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Cai H, Huang Y, Liu Y, Yang L, Zhou Y, Yang S, Chen X, Jiang C, Jiang M, Jiang Y, Singh P. Metabacillus kandeliae sp. nov., isolated from the rhizosphere soil of a decayed mangrove plant Kandelia candel. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we isolated a novel Gram-stain-positive, aerobic, motile, rod-shaped bacterium, named GX 13764T, from the rhizosphere soil of a decayed mangrove plant Kandelia candel collected from Beihai, Guangxi, PR China, and characterized using a polyphasic taxonomic approach. The strain exhibited yellow-orange, round, convex, shiny, smooth, opaque and 2–3 mm diameter colonies on marine agar 2216 media after 3 days of incubation at 30 °C and was capable of growth at 4–45 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0) and 0–4 % NaCl (w/v; optimum, 2 %). The strain was positive for catalase and negative for the oxidase. The main cellular fatty acid was anteiso-C15:0, iso-C15:0, iso-C16:0 and iso-C14:0. The cell-wall peptidoglycan comprised meso-diaminopimelic acid and the main menaquinone was MK-7. The polar lipids included one diphosphatidylglycerol, one phosphatidylglycerol, two glycolipids, two unidentified phospholipids and three unidentified lipids. Based on 16S rRNA gene analysis, GX 13764T presented the highest sequence similarity to
Metabacillus mangrovi
KCTC 33872T (97.04 %). The DNA G+C content of the type strain was 44.2 mol%. The average nucleotide identity values between GX 13764T and
M. mangrovi
KCTC 33872T,
Metabacillus idriensis
DSM 19097T and
Metabacillus indicus
LMG 22858T were 69.39, 68.87 and 68.95 %, respectively, with digital DNA–DNA hybridization values of 19.9, 19.5 and 19.5 %, respectively. Based on the polyphasic data, strain GX 13764T should be nominated as a novel species of the genus
Metabacillus
, for which the name Metabacillus kandeliae sp. nov. is proposed. The type strain is GX 13764T (=MCCC 1K06654T=KCTC 43366T).
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Affiliation(s)
- Hanqin Cai
- School of Marine Science and Biotechnology, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning 530008, PR China
| | - Ying Huang
- School of Marine Science and Biotechnology, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning 530008, PR China
| | - Ying Liu
- School of Chemistry and Chemical Engineering, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning 530008, PR China
| | - Lifang Yang
- School of Chemistry and Chemical Engineering, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning 530008, PR China
| | - Yan Zhou
- School of Marine Science and Biotechnology, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning 530008, PR China
| | - Shaojuan Yang
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Xuemei Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Chenglin Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Mingguo Jiang
- School of Marine Science and Biotechnology, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning 530008, PR China
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Pratiksha Singh
- School of Marine Science and Biotechnology, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning 530008, PR China
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Genomic and Physiological Characterization of Metabacillus flavus sp. nov., a Novel Carotenoid-Producing Bacilli Isolated from Korean Marine Mud. Microorganisms 2022; 10:microorganisms10050979. [PMID: 35630423 PMCID: PMC9146079 DOI: 10.3390/microorganisms10050979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
The newly isolated strain KIGAM252T was found to be facultatively anaerobic, Gram-stain-positive, spore-forming, and rod-shaped. They grew at 10–45 °C, pH 6.0–10.0, and were able to tolerate up to 6% NaCl in the growth medium. Phylogenetic analysis indicated that the KIGAM252T strain was related to the genus Metabacillus. The cell membrane fatty acid composition of strain KIGAM252T included C15:0 anteiso and C15:0 iso (25.6%) as the major fatty acids, and menaquinone 7 was the predominant isoprenoid quinone. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The size of the whole genome was 4.30 Mbp, and the G + C content of the DNA was 43.8%. Average nucleotide and amino acid identity and in silico DNA-DNA hybridization values were below the species delineation threshold. Pan-genomic analysis revealed that 15.8% of all genes present in strain KIGAM252T was unique to the strain. The analysis of the secondary biosynthetic pathway predicted the carotenoid synthetic gene cluster in the strain KIGAM252T. Based on these current polyphasic taxonomic data, strain KIGAM252T represents a novel species of the genus Metabacillus that produces carotenoids, for which we propose the name Metabacillus flavus sp. nov. The type of strain was KIGAM252T (=KCTC 43261T = JCM 34406T).
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Lee SY, Son JS, Hwang YJ, Shin JH, Ghim SY. Metabacillus elymi sp. nov., isolated from the Rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea. Antonie van Leeuwenhoek 2021; 114:1709-1719. [PMID: 34357485 DOI: 10.1007/s10482-021-01634-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 07/27/2021] [Indexed: 12/01/2022]
Abstract
Dokdo islands in Republic of Korea, is not suited to survive plant because strong wind, low organic content and high salinity. Nevertheless, 64 taxa of plants have a symbiotic relationship with microbe. The Metabacillus elymi KUDC1714T was isolated from the rhizosphere of Elymus tsukushiensis collected from Dokdo Islands. This bacterial strain was Gram-stain positive, non-motile, non-spore forming, aerobic and rod-shape bacteria with 0.4-0.5 × 2.5-3.0 μm in size. Colonies were smooth, yellowish-white circular and 2.0-3.0 mm in diameter. KUDC1714T was capable of growing at 10-45 °C (optimum, 30 °C), pH 7-11 (optimum, pH 8) and 0-8.0% (w/v) NaCl (optimum, 1.0-2.0%). Flagella were not observed by transmission electron microscopy. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that KUDC1714T belonged to the genus Metabacillus formed a phyletic lineage within the genus Metabacillus of the family Bacillaceae. The strain KUDC1714T was most closely related to Metabacillus sediminilitoris DSL-17 T (98.2%), Metabacillus litoralis SW-211 T (98.2%) and Metabacillus halosaccharovorans E33T (97.7%) based on 16S rRNA gene sequence. In silico DNA-DNA hybridization using genome-to-genome distance calculator were analysed at 25.8% and 23.5% in strain KUDC1714T and Metabacillus sediminilitoris DSL-17 T, and strain KUDC1714T and Metabacillus litoralis SW-211 T, respectively. Strain KUDC1714T and its closet type strain were all below cut-off point of the average nucleotide identity and average amino acid identity values. The genome contains 5197 CDSs, 3 rRNAs, 118 tRNAs, 5 ncRNAs. The genomic DNA G + C content was 34.8 mol%. Its polar lipids were diphosphatidylglycerol, phosphatidylglycerol and its major fatty acids were anteiso-C15:0 and iso-C15:0. The strain KUDC1714T contained menaquinone-7 as major isoprenoid quinone. Based on its genetic data, physiological and biochemical characteristics, strain KUDC1714T should be considered a novel species of the genus Metabacillus, for which we propose the name Metabacillus elymi sp. nov. the type strain is KUDC1714T (= KCTC 33222 T, = DSM 27608 T).
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Affiliation(s)
- Soo-Yeong Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, 80 Daehakro, 41566, Bukgu, Daegu, Republic of Korea.,School of Life Sciences, Research Institute for Dokdo and Ulleung-do Island, Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea
| | - Jin-Soo Son
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, 80 Daehakro, 41566, Bukgu, Daegu, Republic of Korea.,School of Life Sciences, Research Institute for Dokdo and Ulleung-do Island, Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea
| | - Ye-Ji Hwang
- School of Life Sciences, Research Institute for Dokdo and Ulleung-do Island, Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, 80 Daehakro, 41566, Bukgu, Daegu, Republic of Korea
| | - Sa-Youl Ghim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, 80 Daehakro, 41566, Bukgu, Daegu, Republic of Korea. .,School of Life Sciences, Research Institute for Dokdo and Ulleung-do Island, Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea.
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Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753-5798. [PMID: 33112222 DOI: 10.1099/ijsem.0.004475] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.
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Key Words
- classification of Bacillus species
- conserved signature indels
- emendation of genus Bacillus
- genus Bacillus and the family Bacillaceae
- novel Bacillaceae genera Alteribacter, Ectobacillus, Evansella, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Niallia, Priestia, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sutcliffiella and Weizmannia
- phylogenomic and comparative genomic analyses
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
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Chen P, Wang D, Ren Q, Wu J, Jiang Y, Wu Z, Pan Y, Zhong Y, Guan Y, Chen K, Zhang G. Bacillus aerolatus sp. nov., a novel member of the genus Bacillus, isolated from bioaerosols in a school playground. Arch Microbiol 2020; 202:2373-2378. [PMID: 32583126 DOI: 10.1007/s00203-020-01955-3] [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: 03/01/2020] [Revised: 05/30/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
A Gram-positive, endospore-forming, rod-shaped bacterium with a single flagellum, and a motile strain, designated CX253, was isolated from bioaerosols. The isolate is facultatively anaerobic, is able to grow at 25-45 ℃ (optimum 37 ℃) and pH 6.5-10.0 (optimum 7.5), and can tolerate up to 5.0% NaCl (w/v) under aerobic conditions. The diagnostic diamino acid in the cell wall of strain CX253T is meso-diaminopimelic acid, while major isoprenoid quinone is menaquinone 6 (MK-6) along with a smaller amount of MK-7 (20%). The polar lipid profile is composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids and glycolipids. The major cellular fatty acid is iso-C15:0 and anteiso-C15:0. Phylogenetic analysis based on 16S rRNA gene and genome sequence grouped strain CX253T into the genus Bacillus. The strain was most closely related to Bacillus thermotolerans CCTCC AB 2012108 T by comparison of 16S rRNA gene sequence (97.2% similarity) and to Bacillus wudalianchiensis CCTCC AB 2015266 T by comparison of gyrB gene sequence (80.1% similarity). The draft genome of strain CX253T comprised 3,929,195 bp with a G + C content of 43.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain CX253T and phylogenetically related Bacillus species were lower than 95% and 70%, respectively. Thus, the polyphasic evidence generated through phenotypic, chemotaxonomic and genomic methods confirmed that strain CX253T (= GDMCC 1.1608 T = KACC 21318 T) was a novel species of the genus Bacillus, for which the name Bacillus aerolatus sp. nov. is proposed.
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Affiliation(s)
- Pei Chen
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - DeDong Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - QiaoQiao Ren
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - JiGuo Wu
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - YunXia Jiang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - ZhenDong Wu
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - YiMin Pan
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yi Zhong
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Ying Guan
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Kuncai Chen
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - GuoXia Zhang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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Antimicrobial properties of the novel bacterial isolate Paenibacilllus sp. SMB1 from a halo-alkaline lake in India. Sci Rep 2019; 9:11561. [PMID: 31399607 PMCID: PMC6688988 DOI: 10.1038/s41598-019-47879-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 07/17/2019] [Indexed: 12/23/2022] Open
Abstract
Antibiotic-resistance is ever growing burden on our society for the past many years. Many synthetic chemistry approaches and rational drug-design have been unable to pace up and tackle this problem. Natural resources, more specifically, the microbial diversity, on the other hand, make a traditional and still the best platform to search for new chemical scaffolds and compounds. Here, we report the antimicrobial characteristics of novel bacterial isolate from a salt lake in India. We screened the bacterial isolates for their inhibitory activity against indicator bacteria and found that four novel species were able to prevent the growth of test strains studied in vitro. Further, we characterized one novel species (SMB1T = SL4-2) using polyphasic taxonomic approaches and also purified the active ingredient from this bacterium. We successfully characterized the antimicrobial compound using mass spectroscopy and amino acid analysis. We also allocated two novel biosynthetic gene clusters for putative bacteriocins and one novel non-ribosomal peptide gene cluster in its whole genome. We concluded that the strain SMB1T belonged to the genus Paenibacilllus with the pairwise sequence similarity of 98.67% with Paenibacillus tarimensis DSM 19409T and we proposed the name Paenibacillus sambharensis sp. nov. The type strain is SMB1T (=MTCC 12884 = KCTC 33895T).
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Kumar S, Singh H, Kaur M, Kaur L, Tanuku NRS, Pinnaka AK. Bacillus shivajii sp. nov., isolated from a water sample of Sambhar salt lake, India. Int J Syst Evol Microbiol 2018; 68:3463-3470. [PMID: 30207517 DOI: 10.1099/ijsem.0.003008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, rod-shaped, motile, spore-forming, strictly aerobic, alkali- and halo- tolerant bacterium, designated strain AK72T, was isolated from a water sample collected from Sambhar salt lake, Rajasthan, India. The colony appears circular, shiny, smooth, translucent or slightly pale in colour and convex with an entire margin after 48 h incubation at 37 °C with pH 9. Growth of the bacterium occurred at 10-42 °C (optimum, 25-37 °C), at salinities of 0.5-10 % (w/v) NaCl (optimum 3-5 % NaCl) and pH of 6-10 (optimum pH 9). Strain AK72T was positive for oxidase, catalase, nitrate reductase, phenylalanine deaminase, ornithine decarboxylase, aesculinase, lipase and urease activities. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 and the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, three unidentified phospholipids and three unidentified lipids. The genomic DNA G+C content of the strain AK72T was 36.8 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain AK72T was closely related to Bacillus cellulosilyticus (96.5 %) and Bacillus vedderi (96.3 %), but the novel strain AK72T formed a separate clade with Bacillus aurantiacus whereas B. cellulosilyticus and B. vedderi were clustered in a separate clade. The above data in combination with the phenotypic characteristics and phylogenetic data inferred that strain AK72T represents a novel species of the genus Bacillus, for which the name Bacillusshivajii sp. nov. is proposed. The type strain is AK72T (=MTCC 12636T=KCTC 33981T=JCM 32183T).
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Affiliation(s)
- Shekhar Kumar
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Harjodh Singh
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India.,2Academy of Scientific and Innovative Research (AcSIR), CSIR Campus, Chennai, India.,3CSIR-Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Manpreet Kaur
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India.,2Academy of Scientific and Innovative Research (AcSIR), CSIR Campus, Chennai, India.,3CSIR-Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Lakhwinder Kaur
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Naga Radha Srinivas Tanuku
- 2Academy of Scientific and Innovative Research (AcSIR), CSIR Campus, Chennai, India.,4CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam 530017, India
| | - Anil Kumar Pinnaka
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India.,2Academy of Scientific and Innovative Research (AcSIR), CSIR Campus, Chennai, India
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