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Tran DM, Huynh TU, Do TO, Nguyen AD. Isolation, Plant Growth-Promoting Properties, and Whole-Genome Sequence of a Novel Paenibacillus Species. J Basic Microbiol 2024; 64:e2400119. [PMID: 38894514 DOI: 10.1002/jobm.202400119] [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: 03/02/2024] [Revised: 04/27/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024]
Abstract
This work aimed to isolate and characterize a novel chitin-degrading bacterium from Yok Don National Park, Vietnam, for crop production studies. Among the chitinolytic isolates, strain YSY-4.3 was selected, which grew rapidly and produced a large halo around the colony. 16S rDNA analysis indicated that the strain is a novel species in the genus Paenibacillus, and an in vitro evaluation showed that the strain produced phytohormones (IAA, GA3, and zeatin), biofilms, and siderophores; possessed cellulase; and exerted antifungal activity. The whole genome of the strain was 5,628,400 bp with 49.3% GC content, 5056 coding sequences, 48 tRNA, and 1 rRNA. It shared the highest values of digital DNA-DNA hybridization (67.4%) and average nucleotide identity (89.54%) with those of Paenibacillus woosongensis B2_4 (CP126084.1), suggesting a novel species. Of the coding sequences, 4287 proteins were identified by COG, and 2561 were assigned by KEGG. The genome contained at least 51 genes involved in plant growth and resistance to heavy-metal toxicity and 359 carbohydrate-active enzymes. The chitinolytic system of the strain was composed of 15 enzymes, among them, PsChiC, which contained a GH18 catalytic domain and a GH5 catalytic domain, had not been previously reported. In addition, the genome possessed 15 gene clusters encoding antimicrobial metabolites, 10 of which are possible novel clusters. This study expands knowledge regarding novel chitinolytic bacteria from Yok Don National Park and provides a valuable gene resource for future studies.
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Affiliation(s)
- Dinh Minh Tran
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - To Uyen Huynh
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - Tu Oanh Do
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
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Mispelaere M, De Rop AS, Hermans C, De Maeseneire SL, Soetaert WK, De Mol ML, Hulpiau P. Whole genome-based comparative analysis of the genus Streptomyces reveals many misclassifications. Appl Microbiol Biotechnol 2024; 108:453. [PMID: 39212721 PMCID: PMC11364561 DOI: 10.1007/s00253-024-13290-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/07/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Streptomyces species are experts in the production of bioactive secondary metabolites; however, their taxonomy has fallen victim of the tremendous interest shown by the scientific community, evident in the discovery of numerous synonymous in public repositories. Based on genomic data from NCBI Datasets and nomenclature from the LPSN database, we compiled a dataset of 600 Streptomyces species along with their annotations and metadata. To pinpoint the most suitable taxonomic classification method, we conducted a comprehensive assessment comparing multiple methodologies, including analysis of 16S rRNA, individual housekeeping genes, multilocus sequence analysis (MLSA), and Fast Average Nucleotide Identity (FastANI) on a subset of 409 species with complete data. Due to insufficient resolution of 16S rRNA and inconsistency observed in individual housekeeping genes, we performed a more in-depth analysis, comparing only FastANI and MLSA, which expanded our dataset to include 502 species. With FastANI validated as the preferred method, we conducted pairwise analysis on the entire dataset identifying 59 non-unique species among the 600, and subsequently refined the dataset to 541 unique species. Additionally, we collected data on 724 uncharacterized Streptomyces strains to investigate the uniqueness potential of the unannotated fraction of the Streptomyces genus. Utilizing FastANI, 289 strains could be successfully classified into one of the 541 Streptomyces species. KEY POINTS: • Evaluation of taxonomic classification methods for Streptomyces species. • Whole genome analysis, specifically FastANI, has been chosen as preferred method. • Various reclassifications are proposed within the Streptomyces genus.
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Affiliation(s)
- Marieke Mispelaere
- Bioinformatics Knowledge Center (BiKC), Cluster Life Sciences, Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200, Brugge, Belgium
| | - Anne-Sofie De Rop
- Centre for Industrial Biotechnology and Biocatalysis (InBio.Be), Department of Biotechnology, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Cedric Hermans
- Bioinformatics Knowledge Center (BiKC), Cluster Life Sciences, Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200, Brugge, Belgium
| | - Sofie L De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.Be), Department of Biotechnology, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim K Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.Be), Department of Biotechnology, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Maarten L De Mol
- Centre for Industrial Biotechnology and Biocatalysis (InBio.Be), Department of Biotechnology, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Paco Hulpiau
- Bioinformatics Knowledge Center (BiKC), Cluster Life Sciences, Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200, Brugge, Belgium.
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Golubev S, Rasterkovskaya M, Sungurtseva I, Burov A, Muratova A. Phenanthrene-Degrading and Nickel-Resistant Neorhizobium Strain Isolated from Hydrocarbon-Contaminated Rhizosphere of Medicago sativa L. Microorganisms 2024; 12:1586. [PMID: 39203428 PMCID: PMC11356111 DOI: 10.3390/microorganisms12081586] [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: 07/06/2024] [Revised: 07/24/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
Pollutant degradation and heavy-metal resistance may be important features of the rhizobia, making them promising agents for environment cleanup biotechnology. The degradation of phenanthrene, a three-ring polycyclic aromatic hydrocarbon (PAH), by the rhizobial strain Rsf11 isolated from the oil-polluted rhizosphere of alfalfa and the influence of nickel ions on this process were studied. On the basis of whole-genome and polyphasic taxonomy, the bacterium Rsf11 represent a novel species of the genus Neorhizobium, so the name Neorhizobium phenanthreniclasticum sp. nov. was proposed. Analysis of phenanthrene degradation by the Rsf1 strain revealed 1-hydroxy-2-naphthoic acid as the key intermediate and the activity of two enzymes apparently involved in PAH degradation. It was also shown that the nickel resistance of Rsf11 was connected with the extracellular adsorption of metal by EPS. The joint presence of phenanthrene and nickel in the medium reduced the degradation of PAH by the microorganism, apparently due to the inhibition of microbial growth but not due to the inhibition of the activity of the PAH degradation enzymes. Genes potentially involved in PAH catabolism and nickel resistance were discovered in the microorganism studied. N. phenanthreniclasticum strain Rsf11 can be considered as a promising candidate for use in the bioremediation of mixed PAH-heavy-metal contamination.
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Affiliation(s)
| | | | | | | | - Anna Muratova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), Saratov 410049, Russia; (S.G.); (M.R.); (I.S.); (A.B.)
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Paściak M, Pawlik KJ, Martynowski D, Łaczmański Ł, Ciekot J, Szponar B, Wójcik‐Fatla A, Mackiewicz B, Farian E, Cholewa G, Cholewa A, Dutkiewicz J. Discovery of a new bacterium, Microbacterium betulae sp. nov., in birch wood associated with hypersensitivity pneumonitis in woodworkers. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13311. [PMID: 39135302 PMCID: PMC11319209 DOI: 10.1111/1758-2229.13311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/26/2024] [Indexed: 08/16/2024]
Abstract
A Gram-positive, aerobic, rod-shaped mesophilic bacterium was isolated from birch wood, referred to as the AB strain. Allergological tests suggest that this strain may cause allergic alveolitis in sawmill workers. Employing a polyphasic taxonomic approach, the AB strain's 16S rRNA gene sequence showed high similarity to Microbacterium barkeri and M. oryzae, with 97.25% and 96.91%, respectively, a finding supported by rpoB and gyrB sequence analysis. Further genome sequence comparison with the closely related M. barkeri type strain indicated a digital DNA-DNA hybridization value of 25.5% and an average nucleotide identity of 82.52%. The AB strain's cell wall peptidoglycan contains ornithine, and its polar lipids comprise diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Its major fatty acids include anteiso C15:0, anteiso C17:0, and iso C16:0, while MK-10 is its predominant respiratory quinone. Comprehensive analysis through 16S rRNA, whole-genome sequencing, phenotyping, chemotaxonomy, and MALDI-TOF MS profiling indicates that the AB strain represents a new species within the Microbacterium genus. It has been proposed to name this species Microbacterium betulae sp. nov., with ABT (PCM 3040T = CEST 30706T) designated as the type strain.
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Affiliation(s)
- Mariola Paściak
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Krzysztof J. Pawlik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Dariusz Martynowski
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Łukasz Łaczmański
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Jarosław Ciekot
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Bogumiła Szponar
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Angelina Wójcik‐Fatla
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
| | - Barbara Mackiewicz
- Department of Pneumonology, Oncology and AllergologyMedical UniversityLublinPoland
| | - Ewelina Farian
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
| | - Grażyna Cholewa
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
| | - Alicja Cholewa
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
| | - Jacek Dutkiewicz
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
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He M, Chen G, Li KJ, Tang XX, Liu XX, Ren CB, Liu HH, Luo H, Debnath SC, Wang PM, Chen HX, Zheng DQ. Characterization and Genomic Analysis of Affinirhizobium gouqiense sp. nov. Isolated from Seawater of Gouqi Island Located in the East China Sea and Reclassification of Rhizobium lemnae to the Genus Affinirhizobium as Affinirhizobium lemnae comb. nov. Curr Microbiol 2024; 81:283. [PMID: 39066927 DOI: 10.1007/s00284-024-03807-5] [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: 10/11/2023] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
A novel bacterium designated as SSA5.23T was isolated from seawater. Cells of SSA5.23T are Gram-stain-negative, short, rod-shaped, and exhibit motility via numerous peritrichous flagella. The strain could grow at temperatures ranging from 15 to 35 °C (optimum at 25 °C), in a salinity range of 0-5.0% (w/v) NaCl, and within a pH range of 6.0-9.0 (optimum at pH 7.0). The predominant cellular fatty acid of SSA5.23T was C18:1 ω7c/C18:1 ω6c, and the major respiratory quinones were Q-9 and Q-10. Diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol were identified as the primary polar lipids. The complete genome (5.47 Mb) of SSA5.23T comprises of a circular chromosome of 3.64 Mb and three plasmids, specifically sized at 59.73 kb, 227.82 kb, and 1.54 Mb, respectively. Certain genes located on the plasmids play roles in denitrification, oxidative stress resistance, and osmotic tolerance, which likely contribute to the adaptability of this strain in marine conditions. Core-proteome average amino acid identity analysis effectively identified the strain's affiliation with the genus Affinirhizobium, showing the highest value (89.9%) with Affinirhizobium pseudoryzae DSM 19479T. This classification was further supported by the phylogenetic analysis of concatenated alignment of 170 single-copy orthologous proteins. When compared to related reference strains, SSA5.23T displayed an average nucleotide identity ranging from 74.9 to 80.3% and digital DNA-DNA hybridization values ranging from 19.9 to 23.9%. Our findings confirmed that strain SSA5.23T represents a novel species of the genus Affinirhizobium, for which the name Affinirhizobium gouqiense sp. nov. (type strain SSA5.23T = LMG 32560T = MCCC 1K07165T) was suggested.
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Affiliation(s)
- Min He
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Gen Chen
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Ke-Jing Li
- Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Xing-Xing Tang
- Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Xiao-Xiao Liu
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Chang-Bin Ren
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Hou-Hong Liu
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Hai Luo
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Sanjit Chandra Debnath
- Ocean College, Zhejiang University, Zhoushan, 316021, China
- Biosciences, University of Exeter, Exeter, Geoffrey Pope Building, Devon, EX4 4HB, UK
| | - Pin-Mei Wang
- Ocean College, Zhejiang University, Zhoushan, 316021, China
| | | | - Dao-Qiong Zheng
- Hainan Institute, Zhejiang University, Sanya, 572000, China.
- Ocean College, Zhejiang University, Zhoushan, 316021, China.
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Xie F, Andrews B, Asenjo JA, Goodfellow M, Pathom-Aree W. Atacama desert actinomycetes: taxonomic analysis, drought tolerance and plant growth promoting potential. World J Microbiol Biotechnol 2024; 40:283. [PMID: 39060806 DOI: 10.1007/s11274-024-04077-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
This study was designed to recover representative culturable actinomycetes from the Atacama Desert, and to detect their ability to promote plant growth under drought conditions. Environmental samples were taken from three Atacama Desert habitats, namely, from the Aguas Calientes, Lomas Bayas and Yungay core regions. With one exception higher actinomycete counts were obtained when isolation media were inoculated with mineral particles than with corresponding aliquots of serial dilution. Comparative 16S rRNA gene sequencing showed that representative isolates belonged to thirteen genera including putative novel Blastococcus, Kocuria, Micromonospora, Pseudonocardia, Rhodococcus and Streptomyces species. Representative isolates produced indole-3-acetic acid, siderophore and solubilized phosphate as well as displaying an ability to grow under drought conditions. In conclusion, the current findings open up exciting prospects for the promising potential of actinomycetes from the Atacama Desert to be used as bioinoculants to promote plant growth in arid and semi-arid biomes.
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Affiliation(s)
- Feiyang Xie
- Doctor of Philosophy Program in Applied Microbiology (International Program) in Faculty of Science, Chiang Mai University, under the CMU Presidential Scholarship, Chiang Mai, Thailand
| | - Barbara Andrews
- Department of Chemical Engineering, Biotechnology and Materials, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beaucheff 851, Santiago, Chile
| | - Juan A Asenjo
- Department of Chemical Engineering, Biotechnology and Materials, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beaucheff 851, Santiago, Chile
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Wasu Pathom-Aree
- Center of Excellent in Microbial Diversity and Sustainable Utilization, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
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Tanes C, Tu V, Daniel S, Bittinger K. Unassigning bacterial species for microbiome studies. mSystems 2024; 9:e0051524. [PMID: 38912768 PMCID: PMC11264914 DOI: 10.1128/msystems.00515-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/16/2024] [Indexed: 06/25/2024] Open
Abstract
The method of 16S rRNA marker gene sequencing has fueled microbiome research and continues to be relevant. A perceived weakness of the method is that taxonomic assignments are not possible to make at the rank of species. We show that by working to rule out bacterial or archaeal species membership, we can provide an answer that is more accurate and useful. The Unassigner software operates on 16S rRNA marker gene data and computes a rule-out probability for species membership using a beta-binomial distribution. We demonstrate that our approach is accurate based on full-genome comparisons. Our method is consistent with existing approaches and dramatically improves on them based on the percentage of reads it can associate with a species in a sample. The software is available at https://github.com/PennChopMicrobiomeProgram/unassigner.IMPORTANCEWhile existing methods do not provide reliable species-level assignments for 16S rRNA marker gene data, the Unassigner software solves this problem by ruling out species membership, allowing researchers to reason at the species level.
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Affiliation(s)
- Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Ahn S, Choi DHS, Weerawongwiwat V, Kim JH, Sukhoom A, Kim W. Aquibaculum arenosum gen. nov., sp. nov., a novel member of the family Rhodovibrionaceae, isolated from sea sand. Int J Syst Evol Microbiol 2024; 74:006458. [PMID: 38995165 PMCID: PMC11316597 DOI: 10.1099/ijsem.0.006458] [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: 08/03/2023] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
A Gram-negative, non-motile, and creamy-white coloured bacterium, designated CAU 1616T, was isolated from sea sand collected at Ayajin Beach, Goseong-gun, Republic of Korea. The bacterium was found to grow optimally at 37 °C, pH 8.0-8.5, and with 1-5 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain CAU 1616T within the order Rhodospirillales. The highest 16S rRNA gene sequence similarity was to Fodinicurvata fenggangensis YIM D812T (94.1 %), Fodinicurvata sediminis YIM D82T (93.7 %), Fodinicurvata halophila BA45ALT (93.6 %) and Algihabitans albus HHTR 118T (92.3 %). Comparing strain CAU 1616T with closely related species (Fodinicurvata fenggangensis YIM D812T and Fodinicurvata sediminis YIM D82T), the average nucleotide identity based on blast+ values were 69.7-69.8 %, the average amino acid identity values were 61.3-61.4 %, and the digital DNA-DNA hybridization values were 18.4-18.5 %. The assembled draft genome of strain CAU 1616T had 29 contigs with an N50 value of 385.8 kbp, a total length of 3 490 371 bp, and a DNA G+C content of 65.1 mol%. The predominant cellular fatty acids were C18 : 1 2-OH, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The major respiratory quinone was Q-10. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1616T represents a novel genus in the family Rhodovibrionaceae, for which the name Aquibaculum arenosum gen. nov., sp. nov. is proposed. The type strain is CAU 1616T (=KCTC 82428T=MCCC 1K06089T).
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Affiliation(s)
- Soyeon Ahn
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - David Hyung-Sun Choi
- Faculty of Arts and Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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Raimundo I, Rosado PM, Barno AR, Antony CP, Peixoto RS. Unlocking the genomic potential of Red Sea coral probiotics. Sci Rep 2024; 14:14514. [PMID: 38914624 PMCID: PMC11196684 DOI: 10.1038/s41598-024-65152-8] [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: 03/10/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed via molecular and biochemical assays, followed by genomic screening for BMC traits. Herein, we present a comprehensive in silico framework to explore a set of six putative BMC strains. We extracted high-quality DNA from coral samples collected from the Red Sea and performed PacBio sequencing. We identified BMC traits and mechanisms associated with each strain as well as proposed new traits and mechanisms, such as chemotaxis and the presence of phages and bioactive secondary metabolites. The presence of prophages in two of the six studied BMC strains suggests their possible distribution within beneficial bacteria. We also detected various secondary metabolites, such as terpenes, ectoines, lanthipeptides, and lasso peptides. These metabolites possess antimicrobial, antifungal, antiviral, anti-inflammatory, and antioxidant activities and play key roles in coral health by reducing the effects of heat stress, high salinity, reactive oxygen species, and radiation. Corals are currently facing unprecedented challenges, and our revised framework can help select more efficient BMC for use in studies on coral microbiome rehabilitation, coral resilience, and coral restoration.
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Affiliation(s)
- Inês Raimundo
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Phillipe M Rosado
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Adam R Barno
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Chakkiath P Antony
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Raquel S Peixoto
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia.
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10
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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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11
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Lick S, Wibberg D, Busche T, Blom J, Grimmler C, Goesmann A, Kalinowski J. Pseudomonas kulmbachensis sp. nov. and Pseudomonas paraveronii sp. nov., originating from chilled beef and chicken breast. Int J Syst Evol Microbiol 2024; 74. [PMID: 38587505 DOI: 10.1099/ijsem.0.006293] [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: 04/09/2024] Open
Abstract
By investigating wet and dry age-related ripening of beef, Pseudomonas strains V3/3/4/13T and V3/K/3/5T were isolated. Strain V3/3/4/13T exhibited more than 99 % 16S rRNA gene-based similarity to Pseudomonas fragi and other members of this group, while isolate V3/K/3/5T was very close to Pseudomonas veronii and a number of relatives within the Pseudomonas fluorescens group. Additional comparisons of complete rpoB sequences and draft genomes allowed us to place isolate V3/3/4/13T close to Pseudomonas deceptionensis DSM 26521T. In the case of V3/K/3/5T the closest relative was P. veronii DSM 11331T. Average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values calculated from the draft genomes of V3/3/4/13T and P. deceptionensis DSM 26521T were 88.5 and 39.8 %, respectively. For V3/K/3/5T and its closest relative P. veronii DSM 11331T, the ANIb value was 95.1 % and the dDDH value was 60.7 %. The DNA G+C contents of V3/3/4/13T and V3/K/3/5T were 57.4 and 60.8 mol%, respectively. Predominant fatty acids were C16 : 0, C18 : 1 ω7c, C17 : 0 cyclo and summed feature C16 : 1 ω7ct/C15 : 0 iso 2OH. The main respiratory quinones were Q9, with minor proportions of Q8 and, in the case of V3/K/3/5T, additional Q10. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and, in the case of V3/K/3/5T, additional phosphatidylcholine. Based on the combined data, isolates V3/3/4/13T and V3/K/3/5T should be considered as representatives of two novel Pseudomonas species. The type strain of the newly proposed Pseudomonas kulmbachensis sp. nov. is V3/3/4/13T (=DSM 113654T=LMG 32520T), a second strain belonging to the same species is FLM 004-28 (=DSM 113604=LMG 32521); the type strain for the newly proposed Pseudomonas paraveronii sp. nov. is V3/K/3/5T (=DSM 113573T=LMG 32518T) with a second isolate FLM 11 (=DSM 113572=LMG 32519).
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Affiliation(s)
- Sonja Lick
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
- ELIXIR DE Administration Office, Institute of Bio- and Geosciences IBG-5, Forschungszentrum Jülich GmbH - Branch office Bielefeld, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
- Medical School East Westphalia-Lippe, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Christina Grimmler
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
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12
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Nouioui I, Zimmermann A, Hennrich O, Xia S, Rössler O, Makitrynskyy R, Pablo Gomez-Escribano J, Pötter G, Jando M, Döppner M, Wolf J, Neumann-Schaal M, Hughes C, Mast Y. Challenging old microbiological treasures for natural compound biosynthesis capacity. Front Bioeng Biotechnol 2024; 12:1255151. [PMID: 38361790 PMCID: PMC10867783 DOI: 10.3389/fbioe.2024.1255151] [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: 07/08/2023] [Accepted: 01/03/2024] [Indexed: 02/17/2024] Open
Abstract
Strain collections are a treasure chest of numerous valuable and taxonomically validated bioresources. The Leibniz Institute DSMZ is one of the largest and most diverse microbial strain collections worldwide, with a long tradition of actinomycetes research. Actinomycetes, especially the genus Streptomyces, are renowned as prolific producers of antibiotics and many other bioactive natural products. In light of this, five Streptomyces strains, DSM 40971T, DSM 40484T, DSM 40713T, DSM 40976T, and DSM 40907T, which had been deposited a long time ago without comprehensive characterization, were the subject of polyphasic taxonomic studies and genome mining for natural compounds based on in vitro and in silico analyses. Phenotypic, genetic, and phylogenomic studies distinguished the strains from their closely related neighbors. The digital DNA-DNA hybridization and average nucleotide identity values between the five strains and their close, validly named species were below the threshold of 70% and 95%-96%, respectively, determined for prokaryotic species demarcation. Therefore, the five strains merit being considered as novel Streptomyces species, for which the names Streptomyces kutzneri sp. nov., Streptomyces stackebrandtii sp. nov., Streptomyces zähneri sp. nov., Streptomyces winkii sp. nov., and Streptomyces kroppenstedtii sp. nov. are proposed. Bioinformatics analysis of the genome sequences of the five strains revealed their genetic potential for the production of secondary metabolites, which helped identify the natural compounds cinerubin B from strain DSM 40484T and the phosphonate antibiotic phosphonoalamide from strain DSM 40907T and highlighted strain DSM 40976T as a candidate for regulator-guided gene cluster activation due to the abundance of numerous "Streptomyces antibiotic regulatory protein" (SARP) genes.
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Affiliation(s)
- Imen Nouioui
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alina Zimmermann
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Oliver Hennrich
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Shuning Xia
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Department of Microbiology, Biotechnology, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Oona Rössler
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roman Makitrynskyy
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Juan Pablo Gomez-Escribano
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gabriele Pötter
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marlen Jando
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meike Döppner
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jacqueline Wolf
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Chambers Hughes
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Department of Microbiology, Biotechnology, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Yvonne Mast
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Technische Universität Braunschweig, Institut für Mikrobiologie, Braunschweig, Germany
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13
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Jeong J, Ahn S, Truong TC, Kim JH, Weerawongwiwat V, Lee JS, Yoon JH, Sukhoom A, Kim W. Description of Mycolicibacterium arenosum sp. nov. Isolated from Coastal Sand on the Yellow Sea Coast. Curr Microbiol 2024; 81:73. [PMID: 38253726 DOI: 10.1007/s00284-023-03587-4] [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: 07/18/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
A Gram-staining-positive, aerobic, non-spore-forming bacterium was isolated from coastal sand samples from Incheon in the Republic of Korea and designated as strain CAU 1645T. The optimum conditions for growth were observed at 30 °C in growth media containing 1% (w/v) NaCl at pH 9.0. The predominant respiratory quinone was MK-9 and the major fatty acids were C16:0, C17:1 w7c, and summed feature 7. Similarly, the 16S rRNA gene sequence exhibited the highest similarity with Mycolicibacterium bacteremicum DSM 45578T and Mycolicibacterium neoaurum JCM 6365T, both of which exhibited similarity rates of 97.2%. The genomic DNA G+C content was 68.2%. The whole genome of strain CAU 1645T was obtained and annotated with annotation using RAST server. The pan-genome analysis was determined using Prokka, Roary, and Phandango. In the pan-genome analysis, the strain CAU 1645T shared 40 core genes with closely related Mycolicibacterium species, including the AcpM gene, the meromycolate extension acyl carrier protein involved in forming impermeable cell walls in mycobacteria. Therefore, our findings demonstrated that the isolate represents a novel species of the genus Mycolicibacterium, for which we propose the name Mycolicibacterium arenosum sp. nov. The type strain is CAU 1645T (= KCTC 49724T = MCCC 1K07087T).
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Affiliation(s)
- Jiseon Jeong
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Soyeon Ahn
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Thoi Cong Truong
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkla, 90110, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea.
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14
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Hong T, Ke J, Chen L, Hao Y, Lu P, Chen S. Genomic, Physiological, Biochemical, and Phenotypic Evidences Reveal a New Species, Halomicroarcula salaria sp. nov. Curr Microbiol 2024; 81:71. [PMID: 38253911 DOI: 10.1007/s00284-023-03574-9] [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: 03/29/2023] [Accepted: 12/01/2023] [Indexed: 01/24/2024]
Abstract
An extremely halophilic archaeon strain named FL173T was isolated from a salt mine (Anhui Province, China). Colonies on agar plate are orange-red, moist, and opaque. Cells are motile, Gram-stain-negative, polymorphic, and lyse in distilled water. Cells are able to grow at temperatures, NaCl concentrations, and pH ranging from 20 to 50 °C (optimum 42 °C), 2.6 to 5.1 M NaCl concentration (optimum 3.4 M), and 5.5 to 9.5 pH (optimum 7.0), respectively. Mg2+ is not necessary for growth. The major polar lipids of strain FL173T were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfonate (PGS), sulfonated mannosyl glycolipid (S-DGD-1). It has two copies of the 16S rRNA gene, which share the highest sequence similarity (93.04-99.02% sequence similarity) to the 16S rRNA genes of Halomicroarcula salinisoli F24AT, respectively. The rpoB' gene of strain FL173T showed the highest sequence similarity (93.76%) to that of H. salinisoli F24AT. The genome-based analysis showed that the average amino-acid identity (AAI), orthologous average nucleotide identity (ANI) and in silico DNA-DNA hybridization values between strains FL173T and H. salinisoli F24AT were 84.80%, 85.29%, and 29.70%, respectively, which are far below the threshold for the delineation of a prokaryotic new species. The DNA G+C content of strain FL173T is 64.9%. Genomic, physiological, biochemical, and phenotypic evidences showed that strain FL173T (CGMCC 1.18851=NBRC 114260) represents a new species of the genus Halomicroarcula, for which the name Halomicroarcula salaria sp. nov. is proposed.
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Affiliation(s)
- Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Juntao Ke
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Liangzhon Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Yuling Hao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Peng Lu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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15
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Kusuma AB, Fenylestari G, Ammar F, Nououi I, Goodfellow M. Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al. 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980). Int J Syst Evol Microbiol 2024; 74. [PMID: 38214280 DOI: 10.1099/ijsem.0.006236] [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: 01/13/2024] Open
Abstract
A polyphasic study was designed to determine the taxonomic status of isolate CSLK01-03T, which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus Rhodococcus. The isolate was found to have chemotaxonomic, cultural and morphological properties typical of rhodococci. It has a rod-coccus lifecycle and grows from 10 to 39 °C, from pH 6.5 to 8.0 and in the presence of 0-10 % (w/v) sodium chloride. Whole-organism hydrolysates contain meso-diaminopimelic acid, arabinose and galactose, the predominant menaquinone is MK-8 (H2), the polar lipid pattern consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylmethylethanolamine and two unidentified components, it produces mycolic acids, and C16:0 is the major fatty acid. Whole-genome analyses show that the isolate and Rhodococcus electrodiphilus LMG 29881T (GenBank accession: JAULCK000000000) have genome sizes of 5.5 and 5.1 Mbp, respectively. These strains and Rhodococcus aetherivorans DSM 44752T and Rhodococcus ruber DSM 43338T form well-supported lineages in 16S rRNA and whole-genome trees that are close to sister lineages composed of the type strains of Rhodococcus rhodochrous and related Rhodococcus species. The isolate can be distinguished from its closest evolutionary neighbours using combinations of cultural and phenotypic features, and by low DNA-DNA hybridization values. Based on these data it is proposed that isolate CSLK01-03T (=CCMM B1310T=ICEBB-06T=NCIMB 15214T) be classified in the genus Rhodococcus as Rhodococcus indonesiensis sp. nov. The genomes of the isolate and its closest phylogenomic relatives are rich in biosynthetic gene clusters with the potential to synthesize new natural products, notably antibiotics. In addition, whole-genome-based taxonomy revealed that Rhodococcus electrodiphilus LMG 29881T and Rhodococcus ruber DSM 43338T belong to a single species. It is, therefore, proposed that R. electrodiphilus be recognized as a heterotypic synonym of R. ruber.
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Affiliation(s)
- Ali Budhi Kusuma
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Indonesian Centre for Extremophile Bioresources and Biotechnology (ICEBB), Faculty of Life Sciences and Technology, Sumbawa University of Technology, Sumbawa Besar, 84371, Indonesia
- PT. Archipelago Biotechnology Indonesia (Archi Biotech), Sumbawa Besar, 84316, Indonesia
| | - Gita Fenylestari
- PT. Archipelago Biotechnology Indonesia (Archi Biotech), Sumbawa Besar, 84316, Indonesia
- Department of Research, Innovation and Development, Sumbawa Technopark (STP), Sumbawa Besar, 84371, Indonesia
| | - Fadhil Ammar
- PT. Archipelago Biotechnology Indonesia (Archi Biotech), Sumbawa Besar, 84316, Indonesia
- Department of Research, Innovation and Development, Sumbawa Technopark (STP), Sumbawa Besar, 84371, Indonesia
| | - Imen Nououi
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Imhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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16
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Lasek R, Piszczek I, Krolikowski M, Sówka A, Bartosik D. A Plasmid-Borne Gene Cluster Flanked by Two Restriction-Modification Systems Enables an Arctic Strain of Psychrobacter sp. to Decompose SDS. Int J Mol Sci 2023; 25:551. [PMID: 38203722 PMCID: PMC10779009 DOI: 10.3390/ijms25010551] [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: 11/23/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
The cold-adapted Psychrobacter sp. strain DAB_AL62B, isolated from ornithogenic deposits on the Arctic island of Spitsbergen, harbors a 34.5 kb plasmid, pP62BP1, which carries a genetic SLF module predicted to enable the host bacterium to metabolize alkyl sulfates including sodium dodecyl sulfate (SDS), a common anionic surfactant. In this work, we experimentally confirmed that the pP62BP1-harboring strain is capable of SDS degradation. The slfCHSL genes were shown to form an operon whose main promoter, PslfC, is negatively regulated by the product of the slfR gene in the absence of potential substrates. We showed that lauryl aldehyde acts as an inducer of the operon. The analysis of the draft genome sequence of the DAB_AL62B strain revealed that the crucial enzyme of the SDS degradation pathway-an alkyl sulfatase-is encoded only within the plasmid. The SLF module is flanked by two restriction-modification systems, which were shown to exhibit the same sequence specificity. We hypothesize that the maintenance of pP62BP1 may be dependent on this unique genetic organization.
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Affiliation(s)
- Robert Lasek
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (I.P.); (M.K.); (A.S.)
| | | | | | | | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (I.P.); (M.K.); (A.S.)
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17
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Prescott RD, Chan YL, Tong EJ, Bunn F, Onouye CT, Handel C, Lo CC, Davenport K, Johnson S, Flynn M, Saito JA, Lee H, Wong K, Lawson BN, Hiura K, Sager K, Sadones M, Hill EC, Esibill D, Cockell CS, Santomartino R, Chain PS, Decho AW, Donachie SP. Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance. ASTROBIOLOGY 2023; 23:1348-1367. [PMID: 38079228 PMCID: PMC10750312 DOI: 10.1089/ast.2023.0072] [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: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 12/22/2023]
Abstract
Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).
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Affiliation(s)
- Rebecca D. Prescott
- Department of Biology, University of Mississippi, University, Mississippi, USA
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
- National Aeronautics and Space Administration, Johnson Space Center, Houston, Texas, USA
| | - Yvonne L. Chan
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | - Eric J. Tong
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | - Fiona Bunn
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Chiyoko T. Onouye
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Christy Handel
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Chien-Chi Lo
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Karen Davenport
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Shannon Johnson
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Mark Flynn
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Jennifer A. Saito
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Herb Lee
- Pacific American Foundation, Kailua, Hawai‘i, USA
| | | | - Brittany N. Lawson
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Kayla Hiura
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Kailey Sager
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Mia Sadones
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Ethan C. Hill
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | | | - Charles S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Rosa Santomartino
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Patrick S.G. Chain
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Alan W. Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina, USA
| | - Stuart P. Donachie
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
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18
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Lee SH, Yoo Y, Kwon DY, Khim JS, Xu X, Kim B, Choi IG, Kim JJ. Tenacibaculum tangerinum sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 38117208 DOI: 10.1099/ijsem.0.006203] [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: 12/21/2023] Open
Abstract
An orange-coloured bacterium, designated as strain GRR-S3-23T, was isolated from a tidal flat sediment collected from Garorim Bay, Chuncheongbuk-do, Republic of Korea. Cells of GRR-S3-23T were aerobic, Gram-stain-negative, rod-shaped and motile. GRR-S3-23T grew at 18-40 °C (optimum, 30 °C), pH 7.0-9.0 (optimum, pH 7.0) and with 2-4 % NaCl (optimum, 2-3 % w/v). Results of 16S rRNA gene sequence analysis indicated that GRR-S3-23T was closely related to Tenacibaculum aiptasiae a4T (97.6 %), followed by Tenacibaculum aestuarii SMK-4T (97.5 %), Tenacibaculum mesophilum MBIC 1140T (97.4 %), Tenacibaculum singaporense TLL-A2T (97.3 %), Tenacibaculum crassostreae JO-1T (97.2 %),and Tenacibaculum sediminilitoris YKTF-3T (97.1 %). The average amino acid identity values between GRR-S3-23T and the related strains were 86.8-72.8 %, the average nucleotide identity values were 83.3-74.1 %, and the digital DNA-DNA hybridization values were 27.0-19.6 %. GRR-S3-23T possessed menaquinone-6 (MK-6) as major respiratory quinone and had summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 20.6 %) and iso-C15 : 1G (10.8 %) as major fatty acids (>10.0 %). The polar lipid profiles of GRR-S3-23T contained phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid, three unidentified lipids, one unidentified glycolipid and four unidentified phospholipids. The DNA G+C content of GRR-S3-23T was 33.7%. On the basis of the results of the polyphasic analysis involving phylogenetic, phylogenomic, physiological and chemotaxonomic analyses described in this study, GRR-S3-23T is considered to represent a novel species within the genus Tenacibaculum, for which the name Tenacibaculum tangerinum is proposed. The type strain is GRR-S3-23T (=KCTC 102029T=KACC 23271T=JCM 36353T).
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Affiliation(s)
- Sang Hyun Lee
- Division of Environmental Science and Ecological Engineering, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Yeonjae Yoo
- Division of Environmental Science and Ecological Engineering, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Dae Young Kwon
- Division of Environmental Science and Ecological Engineering, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Science and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Xiaoyue Xu
- Department of Biotechnology, School of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Bogun Kim
- Department of Biotechnology, School of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, School of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science and Ecological Engineering, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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Kammoun I, Hezbri K, Sbissi I, Del Carmen Montero-Calasanz M, Klenk HP, Gtari M, Ghodhbane-Gtari F. Blastococcus carthaginiensis sp. nov., isolated from a monument sampled in Carthage, Tunisia. Int J Syst Evol Microbiol 2023; 73. [PMID: 37994907 DOI: 10.1099/ijsem.0.006178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
A comprehensive polyphasic investigation was conducted to elucidate the taxonomic position of an actinobacterium, designated BMG 814T, which was isolated from the historic ruins of Carthage city in Tunisia. It grew as pink-orange pigmented colonies and displayed versatile growth capabilities, thriving within a temperature range of 20-40 °C, across a pH spectrum ranging from pH 5.5 to 10 and in the presence of up to 4 % NaCl. Chemotaxonomic investigations unveiled specific cell components, including diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified aminoglycophospholipid, six unidentified aminolipids, two unidentified phospholipids and one unidentified lipid in its polar lipid profile. Furthermore, galactose, glucose and ribose were identified as the primary cell-wall sugars. Major menaquinones identified were MK-9(H4), MK-9(H2) and MK-9, while major fatty acids comprised iso-C15 : 0, iso-C16 : 0, C17 : 1 ω8c and C18 : 1 ω9c. Through phylogenetic analysis based on the 16S rRNA gene sequence, the strain was positioned within the genus Blastococcus, with Blastococcus capsiensis BMG 804T showing the closest relationship (99.1 %). In light of this, draft genomes for both strains, BMG 814T and BMG 804T, were sequenced in this study, and comparative analysis revealed that strain BMG 814T exhibited digital DNA-DNA hybridization and average nucleotide identity values below the recommended thresholds for demarcating new species with all available genomes of type strains of validly names species. Based on the polyphasic taxonomy assessment, strain BMG 814T (=DSM 46848T=CECT 8878T) was proposed as the type strain of a novel species named Blastococcus carthaginiensis sp. nov.
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Affiliation(s)
- Ikram Kammoun
- USCR Bactériologie Moléculaire Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Carthage, Tunisia
| | - Karima Hezbri
- USCR Bactériologie Moléculaire Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Carthage, Tunisia
| | - Imed Sbissi
- LR Écologie Pastorale, Institut des Régions Arides, Médenine, Tunisia
| | | | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Maher Gtari
- USCR Bactériologie Moléculaire Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Carthage, Tunisia
| | - Faten Ghodhbane-Gtari
- USCR Bactériologie Moléculaire Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Carthage, Tunisia
- Institut supérieur de Biotechnologie de Sidi Thabet, Université La Manouba, Manouba, Tunisia
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Dhar K, Abinandan S, Sana T, Venkateswarlu K, Megharaj M. Anaerobic biodegradation of phenanthrene and pyrene by sulfate-reducing cultures enriched from contaminated freshwater lake sediments. ENVIRONMENTAL RESEARCH 2023; 235:116616. [PMID: 37437866 DOI: 10.1016/j.envres.2023.116616] [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: 04/26/2023] [Revised: 06/17/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023]
Abstract
Our current understanding of the susceptibility of hazardous polycyclic aromatic hydrocarbons (PAHs) to anaerobic microbial degradation is very limited. In the present study, we obtained phenanthrene- and pyrene-degrading strictly anaerobic sulfate-reducing enrichments using contaminated freshwater lake sediments as the source material. The highly enriched phenanthrene-degrading culture, MMKS23, was dominated (98%) by a sulfate-reducing bacterium belonging to the genus Desulfovibrio. While Desulfovibrio sp. was also predominant (79%) in the pyrene-degrading enrichment culture, MMKS44, an anoxygenic purple non-sulfur bacterium, Rhodopseudomonas sp., constituted a significant fraction (18%) of the total microbial community. Phenanthrene or pyrene biodegradation by the enrichment cultures was coupled with sulfate reduction, as evident from near stoichiometric consumption of sulfate and accumulation of sulfide. Also, there was almost complete inhibition of substrate degradation in the presence of an inhibitor of sulfate reduction, i.e., 20 mM MoO42-, in the culture medium. After 180 days of incubation, about 79.40 μM phenanthrene was degraded in the MMKS23 culture, resulting in the consumption of 806.80 μM sulfate and accumulation of 625.80 μM sulfide. Anaerobic pyrene biodegradation by the MMKS44 culture was relatively slow. About 22.30 μM of the substrate was degraded after 180 days resulting in the depletion of 239 μM sulfate and accumulation of 196.90 μM sulfide. Biodegradation of phenanthrene by the enrichment yielded a metabolite, phenanthrene-2-carboxylic acid, suggesting that carboxylation could be a widespread initial step of phenanthrene activation under sulfate-reducing conditions. Overall, this novel study demonstrates the ability of sulfate-reducing bacteria (SRB), dwelling in contaminated freshwater sediments to anaerobically biodegrade three-ringed phenanthrene and highly recalcitrant four-ringed pyrene. Our findings suggest that SRB could play a crucial role in the natural attenuation of PAHs in anoxic freshwater sediments.
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Affiliation(s)
- Kartik Dhar
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia.
| | - Sudharsanam Abinandan
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Tanmoy Sana
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapur, Andhra Pradesh, 515003, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), University of Newcastle, Callaghan, NSW, 2308, Australia.
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21
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Ates H, Saygin H, Cora M, Kilic AO, Ay H. Genome-based classification of Streptomyces anatolicus sp. nov., an actinobacterium with antimicrobial and cytotoxic activities, and reclassification of Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis. Antonie Van Leeuwenhoek 2023; 116:1073-1090. [PMID: 37606828 DOI: 10.1007/s10482-023-01864-7] [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: 12/13/2022] [Accepted: 07/29/2023] [Indexed: 08/23/2023]
Abstract
During the course of isolating novel actinobacteria producing bioactive metabolites, strain BG9HT was obtained from an arid soil sample in Erzurum, Turkey. Pairwise sequence comparisons for 16S rRNA gene sequences showed the strain was a member of the genus Streptomyces and it shared the highest 16S rRNA gene sequence identity of 99.7% with Streptomyces huasconensis HST28T. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity revealed that strain BG9HT represents a novel species within the genus Streptomyces. The polyphasic analysis also confirmed that the strain has typical characteristics of the genus Streptomyces. The strain has LL-diaminopimelic acid as diagnostic amino acid, and galactose, mannose and trace amounts of glucose and ribose as whole-cell sugars. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unidentified aminolipids, phospholipids and lipids. Major isoprenoid quinones were MK-9(H6), MK-9(H4), and MK-9(H8). Its genome size is approximately 7.2 Mb with 71.2% G+C content. The methanolic extract of strain BG9HT showed antimicrobial and cytotoxic activities. Further genomic analyses of strain BG9HT confirmed its high potential to produce novel secondary metabolites. On the basis of phenotypic and phylogenetic analyses, strain BG9HT represents a novel species of the genus Streptomyces, for which Streptomyces anatolicus sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to the biopharmaceutical industry. We also propose Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis as a result obtained through analysis of overall genome relatedness indices.
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Affiliation(s)
- Hilal Ates
- Department of Biology, Faculty of Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Hayrettin Saygin
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Merve Cora
- Department of Medical Microbiology, Faculty of Medicine, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Ali Osman Kilic
- Department of Medical Microbiology, Faculty of Medicine, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, 34220, Istanbul, Turkey.
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22
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Han R, Hong Y, Xu R, Guo W, Zhang M, Lu Z, Han Q, Mo Z, Dan X, Li Y. Genomic evidence of genetic diversity and functional evolution in Flavobacterium columnare. Front Microbiol 2023; 14:1240471. [PMID: 37840739 PMCID: PMC10568018 DOI: 10.3389/fmicb.2023.1240471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish. Columnaris disease can cause heavy economic losses in aquaculture. In this study, whole-genome sequencing was used to characterize this pathogen. F. columnare isolate AH-01 had a circular chromosome and plasmid that encoded a total of 3,022 genes. Isolate GX-01 only had a circular chromosome and encoded 2,965 genes. Genomic islands, prophage regions, and CRISPR/Cas systems were identified in both genomes. Both genomes presented evidence of gene variation and horizontal transfer, both of which are the essential components of genetic diversity, genome plasticity, and functional evolution. Single-gene phylogeny and comparative genome analyses were performed to investigate the variation and evolution of this pathogen. Genetic analysis of 16S rRNA and housekeeping gene sequences significantly clustered 55 F. columnare isolates into four clades. The intragroup identity of the 16S rRNA gene exceeded 99%, while the intergroup identity was below the species delineation threshold. We discovered significant translocation, inversion, and rearrangement events that influenced local synteny within each group. Notably, the observed alignments varied considerably among all the studied groups. The core genomes of all strains with available sequences comprised 747 genes, corresponding to approximately 25% of the genome. Core genome multilocus sequence typing, genome-wide orthology and phylogenetic analyses, and average nucleotide identity suggested that the currently existing F. columnare was an assemblage of several distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. The present investigation provided genomic evidence of gene variation and horizontal transfer, which were the basis of genetic diversity, genome plasticity, and functional evolution. The findings supported a proposed new taxonomic perspective on F. columnare.
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Affiliation(s)
- Rui Han
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
| | - Yuhao Hong
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Ruilong Xu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wenjie Guo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Mingshu Zhang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Zijun Lu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Qing Han
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zequan Mo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
| | - Xueming Dan
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
| | - Yanwei Li
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
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23
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Sun QL, Xu K, Cao L, Du Z, Wang M, Sun L. Nitrogen and sulfur cycling driven by Campylobacterota in the sediment-water interface of deep-sea cold seep: a case in the South China Sea. mBio 2023; 14:e0011723. [PMID: 37409803 PMCID: PMC10470523 DOI: 10.1128/mbio.00117-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/11/2023] [Indexed: 07/07/2023] Open
Abstract
Chemoautotrophs within Campylobacterota, especially Sulfurovum and Sulfurimonas, are abundant in the seawater-sediment interface of the Formosa cold seep in the South China Sea. However, the in situ activity and function of Campylobacterota are unknown. In this study, the geochemical role of Campylobacterota in the Formosa cold seep was investigated with multiple means. Two members of Sulfurovum and Sulfurimonas were isolated for the first time from deep-sea cold seep. These isolates are new chemoautotrophic species that can use molecular hydrogen as an energy source and CO2 as a sole carbon source. Comparative genomics identified an important hydrogen-oxidizing cluster in Sulfurovum and Sulfurimonas. Metatranscriptomic analysis detected high expression of hydrogen-oxidizing gene in the RS, suggesting that H2 was likely an energy source in the cold seep. Genomic analysis indicated that the Sulfurovum and Sulfurimonas isolates possess a truncated sulfur-oxidizing system, and metatranscriptomic analysis revealed that Sulfurovum and Sulfurimonas with this genotype were active in the surface of RS and likely contributed to thiosulfate production. Furthermore, geochemical and in situ analyses revealed sharply decreased nitrate concentration in the sediment-water interface due to microbial consumption. Consistently, the denitrification genes of Sulfurimonas and Sulfurovum were highly expressed, suggesting an important contribution of these bacteria to nitrogen cycling. Overall, this study demonstrated that Campylobacterota played a significant role in the cycling of nitrogen and sulfur in a deep-sea cold seep. IMPORTANCE Chemoautotrophs within Campylobacterota, in particular Sulfurovum and Sulfurimonas, are ubiquitous in deep-sea cold seeps and hydrothermal vents. However, to date, no Sulfurovum or Sulfurimonas has been isolated from cold seeps, and the ecological roles of these bacteria in cold seeps remain to be investigated. In this study, we obtained two isolates of Sulfurovum and Sulfurimonas from Formosa cold seep, South China Sea. Comparative genomics, metatranscriptomics, geochemical analysis, and in situ experimental study indicated collectively that Campylobacterota played a significant part in nitrogen and sulfur cycling in cold seep and was the cause of thiosulfate accumulation and sharp reduction of nitrate level in the sediment-water interface. The findings of this study promoted our understanding of the in situ function and ecological role of deep-sea Campylobacterota.
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Affiliation(s)
- Qing-lei Sun
- College of Life Science, Qingdao Agricultural University, Qingdao, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Ke Xu
- College of Life Science, Qingdao Agricultural University, Qingdao, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lei Cao
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zengfeng Du
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Minxiao Wang
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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Diouf FS, Beye M, Gaye M, Mbaye B, Alibar S, Sarr M, Dubourg G, Lagier JC, Sokhna C, Fenollar F, Fournier PE, Lo CI. Description of Streptococcus thalassemiae sp. nov., a Bacterium Isolated from Human Blood. Int J Microbiol 2023; 2023:3802590. [PMID: 37559874 PMCID: PMC10409578 DOI: 10.1155/2023/3802590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 08/11/2023] Open
Abstract
Blood is a precious biological liquid that is normally sterile. Therefore, bacteria in the bloodstream are shown a priori anomaly. A blood culture is systematically performed to diagnose the cause of the bacteremia. Indeed, a patient received in our service had a thalassemia major and underwent a genoidentical transplant. Then, a blood test was performed to diagnose a four-day fever. In this context, we have isolated strain Marseille-Q2617 from the blood sample. It revealed a new bacterial strain that belongs to the genus Streptococcus. It is a Gram-positive coccus, nonmotile, and nonspore forming. The major fatty acid found is hexadecanoic acid, with 49.5%. A taxonomic method was used to characterize the strain by studying their phenotypic, phylogenetic, and genomic characteristics. In addition, sequence analysis of the 16S rRNA gene shows that the strain Marseille-Q2617 has 99.94% sequence similarity to Streptococcus mitis. Average nucleotide identity (ANI) analysis for strain Marseille-Q2617T showed the highest similarity of 92.9% with S. mitis. The DNA-DNA hybridization value obtained (50.2%) between strain Marseille-Q2607 and S. mitis, its closest related species, was below the recommended threshold (<70%). Strain Marseille-Q2617T has a genome size of 2.02 Mbp with 40.5 mol% of G + C content. Based on these results, we propose a new species of the genus Streptococcus, for which the name Streptococcus thalassemiae sp. nov., Marseille-Q2617T (=CSUR Q2617 = CECT 30109) was proposed.
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Affiliation(s)
- Fatou Samba Diouf
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Mamadou Beye
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Mapenda Gaye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Babacar Mbaye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Stephane Alibar
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Mariema Sarr
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Gregory Dubourg
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Florence Fenollar
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
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25
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Onouye TC, Busse HJ, Prescott RD, Darris MK, Donachie SP. Chitinophaga pendula, sp. nov., from an air conditioner condensate drain line. Int J Syst Evol Microbiol 2023; 73. [PMID: 37578826 DOI: 10.1099/ijsem.0.006008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
A Gram-negative, rod-shaped and filamentous bacterium designated MD30BT was isolated from a biofilm hanging in water flowing from an air conditioner condensate drain line in Honolulu, Hawai'i. Based on 1517 nucleotides of the strain's 16S rRNA gene, its nearest neighbours are Chitinophaga rhizosphaerae T16R-86T (96.7 %), Chitinophaga caseinilytica S-52T (96.6 %), Chitinophaga lutea ZY74T (96.6 %), Chitinophaga niabensis JS13-10T (96.6 %) and Chitinophaga ginsengisoli Gsoil 052T (96.5 %). MD30BT cells are non-motile, strictly aerobic, and catalase and oxidase positive. Growth occurs between 10 and 45 °C. Major fatty acids in whole cells of MD30BT are 13-methyl tetradecanoic acid (34.1 %), cis-11-hexadecenoic acid (30.3 %), and 3-hydroxy, 15-methyl hexadecanoic acid (13.3 %). The quinone system contains predominantly menaquinone MK-7. The polar lipid profile contains the major lipids phosphatidylethanolamine, one unidentified lipid lacking a functional group, and two unidentified aminolipids. sym-Homospermidine is the major polyamine. The G+C content of the genome is 47.58 mol%. Based on phenotypic and genotypic differences between MD30BT and extant species in the Chitinophaga, we propose that MD30BT represents a new Chitinophaga species, for which the name Chitinophaga pendula sp. nov. is proposed to accommodate strain MD30BT as the type strain (DSM 112477T=NCTC 14606T).
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Affiliation(s)
- T Chiyoko Onouye
- School of Life Sciences, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Rebecca D Prescott
- School of Life Sciences, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
- Astromaterials Research and Exploration Science (ARES) Division, NASA Johnson SpaceCenter, 2101 E NASA Parkway, Houston, TX 77058, USA
| | - Maxwell K Darris
- School of Life Sciences, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
- University of Hawai'i, 200 W. Kāwili Street. Hilo, Hawai'i 96720, USA
| | - Stuart P Donachie
- School of Life Sciences, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
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Świecimska M, Golinska P, Sangal V, Wachnowicz B, Goodfellow M. Streptantibioticus silvisoli sp. nov., acidotolerant actinomycetes from pine litter, reclassification of Streptomyces cocklensis, Streptomyces ferralitis, Streptomyces parmotrematis and Streptomyces rubrisoli as Actinacidiphila cocklensis comb. nov., Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov., and emended descriptions of the genus Streptantibioticus, the family Streptomycetaceae and Streptomyces iconiensis. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486349 DOI: 10.1099/ijsem.0.005978] [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: 07/25/2023] Open
Abstract
Filamentous actinomycetes, designated SL13 and SL54T, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit chemotaxonomic and morphological properties consistent with their classification in the family Streptomycetaceae. They form extensively branched substrate mycelia bearing aerial hyphae that differentiate into straight chains of cylindrical spores. The whole-organism hydrolysates contain ll-diaminopimelic acid, glucose, mannose and ribose, the predominant isoprenologue is MK-9(H8), the polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and glycophospholipids, and the major fatty acids are anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic trees based on 16S rRNA gene sequences and multilocus gene sequences of conserved housekeeping genes show that the isolates form a well-supported lineage that is most closely related to Streptomyces parmotrematis NBRC 115203T. All of these strains form a well-defined clade in the multilocus sequence analysis tree together with Streptantibioticus cattleyicolor DSM 46488T, Streptomyces ferralitis DSM 41836T and Streptomyces rubrisoli DSM 42083T. Draft genomes assemblies of the isolates are rich in biosynthetic gene clusters predicted to produce novel specialized metabolites and stress-related genes which provide an insight into how they have adapted to the harsh conditions that prevail in pine litter. Phylogenomically, both isolates belong to the same lineage as the type strains of S. cattleyicolor, S. ferralitis, S. parmotrematis and S. rubrisoli; these relationships are underpinned by high average amino acid identity, average nucleotide identity and genomic DNA-DNA hybridization values. These metrics confirm that isolates SL13 and SL54T belong to a novel species that is most closely related to S. parmotrematis NBRC 115203T and that these strains together with S. ferralitis DSM 41836T, S. rubrisoli DSM 42083T belong to the genus Streptantibioticus. Consequently, it is proposed that the isolates be recognized as a new Streptantibioticus species, Streptantibioticus silvisoli comb. nov., with isolate SL54T (=DSM 111111T=PCM3044T) as the type strain, and that S. ferralitis, S. parmotrematis and S. rubrisoli be transferred to the genus Streptantibioticus as Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov. Emended descriptions are given for the genus Streptantibioticus, the family Streptomycetaceae and for Streptomyces iconiensis which was found to be a close relative of the isolates in the 16S rRNA gene sequence analyses. It is also proposed that Streptomyces cocklensis be transferred to the genus Actinacidiphila as Actinacidiphila cocklensis comb. nov based on its position in the MLSA and phylogenomic trees and associated genomic data.
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Affiliation(s)
- Magdalena Świecimska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Patrycja Golinska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Bartosz Wachnowicz
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Barbeyron T, Le Duff N, Duchaud E, Thomas F. Zobellia alginiliquefaciens sp. nov., a novel member of the flavobacteria isolated from the epibiota of the brown alga Ericaria zosteroides (C. Agardh) Molinari & Guiry 2020. Int J Syst Evol Microbiol 2023; 73. [PMID: 37266991 DOI: 10.1099/ijsem.0.005924] [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: 06/03/2023] Open
Abstract
Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected from the Mediterranean Sea near Bastia in Corsica, France, was characterised using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30-33 °C, at pH 8-8.5 and with 4-5 % NaCl. LLG6346-3.1T used the seaweed polysaccharide alginic acid as a sole carbon source which was vigorously liquefied. The results of phylogenetic analyses indicated that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae, class Flavobacteriia). LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.6 and 98.3 % to the type strains of Zobellia russellii and Zobellia roscoffensis, respectively, and of 97.4-98.5 % to members of other species of the genus Zobellia. The DNA G+C content of LLG6346-3.1T was determined to be 38.3 mol%. Digital DNA-DNA hybridisation predictions by the average nucleotide identity (ANI) and genome to genome distance calculator (GGDC) methods between LLG6346-3.1T and other members of the genus Zobellia showed values of 76-88 % and below 37 %, respectively. The results of phenotypic, phylogenetic and genomic analyses indicate that LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia, for which the name Zobellia alginiliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (= RCC7657T = LMG 32918T).
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Affiliation(s)
- Tristan Barbeyron
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Eric Duchaud
- INRAE VIM-UR0892 Molecular Immunology and Virology, research group of Infection and Immunity of Fish, Research Center of Jouy-en-Josas, F-78352 Jouy-en-Josas, Ile-de-France, France
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
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Zhang Y, Zhai Y, Mu L, Hu M, Fang W, Xiao Y, Fang Z. Maribacter aquimaris sp. nov., isolated from seawater adjacent to Fildes Peninsula, Antarctica. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01844-x. [PMID: 37225945 DOI: 10.1007/s10482-023-01844-x] [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: 09/06/2022] [Accepted: 05/15/2023] [Indexed: 05/26/2023]
Abstract
A novel Gram-stain-negative, aerobic, and rod-shaped bacterium with gliding motility, named strain ANRC-HE7T, was isolated from the seawater of Biological Bay adjacent to Fildes Peninsula, Antarctica. The optimal growth of this strain occurred at 28 °C, pH 7.5, and in the presence of 1.0% (w/v) NaCl. Strain ANRC-HE7T can produce amylase and harbors gene clusters involved in cellulose degradation. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain ANRC-HE7T formed a distinct lineage within the genus Maribacter and was closely related to Maribacter luteus RZ05T (98.4% sequence similarity), Maribacter polysiphoniae LMG 23671T (98.3%), and Maribacter arenosus CAU 1321T (97.3%). However, digital DNA-DNA hybridization and average nucleotide identity values between strain ANRC-HE7T and closely related strains were 17.4-49.1% and 70.9-92.7%, much lower than the cutoff values of 70% and 95%, respectively. On the other hand, strain ANRC-HE7T shared characteristics with most type strains within the genus. Its respiratory quinone was MK-6. The major fatty acids were iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and anteiso-C15:0. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids, and five unidentified glycolipids. The DNA G + C content of strain ANRC-HE7T was 40.1%. Based on the results of the biochemical, phylogenetic, and chemotaxonomic analyses, strain ANRC-HE7T is suggested to represent a novel species of the genus Maribacter, for which the name Maribacter aquimaris sp. nov. is proposed. The type strain is ANRC-HE7T (= MCCC 1K03787T = KCTC 72532T).
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Affiliation(s)
- Yanfeng Zhang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Yanwu Zhai
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Lulu Mu
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Miaomiao Hu
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Wei Fang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China.
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Thakur M, Kumar P, Rajput D, Yadav V, Dhaka N, Shukla R, Kumar Dubey K. Genome-guided approaches and evaluation of the strategies to influence bioprocessing assisted morphological engineering of Streptomyces cell factories. BIORESOURCE TECHNOLOGY 2023; 376:128836. [PMID: 36898554 DOI: 10.1016/j.biortech.2023.128836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Streptomyces genera serve as adaptable cell factories for secondary metabolites with various and distinctive chemical structures that are relevant to the pharmaceutical industry. Streptomyces' complex life cycle necessitated a variety of tactics to enhance metabolite production. Identification of metabolic pathways, secondary metabolite clusters, and their controls have all been accomplished using genomic methods. Besides this, bioprocess parameters were also optimized for the regulation of morphology. Kinase families were identified as key checkpoints in the metabolic manipulation (DivIVA, Scy, FilP, matAB, and AfsK) and morphology engineering of Streptomyces. This review illustrates the role of different physiological variables during fermentation in the bioeconomy coupled with genome-based molecular characterization of biomolecules responsible for secondary metabolite production at different developmental stages of the Streptomyces life cycle.
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Affiliation(s)
- Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Punit Kumar
- Department of Morphology and Physiology, Karaganda Medical University, Karaganda 100008 Kazakhstan
| | - Deepanshi Rajput
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh 123031, India
| | - Rishikesh Shukla
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura- 281406, U.P., India
| | - Kashyap Kumar Dubey
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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30
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Lin X, Cai R, Cai G, Xie J, Zhou Z, Wang H. Opacimonas viscosa gen. nov., sp. nov., a novel bacterium isolated from phycosphere. Int J Syst Evol Microbiol 2023; 73. [PMID: 37235641 DOI: 10.1099/ijsem.0.005904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
A novel strain of a member of the family Alteromonadaceae was isolated from the phycosphere of a diatom and designated as LMIT007T. LMIT007T could form milk-white, opaque, circular and smooth colonies on 2216E marine agar. LMIT007T cells were around 1.0-1.8 µm long, 0.8-1.8 µm wide, round or oval shaped and had polar flagella but were non-motile. Optimum conditions for growth were 25 °C, pH 7.0 and 6 % (w/v) NaCl. The results of 16S rRNA gene-based analysis indicated that LMIT007T had the highest similarity with the type strains Aestuaribacter halophilus JC2043T (95.95 %), Alteromonas lipolytica JW12T (95.60 %) and Alteromonas halophila KCTC 22164T (94.21 %). Furthermore, the results of phylogenetic analysis based on 16S rRNA gene sequences and of phylogenomic analysis indicated that LMIT007T could be clustered into the family Alteromonadaceae but formed a separate branch. The genome size of the strain was 2.95 Mbp and the DNA G+C content was 41.6 %. The average nucleotide identity (ANI) values of orthologous genes between LMIT007T and species of other closely related genera within the family Alteromonadaceae ranged from 66.9 to 69.2 %, and the average amino acid identity (AAI) values ranged from 60.0 to 65.7 %. The main respiratory quinone was ubiquinone-8. The major fatty acids were summed feature 3 (C16 : 1ω7c / C16 : 1ω6c) and C16 : 0. The polar lipid profile contain phosphatidylethanolamine, phosphatidylglycerol, aminolipid, two phospholipid and an unknown polar lipid. On the basis of the results of the polyphasic analysis, strain LMIT007T is suggested to represent a novel genus and species within the family Alteromonadaceae, for which the name Opacimonas viscosa gen. nov., sp. nov. is proposed. The type strain is LMIT007T (=MCCC 1K08161T=KCTC 92597T).
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Affiliation(s)
- Xuanru Lin
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, PR China
| | - Runlin Cai
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, PR China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, PR China
| | - Guanjing Cai
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, PR China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, PR China
| | - Jianmin Xie
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, PR China
| | - Zhenyuan Zhou
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, PR China
| | - Hui Wang
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, PR China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, PR China
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Dong K, Pu J, Yang J, Zhou G, Gao Y, Kang Z, Lei W, Ji X, Min G, Li H, Li J, Sun B, Xu J. Whole-genome sequencing of Paracoccus species isolated from the healthy human eye and description of Paracoccus shanxieyensis sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37068015 DOI: 10.1099/ijsem.0.005838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Currently, the genus Paracoccus comprises 76 recognized species. Members of Paracoccus are mostly isolated from environmental, animal, and plant sources. This report describes and proposes a novel species of Paracoccus isolated from clinical specimens of the human ocular surface. We isolated two aerobic, Gram-stain-negative, non-spore-forming, coccoid or short rod-shaped, and non-motile strains (designated DK398T and DK608) from conjunctival sac swabs of two healthy volunteers. The results showed that the strains grew best under the conditions of 28°C, pH 7.0, and 1.0 % (w/v) NaCl. Sequence analysis based on the 16S rRNA gene showed that strains DK398T and DK608 were members of Paracoccus, most similar to Paracoccus laeviglucosivorans 43PT (98.54 and 98.62 %), Paracoccus litorisediminis GHD-05T (98.34 and 98.41 %), and Paracoccus limmosus NB88T (98.21 and 98.29 %). Phenotypic analysis showed that DK398T and DK608 were positive for catalase and oxidase, negative for producing N-acetyl-β-glucosaminic acid, arginine dihydrolase, and β-glucuronidase but positive for leucine arylamidase. The predominant isoprenoid quinone was Q-10, and the major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and an unidentified glycolipid. The major fatty acids (>10%) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The meso-diaminopimelic acid was found in the cell wall peptidoglycan of DK398T. The major cell wall sugars were ribose and galactose. Based on the results of phylogenetic analyses, low (<83.22 %) average nucleotide identity, digital DNA-DNA hybridization (<26.0%), chemotaxonomic analysis, and physiological properties, strain DK398T represents a novel species of the genus Paracoccus, for which the name Paracoccus shanxieyensis sp. nov. is proposed. The type strain is DK398T (=CGMCC 1.17227T=JCM 33719T).
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Affiliation(s)
- Kui Dong
- Shanxi Eye Hospital, The Shanxi Province Key Laboratory of Ophthalmology, Taiyuan 030002, PR China
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Guohong Zhou
- Shanxi Eye Hospital, The Shanxi Province Key Laboratory of Ophthalmology, Taiyuan 030002, PR China
| | - Yuqian Gao
- Shanxi Finance & Taxation College, Taiyuan 030002, PR China
| | - Zhiming Kang
- Shanxi Eye Hospital, The Shanxi Province Key Laboratory of Ophthalmology, Taiyuan 030002, PR China
| | - Wenjing Lei
- Shanxi Eye Hospital, The Shanxi Province Key Laboratory of Ophthalmology, Taiyuan 030002, PR China
| | - Xuan Ji
- Shanxi Eye Hospital, The Shanxi Province Key Laboratory of Ophthalmology, Taiyuan 030002, PR China
| | - Guowen Min
- First Hospital of Shanxi Medical University, Taiyuan 030001, PR China
| | - Hong Li
- Shanxi Eye Hospital, The Shanxi Province Key Laboratory of Ophthalmology, Taiyuan 030002, PR China
| | - Junqin Li
- Taiyuan Central Hospital, Taiyuan 030002, PR China
| | - Bin Sun
- Shanxi Eye Hospital, The Shanxi Province Key Laboratory of Ophthalmology, Taiyuan 030002, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
- Institute of Public Health, Nankai University, Tianjin, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
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Komaki H. Recent Progress of Reclassification of the Genus Streptomyces. Microorganisms 2023; 11:microorganisms11040831. [PMID: 37110257 PMCID: PMC10145440 DOI: 10.3390/microorganisms11040831] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
The genus Streptomyces is a representative group of actinomycetes and one of the largest taxa in bacteria, including approximately 700 species with validly published names. Since the classification was mainly based on phenotypic characteristics in old days, many members needed to be reclassified according to recent molecular-based taxonomies. Recent developments of molecular-based analysis methods and availability of whole genome sequences of type strains enables researchers to reclassify these phylogenetically complex members on a large scale. This review introduces reclassifications of the genus Streptomyces reported in the past decade. Appropriately 34 Streptomyces species were transferred to the other genera, such as Kitasatospora, Streptacidiphilus, Actinoalloteichus and recently proposed new genera. As a result of reclassifications of 14 subspecies, the genus Streptomyces includes only four subspecies at present in practice. A total of 63 species were reclassified as later heterotypic synonyms of previously recognized species in 24 published reports. As strong relationships between species and the secondary metabolite-biosynthetic gene clusters become clarified, appropriate classifications of this genus will not only contribute to systematics, but also provide significant information when searching for useful bioactive substances.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan
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Saticioglu IB, Ay H, Altun S, Karakaya E, Gunduz ES, Aydogdu D, Yarim D, Erkek N, Duman M. Genomic insight into Myroides oncorhynchi sp. nov., a new member of the Myroides genus, isolated from the internal organ of rainbow trout (Oncorhynchus mykiss). Antonie Van Leeuwenhoek 2023; 116:291-302. [PMID: 36586048 DOI: 10.1007/s10482-022-01804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023]
Abstract
The strain M-43T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43T. The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25T, M. odoratimimus subsp. odoratimimus CCUG 39352T and M. odoratimimus subsp. xuanwuensis DSM27251T, respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251T, M. profundi D25T, and M. odoratimimus subsp. odoratimimus ATCC BAA-634T, were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C15:0 and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43T as the type strain (JCM 34205T = KCTC 82265T).
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey.
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Enes Said Gunduz
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Duygu Aydogdu
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Dogancan Yarim
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Neslihan Erkek
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
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Heng YC, Menon N, Chen B, Loo BZL, Wong GWJ, Lim ACH, Silvaraju S, Kittelmann S. Ligilactobacillus ubinensis sp. nov., a novel species isolated from the wild ferment of a durian fruit ( Durio zibethinus). Int J Syst Evol Microbiol 2023; 73. [PMID: 36920986 DOI: 10.1099/ijsem.0.005733] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
A Gram-stain-positive, rod-shaped, non-spore-forming, catalase-negative, urease-negative, homofermentative and facultatively anaerobic strain, named WILCCON 0076T, was isolated from a wild ferment of pieces of a 'Kampung' durian fruit collected on the island of Ubin (Pulau Ubin), Singapore. The durian had fallen to the ground from a durian tree (Durio zibethinus), on which a group of long-tailed macaques had been observed picking and eating the fruits. Comparative analyses of 16S rRNA gene sequences indicated that WILCCON 0076T potentially represented a novel species within the genus Ligilactobacillus, with the most closely related type strain being Ligilactobacillus agilis DSM 20509T (16S rRNA gene sequence similarity of 97.2 %). Average nucleotide identity and digital DNA-DNA hybridization prediction values were only 86.0% and 18.9 %, respectively. On the basis of the results of a polyphasic approach that included phylogenomic, chemotaxonomic and morphological analyses, we propose a novel species with the name Ligilactobacillus ubinensis sp. nov. (type strain WILCCON 0076T=DSM 114293T=LMG 32698T).
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Affiliation(s)
- Yu Chyuan Heng
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Nandita Menon
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Binbin Chen
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan Zong Lin Loo
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Garrett Wei Jie Wong
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Amber Ching Han Lim
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Shaktheeshwari Silvaraju
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
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Xu CH, Chen G, Liu Y, Xiao W, Cui XL, Ding ZG, Liu WH, Wang YX. Azospirillum Aestuarii sp. nov., a Novel Nitrogen-Fixting and Aerobic Denitrifying Bacteria Isolated from an Estuary of a Freshwater River. Curr Microbiol 2023; 80:113. [PMID: 36823402 DOI: 10.1007/s00284-023-03213-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
A novel Gram-staining negative, aerobic, rod-shaped bacterium, designated strain YIM DDC1T, was isolated from an estuary sediment sample of Dongda River flowing into Dianchi lake in Yunnan, southwest China. The strain displayed growth at 10-40 °C (optimum of 28 °C), pH 5.0-9.0 (optimum of 7.0-8.0) and in presence of 0-3% (w/v) NaCl (optimum of 0-1%). Strain YIM DDC1T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified aminolipids as the predominant polar lipids; the ubiquinone 10 as the major respiratory quinone; and summed feature 8 (C18:1ω6c and/or C18:1ω7c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C18:1 2-OH as the major cellular fatty acids. Analysis of 16S rRNA showed that YIM DDC1T represents a member of the genus Azospirillum, and was closely related to A. brasilense ATCC 29145 T (98.9%), A. baldaniorum Sp245T (98.2%), A. argentinense Az39T (98.2%) and A. formosense CC-Nfb-7 T (98.2%). The draft genome size was 7.15 Mbp with a 68.4% G + C content. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain YIM DDC1T and the aforementioned closely related strains exhibited similarity in the range of 93.8-93.5% and 53.7-52.7%, respectively. nif gene cluster (nifHDK) and denitrification genes ((napA, nirS, nirK, norBC and nosZ) detected in the genome indicated its potential nitrogen fixation and full-fledged denitrifying function. Based on combined genotypic and phenotypic data, strain YIM DDC1T represents a novel species of the genus Azospirillum, for which the name Azospirillum aestuarii sp. nov. is proposed. The type strain is YIM DDC1T (= KCTC 42887 T = CGMCC 1.17325 T).
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Affiliation(s)
- Can-Hai Xu
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Gen Chen
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Yan Liu
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Wei Xiao
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Xiao-Long Cui
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Zhang-Gui Ding
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Wei-Hong Liu
- College of Agriculture and Biological Sciences, Dali University, Dali, Yunnan, 671003, People's Republic of China
| | - Yong-Xia Wang
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.
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Komaki H, Tamura T, Igarashi Y. Taxonomic Positions and Secondary Metabolite-Biosynthetic Gene Clusters of Akazaoxime- and Levantilide-Producers. Life (Basel) 2023; 13:life13020542. [PMID: 36836900 PMCID: PMC9967187 DOI: 10.3390/life13020542] [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: 12/15/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Micromonospora sp. AKA109 is a producer of akazaoxime and A-76356, whereas Micromonospora sp. AKA38 is that of levantilide C. We aimed to clarify their taxonomic positions and identify biosynthetic gene clusters (BGCs) of these compounds. In 16S rRNA gene and DNA gyrase subunit B gene (gyrB) sequence analyses, strains AKA109 and AKA38 were the most closely related to Micromonospora humidisoli MMS20-R2-29T and Micromonospora schwarzwaldensis HKI0641T, respectively. Although Micromonospora sp. AKA109 was identified as M. humidisoli by the gyrB sequence similarity and DNA-DNA relatedness based on whole genome sequences, Micromonospora sp. AKA38 was classified to a new genomospecies. M. humidisoli AKA109 harbored six type-I polyketide synthase (PKS), one type-II PKS, one type-III PKS, three non-ribosomal peptide synthetase (NRPS) and three hybrid PKS/NRPS gene clusters, among which the BGC of akazaoxime and A-76356 was identified. These gene clusters are conserved in M. humidisoli MMS20-R2-29T. Micromonospora sp. AKA38 harbored two type-I PKS, one of which was responsible for levantilide C, one type-II PKS, one type-III PKS, two NRPS and five hybrid PKS/NRPS gene clusters. We predicted products derived from these gene clusters through bioinformatic analyses. Consequently, these two strains are revealed to be promising sources for diverse non-ribosomal peptide and polyketide compounds.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan
- Correspondence:
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan
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Cryobacterium zhongshanensis sp. nov., an actinobacterium isolated from Antarctic soil. Arch Microbiol 2023; 205:79. [PMID: 36729334 DOI: 10.1007/s00203-023-03408-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 02/03/2023]
Abstract
A Gram-staining-positive, heterotrophic, non-spore-forming, non-motile, rod-shaped, strain ZS14-85T belonging to the genus Cryobacterium was isolated from soil in Antarctica. Growth was observed in the presence of 0-2% (w/v) NaCl, at pH 7.0-9.0 (optimum, pH 7.0) and 4-30 ℃ (optimum, 20 ℃). Phylogenetic analysis showed that strain ZS14-85T formed a lineage in the genus Cryobacterium. The digital DNA-DNA hybridization (dDDH) values between strain ZS14-85T and its close relatives Cryobacterium psychrotolerans CGMCC 1.5382T, Cryobacterium soli MCCC 1K03549T and Cryobacterium breve NBRC 113800T were 22.5, 22.3 and 22.2%, respectively. Orthologous Average Nucleotide Identity (OrthoANI) scores between strain ZS14-85T and C. psychrotolerans CGMCC 1.5382T, C. breve NBRC 113800T and C. soli MCCC 1K03549T were 78.7, 78.1 and 77.7%, respectively. The polar lipids of strain ZS14-85T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), one unidentified glycolipid (GL) and two unidentified lipids (L). The major fatty acids were anteiso-C15:0 (60.7%), iso-C16:0 (17.0%) and anteiso-C17:0 (15.2%). MK-10, MK-11 and MK-9 were the predominant respiratory menaquinones. Based on phenotypic, phylogenetic and genotypic data, a novel species, Cryobacterium zhongshanensis sp. nov. is proposed. The type strain is ZS14-85T (= CCTCC AB 2019396T = KCTC 49384T).
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Crespi S, Drašar V, Salvà-Serra F, Jaén-Luchoro D, Piñeiro-Iglesias B, Lindemann PC, Aliaga-Lozano F, Fernández-Juárez V, Coll-García G, Moore ERB, Bennasar-Figueras A. Legionella maioricensis sp. nov., a new species isolated from the hot water distribution systems of a hospital and a shopping center during routine sampling. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748493 DOI: 10.1099/ijsem.0.005686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Two Legionella-like strains isolated from hot water distribution systems in 2012 have been characterized phenotypically, biochemically and genomically in terms of DNA relatedness. Both strains, HCPI-6T and EUR-108, exhibited biochemical phenotypic profiles typical of Legionella species. Cells were Gram-negative motile rods which grew on BCYEα agar but not on blood agar and displayed phenotypic characteristics typical of the family Legionellaceae, including a requirement for l-cysteine and testing catalase positive. Both strains were negative for oxidase, urease, nitrate reduction and hippurate negative, and non-fermentative. The major ubiquinone was Q12 (59.4 % HCPI-6T) and the dominant fatty acids were C16 : 1 ω7c (28.4 % HCPI-6T, ≈16 % EUR-108), C16 : 0 iso (≈22.5 % and ≈13 %) and C15 : 0 anteiso (19.5 % and ≈23.5 %, respectively). The percent G+C content of genomic DNA was determined to be 39.3 mol %. The 16S rRNA gene, mip sequence and comparative genome sequence-based analyses (average nucleotide identity, ANI; digital DNA-DNA hybridization, dDDH; and phylogenomic treeing) demonstrated that the strains represent a new species of the genus Legionella. The analysis based on the 16S rRNA gene sequences showed that the sequence similarities for both strains ranged from 98.8-90.1 % to other members of the genus. The core genome-based phylogenomic tree (protein-concatemer tree based on concatenation of 418 proteins present in single copy) revealed that these two strains clearly form a separate cluster within the genus Legionella. ANI and dDDH values confirmed the distinctiveness of the strains. Based on the genomic, genotypic and phenotypic findings from a polyphasic study, the isolates are considered to represent a single novel species, for which the name Legionella maioricensis sp. nov. is proposed. The type strain is HCPI-6T (=CCUG 75071T=CECT 30569T).
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Affiliation(s)
- Sebastian Crespi
- Biolinea Int.; Calle Sócrates, 4; ES-07007 Palma de Mallorca, Spain
| | - Vladimír Drašar
- Public Health Institute Ostrava - National Legionella Reference Laboratory; Masarykovo nam., 16; 682 01 Vyškov, Czech Republic
| | - Francisco Salvà-Serra
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Clinical Microbiology, Sahlgrenska University Hospital; Region Västra Götaland, Gothenburg, Sweden.,Microbiologia - Departament de Biologia, Universitat de les Illes Balears; Campus UIB - Ctra. Valldemossa, Km 7.5; ES-07122 Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Beatriz Piñeiro-Iglesias
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Francisco Aliaga-Lozano
- Laboratorio Microbiología. Clínica Rotger, Grupo Quirónsalud - Vía Roma, 3, Carrer de Santiago Rusiñol, 9: ES-07012 Palma de Mallorca, Spain
| | - Victor Fernández-Juárez
- Marine Biology Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Guillem Coll-García
- Microbiologia - Departament de Biologia, Universitat de les Illes Balears; Campus UIB - Ctra. Valldemossa, Km 7.5; ES-07122 Palma de Mallorca, Spain
| | - Edward R B Moore
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Clinical Microbiology, Sahlgrenska University Hospital; Region Västra Götaland, Gothenburg, Sweden
| | - Antoni Bennasar-Figueras
- Microbiologia - Departament de Biologia, Universitat de les Illes Balears; Campus UIB - Ctra. Valldemossa, Km 7.5; ES-07122 Palma de Mallorca, Spain
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Xie L, Yoshida N, Meng L. Polyphasic Characterization of Geotalea uranireducens NIT-SL11 Newly Isolated from a Complex of Sewage Sludge and Microbially Reduced Graphene Oxide. Microorganisms 2023; 11:microorganisms11020349. [PMID: 36838314 PMCID: PMC9961858 DOI: 10.3390/microorganisms11020349] [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: 01/04/2023] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Graphene oxide (GO), a chemically oxidized sheet of graphite, has been used as a conductive carbon carrier of microbes to boost various bioelectrochemical reactions. However, the types of microbes that can reduce GO have rarely been investigated. In this study, a strain of GO-reducing bacteria, named NIT-SL11, which was obtained from a hydrogel of microbially reduced GO and anaerobic sludge that converts sewage to electricity, was phylogenically identified as a novel strain of Geotalea uraniireducens. Considering the current lack of information on the electrogenic ability of the bacterium and its physicochemical and chemotaxonomic characteristics, the polyphasic characterization of the Geotalea uraniireducens strain NIT-SL11 was performed. NIT-SL11 utilized various organic acids, such as lactate, benzoate, and formate, as electron donors and exhibited respiration using GO, electrodes, fumarate, and malate. The strain contained C16:1ω7c and C16:0 as the major fatty acids and MK-8 and 9 as the major respiratory quinones. The complete genome of NIT-SL11 was 4.7 Mbp in size with a G+C content of 60.9%, and it encoded 80 putative c-type cytochromes and 23 type IV pili-related proteins. The possible extracellular electron transfer (EET) pathways of the strain were the porin-cytochrome (Pcc) EET pathway and type IV pili-based pathway.
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Genomic Diversity among Actinomyces naeslundii Strains and Closely Related Species. Microorganisms 2023; 11:microorganisms11020254. [PMID: 36838222 PMCID: PMC9964710 DOI: 10.3390/microorganisms11020254] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
The aim of this study was to investigate and clarify the ambiguous taxonomy of Actinomyces naeslundii and its closely related species using state-of-the-art high-throughput sequencing techniques, and, furthermore, to determine whether sub-clusters identified within Actinomyces oris and Actinomyces naeslundii in a previous study by multi locus sequence typing (MLST) using concatenation of seven housekeeping genes should either be classified as subspecies or distinct species. The strains in this study were broadly classified under Actinomyces naeslundii group as A. naeslundii genospecies I and genospecies II. Based on MLST data analysis, these were further classified as A. oris and A. naeslundii. The whole genome sequencing of selected strains of A. oris (n = 17) and A. naeslundii (n = 19) was carried out using Illumina Genome Analyzer IIxe and Roche 454 allowing paired-end and single-reads sequencing, respectively. The sequences obtained were aligned using CLC Genomic workbench version 5.1 and annotated using RAST (Rapid Annotation using Subsystem Technology) release version 59 accessible online. Additionally, genomes of seven publicly available strains of Actinomyces (k20, MG1, c505, OT175, OT171, OT170, and A. johnsonii) were also included. Comparative genomic analysis (CGA) using Mauve, Progressive Mauve, gene-by-gene, Core, and Pan Genome, and finally Digital DNA-DNA homology (DDH) analysis was carried out. DDH values were obtained using in silico genome-genome comparison. Evolutionary analysis using ClonalFrame was also undertaken. The mutation and recombination events were compared using chi-square test among A. oris and A. naeslundii isolates (analysis methods are not included in the study). CGA results were consistent with previous traditional classification using MLST. It was found that strains of Actinomyces k20, MG1, c505, and OT175 clustered in A. oris group of isolates, while OT171, OT170, and A. johnsonii appeared as separate branches. Similar clustering to MLST was observed for other isolates. The mutation and recombination events were significantly higher in A. oris than A. naeslundii, highlighting the diversity of A. oris strains in the oral cavity. These findings suggest that A. oris forms six distinct groups, whereas A. naeslundii forms three. The correct designation of isolates will help in the identification of clinical Actinomyces isolates found in dental plaque. Easily accessible online genomic sequence data will also accelerate the investigation of the biochemical characterisation and pathogenesis of this important group of micro-organisms.
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Benlaïfaoui M, Richard C, Diop A, Naimi S, Belkaid W, Bernet E, Veyrier F, Elkrief A, Bobay LM, Routy B, Diop K. Tractidigestivibacter montrealensis sp. nov., a new member of human gut microbiota isolated from a healthy volunteer. FEMS Microbiol Lett 2023; 370:fnad058. [PMID: 37348476 PMCID: PMC10396324 DOI: 10.1093/femsle/fnad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/05/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023] Open
Abstract
Strain KD21T, isolated from the fecal sample of a healthy female volunteer, is a strictly anaerobic, non-motile, Gram-staining-positive, saccharolytic small rod that does not produce spores. Strain KD21T was able to grow in the range of temperature 28°C-37°C (optimum, 37 °C), pH 6.0-8.0 (optimum, pH 7.0), and with 0-5.0 g/l NaCl (optimum, 0 g/l NaCl). Bacteria cells reduced nitrates to nitrites. Its major fatty acids were C18:1ω9c, C16:0, C18:0, and summed in feature 8 (C18:1ω7c and/or C18:1ω6c). 16S rRNA gene phylogenetic analysis revealed that KD21T is a member of the genus Tractidigestivibacter and is distinct from any species with validly published names. The sequence showed 98.48% similarity with T. scatoligenes SK9K4T. The DNA G + C content of strain KD21T was 62.6 mol%. The DNA-DNA hybridization and OrthoANI values between strain KD21T and T. scatoligenes SK9K4T were 40.2% and 90.2%, respectively. Differences in phenotypic, phylogenetic, chemotaxonomic, and genomic characteristics indicated that strain KD21T represents a novel species within the genus Tractidigestivibacter. The name T. montrealensis sp. nov. is proposed and the type strain is KD21T (= CSUR Q8103T = DSM 115111T).
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Affiliation(s)
- Myriam Benlaïfaoui
- Laboratory of Immunotherapy and Onco-microbiome, University of Montreal Research Center (CRCHUM), Montreal, H2X 0A9, QC, Canada
| | - Corentin Richard
- Laboratory of Immunotherapy and Onco-microbiome, University of Montreal Research Center (CRCHUM), Montreal, H2X 0A9, QC, Canada
| | - Awa Diop
- Department of Biology, University of North Carolina Greensboro, 321 Mclver Street, Greensboro, NC, United States
| | - Sabrine Naimi
- Laboratory of Immunotherapy and Onco-microbiome, University of Montreal Research Center (CRCHUM), Montreal, H2X 0A9, QC, Canada
| | - Wiam Belkaid
- Laboratory of Immunotherapy and Onco-microbiome, University of Montreal Research Center (CRCHUM), Montreal, H2X 0A9, QC, Canada
| | - Eve Bernet
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC H7V 1B7, QC, Canada
| | - Frederic Veyrier
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC H7V 1B7, QC, Canada
| | - Arielle Elkrief
- Laboratory of Immunotherapy and Onco-microbiome, University of Montreal Research Center (CRCHUM), Montreal, H2X 0A9, QC, Canada
| | - Louis-Marie Bobay
- Department of Biology, University of North Carolina Greensboro, 321 Mclver Street, Greensboro, NC, United States
| | - Bertrand Routy
- Laboratory of Immunotherapy and Onco-microbiome, University of Montreal Research Center (CRCHUM), Montreal, H2X 0A9, QC, Canada
- Hematology-Oncology Service, Department of Medicine, University of Montreal Healthcare Centre (CHUM), Montreal, H2X 0A9, QC, Canada
| | - Khoudia Diop
- Laboratory of Immunotherapy and Onco-microbiome, University of Montreal Research Center (CRCHUM), Montreal, H2X 0A9, QC, Canada
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Selmani Z, Attard E, Lauga B, Barakat M, Ortet P, Tulumello J, Achouak W, Kaci Y, Heulin T. Culturing the desert microbiota. Front Microbiol 2023; 14:1098150. [PMID: 37113232 PMCID: PMC10126307 DOI: 10.3389/fmicb.2023.1098150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that Arthrobacter subterraneus, Arthrobacter tecti, Pseudarthrobacter phenanthrenivorans, Pseudarthrobacter psychrotolerans, and Massilia agri are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera Arthrobacter/Pseudarthrobacter and Kocuria, and a relative underestimation of the genera Blastococcus and Domibacillus by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in Pseudomonadota (Proteobacteria).
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Affiliation(s)
- Zakia Selmani
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Eleonore Attard
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Béatrice Lauga
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Mohamed Barakat
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Philippe Ortet
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Wafa Achouak
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Yahia Kaci
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
| | - Thierry Heulin
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
- *Correspondence: Thierry Heulin,
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Saticioglu IB, Ay H, Altun S, Duman M. Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey. Syst Appl Microbiol 2023; 46:126385. [PMID: 36410095 DOI: 10.1016/j.syapm.2022.126385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
Four strains, designated as C-2, C-17T, C-39T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089T while strains C-2, C-39T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17T, C-39T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17T and C-39T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 - 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17T and C-39T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17T (=JCM 34190T = KCTC 82250T) and C-39T (=JCM 34191T = KCTC 822251T), respectively, are proposed.
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey; Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
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Kumar P, Verma A, Sundharam SS, Ojha AK, Krishnamurthi S. Exploring Diversity and Polymer Degrading Potential of Epiphytic Bacteria Isolated from Marine Macroalgae. Microorganisms 2022; 10:microorganisms10122513. [PMID: 36557766 PMCID: PMC9786321 DOI: 10.3390/microorganisms10122513] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022] Open
Abstract
The macroalgae surface allows specific bacterial communities to colonize, resulting in complex biological interactions. In recent years, several researchers have studied the diversity and function of the epiphytic bacteria associated with algal host, but largely these interactions remain underexplored. In the present study we analysed the cultivable diversity and polymer degradation potential of epiphytic bacteria associated with five different marine macroalgae (Sargassum, Ulva, Padina, Dictyota and Pterocladia sp.) sampled from the central west coast of India. Out of the total 360 strains isolated, purified and preserved, about 238 strains were identified through 16S rRNA gene sequence analysis and processed for polymer (cellulose, pectin, xylan and starch) degrading activities. Phylogeny placed the strains within the classes Actinobacteria, Bacilli, Alpha-proteobacteria, and Gamma-proteobacteria and clustered them into 45 genera, wherein Vibrio, Bacillus, Pseudoalteromonas, Alteromonas, Staphylococcus and Kocuria spp. were the most abundant with 20 strains identified as potentially novel taxa within the genera Bacillus, Cellulosimicrobium, Gordonia, Marinomonas, Vibrio, Luteimonas and Pseudoalteromonas. In terms of polymer hydrolysis potential, 61.3% had xylanase activity, while 59.7%, 58.8%, and 52.2% had amylase, cellulase, and pectinase activity, respectively. Overall, 75.6% of the strains degraded more than one polysaccharide, 24% degraded all polymers, while nine strains (3.8%) degraded raw sugarcane bagasse. This study showed great potential for seaweed-associated bacteria in the bio-remediation of agro-waste based raw materials, which can be employed in the form of green technology.
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Affiliation(s)
- Pravin Kumar
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Ashish Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Shiva S. Sundharam
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anup Kumar Ojha
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Correspondence:
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Yoo Y, Lee H, Khim JS, Xu X, Kim B, Choi IG, Kim JJ. Halomonas getboli sp. nov., a halotolerant bacteria isolated from a salt flat. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748432 DOI: 10.1099/ijsem.0.005634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A novel Gram-stain-negative, rod-shaped, cream-coloured, motile, halotolerant bacterium, designated as YJPS3-2T, was isolated from saltern sediment of the Yellow sea in Yongyu-do, Republic of Korea. Strain YJPS3-2T grew at pH 5.0-10.0 (optimum, pH 7.0), 4-40 °C (optimum, 30 °C) and with 1-15% (w/v) NaCl (optimum 3 %). The 16S rRNA gene sequence analysis indicated that strain YJPS3-2T was closely related to those of Halomonas halophila F5-7T (98.75 %), Halomonas salina F8-11T (98.74 %), Halomonas smyrnensis AAD6T (98.66 %), Halomonas organivorans G-16.1T (98.34 %), Halomonas koreensis SS20T (97.98 %) and Halomonas beimenensis NTU-107T (96.93 %). The average nucleotide identity and digital DNA-DNA hybridization values between YJPS3-2T and related type strains were 86.9-91.6 % and 32.0-44.8 %. Strain YJPS3-2T was characterized as having Q-9 as the predominant respiratory quinone and the principal fatty acids (>10 %) were C16 : 0 (31.4 %), C19 : 0 ω8c cyclo (16.3 %), C17 : 0 cyclo (11.9 %) and C12 : 0 3-OH (10.4 %). The polar lipids consisted of phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain YJPS3-2T is 68.1mol %. Based on the polyphasic taxonomic evidence presented in this study, YJPS3-2T should be classified as representing a novel species within the genus Halmonas, for which name Halomonas getboli is proposed, with the type strain YJPS3-2T (= KCTC 92124T=KACC 22561T=JCM 35085T).
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Affiliation(s)
- Yeonjae Yoo
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Science & Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Xiaoyue Xu
- Department of Biotechnology, School of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Bogun Kim
- Department of Biotechnology, School of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, School of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
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Kim M, Cha IT, Lee KE, Park SJ. Sulfitobacter albidus sp. nov., isolated from marine sediment of Jeju Island. Arch Microbiol 2022; 204:691. [DOI: 10.1007/s00203-022-03305-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/07/2022]
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Möller J, Bodenschatz M, Sangal V, Hofmann J, Burkovski A. Multi-Omics of Corynebacterium Pseudotuberculosis 12CS0282 and an In Silico Reverse Vaccinology Approach Reveal Novel Vaccine and Drug Targets. Proteomes 2022; 10:proteomes10040039. [PMID: 36548458 PMCID: PMC9784263 DOI: 10.3390/proteomes10040039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Corynebacterium pseudotuberculosis is an important animal pathogen, which is also able to infect humans. An optimal treatment of infections with this pathogen is not available today and consequently, more research is necessary to understand the infection process. Here, we present a combined -omics and bioinformatics approach to characterize C. pseudotuberculosis 12CS0282. The genome sequence of strain 12CS0282 was determined, analyzed in comparison with the available 130 C. pseudotuberculosis sequences and used as a basis for proteome analyses. In a reverse vaccinology approach, putative vaccine and drug targets for 12CS0208 were identified. Mass spectrometry analyses revealed the presence of multiple virulence factors even without host contact. In macrophage interaction studies, C. pseudotuberculosis 12CS0282 was highly resistant against human phagocytes and even multiplied within human THP-1 cells. Taken together, the data indicate a high pathogenic potential of the strain.
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Affiliation(s)
- Jens Möller
- Microbiology Division, Department of Biology, Faculty of Sciences, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Mona Bodenschatz
- Microbiology Division, Department of Biology, Faculty of Sciences, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Jörg Hofmann
- Biochemistry Division, Department of Biology, Faculty of Sciences, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Andreas Burkovski
- Microbiology Division, Department of Biology, Faculty of Sciences, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
- Correspondence: ; Tel.: +49-9131-85-28086
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Wintachai P, Surachat K, Chaimaha G, Septama AW, Smith DR. Isolation and Characterization of a Phapecoctavirus Infecting Multidrug-Resistant Acinetobacter baumannii in A549 Alveolar Epithelial Cells. Viruses 2022; 14:v14112561. [PMID: 36423170 PMCID: PMC9695679 DOI: 10.3390/v14112561] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Multidrug-resistant Acinetobacter baumannii (MDR A. baumannii) is an emerging pathogen in the ESKAPE group. The global burden of antimicrobial resistance has led to renewed interest in alternative antimicrobial treatment strategies, including phage therapy. This study isolated and characterized a phage vB_AbaM_ ABPW7 (vABPW7) specific to MDR A. baumannii. Morphological analysis showed that phage vABPW7 belongs to the Myoviridae family. Genome analysis showed that the phage DNA genome consists of 148,647 bp and that the phage is a member of the Phapecoctavirus genus of the order Caudovirales. A short latent period and a large burst size indicated that phage vABPW7 was a lytic phage that could potentially be used in phage therapy. Phage vABPW7 is a high-stability phage that has high lytic activity. Phage vABPW7 could effectively reduce biofilm formation and remove preformed biofilm. The utility of phage vABPW7 was investigated in a human A549 alveolar epithelial cell culture model. Phage vABPW7 was not cytotoxic to A549 cells, and the phage could significantly reduce planktonic MDR A. baumannii and MDR A. baumannii adhesion on A549 cells without cytotoxicity. This study suggests that phage vABPW7 has the potential to be developed further as a new antimicrobial agent against MDR A. baumannii.
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Affiliation(s)
- Phitchayapak Wintachai
- School of Science, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand
- Functional Materials and Nanotechnology Center of Excellence, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand
- Correspondence:
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Ganyalak Chaimaha
- School of Science, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand
| | - Abdi Wira Septama
- Research Centre for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), South Tangerang 15314, Banten, Indonesia
| | - Duncan R. Smith
- Institute of Molecular Biosciences, Mahidol University, Phutthamonthon, Nakhon Pathom 73170, Thailand
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Montero-Calasanz MDC, Yaramis A, Rohde M, Schumann P, Klenk HP, Meier-Kolthoff JP. Genotype-phenotype correlations within the Geodermatophilaceae. Front Microbiol 2022; 13:975365. [PMID: 36439792 PMCID: PMC9686282 DOI: 10.3389/fmicb.2022.975365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.
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Affiliation(s)
- Maria del Carmen Montero-Calasanz
- IFAPA Las Torres-Andalusian Institute of Agricultural and Fisheries Research and Training, Junta de Andalucía, Seville, Spain
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Adnan Yaramis
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Manfred Rohde
- Central Facility for Microscopy, HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jan P. Meier-Kolthoff
- Department Bioinformatics and Databases, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Complete Genome Sequence and Comparative Genome Analysis of Variovorax sp. Strains PAMC28711, PAMC26660, and PAMC28562 and Trehalose Metabolic Pathways in Antarctica Isolates. Int J Microbiol 2022. [DOI: 10.1155/2022/5067074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The complete genomes of Variovorax strains were analyzed and compared along with the genomes of Variovorax strains PAMC28711, PAMC28562, and PAMC26660, Antarctic isolates. The genomic information was collected from the NCBI database and the CAZyme database, and Prokka annotation was used to find the genes that encode for the trehalose metabolic pathway. Likewise, CAZyme annotation (dbCAN2 Meta server) was performed to predict the CAZyme family responsible for trehalose biosynthesis and degradation enzymes. Trehalose has been found to respond to osmotic stress and extreme temperatures. As a result, the study of the trehalose metabolic pathway was carried out in harsh environments such as the Antarctic, where bacteria Variovorax sp. strains PAMC28711, PAMC28562, and PAMC26660 can survive in extreme environments, such as cold temperatures. The trehalose metabolic pathway was analyzed via bioinformatics tools, such as the dbCAN2 Meta server, Prokka annotation, Multiple Sequence Alignment, ANI calculator, and PATRIC database, which helped to predict trehalose biosynthesis and degradation genes’ involvement in the complete genome of Variovorax strains. Likewise, MEGA X was used for evolutionary and conserved genes. The complete genomes of Variovorax strains PAMC28711, PAMC26660, and PAMC28562 are circular chromosomes of length (4,320,000, 7,390,000, and 4,690,000) bp, respectively, with GC content of (66.00, 66.00, and 63.70)%, respectively. The GC content of these three Variovorax strains is lower than that of the other Variovorax strains with complete genomes. Strains PAMC28711 and PAMC28562 exhibit three complete trehalose biosynthetic pathways (OtsA/OtsB, TS, and TreY/TreZ), but strain PAMC26660 only possesses one (OtsA/OtsB). Despite the fact that all three strains contain trehalose, only strain PAMC28711 has two trehaloses according to CAZyme families (GH37 and GH15). Moreover, among the three Antarctica isolates, only strain PAMC28711 exhibits auxiliary activities (AAs), a CAZyme family. To date, although the Variovorax strains are studied for different purposes, the trehalose metabolic pathways in Variovorax strains have not been reported. Further, this study provides additional information regarding trehalose biosynthesis genes and degradation genes (trehalose) as one of the factors facilitating bacterial survival under extreme environments, and this enzyme has shown potential application in biotechnology fields.
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