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Hu X, Yang F, Yang S, Guo W, Ren J, Liu S, Xiao X, Zhu L, Wei W. Roseinatronobacter alkalisoli sp. nov., an alkaliphilic bacterium isolated from soda soil, and genome-based reclassification of the genera Rhodobaca and Roseinatronobacter. Int J Syst Evol Microbiol 2024; 74. [PMID: 38832859 DOI: 10.1099/ijsem.0.006402] [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: 06/06/2024] Open
Abstract
The genera Rhodobaca and Roseinatronobacter are phylogenetically related genera within the family Paracoccaceae. Species of these genera were described using 16S rRNA gene-based phylogeny and phenotypic characteristics. However, the 16S rRNA gene identity and phylogeny reveal the controversy of the taxonomic status of these two genera. In this work, we examined the taxonomic positions of members of both genera using 16S rRNA gene phylogeny, phylogenomic analysis and further validated using overall genome-related indexes, including digital DNA-DNA hybridization, average nucleotide identity, average amino acid identity and percentage of conserved proteins. Based on phylogenetic and phylogenomic results, the current four species of the two genera clustered tightly into one clade with high bootstrap values, suggesting that the genus Rhodobaca should be merged with Roseinatronobacter. In addition, a novel species isolated from a soda soil sample collected from Anda City, PR China, and designated as HJB301T was also described. Phenotypic, chemotaxonomic, genomic and phylogenetic properties suggested that strain HJB301T (=CCTCC AB 2021113T=KCTC 82977T) represents a novel species of the genus Roseinatronobacter, for which the name Roseinatronobacter alkalisoli sp. nov. is proposed.
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Affiliation(s)
- Xinyu Hu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Fan Yang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
| | - Shujing Yang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
| | - Wenjun Guo
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
| | - Jiangtao Ren
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang Agriculture and Forestry University, Hangzhou, PR China
| | - Xiang Xiao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Wei Wei
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
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Pellegrinetti TA, de Cássia Mesquita da Cunha I, Chaves MGD, Freitas ASD, Passos GS, Silva AVRD, Cotta SR, Tsai SM, Mendes LW. Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths. Braz J Microbiol 2024; 55:1817-1828. [PMID: 38358421 PMCID: PMC11153436 DOI: 10.1007/s42770-024-01268-3] [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: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.
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Affiliation(s)
- Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
- Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Piracicaba, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Anderson Santos de Freitas
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Gabriel Schimmelpfeng Passos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Simone Raposo Cotta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil.
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Chantavorakit T, Thanompreechachai J, Suriyachadkun C, Duangmal K. Klenkia sesuvii sp. nov., isolated from leaves of halophyte Sesuvium portulacastrum. Int J Syst Evol Microbiol 2024; 74. [PMID: 38832855 DOI: 10.1099/ijsem.0.006410] [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: 06/06/2024] Open
Abstract
During a study on the diversity of culturable actinobacteria from coastal halophytes in Thailand, strain LSe6-5T was isolated from leaves of sea purslane (Sesuvium portulacastrum L.), and a polyphasic approach was employed to determine its taxonomic position. The 16S rRNA gene sequences analysis indicated that the strain was most closely related to Klenkia brasiliensis Tu 6233T (99.2 %), Klenkia marina YIM M13156T (99.1 %), and Klenkia terrae PB261T (98.7 %). The genome of strain LSe6-5T was estimated to be 4.33 Mbp in size, with DNA G+C contents of 74.3%. A phylogenomic tree based on whole-genome sequences revealed that strain LSe6-5T formed a clade with Klenkia marina DSM 45722T, indicating their close relationship. However, the average nucleotide identity (ANI)-blast, ANI-MUMmer, and dDDH values between strain LSe6-5T with K. marina DSM 45722T (87.1, 88.9, and 33.0 %) were below the thresholds of 95-96 % ANI and 70 % dDDH for identifying a novel species. Furthermore, strain LSe6-5T showed morphological and chemotaxonomic characteristics of the genus Klenkia. Cells were motile, rod-shaped, and Gram-stain-positive. Optimal growth of strain LSe6-5T occurred at 28 °C, pH 7.0, and 0-3 % NaCl. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with galactose, glucose, mannose, and ribose as whole-cell sugars. The predominant menaquinones were MK-9(H4) and MK-9(H0). The polar lipid profile was composed of diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified phospholipid, and an unidentified lipid. Major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, and iso-C17 : 0. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, it is supported that strain LSe6-5T represents a novel species of the genus Klenkia, for which the name Klenkia sesuvii sp. nov. is proposed. The type strain is strain LSe6-5T (=TBRC 16417T= NBRC 115929T).
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Affiliation(s)
- Tanatorn Chantavorakit
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jirun Thanompreechachai
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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Yang X, Garuglieri E, Van Goethem MW, Marasco R, Fusi M, Daffonchio D. Mangrovimonas cancribranchiae sp. nov., a novel bacterial species associated with the gills of the fiddler crab Cranuca inversa (Brachyura, Ocypodidae) from Red Sea mangroves. Int J Syst Evol Microbiol 2024; 74. [PMID: 38865172 DOI: 10.1099/ijsem.0.006415] [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: 06/13/2024] Open
Abstract
Two bacteria, UG2_1T and UG2_2, were isolated from the gill tissues of the mangrove fiddler crab Cranuca inversa collected on the east coast of the Red Sea (Thuwal, Saudi Arabia). The cells are Gram-negative, rod-shaped, orange-pigmented, motile by gliding with no flagella, strictly aerobic, and grow at 20-37 °C (optimum, 28-35 °C), at pH 5.0-9.0 (optimum, pH 6.0-7.0), and with 1-11 % (w/v) NaCl (optimum, 2-4 %). They were positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences indicated that isolates UG2_1T and UG2_2 belong to the genus Mangrovimonas, showing the highest similarity to Mangrovimonas spongiae HN-E26T (99.4 %). Phylogenomic analysis based on the whole genomes, independently using 49 and 120 concatenated genes, showed that strains UG2_1T and UG2_2 formed a monophyletic lineage in a different cluster from other type strain species within the genus Mangrovimonas. The genome sizes were 3.08 and 3.07 Mbp for UG2_1T and UG2_2, respectively, with a G+C content of 33.8 mol% for both strains. Values of average nucleotide identity and digital DNA-DNA hybridization between the strains and closely related species were 91.0 and 43.5 %, respectively. Chemotaxonomic analysis indicated that both strains had iso-C15 : 0 and iso-C15 : 1 G as dominant fatty acids, and the primary respiratory quinone was identified as MK-6. The major polar lipids comprised phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid, two unidentified aminolipids, and four unidentified lipids. Based on phylogenetic, phylogenomic, genome relatedness, phenotypic, and chemotaxonomical data, the two isolates represent a novel species within the genus Mangrovimonas, with the proposed name Mangrovimonas cancribranchiae sp. nov., and the type strain UG2_1T (=KCTC 102158T=DSM 117025T).
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Affiliation(s)
- Xinyuan Yang
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Marc W Van Goethem
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ramona Marasco
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Marco Fusi
- Dove Marine Laboratory, School of Natural and Environmental Sciences Newcastle University, Newcastle-Upon-Tyne, NE1 7RU, UK
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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García-Romero I, Srivastava M, Monjarás-Feria J, Korankye SO, MacDonald L, Scott NE, Valvano MA. Drug efflux and lipid A modification by 4-L-aminoarabinose are key mechanisms of polymyxin B resistance in the sepsis pathogen Enterobacter bugandensis. J Glob Antimicrob Resist 2024; 37:108-121. [PMID: 38552872 DOI: 10.1016/j.jgar.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/26/2024] Open
Abstract
OBJECTIVES A concern with the ESKAPE pathogen, Enterobacter bugandensis, and other species of the Enterobacter cloacae complex, is the frequent appearance of multidrug resistance against last-resort antibiotics, such as polymyxins. METHODS Here, we investigated the responses to polymyxin B (PMB) in two PMB-resistant E. bugandensis clinical isolates by global transcriptomics and deletion mutagenesis. RESULTS In both isolates, the genes of the CrrAB-regulated operon, including crrC and kexD, displayed the highest levels of upregulation in response to PMB. ∆crrC and ∆kexD mutants became highly susceptible to PMB and lost the heteroresistant phenotype. Conversely, heterologous expression of CrrC and KexD proteins increased PMB resistance in a sensitive Enterobacter ludwigii clinical isolate and in the Escherichia coli K12 strain, W3110. The efflux pump, AcrABTolC, and the two component regulators, PhoPQ and CrrAB, also contributed to PMB resistance and heteroresistance. Additionally, the lipid A modification with 4-L-aminoarabinose (L-Ara4N), mediated by the arnBCADTEF operon, was critical to determine PMB resistance. Biochemical experiments, supported by mass spectrometry and structural modelling, indicated that CrrC is an inner membrane protein that interacts with the membrane domain of the KexD pump. Similar interactions were modeled for AcrB and AcrD efflux pumps. CONCLUSION Our results support a model where drug efflux potentiated by CrrC interaction with membrane domains of major efflux pumps combined with resistance to PMB entry by the L-Ara4N lipid A modification, under the control of PhoPQ and CrrAB, confers the bacterium high-level resistance and heteroresistance to PMB.
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Affiliation(s)
- Inmaculada García-Romero
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom; Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Mugdha Srivastava
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Wuerzburg, Wuerzburg, Germany; Core Unit Systems Medicine, University of Wuerzburg, Wuerzburg, Germany
| | - Julia Monjarás-Feria
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Samuel O Korankye
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Lewis MacDonald
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom.
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Bernardino AR, Grosso F, Torres CA, Reis MA, Peixe L. Exploring the biotechnological potential of Acinetobacter soli ANG344B: A novel bacterium for 2-phenylethanol production. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 42:e00839. [PMID: 38633817 PMCID: PMC11021914 DOI: 10.1016/j.btre.2024.e00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/19/2024]
Abstract
A bacterium, Acinetobacter soli ANG344B, isolated from river water, exhibited an exceptional capacity to produce 2-phenylethanol (2-PE) using L-phenylalanine (L-Phe) as a precursor-a capability typically observed in yeasts rather than bacteria. Bioreactor experiments were conducted to evaluate the production performance, using glucose as the carbon source for cellular growth and L-Phe as the precursor for 2-PE production. Remarkably, A. soli ANG344B achieved a 2-PE concentration of 2.35 ± 0.26 g/L in just 24.5 h of cultivation, exhibiting a global volumetric productivity of 0.10 ± 0.01 g/L.h and a production yield of 0.51 ± 0.01 g2-PE/gL-Phe, a result hitherto reported only for yeasts. These findings position A. soli ANG344B as a highly promising microorganism for 2-PE production. Whole-genome sequencing of A. soli strain ANG344 revealed a genome size of 3.52 Mb with a GC content of 42.7 %. Utilizing the Rapid Annotation using Subsystem Technology (RAST) server, 3418 coding genes were predicted, including genes coding for enzymes previously associated with the metabolic pathway of 2-PE production in other microorganisms, yet unreported in Acinetobacter species. Through gene mapping, 299 subsystems were identified, exhibiting 30 % subsystem coverage. The whole genome sequence data was submitted to NCBI GeneBank with the BioProject ID PRJNA982713. These draft genome data offer significant potential for exploiting the biotechnological capabilities of A. soli strain ANG344 and for conducting further comparative genomic studies.
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Affiliation(s)
- Ana R.S. Bernardino
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- LAQV‑REQUIMTE, Chemistry Department, FCT/Universidade NOVA de Lisboa, 2829‑516 Caparica, Portugal
| | - Filipa Grosso
- UCIBIO – Applied Molecular Biosciences Unit, Faculty of Pharmacy, Department of Biological Sciences, Laboratory of Microbiology, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Cristiana A.V. Torres
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Maria A.M. Reis
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Luísa Peixe
- UCIBIO – Applied Molecular Biosciences Unit, Faculty of Pharmacy, Department of Biological Sciences, Laboratory of Microbiology, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP – Culture Collection of Porto-Faculty of Pharmacy, University of Porto, Porto, Portugal
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Maghembe RS, Magulye MAK, Eilu E, Sekyanzi S, Makaranga A, Mwesigwa S, Katagirya E. A sophisticated virulence repertoire and colistin resistance of Citrobacter freundii ST150 from a patient with sepsis admitted to ICU in a tertiary care hospital in Uganda, East Africa: Insight from genomic and molecular docking analyses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 120:105591. [PMID: 38604286 PMCID: PMC11069293 DOI: 10.1016/j.meegid.2024.105591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Sepsis and multidrug resistance comprise a complex of factors attributable to mortality among intensive care unit (ICU) patients globally. Pathogens implicated in sepsis are diverse, and their virulence and drug resistance remain elusive. From a tertiary care hospital ICU in Uganda, we isolated a Citrobacter freundii strain RSM030 from a patient with sepsis and phenotypically tested it against a panel of 16 antibiotics including imipenem levofloxacin, cotrimoxazole and colistin, among others. We sequenced the organism's genome and integrated multilocus sequencing (MLST), PathogenFinder with Virulence Factor analyzer (VFanalyzer) to establish its pathogenic relevance. Thereafter, we combined antiSMASH and PRISM genome mining with molecular docking to predict biosynthetic gene clusters (BGCs), pathways, toxin structures and their potential targets in-silico. Finally, we coupled ResFinder with comprehensive antibiotic resistance database (CARD) to scrutinize the genomic antimicrobial resistance profile of the isolate. From PathogenFinder and MLST, this organism was confirmed to be a human pathogen (p = 0.843), sequence type (ST)150, whose virulence is determined by chromosomal type III secretion system (T3SS) (the injectosome) and plasmid-encoded type IV secretion system (T4SS), the enterobactin biosynthetic gene cluster and biofilm formation through the pgaABCD operon. Pathway and molecular docking analyses revealed that the shikimate pathway can generate a toxin targeting multiple host proteins including spectrin, detector of cytokinesis protein 2 (Dock2) and plasmalemma vesicle-associated protein (PLVAP), potentially distorting the host cell integrity. From phenotypic antibiotic testing, we found indeterminate results for amoxicillin/clavulanate and levofloxacin, with resistance to cotrimoxazole and colistin. Detailed genome analysis revealed chromosomal beta lactam resistance genes, i.e. blaCMY-79, blaCMY-116 and blaTEM-1B, along with multiple mutations of the lipopolysaccharide modifying operon genes PmrA/PmrB, pmrD, mgrA/mgrB and PhoP/PhoQ, conferring colistin resistance. From these findings, we infer that Citrobacter freundii strain RSM030 is implicated in sepsis and resistance to standard antibiotics, including colistin, the last resort.
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Affiliation(s)
- Reuben S Maghembe
- Biological and Marine Sciences Unit, Faculty of Natural and Applied Sciences, Marian University College, P. O. Box 47, Bagamoyo, Tanzania; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda; Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University, Wester Campus, Ishaka, Uganda.; Microbiology Section, Department of Biological Sciences, University of Botswana, Private Bag 0704, Gaborone, Botswana.
| | - Maximilian A K Magulye
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Emmanuel Eilu
- Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University, Wester Campus, Ishaka, Uganda
| | - Simon Sekyanzi
- Department of Medical Microbiology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Abdalah Makaranga
- Biological and Marine Sciences Unit, Faculty of Natural and Applied Sciences, Marian University College, P. O. Box 47, Bagamoyo, Tanzania
| | - Savannah Mwesigwa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
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de Oliveira Sant'Anna L, Dos Santos LS, Olivella JGB, da Cruz Mota M, Ramos JN, Baio PVP, da Rocha DJPG, Vieira VV, Almuzara M, Vay C, Barberis C, Castro TLDP, Seyffert N, Pacheco LGC, Mattos-Guaraldi AL. Description of Corynebacterium hiratae sp. nov. isolated from a human tissue bone a novel member of Corynebacterium Genus. Braz J Microbiol 2024; 55:1405-1414. [PMID: 38598149 PMCID: PMC11153448 DOI: 10.1007/s42770-024-01331-z] [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: 10/09/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Corynebacterium spp. are widely disseminated in the environment, and they are part of the skin and mucosal microbiota of animals and humans. Reports of human infections by Corynebacterium spp. have increased considerably in recent years and the appearance of multidrug resistant isolates around the world has drawn attention. OBJECTIVES To describe a new species of Corynebacterium from human tissue bone is described after being misidentified using available methods. METHODS For taxonomic analyses, phylogenetic analysis of 16S rRNA and rpoB genes, in silico DNA-DNA hybridization, average nucleotide and amino acid identity, multilocus sequence analysis, and phylogenetic analysis based on the complete genome were used. FINDINGS Genomic taxonomic analyzes revealed values of in silico DNA-DNA hybridization, average nucleotide and amino acids identity below the values necessary for species characterization between the analyzed isolates and the closest phylogenetic relative Corynebacterium aurimucosum DSM 44532T. MAIN CONCLUSIONS Genomic taxonomic analyzes indicate that the isolates analyzed comprise a new species of the Corynebacterium genus, which we propose to name Corynebacterium hiratae sp. nov. with isolate 332T (= CBAS 826T = CCBH 35,014T) as the type strain.
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Affiliation(s)
- Lincoln de Oliveira Sant'Anna
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil.
| | - Louisy Sanches Dos Santos
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
| | - Julianna Giordano Botelho Olivella
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
| | - Mariana da Cruz Mota
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
| | - Juliana Nunes Ramos
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
| | | | | | - Verônica Viana Vieira
- Faculty of Pharmacy and Biochemistry and Bacteriology, Department of Clinical Biochemistry, University of Buenos Aires, Autonomous City of Buenos Aires, Argentina
| | - Marisa Almuzara
- Interdisciplinary Laboratory of Medical Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Carlos Vay
- Interdisciplinary Laboratory of Medical Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Claudia Barberis
- Interdisciplinary Laboratory of Medical Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Núbia Seyffert
- Institute of Health Sciences, Department of Biotechnology, Federal University of Bahia, Salvador, Brazil
| | | | - Ana Luíza Mattos-Guaraldi
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
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Hahnke S, Berger M, Schlingloff A, Athale I, Wolf J, Neumann-Schaal M, Adenaya A, Poehlein A, Daniel R, Petersen J, Brinkhoff T. Roseobacter fucihabitans sp. nov., isolated from the brown alga Fucus spiralis. Int J Syst Evol Microbiol 2024; 74. [PMID: 38861315 DOI: 10.1099/ijsem.0.006403] [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: 06/12/2024] Open
Abstract
A Gram-negative, aerobic, pink-pigmented, and bacteriochlorophyll a-containing bacterial strain, designated B14T, was isolated from the macroalga Fucus spiralis sampled from the southern North Sea, Germany. Based on 16S rRNA gene sequences, species of the genera Roseobacter and Sulfitobacter were most closely related to strain B14T with sequence identities ranging from 98.15 % (Roseobacter denitrificans Och 114T) to 99.11 % (Roseobacter litoralis Och 149T), whereas Sulfitobacter mediterraneus CH-B427T exhibited 98.52 % sequence identity. Digital DNA-DNA hybridization and average nucleotide identity values between the genome of the novel strain and that of closely related Roseobacter and Sulfitobacter type strains were <20 % and <77 %, respectively. The novel strain contained ubiquinone-10 as the only respiratory quinone and C18 : 1 ω7c, C16 : 0, C18 : 0, C12 : 1 ω7c, C18 : 2 ω7,13c, and C10 : 0 3-OH as the major cellular fatty acids. The predominant polar lipids of strain B14T were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The genome of strain B14T comprises a chromosome with a size of 4.5 Mbp, one chromid, and four plasmids. The genome contains the complete gene cluster for aerobic anoxygenic photosynthesis required for a photoheterotrophic lifestyle. The results of this study indicate that strain B14T (=DSM 116946T=LMG 33352T) represents a novel species of the genus Roseobacter for which the name Roseobacter fucihabitans sp. nov. is proposed.
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Affiliation(s)
- Sarah Hahnke
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Present address: Department of Human Medicine, University of Oldenburg, Carl-von-Ossietzky Str. 9-11, 26129 Oldenburg, Germany
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Andrea Schlingloff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Isha Athale
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Jacqueline Wolf
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Adenike Adenaya
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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Chinachanta K, Chaiwan F, Luu DT, Pathom-aree W. Draft genome sequence data of Micrococcus yunnanesis strain ORF15-23 from rice rhizosphere soil in Thailand. Data Brief 2024; 54:110466. [PMID: 38774239 PMCID: PMC11106824 DOI: 10.1016/j.dib.2024.110466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/24/2024] Open
Abstract
A Gram-positive bacterium designated as strain ORF15-23 was isolated from a soil sample collected from rainfed organic paddy fields in Roi Et province, Thailand. This strain is previously reported to produce indole-3-acetic acid and 2-acetyl-1-pyrroline (2AP) compound, solubilize potassium feldspar and promote growth of rice seedlings. The genome sequencing was carried out using Illumina MiSeq platform. The draft genome of strain ORF15-23 was 2,562,005 bp in length with 1677 protein coding sequences and an average G + C content of 72.97 mol.%. Phylogenomic tree supports the assignment of strain ORF15-23 as member of the genus Micrococcus. A comparison of average nucleotide identity (ANIb) values revealed that strain ORF15-23 shared 96.95 % identity with the genome of M. yunnanensis DSM 21948T. The draft genome sequence of M. yunnanesis ORF15-23 has been deposited in the DDBJ/EMBL/GenBank databases under the accession number JAZDRZ000000000. This genome sequence data provides insightful information for the taxonomic characterization and further biotechnological exploitation of M. yunnanesis ORF15-23.
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Affiliation(s)
- Kawiporn Chinachanta
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Fapailin Chaiwan
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Doan Trung Luu
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Wasu Pathom-aree
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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61
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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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Liu Q, Yang LL, Xin YH. Pengzhenrongella frigida sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2024; 74. [PMID: 38896461 DOI: 10.1099/ijsem.0.006433] [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: 06/21/2024] Open
Abstract
A Gram-stain-positive, rod-shaped bacterium, designated as HLT2-17T, was isolated from soil sample taken from the Hailuogou glacier in Sichuan province, PR China. Strain HLT2-17T was capable of growing at 4-25°C and in NaCl concentrations ranging from 0 to 2% (w/v). The highest level of 16S rRNA gene sequence similarity was observed with Pengzhenrongella phosphoraccumulans M0-14T (98.3 %) and Pengzhenrongella sicca LRZ-2T (98.2 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain HLT2-17T and its closest relatives, P. phosphoraccumulans M0-14T and P. sicca LRZ-2T, were 80.0-84.0 % and 23.3-27.7 %, respectively. Phylogenomic analysis indicated that strain HLT2-17T clustered together with strains P. phosphoraccumulans M0-14T and P. sicca LRZ-2T. Strain HLT2-17T contained C16 : 0 and anteiso-C15 : 0 as the major fatty acids, and MK-9(H4) as the menaquinone. Therefore, based on a polyphasic approach, we propose that strain HLT2-17T (=CGMCC 1.11116T= NBRC 110443T) represents a novel species of the genus Pengzhenrongella and suggest the name Pengzhenrongella frigida sp. nov.
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Affiliation(s)
- Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lei-Lei Yang
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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63
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Li Y, Wang X, Deng T, Zheng G, Tu Z, Zhang L, Yuan L. Flavobacterium poyangense sp. nov., an ammonifying bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2024; 74. [PMID: 38865183 DOI: 10.1099/ijsem.0.006416] [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: 06/13/2024] Open
Abstract
A Gram-stain-negative, aerobic, non-spore-forming, nonmotile, rod-shaped, and yellow-pigmented bacterium, designated strain JXAS1T, was isolated from a freshwater sample collected from Poyang Lake in China. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the isolate belonged to the genus Flavobacterium, being closest to Flavobacterium pectinovorum DSM 6368T (98.61 %). The genome size of strain JXAS1T was 4.66 Mb with DNA G+C content 35.7 mol%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain JXAS1T and its closest relatives were below the threshold values of 95 and 70 %, respectively. The strain contained menaquinone 6 (MK-6) as the predominant menaquinone and the major polar lipids were phosphatidylethanolamine, one unidentified glycolipid, and one unidentified polar lipid. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0, iso-C17 : 0 3OH, iso-C15 : 0 3OH, and summed feature 9 (iso-C17 : 1 ω9c and/or 10-methyl C16 : 0). Based on phylogenetic, genotypic, and phenotypic evidence, the isolated strain represents a new species in the genus Flavobacterium, and the name Flavobacterium poyangense is proposed. The type strain is JXAS1T (=GDMCC 1.1378T=KCTC 62719T).
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Affiliation(s)
- Ya Li
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Xiyang Wang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Tao Deng
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Guohua Zheng
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Zuxin Tu
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Lili Zhang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Lin Yuan
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
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Mohapatra BR. Genome features and carbohydrate-active enzymes repertoire of a novel Stenotrophomonas sepilia Alg010 strain isolated from Sargassum seaweed waste. Data Brief 2024; 54:110533. [PMID: 38868382 PMCID: PMC11166690 DOI: 10.1016/j.dib.2024.110533] [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: 03/16/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
This study reports the genome sequence data of a novel Stenotrophomonas sepilia Alg010 strain isolated from Sargassum seaweed waste accumulated on the coastline of Barbados. The genome sequence data was obtained via sequencing of the genomic DNA of this isolate with Illumina NextSeq2000 platform and paired-end library preparation protocol. The resulting reads were assembled with the SPAdes Genome Assembler (ver 3.15.4) and annotated with the DDBJ Fast Annotation and Submission Tool. The genome size of this novel isolate was recorded as 4,515,447 bp with a coverage of 270×, a GC content of 66.6 % and a gap ratio of 0.027 %. The lengths of the longest and the N50 contigs were estimated as 246,749 bp and 81,982 bp, respectively. The genome contains 2 rRNA, 66 tRNA, 2 CRISPR, 86 contigs and 4024 CDSs (coding sequences) with a coding ratio of 88.9 %. The annotation of the CDSs for COG (cluster of orthologous groups) and for subsystem features indicated that the metabolism and the amino acids and derivatives were the most dominant categories, respectively. The annotation of the genome via dbCAN3 server for carbohydrate-active genes revealed 98 genes encoding the six functional classes of carbohydrate-active enzymes. The genome sequence data is available in NCBI GenBank with the accession number BTRJ00000000.
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Affiliation(s)
- Bidyut R. Mohapatra
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown BB11000, Barbados
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Mondal R, Dam P, Chakraborty J, Shaw S, Pradhan S, Das S, Nesa J, Meena K, Ghati A, Chaudhuri SD, Bhattacharjee D, Mandal V, Sarkar B, Mandal AK. Genomic dataset of a multiple-drug resistant Pseudomonas sp. strain RAC1 isolated from a flacherie infected Nistari race of Bombyx mori L. Data Brief 2024; 54:110293. [PMID: 38524843 PMCID: PMC10957439 DOI: 10.1016/j.dib.2024.110293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
Species belonging to the genus Pseudomonas is a rod shaped Gram-negative bacteria emerged as an important silkworm pathogen with broad-level multi-drug resistance. The extensive usage of antimicrobials in sericulture farming is gradually leading to the emergence of multi-drug resistance (MDR) strains, posing a significant threat to the well-being of both Bombyx mori L. and serifarmers. Pseudomonas spp. with MDR level may gets transmitted from the infected silkworm to human handlers either via direct contact or through contaminated feces. To understand the emerging concern of antimicrobial resistance (AMR) in Pseudomonas spp. provides insights into their genomic information. Here, we present the draft genome sequence data of Pseudomonas sp. strain RAC1 isolated from a flacherie infected Nistari race of Bombyx mori L. from the silkworm rearing house of Raiganj University, India and sequenced using the Illumina NovaSeq 6000 platform. The estimated genome size of the strain was 4494347 bp with a G + C content of 63.5%. The de novo assembly of the genome generated 38 contigs with an N50 of 200 kb. Our data might help to reveal the genetic diversity, underlying mechanisms of AMR and virulence potential of Pseudomonas spp. This draft-genome shotgun project has been deposited under the NCBI GenBank accession number NZ_JAUTXS000000000.
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Affiliation(s)
- Rittick Mondal
- Department of Sericulture, Raiganj University, North Dinajpur, West Bengal 733134, India
| | - Paulami Dam
- Department of Sericulture, Raiganj University, North Dinajpur, West Bengal 733134, India
| | - Joydeep Chakraborty
- Department of Microbiology, Raiganj University, North Dinajpur, West Bengal 733134, India
| | - Shubhajit Shaw
- Department of Sericulture, Raiganj University, North Dinajpur, West Bengal 733134, India
| | - Sayantan Pradhan
- Department of Sericulture, Raiganj University, North Dinajpur, West Bengal 733134, India
| | - Sandip Das
- Department of Sericulture, Raiganj University, North Dinajpur, West Bengal 733134, India
| | - Jannatun Nesa
- Department of Zoology, Gangarampur College, Dakshin Dinajpur, West Bengal 733124, India
| | - Khemraj Meena
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Rajasthan 305817, India
| | - Amit Ghati
- Department of Microbiology, Barrackpore Rastraguru Surendranath College, Barrackpore, West Bengal 700120, India
| | - Sandip Dev Chaudhuri
- Department of Sericulture, Raiganj University, North Dinajpur, West Bengal 733134, India
| | - Debjoy Bhattacharjee
- Department of Sericulture, Raiganj University, North Dinajpur, West Bengal 733134, India
| | - Vivekananda Mandal
- Plant and Microbial Physiology and Biochemistry Laboratory, Department of Botany, University of Gour Banga, Malda, West Bengal 732103, India
| | - Biraj Sarkar
- Faculty of Allied Health Sciences (FAHS), The ICFAI University, Tripura; Kamalghat, Mohanpur, West Tripura 799210, India
| | - Amit Kumar Mandal
- Department of Sericulture, Raiganj University, North Dinajpur, West Bengal 733134, India
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Kuang D, Liu F, Tian S, Liu W, Li A, Zhou Y, Huang H, Xia Q. Burkholderia semiarida as Cause of Recurrent Pulmonary Infection in Immunocompetent Patient, China. Emerg Infect Dis 2024; 30:1249-1252. [PMID: 38782141 PMCID: PMC11138970 DOI: 10.3201/eid3006.231676] [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: 05/25/2024] Open
Abstract
Burkholderia semiarida was previously identified solely as a plant pathogen within the Burkholderia cepacia complex. We present a case in China involving recurrent pneumonia attributed to B. semiarida infection. Of note, the infection manifested in an immunocompetent patient with no associated primary diseases and endured for >3 years.
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Tseng HC, Matsutani M, Fujimoto N, Ohnishi A. Draft genome sequence and morphological data of Planifilum fimeticola PLACP1, a thermophilic chloramphenicol-resistant bacterium isolated from thermophilic sludge. Data Brief 2024; 54:110447. [PMID: 38708301 PMCID: PMC11068547 DOI: 10.1016/j.dib.2024.110447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Planifilum is a thermophilic aerobic Actinomyces often found in compost that is suggested to play a primary role in the degradation of organic matter and is a potential antibiotic-resistance gene (ARG)-hosting bacterium during the composting process. Planifilum fimeticola PLACP1 was isolated from thermophilic sludge on a Columbia plate supplemented with chloramphenicol. PLACP1 was Gram-stain-positive with cells longer than 20 μm that branched and intertwined with each other. A draft genome sequence of P. fimeticola PLACP1 was generated using the Illumina NovaSeq system and deposited in the National Center for Biotechnology Information database under the BioProject accession numbers PRJDB17484 and SAMD00736731. The genome sequence comprised 3,395,140 bp, with 57.97 % GC content and 3,368 genes, including 3,267 protein-coding, 6 rRNA, and 56 tRNA genes. Based on the Comprehensive Antibiotic Resistance Database, 237 predicted gene products were related to ARGs, including 44 macrolide antibiotic-related genes (19 %) as the largest group. This dataset will be beneficial for the morphological identification, comparative genomic analyses, and ARG research in the genus Planifilum.
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Affiliation(s)
- Hou-Chia Tseng
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Naoshi Fujimoto
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Akihiro Ohnishi
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
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Rolon ML, Voloshchuk O, Bartlett KV, LaBorde LF, Kovac J. Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride. Biofilm 2024; 7:100177. [PMID: 38304489 PMCID: PMC10832383 DOI: 10.1016/j.bioflm.2024.100177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Listeria monocytogenes may survive and persist in food processing environments due to formation of complex multi-species biofilms of environmental microbiota that co-exists in these environments. This study aimed to determine the effect of selected environmental microbiota on biofilm formation and tolerance of L. monocytogenes to benzalkonium chloride in formed biofilms. The studied microbiota included bacterial families previously shown to co-occur with L. monocytogenes in tree fruit packing facilities, including Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae. Biofilm formation ability and the effect of formed biofilms on the tolerance of L. monocytogenes to benzalkonium chloride was measured in single- and multi-family assemblages. Biofilms were grown statically on polystyrene pegs submerged in a R2A broth. Biofilm formation was quantified using a crystal violet assay, spread-plating, confocal laser scanning microscopy, and its composition was assessed using amplicon sequencing. The concentration of L. monocytogenes in biofilms was determined using the most probable number method. Biofilms were exposed to the sanitizer benzalkonium chloride, and the death kinetics of L. monocytogenes were quantified using a most probable number method. A total of 8, 8, 6, and 3 strains of Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae, respectively, were isolated from the environmental microbiota of tree fruit packing facilities and were used in this study. Biofilms formed by Pseudomonadaceae, Xanthomonadaceae, and all multi-family assemblages had significantly higher concentration of bacteria, as well as L. monocytogenes, compared to biofilms formed by L. monocytogenes alone. Furthermore, multi-family assemblage biofilms increased the tolerance of L. monocytogenes to benzalkonium chloride compared to L. monocytogenes mono-species biofilms and planktonic multi-family assemblages. These findings suggest that L. monocytogenes control strategies should focus not only on assessing the efficacy of sanitizers against L. monocytogenes, but also against biofilm-forming microorganisms that reside in the food processing built environment, such as Pseudomonadaceae or Xanthomonadaceae.
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Affiliation(s)
- M. Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Olena Voloshchuk
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Katelyn V. Bartlett
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Luke F. LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
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69
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Show BK, Ross AB, Biswas R, Chaudhury S, Balachandran S. Draft genome sequence data on Bacillus safensis U41 isolated from soils of Santiniketan, India. Data Brief 2024; 54:110547. [PMID: 38882190 PMCID: PMC11179240 DOI: 10.1016/j.dib.2024.110547] [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: 04/10/2024] [Revised: 05/04/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
The draft genome sequence of an isolate of Bacillus safensis U41 from the soils of Santiniketan (23040'12″ N and 87039'52″ E) is reported here. Bacillus safensis is a bacterium that produces cellulases, which is essential for the breakdown of plant biomass. As such, it is a valuable source of digestive enzymes from plant biomass, especially cellulases. The genomic DNA was extracted from a single colony using a QIAgen Blood and Tissue kit (QIAgen Inc., Canada). Sequencing was performed via Illumina HiSeq X using 2 × 150 paired-end chemistry, generating 7,352,576 reads with sequence coverage of 509x. The assembly produced 20 contigs over 200 base pairs (bp) in length, with an N50 value of 901304 and an L50 of 2. The genome size was 3,732,407 bp, and the average GC content was 41.43 %. Genome annotation and gene predictions were performed using Prokka v.1.14.6, which identified 3783 coding sequences, 64 tRNA genes, and 3 rRNA genes.
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Affiliation(s)
- Binoy Kumar Show
- Department of Environmental Studies, Siksha-Bhavana, Visva-Bharati, Santiniketan 731235, West Bengal, India
| | - Andrew B Ross
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Raju Biswas
- Department of Botany, Siksha-Bhavana, Visva-Bharati, Santiniketan 731235, West Bengal, India
| | - Shibani Chaudhury
- Department of Environmental Studies, Siksha-Bhavana, Visva-Bharati, Santiniketan 731235, West Bengal, India
| | - Srinivasan Balachandran
- Department of Environmental Studies, Siksha-Bhavana, Visva-Bharati, Santiniketan 731235, West Bengal, India
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70
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Liou JS, Zhang WL, Hsu LW, Chen CC, Wang YT, Mori K, Hidaka K, Hamada M, Huang L, Watanabe K, Huang CH. Faecalibacterium taiwanense sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2024; 74. [PMID: 38848117 DOI: 10.1099/ijsem.0.006413] [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: 06/09/2024] Open
Abstract
Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21T(98.3-98.1 % and 79.0-79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8-97.9 % and 70.9-80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1-97.3 % and 80.3-80.5 %), Faecalibacterium longum CM04-06T(97.8-98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3-97.4 % and 82.7-82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA-DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T and its closest neighbours were below the species delineation thresholds of 77.6-85.1 %, 71.4-85.2 % and 28.3-30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C18 : 1 ω7c and lacked C15 : 0 and C17 : 1 ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78T (=BCRC 81397T=NBRC 116372T).
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Affiliation(s)
- Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Wei-Ling Zhang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Li-Wen Hsu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 11561, Taiwan, ROC
| | - Koji Mori
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kohei Hidaka
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec 3, Keelung Rd., Taipei 10673, Taiwan, ROC
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
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Paudel S, Zhao M, Stice SP, Dutta B, Kvitko BH. Thiosulfinate Tolerance Gene Clusters Are Common Features of Burkholderia Onion Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:507-519. [PMID: 38489400 DOI: 10.1094/mpmi-01-24-0005-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Burkholderia gladioli pv. alliicola, B. cepacia, and B. orbicola are common bacterial pathogens of onion. Onions produce organosulfur thiosulfinate defensive compounds after cellular decompartmentalization. Using whole-genome sequencing and in silico analysis, we identified putative thiosulfinate tolerance gene (TTG) clusters in multiple onion-associated Burkholderia species similar to those characterized in other Allium-associated bacterial endophytes and pathogens. Sequence analysis revealed the presence of three Burkholderia TTG cluster types, with both Type A and Type B being broadly distributed in B. gladioli, B. cepacia, and B. orbicola in both the chromosome and plasmids. Based on isolate natural variation and generation of isogenic strains, we determined the in vitro and in vivo contribution of TTG clusters in B. gladioli, B. cepacia, and B. orbicola. The Burkholderia TTG clusters contributed to enhanced allicin tolerance and improved growth in filtered onion extracts by all three species. TTG clusters also made clear contributions to B. gladioli foliar necrosis symptoms and bacterial populations. Surprisingly, the TTG cluster did not contribute to bacterial populations in onion bulb scales by these three species. Based on our findings, we hypothesize onion-associated Burkholderia may evade or inhibit the production of thiosulfinates in onion bulb tissues. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Sujan Paudel
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
| | - Mei Zhao
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shaun P Stice
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
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Tambong JT, Xu R, Fleitas MC, Wang L, Akuma M, Chi SI, Kutcher HR. TaqMan Real-Time PCR Assay for Specific Detection and Differentiation of Xanthomonas translucens pv. undulosa from Other Pathovars Targeting a Recombination Mediator Gene, recF. PLANT DISEASE 2024; 108:1869-1878. [PMID: 38345539 DOI: 10.1094/pdis-09-23-1827-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Bacterial leaf streak and black chaff diseases of wheat caused by Xanthomonas translucens pv. undulosa is becoming a major constraint to growers and trade since it is seedborne. Molecular tools for specific detection/differentiation of pv. undulosa are lacking. We report the development of a TaqMan real-time PCR for specific detection/identification of pv. undulosa targeting the recombination mediator gene (recF). Analysis of the complete recF (1,117 bp) sequences identified the gene as a reliable phylogenetic marker for identification of pv. undulosa, differentiating it from the other pathovars; recF-based sequence homology values among the 11 pathovars correlated well with genome-based DNA-DNA hybridization values. The discriminatory power of recF to differentiate pv. undulosa from the other pathovars is due to nucleotide polymorphic positions. We used these nucleotide polymorphisms to develop a TaqMan PCR for specific detection of pv. undulosa. The specificity of the assay was validated using 67 bacterial and fungal/oomycete strains. The selected primers and the double-quenched FAM-labeled TaqMan probe were specific for the detection of 11 pv. undulosa/secalis strains. The 56 strains of other X. translucens pathovars (n = 39) and non-Xanthomonas spp. (n = 17) did not exhibit any detectable fluorescence. Also, greenhouse-inoculated and naturally infected wheat leaf samples showed positive reactions for the presence of pv. undulosa DNA but not healthy control plants. The TaqMan assay reliably detected as low as 1-pg DNA amount and 10 colony forming units of the target pathogen per reaction. This TaqMan assay could be useful to regulatory agencies with economic benefits to wheat growers.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Maria Constanza Fleitas
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Lipu Wang
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Mercy Akuma
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- University of Ottawa, Ottawa, ON, Canada
| | - Sylvia I Chi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Canadian Blood Services, Ottawa, ON, Canada
| | - Hadley R Kutcher
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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73
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Kabiraj A, Halder U, Chitikineni A, Varshney RK, Bandopadhyay R. Insight into the genome of an arsenic loving and plant growth-promoting strain of Micrococcus luteus isolated from arsenic contaminated groundwater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:39063-39076. [PMID: 37864703 DOI: 10.1007/s11356-023-30361-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/05/2023] [Indexed: 10/23/2023]
Abstract
Contamination of arsenic in drinking water and foods is a threat for human beings. To achieve the goal for the reduction of arsenic availability, besides conventional technologies, arsenic bioremediation by using some potent bacteria is one of the hot topics for researchers. In this context, bacterium, AKS4c was isolated from arsenic contaminated water of Purbasthali, West Bengal, India, and through draft genome sequence; it was identified as a strain of Micrococcus luteus that comprised of 2.4 Mb genome with 73.1% GC content and 2256 protein coding genes. As the accessory genome, about 22 genomic islands (GIs) associated with many metal-resistant genes were identified. This strain was capable to tolerate more than 46,800 mg/L arsenate and 390 mg/L arsenite salts as well as found to be tolerable to multi-metals such as Fe, Pb, Mo, Mn, and Zn up to a certain limit of concentrations. Strain AKS4c was able to oxidize arsenite to less toxic arsenate, and its arsenic adsorption property was qualitatively confirmed through X-ray fluorescence (XRF) and Fourier transform infrared spectroscopy (FTIR) analysis. Quantitative estimation of plant growth-promoting attributes like Indole acetic acid (IAA), Gibberellic acid (GA), and proline production and enhancement of rice seedling growth in laboratory condition leads to its future applicability in arsenic bioremediation as a plant growth-promoting rhizobacteria (PGPR).
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Affiliation(s)
- Ashutosh Kabiraj
- Microbiology Section, Department of Botany, The University of Burdwan, Bardhaman, West Bengal, 713104, India
| | - Urmi Halder
- Microbiology Section, Department of Botany, The University of Burdwan, Bardhaman, West Bengal, 713104, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, 6500, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, 6500, Australia
| | - Rajib Bandopadhyay
- Microbiology Section, Department of Botany, The University of Burdwan, Bardhaman, West Bengal, 713104, India.
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74
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Jing X, Su L, Yin X, Chen Y, Guan X, Yang D, Sun Y. Genome Analysis of Pseudomonas viciae G166 Conferring Antifungal Activity in Grapevine. J Fungi (Basel) 2024; 10:398. [PMID: 38921384 PMCID: PMC11205049 DOI: 10.3390/jof10060398] [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: 04/17/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Grapevine (Vitis vinifera) is one of the major economic fruit crops but suffers many diseases, causing damage to the quality of grapes. Strain G166 was isolated from the rhizosphere of grapevine and was found to exhibited broad-spectrum antagonistic activities against fungal pathogens on grapes in vitro, such as Coniella diplodiella, Botrytis cinerea, and Colletotrichum gloeosporioides. Whole-genome sequencing revealed that G166 contained a 6,613,582 bp circular chromosome with 5749 predicted coding DNA sequences and an average GC content of 60.57%. TYGS analysis revealed that G166 belongs to Pseudomonas viciae. Phenotype analysis indicated that P. viciae G166 remarkably reduced the severity of grape white rot disease in the grapevine. After inoculation with C. diplodiella, more H2O2 and MDA accumulated in the leaves and resulted in decreases in the Pn and chlorophyll content. Conversely, G166-treated grapevine displayed less oxidative damage with lower H2O2 levels and MDA contents under the pathogen treatments. Subsequently, G166-treated grapevine could sustain a normal Pn and chlorophyll content. Moreover, the application of P. viciae G166 inhibited the growth of mycelia on detached leaves and berries, while more disease symptoms occurred in non-bacterized leaves and berries. Therefore, P. viciae G166 served as a powerful bioagent against grape white rot disease. Using antiSMASH prediction and genome comparisons, a relationship between non-ribosomal peptide synthase clusters and antifungal activity was found in the genome of P. viciae G166. Taken together, P. viciae G166 shows promising antifungal potential to improve fruit quality and yield in ecological agriculture.
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Affiliation(s)
| | | | | | | | | | - Dongyue Yang
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (X.J.); (L.S.); (X.Y.); (Y.C.); (X.G.)
| | - Yuxia Sun
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (X.J.); (L.S.); (X.Y.); (Y.C.); (X.G.)
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75
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Baysal Ö, Studholme DJ, Jimenez-Quiros C, Tör M. Genome sequence of the plant-growth-promoting bacterium Bacillus velezensis EU07. Access Microbiol 2024; 6:000762.v3. [PMID: 38868377 PMCID: PMC11165630 DOI: 10.1099/acmi.0.000762.v3] [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: 12/21/2023] [Accepted: 04/17/2024] [Indexed: 06/14/2024] Open
Abstract
Many Gram-positive spore-forming rhizobacteria of the genus Bacillus show potential as biocontrol biopesticides that promise improved sustainability and ecological safety in agriculture. Here, we present a draft-quality genome sequence for Bacillus velezensis EU07, which shows growth-promotion in tomato plants and biocontrol against Fusarium head blight. We found that the genome of EU07 is almost identical to that of the commercially used strain QST713, but identified 46 single-nucleotide differences that distinguish these strains from each other. The availability of this genome sequence will facilitate future efforts to unravel the genetic and molecular basis for EU07's beneficial properties.
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Affiliation(s)
- Ömür Baysal
- Department of Molecular Biology and Genetics, Faculty of Science, Mugla Sitki Kocman University, 48000 Menteşe, Turkey
- Department of Biological Sciences, University of Worcester, Worcester, UK
| | | | | | - Mahmut Tör
- Department of Biological Sciences, University of Worcester, Worcester, UK
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76
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Zheng Y, Mo P, Li C, Zhou Z, Zhang Z, Zhu H, Huang K, Wang Y. Streptomyces chengbuensis sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00745-z. [PMID: 38811856 DOI: 10.1038/s41429-024-00745-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024]
Abstract
Strain HUAS CB01T was a novel actinobacterium which was isolated from the rhizosphere soil of Cathaya argyrophylla, Chengbu Miao Autonomous County of Hunan Province, China. The strain formed well-growing substrate mycelium, diffusible pigments, and aerial mycelium, and differentiated into spiral-type spore chains composed of smooth-surface rod-shaped spores. Phylogenetic analysis on account of 16 S rRNA gene sequence demonstrated the strain HUAS CB01T was a member of the genus Streptomyces and had a close relationship with Streptomyces wuyuanensis CGMCC 4.7042 T (100%) and Streptomyces marianii ICN19T (99.86%). Genome-based comparisons indicated that strain HUAS CB01T could be distinctly different from its closest species, Streptomyces wuyuanensis CGMCC 4.7042 T, Streptomyces marianii ICN19T, with ANIm and dDDH results of 92.78% and 45.90%, 92.22% and 43.30%, respectively, far less than 96.7 and 70% cut-off points recommended for delineating species. The main cellular fatty acids concluded anteiso-C15:0, iso-C14:0, iso-C16:0, C16:0 and C16:1 2OH. The menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8) and the whole-cell sugars consisted of ribose and mannose. The polar lipids included phosphatidyl ethanolamine, diphosphatidylglycerol, phosphatidylglycerol, mannosides and unidentified phospholipids. According to these genotypic and phenotypic characteristics, strain HUAS CB01T can be distinguished and representative to be a novel species of the genus Streptomyces, for which the name Streptomyces chengbuensis is proposed. The type strain is HUAS CB01T ( = MCCC 1K08666T = JCM 36277 T).
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Affiliation(s)
- Yaxi Zheng
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, China
| | - Ping Mo
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, China.
| | - Chenxi Li
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, China
| | - Zhibo Zhou
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, China
| | - Zhifang Zhang
- Animal Husbandry and Fisheries Affairs Center of Huaihua, Huaihua, 418000, Hunan Province, China
| | - Haixian Zhu
- Animal Husbandry and Fisheries Affairs Center of Huaihua, Huaihua, 418000, Hunan Province, China
| | - Kerui Huang
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, China.
| | - Yun Wang
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, China
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Rey-Velasco X, Lucena T, Belda A, Gasol JM, Sánchez O, Arahal DR, Pujalte MJ. Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean. Front Microbiol 2024; 15:1407904. [PMID: 38863746 PMCID: PMC11165706 DOI: 10.3389/fmicb.2024.1407904] [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: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024] Open
Abstract
Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.
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Affiliation(s)
| | - Teresa Lucena
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Ana Belda
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David R. Arahal
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - María J. Pujalte
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
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78
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Qi D, Liu Q, Zou L, Zhang M, Li K, Zhao Y, Chen Y, Feng J, Zhou D, Wei Y, Wang W, Zhang L, Xie J. Taxonomic identification and antagonistic activity of Streptomyces luomodiensis sp. nov. against phytopathogenic fungi. Front Microbiol 2024; 15:1402653. [PMID: 38860218 PMCID: PMC11163044 DOI: 10.3389/fmicb.2024.1402653] [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: 03/19/2024] [Accepted: 05/09/2024] [Indexed: 06/12/2024] Open
Abstract
Banana wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is a devastating fungal disease. Biocontrol strategies hold immense potential for inhibiting the spread of Foc TR4. Here, 30 actinobacteria were isolated from soils and screened for their antagonistic activity against Foc TR4. Strain SCA4-21T was selected due to its strongest antagonistic activity against Foc TR4. Strain SCA4-21T also exhibited strong antagonistic activity against the other eight phytopathogenic fungi. The strain was identified as the genus Streptomyces according to its physiological, biochemical, and phenotypic characteristics. The phylogenetic trees of 16S rRNA sequences demonstrated that strain SCA4-21T formed a subclade with S. iranensis HM 35T and/or S. rapamycinicus NRRL B-5491T with low bootstrap values. Considering that 16S rRNAs did not provide sufficient resolution for species-level identification, the whole genome of strain SCA4-21T was sequenced. Multilocus sequence analysis (MLSA) based on five housekeeping gene alleles (atpD, gyrB, recA, rpoB, and trpB) revealed that strain SCA4-21T clustered into S. hygroscopicus subsp. hygroscopicus NBRC 13472T with 100% of bootstrap value. The analysis of the genome-based phylogeny also approved the results. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 91.26 and 44.30%, respectively, with values below the respective species level threshold of 95 and 70%. Hence, strain SCA 4-21T represented a novel species within the genus Streptomyces, named Streptomyces luomodiensis sp. nov. The type strain is SCA4-21T (=GDMCC4.340T = JCM36555T). By the CAZymes analysis, 348 carbohydrate-active enzymes (CAZymes) were detected, including 15 chitinases and eight β-1,3-glucanases. The fermentation broth of strain SCA4-21T, exhibiting strong antagonistic activity against Foc TR4, demonstrated high activities of chitinase and β-1,3-glucanase, which might be involved in antifungal activity. Our results showed an innovative potential biocontrol agent for managing plant fungal diseases, specifically banana fusarium wilt.
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Affiliation(s)
- Dengfeng Qi
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qiao Liu
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Liangping Zou
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Miaoyi Zhang
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kai Li
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yankun Zhao
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yufeng Chen
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Junting Feng
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dengbo Zhou
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yongzan Wei
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Wang
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lu Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jianghui Xie
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Giovannini M, Vieri W, Bosi E, Riccardi C, Lo Giudice A, Fani R, Fondi M, Perrin E. Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica. Mar Drugs 2024; 22:238. [PMID: 38921549 PMCID: PMC11205219 DOI: 10.3390/md22060238] [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: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.
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Affiliation(s)
- Michele Giovannini
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Walter Vieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Emanuele Bosi
- Department of Earth, Environment and Life Sciences—DISTAV, University of Genoa, Corso Europa 26, I-16132 Genova, Italy;
| | - Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA 90089, USA
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council, (CNR.ISP), Spianata San Raineri 86, I-98122 Messina, Italy;
- Italian Collection of Antarctic Bacteria, National Antarctic Museum (CIBAN-MNA), I-98122 Messina, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, I-90133 Palermo, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
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Mannaa M, Lee D, Lee HH, Han G, Kang M, Kim TJ, Park J, Seo YS. Exploring the comparative genome of rice pathogen Burkholderia plantarii: unveiling virulence, fitness traits, and a potential type III secretion system effector. FRONTIERS IN PLANT SCIENCE 2024; 15:1416253. [PMID: 38845849 PMCID: PMC11153758 DOI: 10.3389/fpls.2024.1416253] [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: 04/12/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
This study presents a comprehensive genomic analysis of Burkholderia plantarii, a rice pathogen that causes blight and grain rot in seedlings. The entire genome of B. plantarii KACC 18964 was sequenced, followed by a comparative genomic analysis with other available genomes to gain insights into its virulence, fitness, and interactions with rice. Multiple secondary metabolite gene clusters were identified. Among these, 12 demonstrated varying similarity levels to known clusters linked to bioactive compounds, whereas eight exhibited no similarity, indicating B. plantarii as a source of potentially novel secondary metabolites. Notably, the genes responsible for tropolone and quorum sensing were conserved across the examined genomes. Additionally, B. plantarii was observed to possess three complete CRISPR systems and a range of secretion systems, exhibiting minor variations among the analyzed genomes. Genomic islands were analyzed across the four genomes, and a detailed study of the B. plantarii KACC 18964 genome revealed 59 unique islands. These islands were thoroughly investigated for their gene contents and potential roles in virulence. Particular attention has been devoted to the Type III secretion system (T3SS), a crucial virulence factor. An in silico analysis of potential T3SS effectors identified a conserved gene, aroA. Further mutational studies, in planta and in vitro analyses validated the association between aroA and virulence in rice. Overall, this study enriches our understanding of the genomic basis of B. plantarii pathogenicity and emphasizes the potential role of aroA in virulence. This understanding may guide the development of effective disease management strategies.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Duyoung Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Minhee Kang
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Tae-Jin Kim
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Jungwook Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
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81
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Wódz K, Piechowicz L, Tokarska-Pietrzak E, Gawor J, Gromadka R, Bełkot Z, Strzałkowska Z, Wiśniewski J, Nowak T, Bogdan J, Anusz K, Pławińska-Czarnak J. Does Salmonella diarizonae 58:r:z 53 Isolated from a Mallard Duck Pose a Threat to Human Health? Int J Mol Sci 2024; 25:5664. [PMID: 38891852 PMCID: PMC11171591 DOI: 10.3390/ijms25115664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
Salmonella diarizonae (IIIb) is frequently isolated from reptiles and less frequently from birds and mammals. However, its isolation from invasive human infections has not been widely reported. Migratory mallard ducks are excellent bioindicators of pathogen presence and pathogen antibiotic resistance (AMR). We present the first isolation from a mallard duck in central Europe of the antibiotic-resistant Salmonella enterica subsp. diarizonae with the unique antigenic pattern 58:r:z53 and report its whole-genome sequencing, serosequencing, and genotyping, which enabled the prediction of its pathogenicity and comparison with phenotypic AMR. The isolated strain was highly similar to S. diarizonae isolated from humans and food. Twenty-four AMR genes were detected, including those encoding aminoglycoside, fluoroquinolone, macrolide, carbapenem, tetracycline, cephalosporin, nitroimidazole, peptide antibiotic, and disinfecting agent/antiseptic resistance. Six Salmonella pathogenicity islands were found (SPI-1, SPI-2, SPI-3, SPI-5, SPI-9, and SPI-13). An iron transport system was detected in SPI-1 centisome C63PI. Plasmid profile analyses showed three to be present. Sequence mutations in the invA and invF genes were noted, which truncated and elongated the proteins, respectively. The strain also harbored genes encoding type-III secretion-system effector proteins and many virulence factors found in S. diarizonae associated with human infections. This study aims to elucidate the AMR and virulence genes in S. enterica subsp. diarizonae that may most seriously threaten human health.
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Affiliation(s)
- Karolina Wódz
- Laboratory of Molecular Biology, Vet-Lab Brudzew, 62-720 Brudzew, Poland;
| | - Lidia Piechowicz
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdańsk, 80-204 Gdańsk, Poland; (L.P.); (E.T.-P.)
| | - Ewa Tokarska-Pietrzak
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdańsk, 80-204 Gdańsk, Poland; (L.P.); (E.T.-P.)
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Zbigniew Bełkot
- Department of Food Hygiene of Animal Origin, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-950 Lublin, Poland;
| | - Zuzanna Strzałkowska
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (Z.S.); (J.W.); (J.B.); (K.A.)
| | - Jan Wiśniewski
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (Z.S.); (J.W.); (J.B.); (K.A.)
| | - Tomasz Nowak
- Laboratory of Molecular Biology, Vet-Lab Brudzew, 62-720 Brudzew, Poland;
| | - Janusz Bogdan
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (Z.S.); (J.W.); (J.B.); (K.A.)
| | - Krzysztof Anusz
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (Z.S.); (J.W.); (J.B.); (K.A.)
| | - Joanna Pławińska-Czarnak
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (Z.S.); (J.W.); (J.B.); (K.A.)
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82
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Kim M, Cha IT, Lee KE, Park SJ. Chryseobacterium gotjawalense sp. nov. Isolated from Soil in the Volcanic Forest Gotjawal, Jeju Island. Curr Microbiol 2024; 81:187. [PMID: 38777886 DOI: 10.1007/s00284-024-03711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/21/2024] [Indexed: 05/25/2024]
Abstract
Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4-37 °C and pH 5.0-8.0 in 0-3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA-DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea
| | - In-Tae Cha
- Climate Change and Environmental Biology Research Division, National Institute of Biological Resource, Incheon, 22689, South Korea
| | - Ki-Eun Lee
- Species Diversity Research Division, National Institute of Biological Resource, Incheon, 22689, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea.
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Heckman TI, Yazdi Z, Older CE, Griffin MJ, Waldbieser GC, Chow AM, Medina Silva I, Anenson KM, García JC, LaFrentz BR, Slavic D, Toohey-Kurth KL, Yant P, Fritz HM, Henderson EE, McDowall R, Cai H, Adkison M, Soto E. Redefining piscine lactococcosis. Appl Environ Microbiol 2024; 90:e0234923. [PMID: 38597602 PMCID: PMC11107168 DOI: 10.1128/aem.02349-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/10/2024] [Indexed: 04/11/2024] Open
Abstract
Piscine lactococcosis is a significant threat to cultured and wild fish populations worldwide. The disease typically presents as a per-acute to acute hemorrhagic septicemia causing high morbidity and mortality, recalcitrant to antimicrobial treatment or management interventions. Historically, the disease was attributed to the gram-positive pathogen Lactococcus garvieae. However, recent work has revealed three distinct lactococcosis-causing bacteria (LCB)-L. garvieae, L. petauri, and L. formosensis-which are phenotypically and genetically similar, leading to widespread misidentification. An update on our understanding of lactococcosis and improved methods for identification are urgently needed. To this end, we used representative isolates from each of the three LCB species to compare currently available and recently developed molecular and phenotypic typing assays, including whole-genome sequencing (WGS), end-point and quantitative PCR (qPCR) assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), API 20 Strep and Biolog systems, fatty acid methyl ester analysis (FAME), and Sensititre antimicrobial profiling. Apart from WGS, sequencing of the gyrB gene was the only method capable of consistent and accurate identification to the species and strain level. A qPCR assay based on a putative glycosyltransferase gene was also able to distinguish L. petauri from L. garvieae/formosensis. Biochemical tests and MALDI-TOF MS showed some species-specific patterns in sugar and fatty acid metabolism or protein profiles but should be complemented by additional analyses. The LCB demonstrated overlap in host and geographic range, but there were relevant differences in host specificity, regional prevalence, and antimicrobial susceptibility impacting disease treatment and prevention. IMPORTANCE Lactococcosis affects a broad range of host species, including fish from cold, temperate, and warm freshwater or marine environments, as well as several terrestrial animals, including humans. As such, lactococcosis is a disease of concern for animal and ecosystem health. The disease is endemic in European and Asian aquaculture but is rapidly encroaching on ecologically and economically important fish populations across the Americas. Piscine lactococcosis is difficult to manage, with issues of vaccine escape, ineffective antimicrobial treatment, and the development of carrier fish or biofilms leading to recurrent outbreaks. Our understanding of the disease is also widely outdated. The accepted etiologic agent of lactococcosis is Lactococcus garvieae. However, historical misidentification has masked contributions from two additional species, L. petauri and L. formosensis, which are indistinguishable from L. garvieae by common diagnostic methods. This work is the first comprehensive characterization of all three agents and provides direct recommendations for species-specific diagnosis and management.
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Affiliation(s)
- Taylor I. Heckman
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Zeinab Yazdi
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Caitlin E. Older
- USDA-ARS, Warmwater Aquaculture Research Unit, Stoneville, Mississippi, USA
| | - Matt J. Griffin
- College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi, USA
| | | | - Alexander M. Chow
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Isabella Medina Silva
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Kelsey M. Anenson
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Julio C. García
- USDA-ARS, Aquatic Animal Health Research Unit, Auburn, Alabama, USA
| | | | - Durda Slavic
- Animal Health Laboratory, University of Guelph, Ontario, Canada
| | - Kathy L. Toohey-Kurth
- California Animal Health and Food Safety Laboratory, University of California, Davis, California, USA
| | - Paula Yant
- California Animal Health and Food Safety Laboratory, University of California, Davis, California, USA
| | - Heather M. Fritz
- California Animal Health and Food Safety Laboratory, University of California, Davis, California, USA
| | - Eileen E. Henderson
- California Animal Health and Food Safety Laboratory, University of California, Davis, California, USA
| | | | - Hugh Cai
- Animal Health Laboratory, University of Guelph, Ontario, Canada
| | - Mark Adkison
- California Department of Fish and Wildlife, Rancho Cordova, California, USA
| | - Esteban Soto
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
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Gtari M, Beauchemin NJ, Sarker I, Sen A, Ghodhbane-Gtari F, Tisa LS. An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia. Appl Environ Microbiol 2024; 90:e0028824. [PMID: 38651928 PMCID: PMC11107149 DOI: 10.1128/aem.00288-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems. IMPORTANCE While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.
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Affiliation(s)
- Maher Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Carthage, Tunisia
| | - Nicholas J. Beauchemin
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Indrani Sarker
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri, West Bengal, India
| | - Arnab Sen
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri, West Bengal, India
| | - Faten Ghodhbane-Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Carthage, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of La Manouba, Sidi Thabet, Tunisia
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Smith CM, Anacker M, Bevis DL, Dutton NAM, Powell D, McLaughlin RW. Isolation of a CTX-M-55 (ESBL)-Producing Escherichia coli Strain of the Global ST6448 Clone from a Captive Orangutan in the USA. Curr Microbiol 2024; 81:177. [PMID: 38758473 DOI: 10.1007/s00284-024-03693-x] [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: 09/28/2023] [Accepted: 04/08/2024] [Indexed: 05/18/2024]
Abstract
The purpose of this study was to determine if orangutans (Pongo spp.) living in captivity at a zoo in Wisconsin were colonized with antimicrobial-resistant bacteria and, if found, to identify underlying genetic mechanisms contributing to their resistant phenotypes. We hypothesize that since antimicrobial-resistant bacteria are so prevalent within humans, the animals could also be carriers of such strains given the daily contact between the animals and the zoo staff that care for them. To test this theory, fecal samples from two orangutans were examined for resistant bacteria by inoculation on HardyCHROM™ ESBL and HardyCHROM™ CRE agars. Isolates were identified using MALDI-TOF mass spectrometry and antimicrobial susceptibility testing was performed using a Microscan autoSCAN-4 System. An isolate was selected for additional characterization, including whole genome sequencing (WGS). Using the Type (Strain) Genome Server (TYGS) the bacterium was identified as Escherichia coli. The sequence type identified was (ST/phylogenetic group/β-lactamase): ST6448/B1/CTX-M-55.
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Affiliation(s)
- Carly M Smith
- School of Liberal Arts and Sciences, Gateway Technical College, Kenosha, WI, 53144, USA
| | - Melissa Anacker
- Minnesota Department of Health, Public Health Laboratory - Infectious Disease Laboratory, St. Paul, MN, 55155, USA
| | - Durward L Bevis
- School of Liberal Arts and Sciences, Gateway Technical College, Kenosha, WI, 53144, USA
| | - Nicole A M Dutton
- School of Liberal Arts and Sciences, Gateway Technical College, Kenosha, WI, 53144, USA
| | - Dan Powell
- Racine Zoo, 2131 North Main Street Racine, Racine, WI, 53402, USA
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Duangupama T, Pittayakhajonwut P, Intaraudom C, Suriyachadkun C, Tadtong S, Kuncharoen N, He YW, Tanasupawat S, Thawai C. Pradimicin U, a promising antimicrobial agent isolated from a newly found Nonomuraea composti sp. nov. Sci Rep 2024; 14:10942. [PMID: 38740839 PMCID: PMC11091084 DOI: 10.1038/s41598-024-60744-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Pradimicin U is a new dihydrobenzo[a]naphthacenequinone compound found to be active on a screen designed to investigate compounds with antimicrobial activity, produced by the actinomycete designated strain FMUSA5-5T. The strain was isolated from a bio-fertilizer of Musa spp. collected from Suphanburi province, Thailand. The chemotaxonomic characteristics and 16S rRNA gene analysis revealed that strain FMUSA5-5T is a member of the genus Nonomuraea. Low genome-based taxonomic criteria, average nucleotide identity (ANI) (82.8-88.3%), average amino-acid identity (AAI) (79.4-87.3%), and digital DNA-DNA hybridization (dDDH) (29.5-38.5%) values and several phenotypic differences between strain FMUSA5-5T and its closest type strains of the genus Nonomuraea indicated that strain FMUSA5-5T represents a novel species of the genus Nonomuraea and the name Nonomuraea composti sp. nov. is proposed for the strain. The crude extract from the culture broth of strain FMUSA5-5T displayed promising antimicrobial activity against several pathogens and led to the isolation of a novel secondary metabolite, pradimicin U. Interestingly, this compound displayed a broad spectrum of biological activities such as antimalarial activity against Plasmodium falciparum K1 (IC50 value = 3.65 µg/mL), anti-Mycobacterium tuberculosis H37Ra (MIC value = 25.0 µg/mL), anti-Alternaria brassicicola BCC 42724 (MIC value = 25.0 µg/mL), anti-Bacillus cereus ATCC 11778 and anti-Staphylococcus aureus ATCC 29213 (MIC values = 6.25 and 1.56 µg/mL, respectively). Moreover, the compound possessed strong anti-human small cell lung cancer (NCI-H187) activity with IC50 value of 5.69 µg/mL, while cytotoxicity against human breast cancer (MCF-7) and Vero cells was very weak (IC50 values of 52.49 and 21.84 µg/mL, respectively).
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Affiliation(s)
- Thitikorn Duangupama
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Chakapong Intaraudom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Sarin Tadtong
- Department of Pharmacognosy, Faculty of Pharmacy, Srinakharinwirot University, Nakhon Nayok, 26120, Thailand
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Chitti Thawai
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand.
- Actinobacterial Research Unit, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand.
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87
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Yaxi Z, Aihua D, Xiaoxiao X, Chenxi L, Yi P, Ting T, Jin L, Yiru M, Ping M. Streptomyces camelliae sp. nov., isolated from rhizosphere soil of Camellia oleifera Abel. Arch Microbiol 2024; 206:256. [PMID: 38734826 DOI: 10.1007/s00203-024-03987-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/07/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
A novel actinobacterium strain, designated HUAS 2-6 T, was isolated from the rhizosphere soil of Camellia oleifera Abel collected from Taoyuan County, Northwestern Hunan Province, South China. This strain was subjected to a polyphasic taxonomic study. Strain HUAS 2-6 T is characterized by morphology typical of members of the genus Streptomyces, with deep purplish vinaceous aerial mycelia and deep dull lavender substrate mycelia. Strain HUAS 2-6 T, based on the full-length 16S rRNA gene sequence analysis, exhibited the highest similarities to S. puniciscabiei S77T (99.31%), S. filipinensis NBRC 12860 T (99.10%), S. yaanensis CGMCC 4.7035 T (99.09%), S. fodineus TW1S1T (99.08%), S. broussonetiae CICC 24819 T (98.76%), S. achromogenes JCM 4121 T (98.69%), S. barringtoniae JA03T (98.69%), and less than 98.70% with other validly species. In phylogenomic tree, strain HUAS 2-6 T was clustered together with S. broussonetiae CICC 24819 T, suggesting that they were closely related to each other. However, average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) between them were much less than the species cutoff values (ANI 96.7% and dDDH 70%). Moreover, in phenotypic and chemotaxonomic characteristics, strain HUAS 2-6 T is distinct from S. broussonetiae CICC 24819 T. On the basis of the polyphasic data, strain HUAS 2-6 T is proposed to represent a novel species, Streptomyces camelliae sp. nov. (= MCCC 1K04729T = JCM 35918 T).
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Affiliation(s)
- Zheng Yaxi
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China
| | - Deng Aihua
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China.
| | - Xu Xiaoxiao
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China
| | - Li Chenxi
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China
| | - Peng Yi
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China
| | - Tang Ting
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China
| | - Liu Jin
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China
| | - Ming Yiru
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China
| | - Mo Ping
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing, at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, People's Republic of China
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88
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Jiang CS, Li CY, Gu CT. The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum. Curr Microbiol 2024; 81:168. [PMID: 38733376 DOI: 10.1007/s00284-024-03712-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
In 2018, Nouioui et al. proposed that Bifidobacterium coryneforme was a later synonym of Bifidobacterium indicum on the basis of the digital DNA-DNA hybridization (dDDH) value (85.0%) between B. coryneforme LMG 18911T and B. indicum LMG 11587T. However, in the study of Scardovi et al. (1970), the type strains of B. indicum and B. coryneforme only exhibited 60% DNA-DNA hybridization value. In the present study, the genomes of B. coryneforme CGMCC 1.2279T, B. coryneforme JCM 5819T, B. indicum JCM 1302T, B. indicum CGMCC 1.2275T, B. indicum DSM 20214T, B. indicum LMG 27437T, B. indicum ATCC 25912T, B. indicum KCTC 3230T, B. indicum CCUG 34985T, were sequenced, and the taxonomic relationship between B. coryneforme and B. indicum was re-evaluated. On the basis of the results presented here, (i) ATCC 25912 and DSM 20214 deposited by Vittorio Scardovi are two different strains; (ii) the type strain of B. indicum is ATCC 25912T (= JCM 1302T = LMG 27437T = CGMCC 1.2275T = KCTC 3230T), and not DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587); (iii) B. coryneforme and B. indicum represent two different species of the genus Bifidobacterium; (iv) strain DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587) belongs to B. coryneforme.
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Affiliation(s)
- Cheng-Shan Jiang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chun Yan Li
- College of Food Science, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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89
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Bruna P, Núñez-Montero K, Contreras MJ, Leal K, García M, Abanto M, Barrientos L. Biosynthetic gene clusters with biotechnological applications in novel Antarctic isolates from Actinomycetota. Appl Microbiol Biotechnol 2024; 108:325. [PMID: 38717668 PMCID: PMC11078813 DOI: 10.1007/s00253-024-13154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024]
Abstract
Actinomycetota have been widely described as valuable sources for the acquisition of secondary metabolites. Most microbial metabolites are produced via metabolic pathways encoded by biosynthetic gene clusters (BGCs). Although many secondary metabolites are not essential for the survival of bacteria, they play an important role in their adaptation and interactions within microbial communities. This is how bacteria isolated from extreme environments such as Antarctica could facilitate the discovery of new BGCs with biotechnological potential. This study aimed to isolate rare Actinomycetota strains from Antarctic soil and sediment samples and identify their metabolic potential based on genome mining and exploration of biosynthetic gene clusters. To this end, the strains were sequenced using Illumina and Oxford Nanopore Technologies platforms. The assemblies were annotated and subjected to phylogenetic analysis. Finally, the BGCs present in each genome were identified using the antiSMASH tool, and the biosynthetic diversity of the Micrococcaceae family was evaluated. Taxonomic annotation revealed that seven strains were new and two were previously reported in the NCBI database. Additionally, BGCs encoding type III polyketide synthases (T3PKS), beta-lactones, siderophores, and non-ribosomal peptide synthetases (NRPS) have been identified, among others. In addition, the sequence similarity network showed a predominant type of BGCs in the family Micrococcaceae, and some genera were distinctly grouped. The BGCs identified in the isolated strains could be associated with applications such as antimicrobials, anticancer agents, and plant growth promoters, among others, positioning them as excellent candidates for future biotechnological applications and innovations. KEY POINTS: • Novel Antarctic rare Actinomycetota strains were isolated from soil and sediments • Genome-based taxonomic affiliation revealed seven potentially novel species • Genome mining showed metabolic potential for novel natural products.
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Affiliation(s)
- Pablo Bruna
- Programa de Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco, Chile
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar, 01145, Temuco, Chile
| | - Kattia Núñez-Montero
- Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco, Chile
- Centro de Investigación en Biotecnología, Departamento de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - María José Contreras
- Facultad de Ingeniería, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco, Chile
| | - Karla Leal
- Facultad de Ingeniería, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco, Chile
| | - Matías García
- Programa de Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco, Chile
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar, 01145, Temuco, Chile
- Biocontrol Research Laboratory, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco, Chile
| | - Michel Abanto
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar, 01145, Temuco, Chile.
| | - Leticia Barrientos
- Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco, Chile.
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90
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Cortés-Albayay C, Delgado-Torres M, Larama G, Paredes-Negron C, de la Luz Mora M, Durán P, Barra PJ. Comparative genomics of plant growth promoting phosphobacteria isolated from acidic soils. Antonie Van Leeuwenhoek 2024; 117:76. [PMID: 38705910 DOI: 10.1007/s10482-024-01961-1] [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: 01/25/2024] [Accepted: 03/26/2024] [Indexed: 05/07/2024]
Abstract
Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains-Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198-previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbours, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings.
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Affiliation(s)
- Carlos Cortés-Albayay
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Mabel Delgado-Torres
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - Giovanni Larama
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Cecilia Paredes-Negron
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - María de la Luz Mora
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - Paola Durán
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile.
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile.
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, 4811230, Temuco, Chile.
| | - Patricio Javier Barra
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile.
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Qiao A, Pan H, Zang J, Zhang Y, Yi X, Liu Y, Zhan J, Yang X, Zhao X, Li A, Zhou H. Can xenobiotics support the growth of Mn(II)-oxidizing bacteria (MnOB)? A case of phenol-utilizing bacteria Pseudomonas sp. AN-1. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134095. [PMID: 38521035 DOI: 10.1016/j.jhazmat.2024.134095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
Biogenic manganese oxides (BioMnOx) produced by Mn(II)-oxidizing bacteria (MnOB) have garnered considerable attention for their exceptional adsorption and oxidation capabilities. However, previous studies have predominantly focused on the role of BioMnOx, neglecting substantial investigation into MnOB themselves. Meanwhile, whether the xenobiotics could support the growth of MnOB as the sole carbon source remains uncertain. In this study, we isolated a strain termed Pseudomonas sp. AN-1, capable of utilizing phenol as the sole carbon source. The degradation of phenol took precedence over the accumulation of BioMnOx. In the presence of 100 mg L-1 phenol and 100 µM Mn(II), phenol was entirely degraded within 20 h, while Mn(II) was completely oxidized within 30 h. However, at the higher phenol concentration (500 mg L-1), phenol degradation reduced to 32% and Mn(II) oxidation did not appear to occur. TOC determination confirmed the ability of strain AN-1 to mineralize phenol. Based on the genomic and proteomics studies, the Mn(II) oxidation and phenol mineralization mechanism of strain AN-1 was further confirmed. Proteome analysis revealed down-regulation of proteins associated with Mn(II) oxidation, including MnxG and McoA, with increasing phenol concentration. Notably, this study observed for the first time that the expression of Mn(II) oxidation proteins is modulated by the concentration of carbon sources. This work provides new insight into the interaction between xenobiotics and MnOB, thus revealing the complexity of biogeochemical cycles of Mn and C.
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Affiliation(s)
- Aonan Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Haixia Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Jiaxi Zang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Yiwen Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xianliang Yi
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Yang Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Jingjing Zhan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xiaojing Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xu Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China.
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Miranda-López DC, Pérez-Rueda E, Rojas-Vargas J, Cortez CH, Saldaña-Padilla A, Castelán-Sánchez HG, Castro-Escarpulli G. Comprehensive comparative analysis of the periodontal pathogen Porphyromonas gingivalis: exploring the pan-genome, the reconstruction of the gene regulatory network and genome-scale metabolic network. Lett Appl Microbiol 2024; 77:ovae048. [PMID: 38769598 DOI: 10.1093/lambio/ovae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/23/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Porphyromonas gingivalis is a nonmotile, obligate anaerobic, Gram-negative bacterium known for its association with periodontal disease and its involvement in systemic diseases such as atherosclerosis, cardiovascular disease, colon cancer, and Alzheimer's disease. This bacterium produces several virulence factors, including capsules, fimbriae, lipopolysaccharides, proteolytic enzymes, and hemagglutinins. A comparative genomic analysis revealed the open pangenome of P. gingivalis and identified complete type IV secretion systems in strain KCOM2805 and almost complete type VI secretion systems in strains KCOM2798 and ATCC49417, which is a new discovery as previous studies did not find the proteins involved in secretion systems IV and VI. Conservation of some virulence factors between different strains was observed, regardless of their genetic diversity and origin. In addition, we performed for the first time a reconstruction analysis of the gene regulatory network, identifying transcription factors and proteins involved in the regulatory mechanisms of bacterial pathogenesis. In particular, QseB regulates the expression of hemagglutinin and arginine deaminase, while Rex may suppress the release of gingipain through interactions with PorV and the formatum/nitrate transporter. Our study highlights the central role of conserved virulence factors and regulatory pathways, particularly QseB and Rex, in P. gingivalis and provides insights into potential therapeutic targets.
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Affiliation(s)
- Diana C Miranda-López
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, México
| | - Ernesto Pérez-Rueda
- Unidad Académica del Estado de Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida 97357, México
| | - Jorge Rojas-Vargas
- Department of Biology, University of Western, London, Ontario N6A 3K7, Canada
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western, London, Ontario N6A 3K7, Canada
| | - Cecilia Hernández Cortez
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, México
| | - Andres Saldaña-Padilla
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, México
| | - Hugo G Castelán-Sánchez
- Programa de Investigadoras e Investigadores por México. Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Humanidades, Ciencias y Tecnologías, Ciudad de México 03940, México
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario N6A 3K7, Canada
| | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, México
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93
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Brady C, Crampton B, Kaur S, Maddock D, Kile H, Arnold D, Denman S. Two novel Raoultella species associated with bleeding cankers of broadleaf hosts, Raoultella scottia sp. nov. and Raoultella lignicola sp. nov. Front Microbiol 2024; 15:1386923. [PMID: 38756725 PMCID: PMC11096500 DOI: 10.3389/fmicb.2024.1386923] [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: 02/16/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Seventeen Gram-negative, facultatively anaerobic bacterial strains were isolated from bleeding cankers of various broadleaf hosts and oak rhizosphere soil in Great Britain. The strains were tentatively identified as belonging to the genus Raoultella based on 16S rRNA gene sequencing. Multilocus sequence analysis (MLSA), based on four protein-encoding genes (fusA, leuS, pyrG, and rpoB), separated the strains into three clusters within the Raoultella genus clade. The majority of strains clustered with the type strain of Raoultella terrigena, with the remaining strains divided into two clusters with no known type strain. Whole genome sequencing comparisons confirmed these two clusters of strains as belonging to two novel Raoultella species which can be differentiated phenotypically from their current closest phylogenetic relatives. Therefore, two novel species are proposed: Raoultella scottia sp. nov. (type strain = BAC 10a-01-01T = LMG 33072T = CCUG 77096T) and Raoultella lignicola sp. nov. (type strain = TW_WC1a.1T = LMG 33073T = CCUG 77094T).
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Affiliation(s)
- Carrie Brady
- Centre for Research in Bioscience, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Bridget Crampton
- Centre for Forest Protection, Forest Research, Farnham, United Kingdom
| | - Sundeep Kaur
- Centre for Forest Protection, Forest Research, Farnham, United Kingdom
| | - Daniel Maddock
- Centre for Research in Bioscience, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Helene Kile
- Centre for Research in Bioscience, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Dawn Arnold
- Harper Adams University, Newport, United Kingdom
| | - Sandra Denman
- Centre for Forest Protection, Forest Research, Farnham, United Kingdom
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94
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Suphannarot A, Butdee W, Suriyachadkun C, Duangmal K, Mingma R. Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov., two novel actinobacteria isolated from mangrove sediments and leaves of halophyte Sesuvium portulacastrum in Thailand. Int J Syst Evol Microbiol 2024; 74. [PMID: 38805028 DOI: 10.1099/ijsem.0.006401] [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: 05/29/2024] Open
Abstract
A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1 ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.
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Affiliation(s)
- Aekasit Suphannarot
- Division of Microbiology, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Waranya Butdee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Chanwit Suriyachadkun
- BIOTEC Culture Collection, Biodiversity and Biotechnological Resource Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Kannika Duangmal
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Ratchanee Mingma
- Division of Microbiology, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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95
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Somphong A, Polyiam W, Suriyachadkun C, Sripreechasak P, Harunari E, Igarashi Y, Tanasupawat S, Phongsopitanun W. Streptomyces pyxinae sp. nov. and Streptomyces pyxinicus sp. nov. isolated from lichen Pyxine cocoes (Sw.) Nyl. Int J Syst Evol Microbiol 2024; 74. [PMID: 38713186 DOI: 10.1099/ijsem.0.006364] [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: 05/08/2024] Open
Abstract
Two novel actinobacteria, designated as LP05-1T and LP11T, were isolated from the lichen Pyxine cocoes (Sw.) Nyl. collected in Bangkok, Thailand. Genotypic and phenotypic analyses revealed that both strains represented members of the genus Streptomyces. The 16S rRNA gene of LP05-1T showed the highest similarity to the genome of Streptomyces gelaticus (98.41 %), while the 16S rRNA gene of LP11T was most similar to that of Streptomyces cinerochromogenes (98.93 %). The major menaquinones in LP05-1T were MK-9(H8), MK-9(H6), MK-9(H4) and MK-9(H2), and in LP11T, they were MK-9(H8) and MK-9(H6). Both strains exhibited the major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, with LP05-1T also possessing iso-C17 : 0. The polar lipids of LP05-1T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified lipid, while those of LP11T consisted of phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid and an unidentified glycolipid. The digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) values indicated that both strains are distinct from each other with values below 70 and 95 %, respectively. dDDH, ANI by blast (ANIb) and ANI by MUMmer (ANIm) values between LP05-1T and its closely related type strains were 26.07-26.80 %, 81.24-82.01 % and 86.82-86.96 %, respectively, while those for LP11T and its closely related type strains were 30.70-31.70 %, 84.09-85.31 % and 88.02-88.39 %, respectively. The results of the taxonomic investigation, including dDDH and ANI values, indicate that LP05-1T and LP11T are novel type strains of two novel species within the genus Streptomyces. The names proposed are Streptomyces pyxinae sp. nov. for strain LP05-1T (=TBRC 15494T, =NBRC 115434T) and Streptomyces pyxinicus sp. nov. for strain LP11T (=TBRC 15493T, =NBRC 115421T).
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Affiliation(s)
- Achiraya Somphong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| | - Wetchasart Polyiam
- Lichen Research Unit, Department of Biology, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani 12120, Thailand
| | - Paranee Sripreechasak
- Office of Educational Affairs, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
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96
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Cheng L, Mu H, Zhang X, Jiang P, Liu L, Li J. Deinococcus arenicola sp. nov., a novel radiation-resistant bacterium isolated from sandy soil in Antarctica. Int J Syst Evol Microbiol 2024; 74. [PMID: 38787370 DOI: 10.1099/ijsem.0.006397] [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: 05/25/2024] Open
Abstract
A Gram-stain-positive, aerobic, non-mobile and spherical strain, designated ZS9-10T, belonging to the genus Deinococcus was isolated from soil sampled at the Chinese Zhong Shan Station, Antarctica. Growth was observed in the presence of 0-4 % (w/v) NaCl, at pH 7.0-8.0 and at 4-25 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZS9-10T formed a lineage in the genus Deinococcus. It exhibited highest sequence similarity (97.4 %) to Deinococcus marmoris DSM 12784T. The major phospholipids of ZS9-10T were unidentified phosphoglycolipid, unidentified glycolipids and unidentified lipids. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C16 : 1 ω7c. MK-8 was the predominant respiratory quinone. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZS9-10T and its close relative D. marmoris DSM 12784T were 27.4 and 83.9 %, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, named Deinococcus arenicola sp. nov., is proposed. The type strain iis ZS9-10T (=CCTCC AB 2019392T=KCTC43192T).
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Affiliation(s)
- Li Cheng
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Hongmei Mu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Xinyu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Peiqiang Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Lukuan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Jing Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
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97
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van der Ploeg K, Klaassen CHW, Vos MC, Severin JA, Mason-Slingerland BCGC, Bruno MJ. A search strategy for detecting duodenoscope-associated infections: a retrospective observational study. J Hosp Infect 2024; 147:56-62. [PMID: 38447805 DOI: 10.1016/j.jhin.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Duodenoscope-associated infections (DAIs) are exogenous infections resulting from the use of contaminated duodenoscopes. Though numerous outbreaks of DAI have involved multidrug-resistant micro-organisms (MDROs), outbreaks involving non-MDROs are also likely to occur. Detection challenges arise as these infections often resolve before culture or because causative strains are not retained for comparison with duodenoscope strains. AIM To identify and analyse DAIs spanning a seven-year period in a tertiary care medical centre. METHODS This was a retrospective observational study. Duodenoscope cultures positive for gastrointestinal flora between March 2015 and September 2022 were paired with duodenoscope usage data to identify patients exposed to contaminated duodenoscopes. Analysis encompassed patients treated after a positive duodenoscope culture and those treated within the interval from a negative to a positive culture. Patient identification numbers were cross-referenced with a clinical culture database to identify patients developing infections with matching micro-organisms within one year of their procedure. A 'pair' was established upon a species-level match between duodenoscope and patient cultures. Pairs were further analysed via antibiogram comparison, and by whole-genome sequencing (WGS) to determine genetic relatedness. FINDINGS Sixty-eight pairs were identified; of these, 21 exhibited matching antibiograms which underwent WGS, uncovering two genetically closely related pairs categorized as DAIs. Infection onset occurred up to two months post procedure. Both causative agents were non-MDROs. CONCLUSION This study provides crucial insights into DAIs caused by non-MDROs and it highlights the challenge of DAI recognition in daily practice. Importantly, the delayed manifestation of the described DAIs suggests a current underestimation of DAI risk.
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Affiliation(s)
- K van der Ploeg
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - C H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - M C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - J A Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - B C G C Mason-Slingerland
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - M J Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands.
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98
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Aguilar C, Alwali A, Mair M, Rodriguez-Orduña L, Contreras-Peruyero H, Modi R, Roberts C, Sélem-Mojica N, Licona-Cassani C, Parkinson EI. Actinomycetota bioprospecting from ore-forming environments. Microb Genom 2024; 10:001253. [PMID: 38743050 PMCID: PMC11165632 DOI: 10.1099/mgen.0.001253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.
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Affiliation(s)
- César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Amir Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Madeline Mair
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Carson Roberts
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Elizabeth Ivy Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
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99
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Ahmad T, Erum Ishaq S, Liang L, Hou J, Xie R, Dong Y, Yu T, Wang F. Description of the first cultured representative of "Candidatus Synoicihabitans" genus, isolated from deep-sea sediment of South China Sea. Syst Appl Microbiol 2024; 47:126490. [PMID: 38330528 DOI: 10.1016/j.syapm.2024.126490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
In this study we describe the first cultured representative of Candidatus Synoicihabitans genus, a novel strain designated as LMO-M01T, isolated from deep-sea sediment of South China Sea. This bacterium is a facultative aerobe, Gram-negative, non-motile, and has a globular-shaped morphology, with light greenish, small, and circular colonies. Analysis of the 16S rRNA gene sequences of strain LMO-M01T showed less than 93% similarity to its closest cultured members. Furthermore, employing advanced phylogenomic methods such as comparative genome analysis, average nucleotide identity (ANI), average amino acids identity (AAI), and digital DNA-DNA hybridization (dDDH), placed this novel species within the candidatus genus Synoicihabitans of the family Opitutaceae, Phylum Verrucomicrobiota. The genomic analysis of strain LMO-M01T revealed 175 genes, encoding putative carbohydrate-active enzymes. This suggests its metabolic potential to degrade and utilize complex polysaccharides, indicating a significant role in carbon cycling and nutrient turnover in deep-sea sediment. In addition, the strain's physiological capacity to utilize diverse biopolymers such as lignin, xylan, starch, and agar as sole carbon source opens up possibilities for sustainable energy production and environmental remediation. Moreover, the genome sequence of this newly isolated strain has been identified across diverse ecosystems, including marine sediment, fresh water, coral, soil, plants, and activated sludge highlighting its ecological significance and adaptability to various environments. The recovery of strain LMO-M01T holds promise for taxonomical, ecological and biotechnological applications. Based on the polyphasic data, we propose that this ecologically important strain LMO-M01T represents a novel genus (previously Candidatus) within the family Opitutaceae of phylum Verrucomicrobiota, for which the name Synoicihabitans lomoniglobus gen. nov., sp. nov. was proposed. The type of strain is LMO-M01T (= CGMCC 1.61593T = KCTC 92913T).
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Affiliation(s)
- Tariq Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Sidra Erum Ishaq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Lewen Liang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jialin Hou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ruize Xie
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yijing Dong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Tiantian Yu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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100
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Liu FL, Abdugheni R, Ran CG, Zhou N, Liu SJ. Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human. Int J Syst Evol Microbiol 2024; 74. [PMID: 38739685 DOI: 10.1099/ijsem.0.006380] [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: 05/16/2024] Open
Abstract
An oval to rod-shaped, Gram-stain-positive, strictly anaerobic bacterium, designated LFL-14T, was isolated from the faeces of a healthy Chinese woman. Cells of the strain were non-spore-forming, grew optimally at 37 °C (growth range 30-45 °C) and pH 7.0 (growth range 6.0-9.0) under anaerobic conditions in the liquid modified Gifu anaerobic medium (mGAM). The result of 16S rRNA gene-based analysis indicated that LFL-14T shared an identity of 94.7 0% with Eubacterium ventriosum ATCC 27560T, indicating LFL-14T represented a novel taxon. The results of genome-based analysis revealed that the average nucleotide identity (ANI), the digital DNA-DNA hybridisation (dDDH) and average amino acid identity (AAI) between LFL-14T and its phylogenetically closest neighbour, Eubacterium ventriosum ATCC 27560T, were 77.0 %, 24.6 and 70.9 %, respectively, indicating that LFL-14T represents a novel species of the genus Eubacterium. The genome size of LFL-14T was 2.92 Mbp and the DNA G+C content was 33.14 mol%. We analysed the distribution of the genome of LFL-14T in cohorts of healthy individuals, type 2 diabetes patients (T2D) and patients with non-alcoholic fatty liver disease (NAFLD). We found that its abundance was higher in the T2D cohort, but it had a low average abundance of less than 0.2 % in all three cohorts. The percentages of frequency of occurrence in the T2D, healthy and NAFLD cohorts were 48.87 %, 16.72 % and 13.10 % respectively. The major cellular fatty acids of LFL-14T were C16 : 0 (34.4 %), C17 : 0 2-OH (21.4 %) and C14 : 0 (11.7 %). Additionally, the strain contained diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE), as well as unidentified phospholipids and unidentified glycolipids. The glucose fermentation products of LFL-14T were acetate and butyrate. In summary, On the basis of its chemotaxonomic, phenotypic, phylogenetic and phylogenomic properties, strain LFL-14T (= CGMCC 1.18005T = KCTC 25580T) is identified as representing a novel species of the genus Eubacterium, for which the name Eubacterium album sp. nov. is proposed.
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Affiliation(s)
- Feng-Lan Liu
- College of Life Sciences, Hebei University, Baoding, 071000, PR China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Cong-Guo Ran
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of the Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of the Chinese Academy of Sciences, Beijing, 100049, PR China
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