMD, Christie G, Hong HA, Cutting SM. Prophylactic immunization to Helicobacter pylori infection using spore vectored vaccines. Helicobacter 2023; 28:e12997. [PMID: 37314018 PMCID: PMC10909515 DOI: 10.1111/hel.12997] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/08/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Helicobacter pylori infection remains a major public health threat leading to gastrointestinal illness and increased risk of gastric cancer. Mostly affecting populations in developing countries no vaccines are yet available and the disease is controlled by antimicrobials which, in turn, are driving the emergence of AMR. MATERIALS AND METHODS We have engineered spores of Bacillus subtilis to display putative H. pylori protective antigens, urease subunit A (UreA) and subunit B (UreB) on the spore surface. Following oral dosing of mice with these spores, we evaluated immunity and colonization in animals challenged with H. pylori. RESULTS Oral immunization with spores expressing either UreA or UreB showed antigen-specific mucosal responses (fecal sIgA) including seroconversion and hyperimmunity. Following challenge, colonization by H. pylori was significantly reduced by up to 1-log. CONCLUSIONS This study demonstrates the utility of bacterial spores for mucosal vaccination to H. pylori infection. The heat stability and robustness of Bacillus spores coupled with their existing use as probiotics make them an attractive solution for either protection against H. pylori infection or potentially for therapy and control of active infection.
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Affiliation(s)
| | - Van Duy Nguyen
- Institute of Biotechnology and EnvironmentNha Trang UniversityNha TrangVietnam
| | | | - Thi Kim Cuc Nguyen
- Institute of Biotechnology and EnvironmentNha Trang UniversityNha TrangVietnam
| | - Gabrielle Mills
- Department of Chemical Engineering & BiotechnologyUniversity of CambridgeCambridgeUK
| | - David M. D. Bailey
- Department of Chemical Engineering & BiotechnologyUniversity of CambridgeCambridgeUK
| | - Graham Christie
- Department of Chemical Engineering & BiotechnologyUniversity of CambridgeCambridgeUK
| | - Huynh Anh Hong
- Department of Biological SciencesRoyal Holloway University of LondonEghamUK
| | - Simon M. Cutting
- Department of Biological SciencesRoyal Holloway University of LondonEghamUK
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14
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Straková D, Sánchez-Porro C, de la Haba RR, Ventosa A. Natrinema salsiterrestre sp. nov., an extremely halophilic archaeon isolated from a hypersaline soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37578894 DOI: 10.1099/ijsem.0.005960] [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] [Indexed: 08/16/2023] Open
Abstract
An extremely halophilic archaeal strain, designated S1CR25-10T, was isolated from hypersaline soil sampled in the Odiel Saltmarshes Natural Area in Southwestern Spain (Huelva) and subjected to a polyphasic taxonomic characterization. The cells were Gram-stain-negative, motile and their colonies were pink-pigmented. It was a strictly aerobic haloarchaeon that could grow at 25-55 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 12-30 % (w/v) total salts (optimum, 20-25 %, w/v). The phylogenetic analysis based on the comparison of the 16S rRNA gene sequences revealed that strain S1CR25-10T belongs to the genus Natrinema, with 98.9 % similarity to Natrinema salinisoli SLN56T. In addition, the values of orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity were below the threshold limits accepted for prokaryotic species delineation, with N. salinisoli SLN56T showing the highest relatedness values (92.6 % and 48.4 %, respectively). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content of the isolate was 63.8 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic characterization and the whole genome results, strain S1CR25-10T represents a new species within the genus Natrinema, for which the name Natrinema salsiterrestre sp. nov., with type strain S1CR25-10T (=CECT 30623T=CCM 9251T), is proposed.
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Affiliation(s)
- Dáša Straková
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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15
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Coelho RA, Figueiredo-Carvalho MHG, Almeida-Silva F, de Souza Rabello VB, de Souza GR, Sangenito LS, Joffe LS, Santos ALSD, da Silva Lourenço MC, Rodrigues ML, Almeida-Paes R. Repurposing Benzimidazoles against Causative Agents of Chromoblastomycosis: Albendazole Has Superior In Vitro Activity Than Mebendazole and Thiabendazole. J Fungi (Basel) 2023; 9:753. [PMID: 37504741 PMCID: PMC10381309 DOI: 10.3390/jof9070753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
Chromoblastomycosis (CBM) is a neglected human implantation mycosis caused by several dematiaceous fungal species. Currently available therapy is usually associated with physical methods, especially surgery, and with high refractoriness. Therefore, drug discovery for CBM is essential. Drug repositioning is a strategy used to facilitate the discovery of new treatments for several diseases. The aim of this study was to discover substances with antifungal activity against CBM agents from a collection of drugs previously approved for use in human diseases. A screening was performed with the NIH Clinical Collection against Fonsecaea pedrosoi. Ten substances, with clinical applicability in CBM, inhibited fungal growth by at least 60%. The minimum inhibitory concentration (MIC) of these substances was determined against other CBM agents, and the benzimidazoles albendazole, mebendazole and thiabendazole presented the lowest MIC values. The selectivity index, based on MIC and cytotoxicity of these substances, revealed albendazole to be more selective. To investigate a possible synergism of this benzimidazole with itraconazole and terbinafine, the chequerboard method was used. All interactions were classified as indifferent. Our current results suggest that benzimidazoles have repositioning potential against CBM agents. Albendazole seems to be the most promising, since it presented the highest selectivity against all dematiaceous fungi tested.
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Affiliation(s)
- Rowena Alves Coelho
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, INI/Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | | | - Fernando Almeida-Silva
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, INI/Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Vanessa Brito de Souza Rabello
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, INI/Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Gabriela Rodrigues de Souza
- Plataforma de Bioensaios RPT 11B, Instituto Nacional de Infectologia Evandro Chagas, INI/Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Leandro Stefano Sangenito
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Nilópolis 26530-060, RJ, Brazil
| | - Luna Sobrino Joffe
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11792, USA
| | - André Luis Souza Dos Santos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Rede Micologia RJ, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Rio de Janeiro 21941-901, RJ, Brazil
| | - Maria Cristina da Silva Lourenço
- Plataforma de Bioensaios RPT 11B, Instituto Nacional de Infectologia Evandro Chagas, INI/Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81350-010, PR, Brazil
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, RJ, Brazil
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, INI/Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
- Rede Micologia RJ, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Rio de Janeiro 21941-901, RJ, Brazil
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16
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Ait Bessai S, Cruz J, Carril P, Melo J, Santana MM, Mouazen AM, Cruz C, Yadav AN, Dias T, Nabti EH. The Plant Growth-Promoting Potential of Halotolerant Bacteria Is Not Phylogenetically Determined: Evidence from Two Bacillus megaterium Strains Isolated from Saline Soils Used to Grow Wheat. Microorganisms 2023; 11:1687. [PMID: 37512860 PMCID: PMC10384442 DOI: 10.3390/microorganisms11071687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
(1) Background: Increasing salinity, further potentiated by climate change and soil degradation, will jeopardize food security even more. Therefore, there is an urgent need for sustainable agricultural practices capable of maintaining high crop yields despite adverse conditions. Here, we tested if wheat, a salt-sensitive crop, could be a good reservoir for halotolerant bacteria with plant growth-promoting (PGP) capabilities. (2) Methods: We used two agricultural soils from Algeria, which differ in salinity but are both used to grow wheat. Soil halotolerant bacterial strains were isolated and screened for 12 PGP traits related to phytohormone production, improved nitrogen and phosphorus availability, nutrient cycling, and plant defence. The four 'most promising' halotolerant PGPB strains were tested hydroponically on wheat by measuring their effect on germination, survival, and biomass along a salinity gradient. (3) Results: Two halotolerant bacterial strains with PGP traits were isolated from the non-saline soil and were identified as Bacillus subtilis and Pseudomonas fluorescens, and another two halotolerant bacterial strains with PGP traits were isolated from the saline soil and identified as B. megaterium. When grown under 250 mM of NaCl, only the inoculated wheat seedlings survived. The halotolerant bacterial strain that displayed all 12 PGP traits and promoted seed germination and plant growth the most was one of the B. megaterium strains isolated from the saline soil. Although they both belonged to the B. megaterium clade and displayed a remarkable halotolerance, the two bacterial strains isolated from the saline soil differed in two PGP traits and had different effects on plant performance, which clearly shows that PGP potential is not phylogenetically determined. (4) Conclusions: Our data highlight that salt-sensitive plants and non-saline soils can be reservoirs for halotolerant microbes with the potential to become effective and sustainable strategies to improve plant tolerance to salinity. However, these strains need to be tested under field conditions and with more crops before being considered biofertilizer candidates.
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Affiliation(s)
- Sylia Ait Bessai
- Laboratoire de Maitrise des Energies Renouvelables, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia 06000, Algeria
| | - Joana Cruz
- cE3c-Centre for Ecology, Evolution and Environmental Changes and CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Competence Centre for Molecular Biology, SGS Molecular, Polo Tecnológico de Lisboa, Rua Cesina Adães Bermudes, Lt 11, 1600-604 Lisboa, Portugal
| | - Pablo Carril
- cE3c-Centre for Ecology, Evolution and Environmental Changes and CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Juliana Melo
- cE3c-Centre for Ecology, Evolution and Environmental Changes and CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Margarida M Santana
- cE3c-Centre for Ecology, Evolution and Environmental Changes and CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Abdul M Mouazen
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium
| | - Cristina Cruz
- cE3c-Centre for Ecology, Evolution and Environmental Changes and CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Ajar Nath Yadav
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
| | - Teresa Dias
- cE3c-Centre for Ecology, Evolution and Environmental Changes and CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - El-Hafid Nabti
- Laboratoire de Maitrise des Energies Renouvelables, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia 06000, Algeria
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17
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Zakrzewska M, Rzepa G, Musialowski M, Goszcz A, Stasiuk R, Debiec-Andrzejewska K. Reduction of bioavailability and phytotoxicity effect of cadmium in soil by microbial-induced carbonate precipitation using metabolites of ureolytic bacterium Ochrobactrum sp. POC9. FRONTIERS IN PLANT SCIENCE 2023; 14:1109467. [PMID: 37416890 PMCID: PMC10321601 DOI: 10.3389/fpls.2023.1109467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 05/26/2023] [Indexed: 07/08/2023]
Abstract
The application of ureolytic bacteria for bioremediation of soil contaminated with heavy metals, including cadmium (Cd), allows for the efficient immobilization of heavy metals by precipitation or coprecipitation with carbonates. Microbially-induced carbonate precipitation process may be useful also in the case of the cultivation of crop plants in various agricultural soils with trace but legally permissible Cd concentrations, which may be still uptaken by plants. This study aimed to investigate the influence of soil supplementation with metabolites containing carbonates (MCC) produced by the ureolytic bacterium Ochrobactrum sp. POC9 on the Cd mobility in the soil as well as on the Cd uptake efficiency and general condition of crop plants (Petroselinum crispum). In the frame of the conducted studies (i) carbonate productivity of the POC9 strain, (ii) the efficiency of Cd immobilization in soil supplemented with MCC, (iii) crystallization of cadmium carbonate in the soil enriched with MCC, (iv) the effect of MCC on the physico-chemical and microbiological properties of soil, and (v) the effect of changes in soil properties on the morphology, growth rate, and Cd-uptake efficiency of crop plants were investigated. The experiments were conducted in soil contaminated with a low concentration of Cd to simulate the natural environmental conditions. Soil supplementation with MCC significantly reduced the bioavailability of Cd in soil with regard to control variants by about 27-65% (depending on the volume of MCC) and reduced the Cd uptake by plants by about 86% and 74% in shoots and roots, respectively. Furthermore, due to the decrease in soil toxicity and improvement of soil nutrition with other metabolites produced during the urea degradation (MCC), some microbiological properties of soil (quantity and activity of soil microorganisms), as well as the general condition of plants, were also significantly improved. Soil supplementation with MCC enabled efficient Cd stabilization and significantly reduced its toxicity for soil microbiota and plants. Thus, MCC produced by POC9 strain may be used not only as an effective Cd immobilizer in soil but also as a microbe and plant stimulators.
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Affiliation(s)
- Marta Zakrzewska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Grzegorz Rzepa
- Department of Mineralogy, Petrography and Geochemistry, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Krakow, Poland
| | - Marcin Musialowski
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Goszcz
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Department of Ecotoxicology, Institute of Environmental Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Robert Stasiuk
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Klaudia Debiec-Andrzejewska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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18
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Van Wylick A, Vandersanden S, Jonckheere K, Rahier H, De Laet L, Peeters E. Screening fungal strains isolated from a limestone cave on their ability to grow and precipitate CaCO 3 in an environment relevant to concrete. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000764. [PMID: 37223428 PMCID: PMC10202147 DOI: 10.17912/micropub.biology.000764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023]
Abstract
Fungi-mediated self-healing concrete is a novel approach that promotes the precipitation of calcium carbonate (CaCO 3 ) on fungal hyphae to heal the cracks in concrete. In this study, we set out to explore the potential of fungal species isolated from a limestone cave by investigating their ability to precipitate CaCO 3 and to survive and grow in conditions relevant to concrete. Isolated strains belonging to the genera Botryotrichum sp. , Trichoderma sp. and Mortierella sp. proved to be promising candidates for fungi-mediated self-healing concrete attributed to their growth properties and CaCO 3 precipitation capabilities in the presence of cement.
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Affiliation(s)
- Aurélie Van Wylick
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
- Research Group of Physical Chemistry and Polymer Science, Department of Materials and Chemistry, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
| | - Simon Vandersanden
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
- Current Address: Centre for Environmental Sciences, Hasselt University, Hasselt, Flanders, Belgium
| | - Karl Jonckheere
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
| | - Hubert Rahier
- Research Group of Physical Chemistry and Polymer Science, Department of Materials and Chemistry, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
| | - Lars De Laet
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
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19
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Nováková D, Koublová V, Sedlář K, Staňková E, Králová S, Švec P, Neumann-Schaal M, Wolf J, Koudelková S, Barták M, Sedláček I. Pseudomonas petrae sp. nov. isolated from regolith samples in Antarctica. Syst Appl Microbiol 2023; 46:126424. [PMID: 37167755 DOI: 10.1016/j.syapm.2023.126424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/06/2023] [Accepted: 04/23/2023] [Indexed: 05/13/2023]
Abstract
A polyphasic taxonomic approach was used to characterize the four strains P2653T, P2652, P2498, and P2647, isolated from Antarctic regolith samples. Initial genotype screening performed by PCR fingerprinting based on repetitive sequences showed that the isolates studied formed a coherent cluster separated from the other Pseudomonas species. Identification results based on 16S rRNA gene sequences showed the highest sequence similarity with Pseudomonas graminis (99.7%), which was confirmed by multilocus sequence analysis using the rpoB, rpoD, and gyrB genes. Genome sequence comparison of P2653T with the most related P. graminis type strain DSM 11363T revealed an average nucleotide identity of 92.1% and a digital DNA-DNA hybridization value of 46.6%. The major fatty acids for all Antarctic strains were C16:0, Summed Feature 3 (C16:1ω7c/C16:1ω6c) and Summed Feature 8 (C18:1ω7c/C18:1ω6c). The predominant respiratory quinone was Q-9, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The regolith strains could be differentiated from related species by the absence of arginine dihydrolase, ornithine and lysine decarboxylase and by negative tyrosine hydrolysis. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of four analysed strains from the closest related species, which confirmed that the strains represent a novel species within the genus Pseudomonas, for which the name Pseudomonas petrae sp. nov. is proposed with P2653T (CCM 8850T = DSM 112068T = LMG 30619T) as the type strain.
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Affiliation(s)
- Dana Nováková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Vendula Koublová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic; Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, 803 33 Munich, Germany
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Sylva Koudelková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miloš Barták
- Department of Experimental Biology, Section of Experimental Plant Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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20
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de Andrade IB, Corrêa-Junior D, Alves V, Figueiredo-Carvalho MHG, Santos MV, Almeida MA, Valdez AF, Nimrichter L, Almeida-Paes R, Frases S. Cyclosporine Affects the Main Virulence Factors of Cryptococcus neoformans In Vitro. J Fungi (Basel) 2023; 9:jof9040487. [PMID: 37108941 PMCID: PMC10140927 DOI: 10.3390/jof9040487] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
This study aimed to investigate the effects of cyclosporine on the morphology, cell wall structure, and secretion characteristics of Cryptococcus neoformans. The minimum inhibitory concentration (MIC) of cyclosporine was found to be 2 µM (2.4 µg/mL) for the H99 strain. Yeast cells treated with cyclosporine at half the MIC showed altered morphology, including irregular shapes and elongated projections, without an effect on cell metabolism. Cyclosporine treatment resulted in an 18-fold increase in chitin and an 8-fold increase in lipid bodies, demonstrating changes in the fungal cell wall structure. Cyclosporine also reduced cell body and polysaccharide capsule diameters, with a significant reduction in urease secretion in C. neoformans cultures. Additionally, the study showed that cyclosporine increased the viscosity of secreted polysaccharides and reduced the electronegativity and conductance of cells. The findings suggest that cyclosporine has significant effects on C. neoformans morphology, cell wall structure, and secretion, which could have implications for the development of new antifungal agents.
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Affiliation(s)
- Iara Bastos de Andrade
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Dario Corrêa-Junior
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Vinicius Alves
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | | | - Marcos Vinicius Santos
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21941-902, Brazil
| | - Marcos Abreu Almeida
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21941-902, Brazil
| | - Alessandro Fernandes Valdez
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Rede Micologia RJ, FAPERJ, Rio de Janeiro 21941-902, Brazil
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21941-902, Brazil
- Rede Micologia RJ, FAPERJ, Rio de Janeiro 21941-902, Brazil
| | - Susana Frases
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Rede Micologia RJ, FAPERJ, Rio de Janeiro 21941-902, Brazil
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21
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Sritongon N, Boonlue S, Mongkolthanaruk W, Jogloy S, Riddech N. The combination of multiple plant growth promotion and hydrolytic enzyme producing rhizobacteria and their effect on Jerusalem artichoke growth improvement. Sci Rep 2023; 13:5917. [PMID: 37041302 PMCID: PMC10090049 DOI: 10.1038/s41598-023-33099-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/07/2023] [Indexed: 04/13/2023] Open
Abstract
Rhizobacteria are well recognized for their beneficial multifunctions as key promoters of plant development, suppressing pathogens, and improving soil health. In this study, experiments focused on characterizing the plant growth promotion (PGP) and extracellular hydrolase production traits of rhizobacteria, and their impact on Jerusalem artichoke growth. A total of 50 isolates proved capable of either direct PGP or hydrolase-producing traits. Two promising strains (Enterobacter cloacae S81 and Pseudomonas azotoformans C2-114) showed potential on phosphate and potassium solubilization, IAA production, and 1-aminocyclopropane-1-carboxylic acid deaminase activity and hydrolase production. A hydrolase-producing strain (Bacillus subtilis S42) was able to generate cellulase, protease, amylase, β-glucosidase, and phosphatase. These three selected strains also gave positive results for indirect PGP traits such as siderophore, ammonia, oxalate oxidase, polyamine, exopolysaccharide, biofilm, motility, and tolerance to salinity and drought stress. Colonization was observed using a scanning electron microscope and rhizobacteria appeared at the root surface. Interestingly, inoculation with consortia strains (S42, S81, and C2-114) significantly increased all plant parameters, including height, biomass, root (length, surface, diameter, and volume), and tuber fresh weight. Therefore, we recommend that potential consortia of PGP and hydrolase-producing rhizobacteria be employed as a biofertilizer to improve soil and boost crop productivity.
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Affiliation(s)
- Natthawat Sritongon
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sophon Boonlue
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Wiyada Mongkolthanaruk
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sanun Jogloy
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nuntavun Riddech
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
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22
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Gutierrez-Gongora D, Raouf-Alkadhimi F, Prosser RS, Geddes-McAlister J. Differentiated extracts from freshwater and terrestrial mollusks inhibit virulence factor production in Cryptococcus neoformans. Sci Rep 2023; 13:4928. [PMID: 36967422 PMCID: PMC10040410 DOI: 10.1038/s41598-023-32140-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
The human fungal pathogen, Cryptococcus neoformans, is responsible for deadly infections among immunocompromised individuals with the evolution of antifungal resistance driving the solution to discover new compounds that inhibit fungal virulence factors rather than kill the pathogen. Recently, exploration into natural sources (e.g., plants, invertebrates, microbes) of antifungal agents has garnered attention by integrating a One Health approach for new compound discovery. Here, we explore extracts from three mollusk species (freshwater and terrestrial) and evaluate effects against the growth and virulence factor production (i.e., thermotolerance, melanin, capsule, and biofilm) in C. neoformans. We demonstrate that clarified extracts of Planorbella pilsbryi have a fungicidal effect on cryptococcal cells comparable to fluconazole. Similarly, all extracts of Cipangopaludina chinensis affect cryptococcal thermotolerance and impair biofilm and capsule production, with clarified extracts of Cepaea nemoralis also conveying the latter effect. Next, inhibitory activity of extracts against peptidases related to specific virulence factors, combined with stress assays and quantitative proteomics, defined distinct proteome signatures and proposed proteins driving the observed anti-virulence properties. Overall, this work highlights the potential of compounds derived from natural sources to inhibit virulence factor production in a clinically important fungal pathogen.
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Affiliation(s)
| | | | - Ryan S Prosser
- Department of Environmental Toxicology, University of Guelph, Guelph, ON, Canada
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23
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Choi CY, Lee CH, Yang J, Kang SJ, Park IB, Park SW, Lee NY, Hwang HB, Yun HS, Chun T. Efficacies of Potential Probiotic Candidates Isolated from Traditional Fermented Korean Foods in Stimulating Immunoglobulin A Secretion. Food Sci Anim Resour 2023; 43:346-358. [PMID: 36909859 PMCID: PMC9998188 DOI: 10.5851/kosfa.2023.e2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
The aim of this study was to evaluate efficacies of selected lactic acid bacteria (LAB) in inducing immunoglobulin A (IgA) secretion. Twenty-five different LAB isolated from traditional fermented Korean foods were characterized for their probiotic properties and screened to identify those that could stimulate lamina propria cells (LPCs) from Peyer's patch to secret IgA in vitro. Among them, four strains (Lactiplantibacillus plantarum CJW55-10, Lactiplantibacillus pentosus CJW18-6, L. pentosus CJW56-11, and Pediococcus acidilactici CJN2696) were found to be strong IgA inducers. The number of IgA positive B cells and soluble IgA level were increased when LPCs were co-cultured with these LAB. Expression levels of toll-like receptor (TLR) such as TLR2 and TLR4 and secretion of interleuckin-6 were augmented in LPCs treated with these LAB. Further, we determined whether oral intake of these LAB enhanced IgA production in vivo. After one-week of daily oral administration, these LAB feed mice increased mucosal IgA and serum IgA. In conclusion, selected strains of LAB could induce systemic IgA secretion by activating lamina propria B cells in Peyer's patch and oral intake of selected strains of LAB can enhance systemic immunity by inducing mucosal IgA secretion.
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Affiliation(s)
- Chang-Yong Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Chang-Hee Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Jun Yang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Seok-Jin Kang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - In-Byung Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Si-Won Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Na-Young Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Hyun-Been Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | | | - Taehoon Chun
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
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24
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Reyad AM, Mokhtar G. Impact of the immobilized Bacillus cereus MG708176 on the characteristics of the bio-based self-healing concrete. Sci Rep 2023; 13:500. [PMID: 36627411 PMCID: PMC9832136 DOI: 10.1038/s41598-023-27640-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
Novel carrier units were evaluated for their bio-healing benefits in our study to increase the efficacy of concrete healing. Bacillus cereus MG708176, an alkali-tolerant, calcite precipitating, endospore-forming strain was added as a bio-healing agent after its immobilization on wood ash units. A spore concentration of [1.3 × 107 spore/cm3] combined with 2.5% w/w urea was added to cement. Beams of 40 × 40 × 160 mm were used and tested for completely damaged mortar specimens after 7, 14, and 28 days of water treatment. Using wood ash bacterial mortars, totally destructed specimens were fully healed in all time intervals. Positive changes in concrete mechanical properties in bacterial wood ash treatment that were 24.7, 18.9, and 28.6% force for compressive, flexural, and tensile strengths more than control. The micro-images of the Scanning Electron Microscope (SEM) showed the dense concrete structure via calcite, Bacillafilla, and ettringite formation. Our results have shown improvements in the concrete healing efficiency and the mechanical concrete properties by filling the concrete cracks using a calcite-producing bacterium that is immobilized on wood ash units.
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Affiliation(s)
- Amany M. Reyad
- grid.411170.20000 0004 0412 4537Department of Botany, Faculty of Science, Fayoum University, Faiyum, Egypt
| | - Gehad Mokhtar
- Civil Engineering, Future High Institute of Engineering in Fayoum, Faiyum, Egypt
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25
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Corynebacterium antarcticum sp. nov., Corynebacterium marambiense sp. nov., Corynebacterium meridianum sp. nov., and Corynebacterium pygosceleis sp. nov., isolated from Adélie penguins (Pygoscelis adeliae). Syst Appl Microbiol 2023; 46:126390. [PMID: 36566621 DOI: 10.1016/j.syapm.2022.126390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
A taxonomic study was conducted on 16 bacterial strains isolated from wild Adélie penguins (Pygoscelis adeliae) from Seymour (Marambio) Island and James Ross Island. An initial screening by repetitive sequence-based PCR fingerprinting divided the strains studied into four coherent groups. Phylogenetic analysis based on 16S rRNA gene sequences assigned all groups to the genus Corynebacterium and showed that Corynebacterium glyciniphilum and Corynebacterium terpenotabidum were the closest species with 16S rRNA gene sequence similarities between 95.4 % and 96.5 %. Further examination of the strains studied with ribotyping, MALDI-TOF mass spectrometry, comprehensive biotyping and calculation of average nucleotide identity and digital DNA-DNA hybridisation values confirmed the separation of the four groups from each other and from the other Corynebacterium species. Chemotaxonomically, the four strains P5828T, P5850T, P6136T, P7210T representing the studied groups were characterised by C16:0 and C18:1ω9c as the major fatty acids, by the presence of meso-diaminopimelic acid in the peptidoglycan, the presence of corynemycolic acids and a quinone system with the predominant menaquinone MK-9(H2). The results of this study show that the strains studied represent four new species of the genus Corynebacterium, for which the names Corynebacterium antarcticum sp. nov. (type strain P5850T = CCM 8835T = LMG 30620T), Corynebacterium marambiense sp. nov. (type strain P5828T = CCM 8864T = LMG 31626T), Corynebacterium meridianum sp. nov. (type strain P6136T = CCM 8863T = LMG 31628T) and Corynebacterium pygosceleis sp. nov. (type strain P7210T = CCM 8836T = LMG 30621T) are proposed.
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26
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Lynch C, Peeters C, Walsh N, McCarthy C, Coffey A, Lucey B, Vandamme P. Campylobacter majalis sp. nov. and Campylobacter suis sp. nov., novel Campylobacter species isolated from porcine gastrointestinal mucosa. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748456 DOI: 10.1099/ijsem.0.005510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Strains LMG 7974T and LMG 8286T represent single, novel Campylobacter lineages with Campylobacter pinnipediorum and Campylobacter mucosalis as nearest phylogenomic neighbours, respectively. The results of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses of LMG 7974T, LMG 8286T and type strains of species of the genus Campylobacter confirmed that these strains represent novel species of the genus Campylobacter. The 16S rRNA gene sequences of both strains showed highest identity towards C. mucosalis (97.84 and 98.74 %, respectively). Strains LMG 7974T and LMG 8286T shared 72.5 and 73.7% ANI, respectively, with their nearest phylogenomic neighbours and less than 21 % dDDH. The draft genome sizes of LMG 7974T and LMG 8286T are 1 945429 bp and 1 708214 bp in length with percentage DNA G+C contents of 33.8 and 37.2 %, respectively. Anomalous biochemical characteristics and low MALDI-TOF mass spectrometry log scores supported their designation as representing novel species of the genus Campylobacte. We therefore propose to classify strain LMG 7974T (=CCUG 20705T) as the type strain of the novel species Campylobacter majalis sp. nov. and strain LMG 8286T (=CCUG 24193T, NCTC 11879T) as the type strain of the novel species Campylobacter suis sp. nov.
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Affiliation(s)
- Caoimhe Lynch
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Niamh Walsh
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Conor McCarthy
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland.,APC Microbiome Institute, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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27
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Riesco R, Rose JJA, Batinovic S, Petrovski S, Sánchez-Juanes F, Seviour RJ, Goodfellow M, Trujillo ME. Gordonia pseudamarae sp. nov., a home for novel actinobacteria isolated from stable foams on activated sludge wastewater treatment plants. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The taxonomic status of two
Gordonia
strains, designated BEN371 and CON9T, isolated from stable foams on activated sludge plants was the subject of a polyphasic study which also included the type strains of
Gordonia
species and three authenticated
Gordonia amarae
strains recovered from such foams. Phylogenetic analyses of 16S rRNA gene sequences showed that these isolates formed a compact cluster suggesting a well-supported lineage together with a second branch containing the
G. amarae
strains. A phylogenomic tree based on sequences of 92 core genes extracted from whole genome sequences of the isolates, the
G. amarae
strains and
Gordonia
type strains confirmed the assignment of the isolates and the
G. amarae
strains to separate but closely associated lineages. Average nucleotide index (ANI) and digital DNA–DNA hybridisation (dDDH) similarities showed that BEN371 and CON9T belonged to the same species and had chemotaxonomic and morphological features consistent with their assignment to the genus
Gordonia
. The isolates and the
G. amarae
strains were distinguished using a range of phenotypic features and by low ANI and dDDH values of 84.2 and 27.0 %, respectively. These data supplemented with associated genome characteristics show that BEN371 and CON9T represent a novel species of the genus
Gordonia
. The name proposed for members of this taxon is Gordonia pseudamarae sp. nov. with isolate CON9T (=DSM 43602T=JCM 35249T) as the type strain.
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Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Jayson J. A. Rose
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steven Batinovic
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, CSIC, Salamanca, Spain
- Department of Biochemistry and Molecular Biology, University of Salamanca, Salamanca, Spain
| | - Robert J. Seviour
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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28
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Medically important bacteria isolated from commercial herbal medicines in Kampala city indicate the need to enhance safety frameworks. Sci Rep 2022; 12:16647. [PMID: 36198745 PMCID: PMC9533980 DOI: 10.1038/s41598-022-21065-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/22/2022] [Indexed: 11/08/2022] Open
Abstract
The high global bacterial infection burden has created need to investigate the neglected potential drivers of pathogenic bacteria, to inform disease prevention. Kampala is facing a proliferation of herbalists, selling herbal medicine (HM), of largely unregulated microbiological quality. We evaluated the bacterial contamination burden in HM sold in Kampala, to support evidence-based redress. The total viable loads (TVL), total coliform counts (TCC), E. coli counts, and prevalence of selected bacterial strains in 140 HM were examined using conventional culture, following the guidelines of World Health Organization (WHO), and Uganda National Drug Authority (NDA). Data were analyzed using D'Agostino-Pearson test, frequencies, proportions, Chi-square, and Mann-Whitney U test with STATA version-15.0. Fifty (35.7%), fifty-nine (42.1%), and twelve (8.6%) HM were unsafe for human use because they exceeded WHO's permissible limits for TVL, TCC, and E. coli counts respectively. Solids had significantly higher mean TVL than liquids. Violation of NDA's guidelines was significantly associated with high TVL. Fifty-nine bacteria, viz., Klebsiella pneumoniae (n = 34; 57.6%), Escherichia. coli (12; 20.3%), Staphylococcus aureus (7; 11.9%), Klebsiella oxytoca (3; 5.1%), Bacillus cereus, Pseudomonas aeruginosa, and Enterobacter spp. (1; 1.7% each), were isolated from 45 (32.1%) samples. These bacteria can cause severe clinical diseases, and promote deterioration of HM potency.
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29
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Zhang K, Hu J, Yang S, Xu W, Wang Z, Zhuang P, Grossart HP, Luo Z. Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129406. [PMID: 35753302 DOI: 10.1016/j.jhazmat.2022.129406] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/08/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 ℃ by breaking the carbonyl groups (1732 cm-1) and C-N-H bonds (1532 cm-1 and 1247 cm-1) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation" was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.
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Affiliation(s)
- Kai Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Jiege Hu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Zhichao Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Peiwen Zhuang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin 16775, Germany; Institute of Biochemistry and Biology, Potsdam University, Potsdam 14469, Germany
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China; School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing 210044, PR China; Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang 222005, PR China.
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30
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Švec P, Králová S, Staňková E, Holochová P, Sedlář K, Koudelková S, Krsek D, Grzesiak J, Šedo O, Váczi P, Urvashi, Gupta V, Sood U, Lal R, Korpole S, Sedláček I. Pedobacter fastidiosus sp. nov., isolated from glacial habitats of maritime Antarctica. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains P8930T and 478 were isolated from Antarctic glaciers located on James Ross Island and King George Island, respectively. They comprised Gram-stain-negative short rod-shaped cells forming pink pigmented colonies and exhibited identical 16S rRNA gene sequences and highly similar MALDI TOF mass spectra, and hence were assigned as representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences assigned both isolates to the genus
Pedobacter
and showed
Pedobacter frigidisoli
and
Pedobacter terrae
to be their closest phylogenetic neighbours, with 97.4 and 97.2 % 16S rRNA gene sequence similarities, respectively. These low similarity values were below the threshold similarity value of 98.7%, confirming the delineation of a new bacterial species. Further genomic characterization included whole-genome sequencing accompanied by average nucleotide identity (ANI) and digital DNA–DNA hybridization calculations, and characterization of the genome features. The ANI values between P8930T and
P. frigidisoli
RP-3-11T and
P. terrae
DSM 17933T were 79.7 and 77.6 %, respectively, and the value between
P. frigidisoli
RP-3-11T and
P. terrae
DSM 17933T was 77.7 %, clearly demonstrating the phylogenetic distance and the novelty of strain P8930T. Further characterization included analysis of cellular fatty acids, quinones and polar lipids, and comprehensive biotyping. All the obtained results proved the separation of strains P8930T and 478 from the other validly named
Pedobacter
species, and confirmed that they represent a new species for which the name Pedobacter fastidiosus sp. nov. is proposed. The type strain is P8930T (=CCM 8938T=LMG 32098T).
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Affiliation(s)
- Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 12, 616 00 Brno, Czech Republic
| | - Sylva Koudelková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, The National Institute of Public Health, Šrobárova 49/48 100 00 Prague 10, Czech Republic
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Peter Váczi
- Department of Experimental Biology, Division of Experimental Plant Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Urvashi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - Vipin Gupta
- Ministry of Environment Forest & Climate Change, Integrated Regional Office, Dehradun, 248001, India
| | - Utkarsh Sood
- The Energy and Resources Institute, Lodhi Road New Delhi-110003, India
| | - Rup Lal
- The Energy and Resources Institute, Lodhi Road New Delhi-110003, India
| | - Suresh Korpole
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Chauhan P, Bhattacharya A, Giri VP, Singh SP, Gupta SC, Verma P, Dwivedi A, Rajput LS, Mishra A. Bacillus subtilis suppresses the charcoal rot disease by inducing defence responses and physiological attributes in soybean. Arch Microbiol 2022; 204:266. [PMID: 35437612 DOI: 10.1007/s00203-022-02876-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/18/2022] [Accepted: 03/24/2022] [Indexed: 11/02/2022]
Abstract
Endophytes can induce the defence responses and modulates physiological attributes in host plants during pathogen attacks. In the present study, 127 bacterial endophytes (BEs) were isolated from different parts of healthy soybean plant. Among them, two BEs (M-2 and M-4) resulted a significant antagonistic property against Macrophomina phaseolina, causes charcoal rot disease in soybean. The antagonistic potential was evaluated through dual culture plate assay, where M-4 expressed higher antifungal activity than M-2 against M. phaseolina. The M-4 produces cell wall degrading enzymes viz. cellulase (145.71 ± 1.34 μgmL-1), chitinase (0.168 ± 0.0009 unitmL-1) and β,1-3 endoglucanase (162.14 ± 2.5 μgmL-1), which helps in cell wall disintegration of pathogens. Additionally, M-4 also can produce siderophores, indole-3-acetic acid (IAA) (17.03 ± 1.10 μgmL-1) and had a phosphate solubilization potential (19.89 ± 0.26 μgmL-1). Further, GC-MS profiling of M-4 has been carried out to demonstrate the production of lipophilic secondary metabolites which efficiently suppress the M. phaseolina defensive compounds under co-culture conditions. Bio-efficacy study of M-4 strain shown a significant reduction in disease incidence around 60 and 80% in resistant and susceptible varieties of soybean, respectively. The inoculation of M-4 potentially enhances the physiological attributes and triggers various defence responsive enzymes viz. superoxide dismutase (SOD), phenol peroxidase (PPO), peroxidase (PO) and catalase (CAT). The histopathological study also confirmed that M-4 can reduce the persistence of microsclerotia in root and shoot tissue. Conclusively, M-4 revealed as an efficient biocontrol agent that can uses multifaceted measures for charcoal rot disease management, by suppress the M. phaseolina infection and enhance the physiological attributes of soybean.
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Affiliation(s)
- Priyanka Chauhan
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Arpita Bhattacharya
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ved Prakash Giri
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
- Department of Botany, Lucknow University, Hasanganj, Lucknow, 226007, Uttar Pradesh, India
| | - Satyendra Pratap Singh
- Pharmacognosy Division, CSIR-National Botanical Research Institute, Lucknow, 226001, Uttar Pradesh, India
| | - Sateesh Chandra Gupta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Phytochemistry Division, CSIR-National Botanical Research Institute, Lucknow, 226001, Uttar Pradesh, India
| | - Pratibha Verma
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashish Dwivedi
- Photobiology Division, CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - Laxman Singh Rajput
- Division of Crop Protection, ICAR-Indian Institute of Soybean Research, Indore, 452001, Madhya Pradesh, India
| | - Aradhana Mishra
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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32
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Acidic Neutralization by Indigenous Bacteria Isolated from Abandoned Mine Areas. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soil acidification has been a serious problem in abandoned mine areas, and could be exacerbated by acid deposition with the release of mine wastes. In this study, three different indigenous bacterial consortia were isolated from abandoned mines in South Korea, from which the potential for acid neutralization of microorganisms was evaluated. They were all able to neutralize acidity within 24 h in the liquid nutrient medium. Moreover, a strong positive correlation (R = +0.922, p < 0.05) was established between the ammonium ion (NH4+) production yield and the resulting pH, indicating that NH4+ served as an important metabolite for biological neutralization. Serratialiquefaciens, Citrobacter youngae, Pseudescherichia vulneris, and Serratia grimesii had higher acid neutralization ability to generate NH4+ by the metabolism of nitrogen compounds such as carboxylation and urea hydrolysis. Therefore, acidic soils can be expected to be ameliorated by indigenous microorganisms through in situ biostimulation with the adequate introduction of nitrogenous substances into the soil environments.
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33
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Duran Ramirez JM, Gomez J, Obernuefemann CLP, Gualberto NC, Walker JN. Semi-Quantitative Assay to Measure Urease Activity by Urinary Catheter-Associated Uropathogens. Front Cell Infect Microbiol 2022; 12:859093. [PMID: 35392611 PMCID: PMC8980526 DOI: 10.3389/fcimb.2022.859093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Catheter-associated urinary tract infections (CAUTIs) are one of the most common healthcare-associated infections in the US, accounting for over 1 million cases annually and totaling 450 million USD. CAUTIs have high morbidity and mortality rates and can be caused by a wide range of pathogens, making empiric treatment difficult. Furthermore, when urease-producing uropathogens cause symptomatic CAUTI or asymptomatic catheter colonization, the risk of catheter failure due to blockage increases. The enzyme urease promotes catheter blockage by hydrolyzing urea in urine into ammonia and carbon dioxide, which results in the formation of crystals that coat the catheter surface. If CAUTI is left untreated, the crystals can grow until they block the urinary catheter. Catheter blockage and subsequent failure reduces the quality of life for the chronically catheterized, as it requires frequent catheter exchanges and can promote more severe disease, including dissemination of the infection to the kidneys or bloodstream. Thus, understanding how urease contributes to catheter blockages and/or more severe disease among the broad range of urease-producing microbes may provide insights into better prevention or treatment strategies. However, clinical assays that detect urease production among clinical isolates are qualitative and prioritize the detection of urease from Proteus mirabilis, the most well-studied uropathogenic urease producer. While urease from other known urease producers, such as Morganella morganii, can also be detected with these methods, other uropathogens, including Staphylococcus aureus and Klebsiella pneumonia, are harder to detect. In this study, we developed a high throughput, semiquantitative assay capable of testing multiple uropathogens in a rapid and efficient way. We validated the assay using Jack Bean urease, the urease producing species: Proteus spp., M. morganii, K. pneumonia, and S. aureus strains, and the non-urease producer: Escherichia coli. This modified assay more rapidly detected urease-producing strains compared to the current clinical test, Christensen Urea Agar, and provided semiquantitative values that may be used to further investigate different aspects of urease regulation, production, or activity in these diverse species. Furthermore, this assay can be easily adapted to account for different environmental stimuli affecting urease production, including bacterial concentration, aeration, or addition of anti-urease compounds.
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Affiliation(s)
- Jesus M. Duran Ramirez
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX, United States
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Center for Infectious Diseases, School of Public Health, The University of Texas Health Science Center, Houston, TX, United States
| | - Jana Gomez
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX, United States
| | - Chloe L. P. Obernuefemann
- The Center for Women’s Infectious Disease Research, Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Nathaniel C. Gualberto
- The Center for Women’s Infectious Disease Research, Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Jennifer N. Walker
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX, United States
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Center for Infectious Diseases, School of Public Health, The University of Texas Health Science Center, Houston, TX, United States
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34
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Almeida E, Henriques V, Wiegand S, Albuquerque L, Schumann P, Kohn T, Jogler C, Simões da Costa M, Lobo-da-Cunha A, de Fátima Carvalho M, Lage OM. Salsipaludibacter albus gen. nov., sp. nov., a novel actinobacterial strain isolate from a Portuguese solar saltern and proposal of Salsipaludibacteraceae fam. nov. and Salsipaludibacterales ord. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005228] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A novel micro-organism designated AS10T was isolated from dry salt collected from Aveiro saltern in the north of Portugal. Cells were Gram-stain-positive, non-motile, non-endospore-forming, rod-shaped and aerobic. Strain AS10T was characterized by long filaments of rod-shaped cells, presenting also coccoid cellular forms at the end of the filaments, unveiling some pleomorphism. Rod-shaped cells varied from 0.3 to 0.6 µm wide and from 0.6 to 2 µm long. Growth of AS10T occurred at 15–40 °C (optimum, 20–30 °C), 0–10% (w/v) NaCl (optimum, 2%) and pH 4.5–11.0 (optimum, pH 8.0–11.0). The peptidoglycan type was A1ϒ-type with 3-hydroxy-diaminopimelic acid. The major fatty acids were C16:0, iso-C14:0, C17:0 and C14:0. The major respiratory quinone was MK-9(H4). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AS10T was similar to actinobacterial members of the class
Nitriliruptoria
, with
Nitriliruptor alkaliphilus
ANL-iso2T being the closest relative the species with a sequence pairwise similarity of 91.21%. Average nucleotide identity, average amino acid identity and in silico DNA–DNA hybridization values between strain AS10T and
N. alkaliphilus
ANL-iso2T were 71.34, 53.57 and 18.90%, respectively. The genome DNA G+C content of AS10T was 71.8 mol%. Based on genomic, phylogenetic, phenotypic and chemotaxonomic studies, we describe a new species of a novel genus represented by strain AS10T (=LMG 31937T=CECT 30148T) for which we propose the name Salsipaludibacter albus gen. nov., sp. nov. We also propose that this organism represents a new family named Salsipaludibacteraceae fam. nov. of a novel order named Salsipaludibacterales ord. nov.
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Affiliation(s)
- Eduarda Almeida
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
- Faculty of Sciences, University of Porto (FCUP), Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Valentina Henriques
- Faculty of Sciences, University of Porto (FCUP), Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Sandra Wiegand
- Institute for Biological Surfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Luciana Albuquerque
- CNC – Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Timo Kohn
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Milton Simões da Costa
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- CNC – Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Alexandre Lobo-da-Cunha
- Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Maria de Fátima Carvalho
- Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Olga Maria Lage
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
- Faculty of Sciences, University of Porto (FCUP), Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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35
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Chlebek D, Płociniczak T, Gobetti S, Kumor A, Hupert-Kocurek K, Pacwa-Płociniczak M. Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits. Int J Mol Sci 2021; 23:ijms23010214. [PMID: 35008639 PMCID: PMC8745256 DOI: 10.3390/ijms23010214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022] Open
Abstract
The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca3(PO4)2, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg−1 h−1). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5, 15, and 10 mM metal, respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis.
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36
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LaFrentz BR, Králová S, Burbick CR, Alexander TL, Phillips CW, Griffin MJ, Waldbieser GC, García JC, de Alexandre Sebastião F, Soto E, Loch TP, Liles MR, Snekvik KR. The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare, Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare. Syst Appl Microbiol 2021; 45:126293. [PMID: 35026686 DOI: 10.1016/j.syapm.2021.126293] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 01/09/2023]
Abstract
Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT shared less than <98.8 % sequence identity to F. columnare ATCC 23463T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463T, genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36T), F. davisii sp. nov. (90-106T), and F. oreochromis sp. nov. (Costa Rica 04-02-TNT) are proposed to represent genetic groups 2, 3, and 4, respectively.
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Affiliation(s)
- Benjamin R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Auburn, AL, United States.
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States
| | - Conner W Phillips
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States
| | - Matt J Griffin
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, MS, United States
| | - Geoffrey C Waldbieser
- Warmwater Aquaculture Research Unit, USDA-ARS, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, United States
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Auburn, AL, United States
| | | | - Esteban Soto
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Thomas P Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Kevin R Snekvik
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
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Domestic Birds as Source of Cryptococcus deuterogattii (AFLP6/VGII): Potential Risk for Cryptococcosis. Mycopathologia 2021; 187:103-111. [PMID: 34762221 PMCID: PMC8807445 DOI: 10.1007/s11046-021-00601-w] [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: 09/08/2021] [Accepted: 10/18/2021] [Indexed: 11/29/2022]
Abstract
Cryptococcosis is an infection caused by encapsulated basidiomycetous yeasts belonging to the Cryptococcus neoformans/Cryptococcus gattii species complexes. It is acquired through inhalation of infectious propagules, often resulting in meningitis and meningoencephalitis. The ecological niche of these agents is a wide variety of trees species, as well as pigeon, parrot and passerine excreta. The objective of this study was to isolate Cryptococcus yeasts from excreta of commercially traded parrots and passerines. The 237 samples were collected between October 2018 and April 2019 and processed using conventional methodologies. Nineteen colonies with a dark brown phenotype, caused by phenol oxidase activity, were isolated, suggesting the presence of pathogenic Cryptococcus yeasts. All isolates tested positive for urease activity. URA5-RFLP fingerprinting identified 14 isolates (68.4%) as C. neoformans (genotype AFLP1/VNI) and 5 (26.3%) as C. deuterogattii (genotype AFLP6/VGII). Multi-locus sequence typing was applied to investigate the relatedness of the C. deuterogattii isolates with those collected globally, showing that those originating from bird-excreta were genetically indistinguishable from some clinical isolates collected during the past two decades.
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Králová S, Busse HJ, Bezdíček M, Sandoval-Powers M, Nykrýnová M, Staňková E, Krsek D, Sedláček I. Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Front Microbiol 2021; 12:729977. [PMID: 34745033 PMCID: PMC8570120 DOI: 10.3389/fmicb.2021.729977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Vienna, Austria
| | - Matěj Bezdíček
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, Masaryk University, Brno, Czechia
| | | | - Markéta Nykrýnová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, National Institute of Public Health, Prague, Czechia
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
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Yang Z, Liu Z, Dabrowska M, Debiec-Andrzejewska K, Stasiuk R, Yin H, Drewniak L. Biostimulation of sulfate-reducing bacteria used for treatment of hydrometallurgical waste by secondary metabolites of urea decomposition by Ochrobactrum sp. POC9: From genome to microbiome analysis. CHEMOSPHERE 2021; 282:131064. [PMID: 34118631 DOI: 10.1016/j.chemosphere.2021.131064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/25/2021] [Accepted: 05/28/2021] [Indexed: 06/12/2023]
Abstract
Sulfate-reducing bacteria (SRB) are key players in many passive and active systems dedicated to the treatment of hydrometallurgical leachates. One of the main factors reducing the efficiency and activity of SRB is the low pH and poor nutrients in leachates. We propose an innovative solution utilizing biogenic ammonia (B-NH3), produced by urea degrading bacteria, as a pretreatment agent for increasing the pH of the leachate and spontaneously stimulating SRB activity via bacterial secondary metabolites. The selected strain, Ochrobactrum sp. POC9, generated 984.7 mg/L of ammonia in 24 h and promotes an effective neutralization of B-NH3. The inferred metabolic traits indicated that the Ochrobactrum sp. POC9 can synthesize a group of vitamins B, and the production of various organic metabolites was confirmed by GC-MS analysis. These metabolites comprise alcohols, organic acids, and unsaturated hydrocarbons that may stimulate biological sulfate reduction. With the pretreatment of B-NH3, sulfate removal efficiency reached ~92.3% after 14 days of incubation, whereas SRB cell count and abundance were boosted (~107 cell counts and 88 OTUs of SRB) compared to synthetic ammonia (S-NH3) (~103 cell counts and 40 OTUs of SRB). The dominant SRB is Desulfovibrio in both S-NH3 and B-NH3 pretreated leachate, however, it belonged to two different clades. By reconstructing the ecological network, we found that B-NH3 not only directly increases SRB performance but also promotes other strains with positive correlations with SRB.
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Affiliation(s)
- Zhendong Yang
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Zhenghua Liu
- Central South University, School of Resource Processing and Bioengineering, No. 932 Lushan South Road, Changsha, China
| | - Maria Dabrowska
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Klaudia Debiec-Andrzejewska
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Robert Stasiuk
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Huaqun Yin
- Central South University, School of Resource Processing and Bioengineering, No. 932 Lushan South Road, Changsha, China
| | - Lukasz Drewniak
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
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Mališová L, Španělová P, Sedláček I, Pajer P, Musílek M, Puchálková B, Jakubů V, Žemličková H, Šafránková R. The first case of Planococcus glaciei found in blood, a report from the Czech Republic. Folia Microbiol (Praha) 2021; 67:121-127. [PMID: 34590203 DOI: 10.1007/s12223-021-00919-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/07/2021] [Indexed: 11/27/2022]
Abstract
The isolation of Planococcus glaciei (designed strain CNCTC 7660) from blood of a patient with appendicitis is reported. Species P. glaciei (type strain CGMCC 1.6846 T) was for the first time identified as an environmental bacterium acquired from a glacier in China in 2009. To reveal the identity of the isolate CNCTC 7660, the 16S rDNA sequencing and the whole genome sequencing (Illumina MiSeq, Oxford Nanopore) were performed. The level of 16S rDNA gene sequencing similarity between CNCTC 7660 and CGMCC 1.6846 T was 99.55%. Phylogenetic analysis and average nucleotide analysis (ANI) based on the whole genome sequencing confirmed that the isolate CNCTC 7660 and CGMCC1.6846 T had ANI value above the taxonomic threshold for belonging to the same species (95%). The G + C content of CNCTC 7660 DNA was 46.8% (mol/mol). Except for the growth temperature, strains CGMCC1.6846 T and CNCTC 7660 were distinguished also biochemically. Due to the lack of information about the pathogenicity of P. glaciei, the possibility that it exerts pathogenicity in persons is suggested. But for understanding the nature of this species, further cases are needed.
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Affiliation(s)
- Lucia Mališová
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Microbiology, 3Rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
| | - Petra Španělová
- Czech National Collection of Type Cultures, National Institute of Public Health, Prague, Czech Republic.
| | - Ivo Sedláček
- Department of Experimental Biology, Faculty of Science, Czech Collection of Microorganisms, Masaryk University, Brno, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Martin Musílek
- National Reference Laboratory for Meningococcal Infections, National Institute of Public Health, Prague, Czech Republic
| | - Blanka Puchálková
- Department of Clinical Microbiology, Karlovy Vary Regional Hospital, Hradec Kralove, Czech Republic
| | - Vladislav Jakubů
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Microbiology, 3Rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
- Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic
| | - Helena Žemličková
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Microbiology, 3Rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
- Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic
| | - Renáta Šafránková
- Czech National Collection of Type Cultures, National Institute of Public Health, Prague, Czech Republic
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Fayez Hassan N, Khaled Ibrahim M, Yousef El Tablawy S, Abd Allah Farrag H. Characterization of Biofilm Producer Nanobacteria Isolated from Kidney Stones of Some Egyptian Patients. Pak J Biol Sci 2021; 24:953-970. [PMID: 34585548 DOI: 10.3923/pjbs.2021.953.970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
<b>Background and Objective:</b> Nanobacteria (NB) appear to contribute to many calcifying diseases including kidney stones which represent a common problem with inadequate prevention exist. NB framing itself with a mineral coat that assists as a primary defence shield against the immune system, antibiotics. This study aims to collect and detect nanobes from different kidney stones from patients with active urolithiasis then investigated the anti-nano-bacterial activity of some antibiotics alone or in combination with extracts of irradiated herbs of certain medicinal plants which will represent a new approach to therapy for patients with kidney stones. <b>Materials and Methods:</b> Total of 32 nanobes were isolated from 54 kidney stones. Fourier Transforms Infrared Spectroscopy (FTIR) revealed that calcium and phosphate are the main components of stones. Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray spectroscopy (EDX) and Transmission Electron Microscope (TEM), showed that nanobes were Gram-ve cocci with size ranged from (375:600 nm). The biofilm production ability of nanobes was estimated qualitatively and quantitatively. <b>Results:</b> The results revealed that all were strong biofilm producers. Further, the antibiotic susceptibility test indicates their resistance towards most of the tested antibiotics. Molecular identification of the strong biofilm producer isolates by ribosomal ribonucleic acid (rRNA) revealed that it is indicated by 85.37% to <i>Bartonella apis</i> strain PEB0122. <b>Conclusion:</b> The findings of the current study evidenced that combination treatment between Doxycycline (DO) and water extract of khella exhibited a significant reduction in biofilm formation ability of the strongest producers nanobes. Therefore, this treatment can play a role in enhancing public health, especially with patients who suffer from recurrent kidney stone formation.
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Mokhtar G, Ahmed AAEA, Reyad AM. The effect of isolated Bacillus ureolytic bacteria in improving the bio-healing of concrete cracks. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1186/s43088-021-00142-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Reinforcement corrosion and the concrete strength reduction are critical problems that resulted from crack creation in concrete. Very expensive and hazardous technologies based on chemical materials have been provided for repairing the cracks. Recently, crack repair using bio-catalysis precipitating bacteria has been developed as a viable and ecofriendly alternative technique. The main target of this study was to select and identify bacterial isolates with high urease activity to use in filling the cracks by the precipitation of CaCO3.
Results
Two endospore-forming and alkali-resistant ureolytic bacteria were combined with concrete to tolerate the mechanical stresses generated by mixing. The two isolates designated as (B1 and B2) were selected and identified as Bacillus wiedmannii strain FSL W8-0169 and Bacillus paramycoides strain MCCC 1A04098, respectively, using 16SrDNA gene sequencing. Both bacterial species completely heal cracks in fully destructed concrete and significant enhancement in compressive strength was illustrated. The calcite filling of cracks and CaCO3 crystals that were screened using a scanning electron microscope may explain the crack healing and the enhancement in concrete strength.
Conclusions
Bacillus wiedmannii strain FSL W8-0169 and Bacillus paramycoides strain MCCC 1A04098 can be inserted with the concrete to improve the compressive strength and the self-healing of cracks. The two ureolytic bacterial strains can be used to protect water buildings from exposure to frequent cracks.
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43
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Rodríguez-Andrade E, Cano-Lira JF, Wiederhold N, Pérez-Cantero A, Guarro J, Stchigel AM. A revision of malbranchea-like fungi from clinical specimens in the United States of America reveals unexpected novelty. IMA Fungus 2021; 12:25. [PMID: 34493345 PMCID: PMC8422767 DOI: 10.1186/s43008-021-00075-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/23/2021] [Indexed: 11/10/2022] Open
Abstract
The fungi of the order Onygenales can cause important human infections; however, their taxonomy and worldwide occurrence is still little known. We have studied and identified a representative number of clinical fungi belonging to that order from a reference laboratory in the USA. A total of 22 strains isolated from respiratory tract (40%) and human skin and nails (27.2%) showed a malbranchea-like morphology. Six genera were phenotypically and molecularly identified, i.e. Auxarthron/Malbranchea (68.2%), Arachnomyces (9.1%), Spiromastigoides (9.1%), and Currahmyces (4.5%), and two newly proposed genera (4.5% each). Based on the results of the phylogenetic study, we synonymized Auxarthron with Malbranchea, and erected two new genera: Pseudoarthropsis and Pseudomalbranchea. New species proposed are: Arachnomyces bostrychodes, A. graciliformis, Currahmyces sparsispora, Malbranchea gymnoascoides, M. multiseptata, M. stricta, Pseudoarthropsis crassispora, Pseudomalbranchea gemmata, and Spiromastigoides geomycoides, along with a new combination for Malbranchea gypsea. The echinocandins showed the highest in vitro antifungal activity against the studied isolates, followed by terbinafine and posaconazole; in contrast, amphotericin B, fluconazole, itraconazole and 5-fluorocytosine were less active or lacked in vitro activity against these fungi.
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Affiliation(s)
- Ernesto Rodríguez-Andrade
- Mycology Unit, Medical School, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201, Reus, Tarragona, Spain
| | - José F Cano-Lira
- Mycology Unit, Medical School, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201, Reus, Tarragona, Spain.
| | - Nathan Wiederhold
- Fungus Testing Laboratory, University of Texas Health Science Center, San Antonio, TX, USA
| | - Alba Pérez-Cantero
- Mycology Unit, Medical School, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201, Reus, Tarragona, Spain
| | - Josep Guarro
- Mycology Unit, Medical School, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201, Reus, Tarragona, Spain
| | - Alberto M Stchigel
- Mycology Unit, Medical School, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201, Reus, Tarragona, Spain
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Rakitin AL, Ermakova AY, Beletsky AV, Petrova M, Mardanov AV, Ravin NV. Genome Analysis of Acinetobacter lwoffii Strains Isolated from Permafrost Soils Aged from 15 Thousand to 1.8 Million Years Revealed Their Close Relationships with Present-Day Environmental and Clinical Isolates. BIOLOGY 2021; 10:871. [PMID: 34571748 PMCID: PMC8472584 DOI: 10.3390/biology10090871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 01/21/2023]
Abstract
Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. Acinetobacter lwoffii is a typical soil bacterium that has been increasingly reported as hospital pathogens associated with bacteremia. In order to identify the specific genetic characteristics of ancient permafrost-conserved strains of A. lwoffii and their differences from present-day clinical isolates, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not identify chromosomal genetic determinants that distinguish permafrost strains from clinical A. lwoffii isolates and strains from other natural habitats. Phylogenetic analysis based on whole genome sequences showed that permafrost strains do not form a separate cluster and some of them are most closely related to clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal transfer of genetic material. Comparison of plasmids of modern and permafrost strains showed that plasmids from the modern strains are enriched with antibiotic resistance genes, while the content of genes for resistance to heavy metals and arsenic is nearly the same. The thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter.
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Affiliation(s)
- Andrey L. Rakitin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia; (A.L.R.); (A.Y.E.); (A.V.B.); (A.V.M.)
| | - Alexandra Y. Ermakova
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia; (A.L.R.); (A.Y.E.); (A.V.B.); (A.V.M.)
| | - Alexey V. Beletsky
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia; (A.L.R.); (A.Y.E.); (A.V.B.); (A.V.M.)
| | - Mayya Petrova
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123098 Moscow, Russia;
| | - Andrey V. Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia; (A.L.R.); (A.Y.E.); (A.V.B.); (A.V.M.)
| | - Nikolai V. Ravin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia; (A.L.R.); (A.Y.E.); (A.V.B.); (A.V.M.)
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Králová S, Sandoval-Powers M, Fawwal DV, Degnes KF, Lewin AS, Klinkenberg G, Nguyen GS, Liles MR, Wentzel A. Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord. Front Microbiol 2021; 12:714233. [PMID: 34421874 PMCID: PMC8371330 DOI: 10.3389/fmicb.2021.714233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01T, was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269T (98.3%). Predominant fatty acids were C16:0 iso, C16:0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G + C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01T = CCM 9049T = DSM 111582T) is proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Biological Sciences, Auburn University, Auburn, AL, United States.,Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Dorelle V Fawwal
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Kristin F Degnes
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Anna Sofia Lewin
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Giang-Son Nguyen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
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Chua SMH, Wizrah MSI, Luo Z, Lim BYJ, Kappler U, Kobe B, Fraser JA. Structural features of Cryptococcus neoformans bifunctional GAR/AIR synthetase may present novel antifungal drug targets. J Biol Chem 2021; 297:101091. [PMID: 34416230 PMCID: PMC8449271 DOI: 10.1016/j.jbc.2021.101091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Cryptococcus neoformans is a fungus that causes life-threatening systemic mycoses. During infection of the human host, this pathogen experiences a major change in the availability of purines; the fungus can scavenge the abundant purines in its environmental niche of pigeon excrement, but must employ de novo biosynthesis in the purine-poor human CNS. Eleven sequential enzymatic steps are required to form the first purine base, IMP, an intermediate in the formation of ATP and GTP. Over the course of evolution, several gene fusion events led to the formation of multifunctional purine biosynthetic enzymes in most organisms, particularly the higher eukaryotes. In C. neoformans, phosphoribosyl-glycinamide synthetase (GARs) and phosphoribosyl-aminoimidazole synthetase (AIRs) are fused into a bifunctional enzyme, while the human ortholog is a trifunctional enzyme that also includes GAR transformylase. Here we functionally, biochemically, and structurally characterized C. neoformans GARs and AIRs to identify drug targetable features. GARs/AIRs are essential for de novo purine production and virulence in a murine inhalation infection model. Characterization of GARs enzymatic functional parameters showed that C. neoformans GARs/AIRs have lower affinity for substrates glycine and PRA compared with the trifunctional metazoan enzyme. The crystal structure of C. neoformans GARs revealed differences in the glycine- and ATP-binding sites compared with the Homo sapiens enzyme, while the crystal structure of AIRs shows high structural similarity compared with its H. sapiens ortholog as a monomer but differences as a dimer. The alterations in functional and structural characteristics between fungal and human enzymes could potentially be exploited for antifungal development.
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Affiliation(s)
- Sheena M H Chua
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Maha S I Wizrah
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Zhenyao Luo
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Bryan Y J Lim
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
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Sandoval-Powers M, Králová S, Nguyen GS, Fawwal DV, Degnes K, Lewin AS, Klinkenberg G, Wentzel A, Liles MR. Streptomyces poriferorum sp. nov., a novel marine sponge-derived Actinobacteria species expressing anti-MRSA activity. Syst Appl Microbiol 2021; 44:126244. [PMID: 34392062 DOI: 10.1016/j.syapm.2021.126244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022]
Abstract
Marine sponges represent a rich source of uncharacterized microbial diversity, and many are host to microorganisms that produce biologically active specialized metabolites. Here, a polyphasic approach was used to characterize two Actinobacteria strains, P01-B04T and P01-F02, that were isolated from the marine sponges Geodia barretti (Bowerbank, 1858) and Antho dichotoma (Esper, 1794), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains P01-B04T and P01-F02 are closely related to Streptomyces beijiangensis DSM 41794T, Streptomyces laculatispora NRRL B-24909T, and Streptomyces brevispora NRRL B-24910T. The two strains showed nearly identical 16S rRNA gene sequences (99.93%), and the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values were 99.96% and 99.6%, respectively, suggesting that these strains are affiliated with the same species. Chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons, and phylogenomic analyses distinguished strains P01-B04T and P01-F02 from their closest phylogenetic relatives. In silico analysis predicted that the 8.9 Mb genome of P01-B04T contains at least 41 biosynthetic gene clusters (BGCs) encoding secondary metabolites, indicating that this strain could express diverse bioactive metabolites; in support of this prediction, this strain expressed antibacterial activity against Gram-positive bacteria including a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA) EAMC30. Based on these results, the marine sponge-associated isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces poriferorum sp. nov. is proposed, with P01-B04T (=DSM 111306T = CCM 9048T) as the type strain.
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Affiliation(s)
| | - Stanislava Králová
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA; Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Giang-Son Nguyen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Dorelle V Fawwal
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Kristin Degnes
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Anna Sofia Lewin
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
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Graddy CMR, Gomez MG, DeJong JT, Nelson DC. Native Bacterial Community Convergence in Augmented and Stimulated Ureolytic MICP Biocementation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10784-10793. [PMID: 34279077 DOI: 10.1021/acs.est.1c01520] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microbially induced calcite precipitation is a biomineralization process with numerous civil engineering and ground improvement applications. In replicate soil columns, the efficacy and microbial composition of soil bioaugmented with the ureolytic bacterium Sporosarcina pasteurii were compared to a biostimulation method that enriches native ureolytic soil bacteria in situ under conditions analogous to field implementation. The selective enrichment resulting from sequential stimulation treatments strongly selected for Firmicutes (>97%), with Sporosarcina and Lysinibacillus comprising 60 to 94% of high-throughput 16S rDNA sequences in each suspended community sample. Seven species of the former and two of the latter were present in greater than 10% abundance at different times, demonstrating unexpected within-genus diversity and robustness in the suspended phase of this highly selective environment. Based on longer 16S sequences, it was inferred that augmented S. pasteurii competed poorly with natural bacteria, decreasing to below detection after nine treatments, while the native microbial community was enriched to approximately that present in the stimulated columns. These analyses were corroborated by the observed convergence in bulk ureolytic rates and calcite contents between techniques. However, a 10-fold discrepancy between the observed cell density and an activity-based estimate indicates the attached community, uncharacterized despite efforts, substantially contributes to bulk behavior.
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Affiliation(s)
- Charles M R Graddy
- Department of Microbiology and Molecular Genetics, University of California, Davis 95616, California, United States
| | - Michael G Gomez
- Department of Civil and Environmental Engineering, University of Washington, Seattle 98195-2700, Washington, United States
| | - Jason T DeJong
- Department of Civil and Environmental Engineering, University of California, Davis 95616, California, United States
| | - Douglas C Nelson
- Department of Microbiology and Molecular Genetics, University of California, Davis 95616, California, United States
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Sphingomonas horti sp. nov., a novel bacterial species isolated from soil of a tomato garden. Arch Microbiol 2020; 203:543-548. [PMID: 32970222 DOI: 10.1007/s00203-020-02056-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/10/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
A novel bacterial strain, designated MAH-20T, was isolated from a soil sample of a tomato garden. Cells of strain MAH-20T were Gram-stain negative, aerobic, motile, and rod-shaped. The colonies were light brown colored, smooth, spherical, and 0.2-0.7 mm in diameter when grown on Luria-Bertani agar for 2 days. Strain MAH-20T grows at 15-40 °C (optimum growth temperature 30-32 °C), at pH 5.0-10.0 (optimum growth pH 7.0) and at 0-2.0% NaCl. The strain showed positive activity for both oxidase and catalase tests. Cells were able to hydrolyze starch, DNA, urea, gelatin, L-arginine, and Tween 20. According to the 16S rRNA gene sequence similarity, the strain MAH-20T was identified as a new member of the genus Sphingomonas and had the close sequence similarity with Sphingomonas changbaiensis V2M44T (98.9%) and Sphingomonas tabacisoli X1-8T (98.1%). The genomic ANI value between strain MAH-20T and S. changbaiensis NBRC 104936T was 84.4%. The novel strain MAH-20T has a draft genome size of 3,350,026 bp (25 contigs), annotated with 3210 protein-coding genes, 46 tRNA, and 3 rRNA genes. The genomic DNA G + C content of isolate was 67.3 mol%, the predominant quinone was ubiquinone 10 and the major fatty acids were C16:0, C17:1 ω6c and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). On the basis of DNA-DNA hybridization results, phenotypic, genotypic, and chemotaxonomic data, the isolated strain MAH-20T represents a novel species, for which the name Sphingomonas horti sp. nov. is proposed, with MAH-20T as the type strain (= KACC 19746T = CGMCC1.13658T).
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Anter A, El-Ghany MA, Abou El Dahab M, Mahana N. Does Curcumin Have a Role in the Interaction between Gut Microbiota and Schistosoma mansoni in Mice? Pathogens 2020; 9:pathogens9090767. [PMID: 32961786 PMCID: PMC7558489 DOI: 10.3390/pathogens9090767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022] Open
Abstract
There is strong correlation between changes in abundance of specific bacterial species and several diseases including schistosomiasis. Several studies have described therapeutic effects of curcumin (CUR) which may arise from its regulative effects on intestinal microbiota. Thus, we examined the impact of CUR on the diversity of intestinal microbiota with/without infection by Schistosoma mansoni cercariae for 56 days. Enterobacteriaceae was dominating in a naive and S. mansoni infected mice group without CUR treatment, the most predominant species was Escherichia coli with relative density (R.D%) = 80.66% and the least one was Pseudomonas sp. (0.52%). The influence of CUR on murine microbiota composition was examined one week after oral administration of high (40) and low (20 mg/kg b.w.) CUR doses were administered three times, with two day intervals. CUR induced high variation in the Enterobacteriaceae family, characterized by a significant (p < 0.001) reduction in E. coli and asignificant (p < 0.001) increase in Pseudomonas sp. in both naïve and S. mansoni-infected mice, compared to untreated mice, in a dose-dependent manner. Additionally, our study showed the effects of high CUR doses on S. mansoni infection immunological and parasitological parameters. These data support CUR’s ability to promote Pseudomonas sp. known to produce schistosomicidal toxins and offset the sequelae of murine schistosomiasis.
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Affiliation(s)
- Assmaa Anter
- Zoology Department, Faculty of Science, Cairo University, Giza 12613, Egypt;
| | - Mohamed Abd El-Ghany
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt;
| | - Marwa Abou El Dahab
- Zoology Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt;
| | - Noha Mahana
- Zoology Department, Faculty of Science, Cairo University, Giza 12613, Egypt;
- Correspondence: or ; Tel.: +20-2-3567-6708
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