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Lin SY, Hameed A, Tsai CF, Young CC. Description of Flavobacterium agricola sp. nov., an auxin producing bacterium isolated from paddy field. Antonie Van Leeuwenhoek 2023; 116:1345-1357. [PMID: 37837564 DOI: 10.1007/s10482-023-01891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
An auxin-producing bacterial strain, CC-SYL302T, was isolated from paddy soil in Taiwan and identified using a polyphasic taxonomic approach. The cells were observed to be aerobic, non-motile, non-spore-forming rods, and tested positive for catalase and oxidase. Produced carotenoid but flexirubin-type pigments were absent. Optimal growth of strain CC-SYL302T was observed at 25 °C, pH 7.0, and with 2% (w/v) NaCl present. Based on analysis of 16S rRNA gene sequences, it was determined that strain CC-SYL302T belongs to the genus Flavobacterium of the Flavobacteriaceae family. The closest known relatives of this strain are F. tangerinum YIM 102701-2 T (with 93.3% similarity) and F. cucumis R2A45-3 T (with 93.1% similarity). Digital DNA-DNA hybridization (dDDH) values were calculated to assess the genetic distance between strain CC-SYL302T and its closest relatives, with mean values of 21.3% for F. tangerinum and 20.4% for F. cucumis. Strain CC-SYL302T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the Flavobacterium genus, ranging from 67.2 to 72.1% (n = 22). The dominating cellular fatty acids (> 5%) included iso-C14:0, iso-C15:0, iso-C16:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C16:1 ω6c/C16:1 ω7c and C16:0 10-methyl/iso-C17:1 ω9c. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and nine unidentified polar lipids. The genome (2.7 Mb) contained 33.6% GC content, and the major polyamines were putrescine and sym-homospermidine. Strain CC-SYL302T exhibits distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, dDDH, and phylogenomic placement. Therefore, it is proposed that this strain represents a new species of the Flavobacterium genus, for which the name Flavobacterium agricola sp. nov. is proposed. The type strain is CC-SYL302T (= BCRC 81320 T = JCM 34764 T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan.
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Lin SY, Lin TY, Hameed A, Tang YS, Young CC. Neopusillimonas aromaticivorans sp. nov. isolated from poultry manure. Int J Syst Evol Microbiol 2023; 73. [PMID: 37962187 DOI: 10.1099/ijsem.0.006146] [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: 11/15/2023] Open
Abstract
A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST667T, isolated from poultry manure sampled in Taiwan. The cells were observed to be aerobic, motile and non-spore-forming rods, displaying positive reactions for oxidase. Optimal growth of CC-YST667T was observed at 25 °C, pH 8.0 and with 1 % (w/v) NaCl. The polar lipid profile consisted of phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and multiple unidentified polar lipids. The major polyamine was spermidine. The major cellular fatty acids (>5 %) included C16 : 0, C17 : 0cyclo, C19 : 0cyclo ω8c and C14 : 0 3OH/iso-C16 : 1 I. On the basis of the results of analysis of 16S rRNA gene sequences, this isolate showed the closest phylogenetic relationship with 'Neopusillimonas minor' (with 98.2 % similarity) and Paralcaligenes ureilyticus (with 97.3 % similarity) of the family Alcaligenaceae. The draft genome, (3.3 Mb) with a DNA G+C content of 57.2 mol%, harboured various genes involved in the biodegradation of aromatic hydrocarbons. CC-YST667T shared highest orthologous average nucleotide identity (OrthoANI) with the type strains of species of of the genera Neopusillimonas (72.4‒77.9 %, n=2), Pusillimonas (72.8‒73.0 %, n=2) and Pollutimonas (71.7‒73.0 %, n=5). On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with the results of comparative 16S rRNA gene sequencing, OrthoANI, digital DNA-DNA hybridization (DDH) and the phylogenomic placement, strain CC-YST667T is considered to represent a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aromaticivorans sp. nov. is proposed. The type strain is CC-YST667T (=BCRC 81321T =JCM 34761T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan, ROC
| | - Tzu-Yu Lin
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte 575018, Mangalore, Karnataka, India
| | - Yu-Shan Tang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan, ROC
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan, ROC
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Lin SY, Hameed A, Tsai CF, Tang YS, Young CC. Description of Pseudogemmobacter faecipullorum sp. nov., isolated from poultry manure. FEMS Microbiol Lett 2022; 369:6840210. [PMID: 36413463 DOI: 10.1093/femsle/fnac112] [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: 08/11/2022] [Revised: 10/07/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST710T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST710T were aerobic, Gram-stain-negative, nonmotile, nonspore-forming rods, displaying positive reactions for catalase, and oxidase activities. Strain CC-YST710T was found to grow optimally at 30°C, pH 7.0, and in the presence of 2% (w/v) NaCl. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, four unidentified aminolipids, one unidentified aminophospholipid, and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C16:0, C18:0, and C18:1ω7c/C18:1ω6c. Based on 16S rRNA gene analysis, this isolate showed the closest phylogenetic relationship with 'Pseudogemmobacter humicola' (97.6%), followed by Pseudogemmobacter bohemicus (97.2%) and 'Pseudogemmobacter hezensis' (97.5%). The draft genome (4.3 Mb) had 62.9 mol% G + C content. CC-YST710T can be distinguished from other Pseudogemmobacter species due to the exclusive presence of key genes encoding p-hydroxybenzoate hydroxylase, protocatechuate 3, 4-dioxygenase (α and β chain), and homogentisate 1, 2-dioxygenase involved in the degradation of phenolic compounds such as p-hydroxybenzoic acid, protocatechuate, and homogentisate, respectively. Orthologous average nucleotide identity (OrthoANI) of the isolate with the type strains of the genera Pseudogemmobacter were 77.6%‒78.0% (n = 3), followed by Tabrizicola (72.3%‒73.7%, n = 5), and Gemmobacter(72.3%‒73.5%, n = 7). Based on its distinct phylogenetic, phenotypic, and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST710T is considered to represent a novel Pseudogemmobacter species, for which the name Pseudogemmobacter faecipullorum sp. nov. (type strain CC-YST710T = BCRC 81286T = JCM 34182T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung 40227, Taiwan
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, University Road Deralakatte Mangalore 575018, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung 40227, Taiwan
| | - Yu-Shan Tang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung 40227, Taiwan.,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, 145, XingDa Rd., Taichung 40227, Taiwan
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Lin SY, Tsai CF, Hameed A, Lee TH, Young CC. Niabella agricola sp. nov., isolated from paddy soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a Gram-stain-negative, orange-coloured bacterium (designated strain CC-SYL272T) isolated from paddy soil. Cells were observed to be strictly aerobic, non-motile and non-spore-forming rods, exhibiting positive catalase and oxidase. Strain CC-SYL272T was found to grow optimally at 20–40 °C, pH 6.0–8.0 and NaCl 0–2 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CC-SYL272T belongs to the genus
Niabella
, family
Chitinophagaceae
, and is most closely related to
Niabella pedocola
(97.8 %) followed by
Niabella drilacis
(97.2 %) and established a distinct taxonomic lineage associated with these species. The highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-SYL272T
versus Niabella species (69.1–83.5 %, n=8). The mean digital DNA–DNA hybridization (dDDH) value obtained for strain CC-SYL272T against
N. pedocola
was 27.3 %. The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The major polyamines were putrescine and sym-homospermidine. The dominating cellular fatty acids (>5 %) included iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3OH and C16 : 1
ω6c/C16 : 1
ω7c. The draft genome (6.25 Mb) of strain CC-SYL272T spanned three contigs having 47.1 mol% DNA G+C content, 5087 protein-encoding genes, 10 rRNA genes and 44 tRNA genes. The genome harboured genes involved in the depolymerization of both animal and plant polysaccharides. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH and the phylogenomic placement, strain CC-SYL272T is considered to represent a novel species of the genus
Niabella
, affiliated to the family
Chitinophagaceae
, for which the name Niabella agricola sp. nov. is proposed. The type strain is CC-SYL272T (=BCRC 81319T=JCM 34758T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
| | - Tzung-Han Lee
- Taoyuan District Agricultural Research and Extension Station, Council of Agriculture Executive Yuan, Taoyuan City, Taiwan, ROC
| | - Chiu-Chung Young
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
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Rawat A, Sharma M, Vignesh P, Jindal AK, Suri D, Das J, Joshi V, Tyagi R, Sharma J, Kaur G, Lau YL, Imai K, Nonoyama S, Lenardo M, Singh S. Utility of targeted next generation sequencing for inborn errors of immunity at a tertiary care centre in North India. Sci Rep 2022; 12:10416. [PMID: 35729272 PMCID: PMC9213413 DOI: 10.1038/s41598-022-14522-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022] Open
Abstract
Inborn errors of immunity (IEI) are a heterogeneous group of monogenic disorders that include primary immunodeficiency's and other disorders affecting different aspects of the immune system. Next-Generation Sequencing (NGS) is an essential tool to diagnose IEI. We report our 3-year experience in setting up facilities for NGS for diagnosis of IEI in Chandigarh, North India. We used a targeted, customized gene panel of 44 genes known to result in IEI. Variant analysis was done using Ion Reporter software. The in-house NGS has enabled us to offer genetic diagnoses to patients with IEI at minimal costs. Of 121 patients who were included pathogenic variants were identified in 77 patients. These included patients with Chronic Granulomatous Disease, Severe Combined Immune Deficiency, leukocyte adhesion defect, X-linked agammaglobulinemia, Ataxia Telangiectasia, Hyper-IgE syndrome, Wiskott Aldrich syndrome, Mendelian susceptibility to mycobacterial diseases, Hyper-IgM syndrome, autoimmune lymphoproliferative syndrome, and GATA-2 deficiency. This manuscript discusses the challenges encountered while setting up and running targeted NGS for IEI in our unit. Genetic diagnosis has helped our patients with IEI in genetic counselling, prenatal diagnosis, and accessing appropriate therapeutic options.
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Affiliation(s)
- Amit Rawat
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India.
| | - Madhubala Sharma
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Pandiarajan Vignesh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Ankur Kumar Jindal
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Deepti Suri
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Jhumki Das
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Vibhu Joshi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Rahul Tyagi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Jyoti Sharma
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Gurjit Kaur
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kohsuke Imai
- Department of Pediatric, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, National Defence Medical College, Tokyo, 113-8519, Japan
| | - Shigeaki Nonoyama
- Department of Pediatric, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, National Defence Medical College, Tokyo, 113-8519, Japan
| | - Michael Lenardo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA
| | - Surjit Singh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
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Lin SY, Hameed A, Tsai CF, Hung MH, Young CC. Agrilactobacillus fermenti sp. nov. isolated from fermented vegetable residue. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a Gram-stain-positive fermentative bacterium, designated strain CC-MHH1034T, isolated from a fermented vegetable residue. Cells of strain CC-MHH1034T were facultatively anaerobic, non-motile, and non-spore-forming rods, exhibiting positive catalase, oxidase and protease activities. Optimal growth occurred at 30 °С and pH 6.0. Strain CC-MHH1034T shared the highest 16S rRNA gene sequence similarities with
Agrilactobacillus composti
(95.9 %) followed by
Agrilactobacillus yilanensis
(95.1 %) and established a distinct taxonomic lineage associated with these species. Highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-MHH1034T versus
Agrilactobacillus
(71.1–71.6 %, n=2) followed by
Ligilactobacillus
(66.5–66.8 %, n=2),
Lactobacillus
(64.1–65.8 %, n=4). The mean digital DNA–DNA hybridization (dDDH) value obtained for strain CC-MHH1034T against
Agrilactobacillus
was 19.2–19.5 % (n=2). The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, four unidentified glycolipids, four unidentified phospholipids and one unidentified lipid. The major polyamine was sym-homospermidine and meso-diaminopimelic acid was detected as the cell-wall peptidoglycan. The dominating cellular fatty acids (>5 %) included C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and C18 : 1
ω9c. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH, and the phylogenomic placement, strain CC-MHH1034T is considered to represent a novel species of the genus
Agrilactobacillus
, affiliated to the family
Lactobacillaceae
, for which the name Agrilactobacillus fermenti sp. nov. is proposed. The type strain is CC-MHH1034T (=BCRC 81220T=JCM 33476T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC
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Lin SY, Hameed A, Tsai CF, Tang YS, Young CC. Pusillimonas faecipullorum sp. nov., isolated from the poultry manure. Arch Microbiol 2022; 204:256. [PMID: 35414138 DOI: 10.1007/s00203-022-02859-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/02/2022]
Abstract
A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST705T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST705T were aerobic, Gram-stain-negative, non-motile, non-spore-forming rods, displaying positive reactions for catalase, oxidase and β-glucosidase. Optimal growth occurred at 30 °C and pH 8. Strain CC-YST705T shared the highest (> 96.0%) pair-wise 16S rRNA gene sequence similarity with Pusillimonas noertemannii (96.7%), followed by Pusillimonas caeni (96.6%), Eoetvoesia caeni (96.1%) and Paracandidimonas soli (96.0%), and formed a distinct phyletic lineage associate with the clade that accommodated Pusillimonas species. The draft genome (3.1 Mb) having 57.4 mol % G + C content contained genes involved in the catabolism of aromatic hydrocarbons. The orthologous average nucleotide identity (OrthoANI) values were 62.8-73.1% (n = 8), 72.6 (n = 1), 71.5% (n = 1) compared within the type strains of the genera Pusillimonas, Eoetvoesia and Paracandidimonas, respectively. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C12:0, C16:0, C17:0 cyclo, C19:0 cyclo ω8c and 2 C14:0 3OH/iso-C16:1 I. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST705T is considered to represent a novel species of the genus Pusillimonas, for which the name Pusillimonas faecipullorum sp. nov. is proposed. The type strain is CC-YST705T (= BCRC 81285 T = JCM 34168 T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan
| | - Yu-Shan Tang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan. .,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan.
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8
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Nagamatsu S, Wada T, Matsushima R, Fujita N, Miura S, Crofts N, Hosaka Y, Yamaguchi O, Kumamaru T. Mutation in BEIIb mitigates the negative effect of the mutation in ISA1 on grain filling and amyloplast formation in rice. PLANT MOLECULAR BIOLOGY 2022; 108:497-512. [PMID: 35083581 DOI: 10.1007/s11103-022-01242-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Mutation of the BEIIb gene in an isa1 mutant background mitigates the negative effect of the ISA1 mutation on grain filling, and facilitates recovery of amyloplast formation in rice endosperm. In this study, the effect of branching enzyme IIb and isoamylase 1 deficiency on starch properties was demonstrated using high resistant starch rice lines, Chikushi-kona 85 and EM129. Both lines harbored a mutation in the BEIIb and ISA1 genes and showed no BEIIb and ISA1 activity, implying that both lines are beIIb isa1 double mutants. The amylopectin long chain and apparent amylose content of both mutant lines were higher than those of the wild-type. While both mutants contained loosely packed, round starch grains, a trait specific to beIIb mutants, they also showed collapsed starch grains at the center of the endosperm, a property specific to isa1 mutants. Furthermore, beIIb isa1 double mutant F2 lines derived from a cross between Chikushi-kona 85 and Nishihomare (wild-type cultivar) showed significantly heavier seed weight than the beIIb and isa1 single mutant lines. These results suggest that co-occurrence of beIIb and isa1 mutant alleles in a single genetic background mitigates the negative effect of the isa1 allele on grain filling, and contributes to recovery of the amyloplast formation defect in the isa1 single mutant.
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Affiliation(s)
- Shiro Nagamatsu
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka, 818-8549, Japan.
| | - Takuya Wada
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka, 818-8549, Japan
| | - Ryo Matsushima
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo Kurashiki, Okayama, 710-0046, Japan
| | - Naoko Fujita
- Department of Biological Production, Akita Prefectural University, 241-438 Kaidobata-Nishi Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Satoko Miura
- Department of Biological Production, Akita Prefectural University, 241-438 Kaidobata-Nishi Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Naoko Crofts
- Department of Biological Production, Akita Prefectural University, 241-438 Kaidobata-Nishi Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Yuko Hosaka
- Department of Biological Production, Akita Prefectural University, 241-438 Kaidobata-Nishi Nakano Shimoshinjo, Akita, 010-0195, Japan
| | - Osamu Yamaguchi
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka, 818-8549, Japan
| | - Toshihiro Kumamaru
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
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Lin SY, Hameed A, Tsai CF, Young CC. Vineibacter terrae gen. nov., sp. nov., an ammonium-assimilating and nitrate-reducing bacterium isolated from vineyard soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878378 DOI: 10.1099/ijsem.0.005111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT640T, isolated from vineyard soil sampled in Taiwan. Cells of strain CC-CFT640T were aerobic, non-motile, nitrate-reducing rods. Test results were positive for catalase, oxidase and proteinase activities. Optimal growth occurred at 30 °С and pH 7. Strain CC-CFT640T showed highest 16S rRNA gene sequence similarity to members of the genus Enhydrobacter (90.0 %, n=1) followed by Hypericibacter (89.4-90.0 %, n=2), Reyranella (88.8-89.8 %, n=5) and Nitrospirillum (89.2-89.4 %, n=2), and formed a distinct phyletic lineage distantly associated with the clade that predominately accommodated Reynerella species. The DNA G+C composition of the genome (2.1 Mb) was 67.9 mol%. Genes involved in the reduction of nitrate to nitrite, nitric oxide and nitrous oxide were found. In addition, genes encoding dissimilatory nitrate reduction to ammonia, ammonium transport and ammonium assimilation were also detected. Average nucleotide identity values were 73.3 % (n=1), 74.0-74.6 % (n=2), 67.5-68.3 % (n=2) when compared within the type strains of the genera Enhydrobacter, Reyranella and Niveispirillum, respectively. The dominant cellular fatty acids (>5 %) included C16 : 0, iso-C17 : 1 ω10c, C19 : 0 cyclo ω8c, C18 : 1 2-OH and C18 : 1 ω7c/C18 : 1 ω6c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, three unidentified phospholipids and an unidentified aminophospholipid. The major respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequencing, digital DNA-DNA hybridization, average nucleotide identity and phylogenomic placement, strain CC-CFT640T is considered to represent a novel genus and species of the family Rhodospirillaceae, for which the name Vineibacter terrae gen. nov., sp. nov. is proposed. The type strain is CC-CFT640T (=BCRC 81219T=JCM 33507T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC.,Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC.,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC
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Lin SY, Hameed A, Tsai CF, Young CC. Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field. Antonie van Leeuwenhoek 2021; 114:2101-2111. [PMID: 34599477 DOI: 10.1007/s10482-021-01664-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 09/19/2021] [Indexed: 11/25/2022]
Abstract
A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT501T, harboring xenobiotic- and allelochemical-metabolizing genes, isolated from a long-term ecological research field in Taiwan. Cells of strain CC-CFT501T were catalase- and oxidase-positive, non-motile and short rods. Optimal growth occurred at 30 °C, pH 8 and 1% NaCl. Strain CC-CFT501T was found to share high 16S rRNA gene sequence similarity with the members of genera Quisquiliibacterium (94.3%, n = 1), Pandoraea (93.4-94.0%, n = 23) and Paraburkholderia (93.3-94.0%, n = 9), affiliated to the family Burkholderiaceae. Strain CC-CFT501T shared 76.4% orthologous average nucleotide identity (OrthoANI) and 20.9% digital DNA-DNA hybridization (dDDH) values with Quisquiliibacterium transsilvanicum DSM 29781T. Draft genome sequence (3.83 Mb) of strain CC-CFT501T revealed several genes encoding the proteins involved in biphenyl and phenolic acid metabolism. Fatty acid profile contained C16:0, C18:0, C10:0 3-OH, C16:1 ω7c/C16:1 ω6c and C18:1 ω7c/C18:1 ω6c in predominant amounts. The polar lipid profile consisted of phosphatidylethanolamine, thirteen unidentified amino lipids, two unidentified phospholipids and two unidentified glycolipids. The major polyamine was spermidine and ubiquinone Q-8 was the sole respiratory quinone. The DNA G + C content was 70.0 mol%. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT501T is considered to represent a novel genus and species of the family Burkholderiaceae, for which the name Zeimonas arvi gen. nov., sp. nov. is proposed. The type strain of the type species is CC-CFT501T (= BCRC 81218T = JCM 33506T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan.
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Lin SY, Tsai CF, Hameed A, Tang YS, Young CC. Description of Devosia faecipullorum sp. nov., harboring antibiotic- and toxic compound-resistace genes, isolated from poultry manure. Int J Syst Evol Microbiol 2021; 71. [PMID: 34287119 DOI: 10.1099/ijsem.0.004901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696T, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696T were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696T associated with Devosia chinhatensis (97.9 % sequence identity), Devosia riboflavina (97.3 %) and Devosia indica (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8-80.0 % (n=17) compared within the type strains of species of of the genus Devosia. CC-YST696T contained C16:0, C18:0, C18:1ω7c 11-methyl and C18:1ω6c/ C18:1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696T is proposed to represent a novel species of the genus Devosia, for which the name Devosia faecipullorum sp. nov. (type strain CC-YST696T=BCRC 81284T=JCM 34167T) is proposed.
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yu-Shan Tang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC
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Lin SY, Tsai CF, Hameed A, Young CC. Aeromicrobium terrae sp. nov., isolated from a maize field. Int J Syst Evol Microbiol 2021; 71. [PMID: 33400640 DOI: 10.1099/ijsem.0.004616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT486T, isolated from soil sampled in a maize field in Taiwan. Cells of strain CC-CFT486T were short rods, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT486T associated with Aeromicrobium panacisoli (97.0 % sequence identity), Aeromicrobium lacus (97.0 %), Aeromicrobium erythreum (96.8 %) and Aeromicrobium alkaliterrae (96.8 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 70.6-77.8 % (n=11) compared within the type strains of the genus Aeromicrobium. Strain CC-CFT486T contained C16 : 0, C17 : 0, C17 : 1 ω8c and C18 : 1 ω9c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified aminophospholipids and three unknown phospholipids. The cell wall peptidoglycan of strains CC-CFT486T contained ll-diaminopimelic acid (ll-DAP) and the major polyamine was spermidine. The DNA G+C content was 70.6 mol% and the predominant quinone was menaquinone 9 (MK-9). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-CFT486T is proposed to represent a novel Aeromicrobium species, for which the name Aeromicrobium terrae sp. nov. (type strain CC-CFT486T=BCRC 81217T=JCM 33499T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chiu-Chung Young
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
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Lin SY, Tsai CF, Hameed A, Young CC. Cerasibacillus terrae sp. nov., isolated from maize field, and emended description of Cerasibacillus quisquiliarum Nakamura et al. 2004. Int J Syst Evol Microbiol 2020; 70:5725-5733. [PMID: 32941128 DOI: 10.1099/ijsem.0.004470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT480T, isolated from soil sampled in a maize field in Taiwan, ROC. Cells of strain CC-CFT480T were rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 3 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT480T associated with Cerasibacillus quisquiliarum (97.2 % sequence identity), Virgibacillus soli (95.7 %), Virgibacillus carmonensis (95.4 %) and Virgibacillus byunsanensis (95.2 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-CFT480T and C. quisquiliarum were 74.2 and 20.1 %, respectively. Strain CC-CFT480T contained iso-C15:0, C16:1 ω7c alcohol and iso-C17:1 ω10c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown aminophospholipids, one uncharacterized aminophospholipid and two unknown phospholipids. The major polyamine was spermidine. The DNA G+C content was 34.8 mol% and the predominant quinone was menaquinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT480T is proposed to represent a novel Cerasibacillus species, for which the name Cerasibacillus terrae sp. nov. (type strain CC-CFT480T=BCRC 81216T=JCM 33498T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chiu-Chung Young
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
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Lin SY, Chen WM, Huang GH, Hameed A, Chang CT, Tsai CF, Young CC. Flavobacterium supellecticarium sp. nov., isolated from an abandoned construction timber. Int J Syst Evol Microbiol 2020; 70:3731-3739. [PMID: 32453684 DOI: 10.1099/ijsem.0.004227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain CC-CTC003T was isolated from a synthetic wooden board. Cells of strain CC-CTC003T were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003T belonged to the genus Flavobacterium and was most closely related to Flavobacterium cerinum (95.3 % sequence identity), Flavobacterium maris (94.9 % sequence identity), Flavobacterium qiangtangense (94.8 %) and Flavobacterium subsaxonicum (94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003T and the type strains of other closely related species were 70.1-74.1 %. The digital DNA-DNA hybridization (dDDH) with F. cerinum was 19.4 %. Strain CC-CTC003T contained C15 : 0, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω6c / C16 : 1 ω7c) and summed feature 9 (C16 : 0 10-methyl / iso-C17 : 1 ω9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was sym-homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003T should be classified as a novel species, for which the name Flavobacterium supellecticarium sp. nov. is proposed. The type strain is CC-CTC003T (=BCRC 81146T=JCM 32838T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan, ROC
| | - Guan-Hua Huang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chun-Tse Chang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chiu-Chung Young
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
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Description of Azoarcus nasutitermitis sp. nov. and Azoarcus rhizosphaerae sp. nov., two nitrogen-fixing species isolated from termite nest and rhizosphere of Ficus religiosa. Antonie van Leeuwenhoek 2020; 113:933-946. [PMID: 32222862 DOI: 10.1007/s10482-020-01401-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/06/2020] [Indexed: 10/24/2022]
Abstract
A polyphasic taxonomic approach was used to characterise two presumably novel bacteria, designated strains CC-YHH838T and CC-YHH848T isolated from termite nest and rhizosphere of Ficus religiosa, respectively. These two nitrogen-fixing strains were observed to be Gram-staining-negative, aerobic rod, and colonies were yellowish in color. Growth of strains was observed at 20-37 °C, pH 7-8, and in the presence of 1-2% NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-YHH838T and CC-YHH848T associated with Thauera hydrothermalis (97.1% sequence identity), and formed a separate branch with Azoarcus indigens (95.4%), Aromatoleum aromaticum (96.2%), and lower sequence similarity to other species. The calculation of OrthoANI values pointed out strains CC-YHH838T and CC-YHH848T gave 78.9% and 79.8% compared to Thauera hydrothermalis, respectively. The major fatty acids (> 5%) were C16:0, C17:0 cyclo, C10:0 3-OH, C16:1ω7c/C16:1ω6c and C18:1ω7c/C18:1ω6c. The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminophospholipid and phospholipids; the predominant polyamines were putrescine and spermidine. The predominant respiratory system was ubiquinone (Q-8) and the DNA G + C contents were 61.4 ± 0.1 mol% and 60.2 ± 1.3 mol%, respectively. Based on the phylogenetic and polyphasic comparisons, strains CC-YHH838T and CC-YHH848T are proposed to represent two novel species within the genus Azoarcus in the family Rhodocyclaceae, for which the name Azoarcus nasutitermitis sp. nov. (type strain CC-YHH838T = BCRC 81059T = JCM 32001T) and Azoarcus rhizosphaerae sp. nov. (type strain CC-YHH848T = BCRC 81060T = JCM 32002T) were proposed.
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Lin SY, Chen WM, Hameed A, Huang GH, Hung MH, Young CC. Cohnella fermenti sp. nov., isolated from a fermentation process. Int J Syst Evol Microbiol 2020; 70:2602-2610. [PMID: 32160142 DOI: 10.1099/ijsem.0.004080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CC-MHH1044T, was isolated from a preserved vegetable sample. A polyphasic taxonomic approach was applied to the isolates in order to clarify its taxonomic position. Growth of the strain CC-MHH1044T occurred at 15-50 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-2.0 % (w/v) NaCl (optimum, 1 %, w/v). The genome of strain CC-MHH1044T consisted of 8.5 Mb and the genomic DNA G+C content was 58.5 mol%. Comparison of the 16S rRNA gene sequences showed that CC-MHH1044T belonged to the genus Cohnella and showed a close relationship with the type strains of Cohnella damuensis (96.2 %) and Cohnella panacarvi (95.9 %), and lower sequence similarity to other species. Average nucleotide identity values calculated from whole-genome sequencing data proved that CC-MHH1044T represents a distinct Cohnella species. The dominant cellular fatty acids (>5 %) included iso-C14 : 0(7.4 %), iso-C15 : 0 (6.4 %), anteiso-C15 : 0(40.3 %), C16 : 0 (6.6 %) and iso-C16 : 0 (27.0 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids, one unidentified phospholipid and glycolipid. The major polyamine was spermidine. The predominant isoprenoid quinone was menaqinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits, together with results of comparative 16S rRNA gene sequence, average nucleotide identity and digital DNA-DNA hybridization analyses, we conclude that strain CC-MHH1044T represents a novel member of the genus Cohnella, for which the name Cohnella fermenti sp. nov. is proposed. The type strain is CC-MHH1044T (=BCRC 81147T=JCM 32834T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Wen-Ming Chen
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Guan-Hua Huang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
| | - Chiu-Chung Young
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City, Taiwan, ROC
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Lin SY, Hameed A, Huang HI, Young CC. Allorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov. Int J Syst Evol Microbiol 2020; 70:397-405. [PMID: 31626583 DOI: 10.1099/ijsem.0.003770] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a nitrogen-fixing bacterium, designated strain CC-HIH110T, isolated from paddy soil in Taiwan. Cells of strain CC-HIH110T were Gram-stain-negative, rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 7 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-HIH110T associated with Rhizobium oryziradicis (98.4 % sequence identity), Allorhizobium vitis (97.8 %), Allorhizobium taibaishanense (97.7 %) and Allorhizobium undicola (96.0 %), and lower sequence similarity to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-HIH110T and the type strains of other closely related species were 71.5-88.6 % and 19.6-35.5 %, respectively. Strain CC-HIH110T contained C16 : 0 3-OH, C14 : 0 3-OH/iso C16 : 1 I and C18 : 1 ω7c/C18 : 1 ω6c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, three unknown aminophospholipids, two unknown phospholipids and an unknown lipid. The major polyamine was homospermidine. The DNA G+C content was 55.0 mol% and the predominant quinone was ubiquinone (Q-10). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-HIH110T is proposed to represent a novel Allorhizobium species, for which the name Allorhizobium terrae sp. nov. (type strain CC-HIH110T=BCRC 80932T=JCM 31228T). In addition, Rhizobium oryziradicis is reclassified as Allorhizobium oryziradicis (type strain N19T=ACCC 19962T=KCTC 52413T) comb. nov.
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Hsin-I Huang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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Hameed A, Shahina M, Lin SY, Chen WM, Hsu YH, Lai WA, Young CC. Description of Gemmobacter aestuarii sp. nov., isolated from estuarine surface water and reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013. Arch Microbiol 2020; 202:1035-1042. [DOI: 10.1007/s00203-020-01809-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 10/25/2022]
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Akram N, Mustafa G, Hanif AA, Tawwab S, Hussain S, Kaul H, Mohsin S. Cytochrome 2C19 and paraoxonase-1 polymorphisms and clopidogrel resistance in ischemic heart disease patients. Per Med 2019; 16:379-386. [PMID: 31591927 DOI: 10.2217/pme-2018-0030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aim: Polymorphisms in cytochrome P450 (CYP) 2C19 and paraoxonase-1 (PON-1) genes are thought to be involved in clopidogrel high on treatment reactivity in ischemic heart disease (IHD) patients. Methods: A total of 240 patients with IHD were screened for CYP2C19 loss-of-function alleles (LOF; *2, *3) and PON-1 Q192R. Patients were classified as responders and nonresponders to clopidogrel based upon platelet aggregation studies. Genotyping of the CYP2C19 and PON-1 allele was carried out by PCR-RFLP. Results: Results showed that 14.3% of the patients were nonresponders, whereas 85.7% were responders to the clopidogrel therapy. CYP2C19*3 allele showed significant association with clopidogrel high on treatment reactivity in IHD patients. Conclusion: Result of our study demonstrate that IHD patients with CYP2C19*3 allele can face the problem of clopidogrel high on treatment reactivity in Punjabi Pakistani population.
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Affiliation(s)
- Nabila Akram
- Department of Haematology, University of Health Sciences, Lahore, Pakistan
| | - Ghulam Mustafa
- Department of Haematology, University of Health Sciences, Lahore, Pakistan
| | - Anum A Hanif
- Department of Haematology, University of Health Sciences, Lahore, Pakistan
| | | | - Shabbir Hussain
- Department of Biochemistry, University of Health Sciences, Lahore, Pakistan
| | - Haiba Kaul
- Department of Biochemistry, University of Health Sciences, Lahore, Pakistan.,Genetics Division, Department of Livestock Production, University of Veterinary & Animal Sciences, Ravi Campus, Pattoki, Pakistan
| | - Shahida Mohsin
- Department of Haematology, University of Health Sciences, Lahore, Pakistan
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20
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Bowman LL, MacGuigan DJ, Gorchels ME, Cahillane MM, Moore MV. Revealing paraphyly and placement of extinct species within Epischura (Copepoda: Calanoida) using molecular data and quantitative morphometrics. Mol Phylogenet Evol 2019; 140:106578. [PMID: 31401068 DOI: 10.1016/j.ympev.2019.106578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/02/2019] [Accepted: 08/07/2019] [Indexed: 10/26/2022]
Abstract
Epischura (Calanoida: Temoridae) is a Holarctic group of copepods serving important ecological roles, but it is difficult to study because of small range sizes of individual species and widespread distribution of the genus. This genus includes Tertiary relicts, some endemic to single, isolated lakes and can play major roles in unique ecosystems like Lakes Baikal and Tahoe. We present the first molecular and morphological analysis of Epischura that reveals their spatio-temporal evolutionary history. Morphological measurements of mandibles and genetics estimated phylogenetic relationships among all species represented in Epischura, including E. massachusettsensis, whose extinction status is of concern. Analyses used three gene regions for six previously unsequenced species to infer highly-resolved and well-supported phylogenies confirming a split between Siberian and North American species. Previously published age estimates and sequence data from broad taxonomic sampling of calanoid copepods estimated divergence times between the two Epischura groups. Divergence time estimates for Epischura were consistent with earlier molecular clock estimates and late-Miocene cooling events. Additionally, we provide the first taxonomically broad estimates of divergence times within Calanoida. The paraphyletic nature of the genus Epischura (and the family Temoridae) is apparent and requires the resurrection of the genus Epischurella (Smirnov, 1936) to describe the Siberian species.
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Affiliation(s)
- Larry L Bowman
- Department of Ecology and Evolutionary Biology, Yale University, Osborn Memorial Laboratories, 165 Prospect St., New Haven, CT 06511, USA.
| | - Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, Osborn Memorial Laboratories, 165 Prospect St., New Haven, CT 06511, USA
| | - Madeline E Gorchels
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
| | - Madeline M Cahillane
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
| | - Marianne V Moore
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
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21
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Lin SY, Hameed A, Hsieh YT, Young CC. Mesorhizobium composti sp. nov., isolated from compost. Antonie van Leeuwenhoek 2019; 112:1387-1398. [PMID: 31055717 DOI: 10.1007/s10482-019-01270-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/26/2019] [Indexed: 11/26/2022]
Abstract
A polyphasic taxonomic approach was used to characterize a presumptively novel diazotrophic bacterium, designated strain CC-YTH430T, isolated from a compost sample in Taiwan. Cells of strain CC-YTH430T were found to be Gram-stain negative, facultative anaerobic rods that formed yellow-colored colonies on nutrient agar. Cell growth occurred at 15-40 °C, pH 5.0-9.0 and in the presence of 0-2% NaCl. Strain CC-YTH430T resembled Mesorhizobium species while sharing high pair-wise 16S rRNA gene sequence similarities with Mesorhizobium silamurunense, Mesorhizobium thiogangeticum, Mesorhizobium plurifarium, Mesorhizobium tamadayense, Mesorhizobium amorphae (96.9% each), Mesorhizobium sediminum (96.8%), and Mesorhizobium soli (96.5%) and < 96.5% similarity to other species. Strain CC-YTH430T showed 78.8-79.7% average nucleotide identity compared to the type strains of M. amorphae, M. plurifarium, M. soli, M. tamadayense and M. wenxiniae. The N2-fixing activity of strain CC-YTH430T was 0.2 nmol ethylene h-1 at 30 °C. The respiratory system was ubiquinone 10 (Q-10) and the DNA G+C content was 62.0 ± 0.2 mol%. The major fatty acids (> 5%) were C16:0, C17:0 cyclo, C19:0 cyclo ω8c, C14:0 3OH/C16:1 iso I and C18:1ω7c/C18:1ω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and an unidentified aminolipid in major amounts. In addition, phosphatidylethanolamine, an unidentified lipid and several unidentified polar lipids were also found in moderate-to-trace amounts. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-YTH430T is proposed to represent a novel Mesorhizobium species, for which the name Mesorhizobium composti sp. nov. (type strain CC-YTH430T = BCRC 81024T = JCM 31762T) is proposed.
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xingda Rd, Taichung, 40227, Taiwan
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xingda Rd, Taichung, 40227, Taiwan
| | - Yu-Ting Hsieh
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xingda Rd, Taichung, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xingda Rd, Taichung, 40227, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan.
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22
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Ganapathy B, Yahya A, Ibrahim N. Bioremediation of palm oil mill effluent (POME) using indigenous Meyerozyma guilliermondii. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:11113-11125. [PMID: 30788704 DOI: 10.1007/s11356-019-04334-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Despite being a key Malaysian economic contributor, the oil palm industry generates a large quantity of environmental pollutant known as palm oil mill effluent (POME). Therefore, the need to remediate POME has drawn a mounting interest among environmental scientists. This study has pioneered the application of Meyerozyma guilliermondii with accession number (MH 374161) that was isolated indigenously in accessing its potential to degrade POME. This strain was able to treat POME in shake flask experiments under aerobic condition by utilising POME as a sole source of carbon. However, it has also been shown that the addition of suitable carbon and nitrogen sources has significantly improved the degradation potential of M. guilliermondii. The remediation of POME using this strain resulted in a substantial reduction of chemical oxygen demand (COD) of 72%, total nitrogen of 49.2% removal, ammonical nitrogen of 45.1% removal, total organic carbon of 46.6% removal, phosphate of 60.6% removal, and 92.4% removal of oil and grease after 7 days of treatment period. The strain also exhibited an extracellular lipase activity which promotes better wastewater treatment. Additionally, Fourier transform infrared spectroscopy (FTIR) and gas chromatography-mass spectrometry (GC-MS) analyses have specifically shown that M. guilliermondii strain can degrade hydrocarbons, fatty acids, and phenolic compounds present in the POME. Ultimately, this study has demonstrated that M. guilliermondii which was isolated indigenously exhibits an excellent degrading ability. Therefore, this strain is suitable to be employed in the remediation of POME, contributing to a safe discharge of the effluent into the environment.
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Affiliation(s)
- Birintha Ganapathy
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Johor, Malaysia
| | - Adibah Yahya
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Johor, Malaysia
| | - Norahim Ibrahim
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Johor, Malaysia.
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23
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Faucher M, Nouvel LX, Dordet-Frisoni E, Sagné E, Baranowski E, Hygonenq MC, Marenda MS, Tardy F, Citti C. Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer. PLoS Genet 2019; 15:e1007910. [PMID: 30668569 PMCID: PMC6358093 DOI: 10.1371/journal.pgen.1007910] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/01/2019] [Accepted: 12/19/2018] [Indexed: 11/18/2022] Open
Abstract
Horizontal Gene Transfer was long thought to be marginal in Mycoplasma a large group of wall-less bacteria often portrayed as minimal cells because of their reduced genomes (ca. 0.5 to 2.0 Mb) and their limited metabolic pathways. This view was recently challenged by the discovery of conjugative exchanges of large chromosomal fragments that equally affected all parts of the chromosome via an unconventional mechanism, so that the whole mycoplasma genome is potentially mobile. By combining next generation sequencing to classical mating and evolutionary experiments, the current study further explored the contribution and impact of this phenomenon on mycoplasma evolution and adaptation using the fluoroquinolone enrofloxacin (Enro), for selective pressure and the ruminant pathogen Mycoplasma agalactiae, as a model organism. For this purpose, we generated isogenic lineages that displayed different combination of spontaneous mutations in Enro target genes (gyrA, gyrB, parC and parE) in association to gradual level of resistance to Enro. We then tested whether these mutations can be acquired by a susceptible population via conjugative chromosomal transfer knowing that, in our model organism, the 4 target genes are scattered in three distinct and distant loci. Our data show that under antibiotic selective pressure, the time scale of the mutational pathway leading to high-level of Enro resistance can be readily compressed into a single conjugative step, in which several EnroR alleles were transferred from resistant to susceptible mycoplasma cells. In addition to acting as an accelerator for antimicrobial dissemination, mycoplasma chromosomal transfer reshuffled genomes beyond expectations and created a mosaic of resistant sub-populations with unpredicted and unrelated features. Our findings provide insights into the process that may drive evolution and adaptability of several pathogenic Mycoplasma spp. via an unconventional conjugative mechanism.
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Affiliation(s)
- Marion Faucher
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- UMR Mycoplasmoses of ruminants, ANSES, VetAgro Sup, University of Lyon, Lyon, France
| | | | | | - Eveline Sagné
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
| | | | | | - Marc-Serge Marenda
- Asia-Pacific Centre for Animal Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Florence Tardy
- UMR Mycoplasmoses of ruminants, ANSES, VetAgro Sup, University of Lyon, Lyon, France
| | - Christine Citti
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- * E-mail: (LXN); (CC)
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24
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Lin SY, Hameed A, Hsieh YT, Hsu YH, Lai WA, Young CC. Castellaniella fermenti sp. nov., isolated from a fermented meal. Int J Syst Evol Microbiol 2017; 68:52-57. [PMID: 29116034 DOI: 10.1099/ijsem.0.002436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a presumably novel bacterium, designated strain CC-YTH191T, isolated from a fermented meal in Taiwan. Cells of strain CC-YTH191T were Gram-stain-negative aerobic rods, which grew at 15-40 °C (optimal 25-30 °C), pH 6.0-9.0 (optimal 7.0) and 1-2 % (w/v) NaCl (optimal 1 %). On the basis of 16S rRNA gene sequence analysis, strain CC-YTH191T appeared to belong to the genus Castellaniella, and was closely related to Castellaniella hirudinis (96.7 % similarity), Castellaniella ginsengisoli (96.7 %) and Castellaniella caeni (96.0 %), while with other related species it shared <96.0 % similarity. The major cellular fatty acids of the isolate were C16 : 0, C17 : 0cyclo, C14 : 0 3OH/C16 : 1iso I and C18 : 1ω7c/C18 : 1ω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, three unidentified phospholipids, an unidentified aminolipid and an unidentified aminophospholpid. Putrescine was the predominant polyamine followed by spermidine. The DNA G+C content was 62.2 mol% and the predominant quinone system was ubiquinone 8 (Q-8). All these features confirmed the placement of the strain CC-YTH191T as a novel species within the genus Castellaniella, for which the name Castellaniella fermenti sp. nov. is proposed. The type strain is CC-YTH191T (=BCRC 81023T=JCM 31755T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yu-Ting Hsieh
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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25
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Lin SY, Hameed A, Hsu YH, Liu YC, Hung MH, Lai WA, Young CC. Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta). Int J Syst Evol Microbiol 2017; 68:133-140. [PMID: 29116039 DOI: 10.1099/ijsem.0.002471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic approach was used to characterize an aerobic, Gram-stain-negative, rod-shaped bacterium (designed as strain CC-MHH0539T) isolated from the chopped tuber of taro (Colocasia esculanta) in Taiwan. Strain CC-MHH0539T was able to grow at 15-30 °C (optimum, 25 °C), at pH 6.0-9.0 (optimum, 7.0) and with 0-1 % (w/v) NaCl. Strain CC-MHH0539T showed highest 16S rRNA gene sequence similarity to Sphingomonas laterariae LNB2T (96.8 %), Sphingobium boeckii 469T (96.5 %), Sphingomonas faucium E62-3T (96.4 %) and Sphingosinicella vermicomposti YC7378T (96.2 %) and <96.1 % similarity to other sphingomonads. Strain CC-MHH0539T was found to cluster mainly with the clade that accommodated members of the genus Sphingomonas. The dominant cellular fatty acids were C16 : 0, C16 : 1ω5c, C14 : 0 2-OH, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two sphingoglycolipids and two unidentified phospholipids were detected in strain CC-MHH0539T. The DNA G+C content was 69.5 mol%. The respiratory quinone system and predominant polyamine was ubiquinone 10 (Q-10) and sym-homospermidine, respectively, which is in line with Sphingomonas representatives. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits, strain CC-MHH0539T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas colocasiae sp. nov. is proposed. The type strain is CC-MHH0539T (=BCRC 80933T=JCM 31229T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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26
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Hydrogenophaga aquatica sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2017; 67:3716-3721. [DOI: 10.1099/ijsem.0.002146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Lin SY, Hameed A, Hsu YH, Liu YC, Lai WA, Young CC. Filimonas aquilariae sp. nov., isolated from agarwood chips. Int J Syst Evol Microbiol 2017; 67:3219-3225. [DOI: 10.1099/ijsem.0.002087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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28
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Lin SY, Hameed A, Liu YC, Hsu YH, Hung MH, Lai WA, Young CC. Ruficoccus amylovorans gen. nov., sp. nov., an amylolytic and nitrate-reducing diazotroph of the family Puniceicoccaceae. Int J Syst Evol Microbiol 2017; 67:956-962. [DOI: 10.1099/ijsem.0.001723] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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29
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Liu CT, Lin SY, Hameed A, Liu YC, Hsu YH, Wong WT, Tseng CH, Lur HS, Young CC. Oryzomicrobium terrae gen. nov., sp. nov., of the family Rhodocyclaceae isolated from paddy soil. Int J Syst Evol Microbiol 2017; 67:183-189. [DOI: 10.1099/ijsem.0.001565] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chi-Te Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
- Institute of Biotechnology, National Taiwan University, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wai-Tak Wong
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Ching-Han Tseng
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan, ROC
| | - Huu-Sheng Lur
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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30
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Lin SY, Hameed A, Chiu KY, Liu YC, Hsu YH, Lai WA, Young CC. Olivibacter composti sp. nov., isolated from compost collected at a greenhouse. Int J Syst Evol Microbiol 2017; 67:148-152. [PMID: 28211312 DOI: 10.1099/ijsem.0.001593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic approach was used to characterize a presumably novel bacterium, designated strain CC-KYC063T, isolated from a compost sample collected at a greenhouse facility within Taiwan. Strain CC-KYC063T was Gram-stain-negative and aerobic, able to grow at 15-37 °C (optimal 30 °C), at pH 7.0-9.0 (optimal pH 7.0) and with 0-2 % (w/v) NaCl. The 16S rRNA gene sequence of strain CC-KYC063T showed highest similarity to Olivibacter ginsengisoli Gsoil 060T (96.2 %) and Olivibacter terrae Jip13T (95.5 %). The DNA G+C content was 43.0 mol% and the predominant quinone system was menaquinone-7 (MK-7). The polyamine pattern showed a predominance of sym-homospermidine. The major fatty acids found in strain CC-KYC063T were iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω6c/C16 : 1ω7c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-KYC063T is considered to represent a novel species of the genus Olivibacter, for which the name Olivibacter composti sp. nov. is proposed. The type strain is CC-KYC063T (=BCRC 80939T=JCM 31198T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Kai-Yeh Chiu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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Lin SY, Hameed A, Liu YC, Hsu YH, Hsieh YT, Lai WA, Young CC. Humibacter aquilariae sp. nov., an actinobacterium isolated from an agarwood chip. Int J Syst Evol Microbiol 2016; 67:1468-1472. [PMID: 27983468 DOI: 10.1099/ijsem.0.001740] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a presumably novel bacterium, designated strain CC-YTH161T, isolated from an agarwood sample. Cells of strain CC-YTH161T were Gram-stain-positive aerobic rods, which grew at 20-40 °C, at pH 5.0-9.0 and with 0-5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain CC-YTH161T appeared to belong to the genus Humibacter, and was closely related to Humibacter antri D7-27T (96.6 % similarity) and Humibacter ginsengiterrae DCY60T (96.2 %). The DNA G+C content was 67.0 mol% and the predominant quinone system was menaquinones (MK) 11 and 12. The major cellular fatty acids of the isolate were C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and C18 : 1ω7c/C18 : 1ω6c. The polar lipid profile comprised predominant amounts of diphosphatidylglycerol followed by two unidentified co-migrating glycolipids and phosphatidylglycerol in significant amounts. The diagnostic diamino acid was 2,4-diaminobutyric acid. All these features confirmed the placement of strain CC-YTH161T within the genus Humibacter. On the basis of evidence from this study, strain CC-YTH161T is considered to represent a novel species of the genus Humibacter, for which the name Humibacter aquilariae sp. nov. is proposed. The type strain is CC-YTH161T (=BCRC 80936T=JCM 31199T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yu-Ting Hsieh
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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Lin SY, Hameed A, Liu YC, Hsu YH, Hsieh YT, Lai WA, Young CC. Chryseobacterium endophyticum sp. nov., isolated from a maize leaf. Int J Syst Evol Microbiol 2016; 67:570-575. [PMID: 27902278 DOI: 10.1099/ijsem.0.001656] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, yellow-pigmented, flexirubin-producing, rod-shaped and endophytic bacterium, designated strain CC-YTH209T, was isolated from a maize leaf and subjected to a taxonomic study. Strain CC-YTH209T was found to grow at 15-40 °C (optimal 30 °C), at pH 6.0-8.0 (optimal pH 7.0) and in the presence of 0-2 % (optimal 1 %) (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain CC-YTH209T appeared to belong to the genus Chryseobacterium within the class Flavobacteriia, and was closely related to Chryseobacterium rigui CJ16T (97.5 % similarity) and Chryseobacterium taeanense PHA3-4T (96.9 %). The level of DNA-DNA relatedness between strain CC-YTH209T and Chryseobacterium rigui CJ16T was 14.4 % (reciprocal, 13.0 %). Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-YTH209T within the clade that accommodated Chryseobacterium species. The DNA G+C content was 37.2 mol%. Strain CC-YTH209T contained menaquinone MK-6 as the predominant respiratory quinone and sym-homospermidine as the major polyamine. The major cellular fatty acids of the isolate were iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω6c/C16 : 1ω7c. The polar lipid profile comprised phosphatidylethanolamine and five aminolipids, three lipids, one glycolipid, one aminophospholipid and one phospholipid, which are presently uncharacterized. On the basis of evidence presented in this study, strain CC-YTH209T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium endophyticum sp. nov. is proposed. The type strain is CC-YTH209T (=BCRC 80938T=JCM 31226T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yu-Ting Hsieh
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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Hameed A, Lin SY, Lai WA, Shahina M, Liu YC, Hsu YH, Young CC. Idiomarina tyrosinivorans sp. nov., isolated from estuarine surface water. Int J Syst Evol Microbiol 2016; 66:5384-5391. [DOI: 10.1099/ijsem.0.001525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Mariyam Shahina
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
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Lin SY, Young CC, Hameed A, Liu YC, Hsu YH, Chung WC, Young LS. Actibacterium ureilyticum sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:2769-2773. [DOI: 10.1099/ijsem.0.001052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-Ching Chung
- Department of Biotechnology, College of Applied Arts and Sciences, National Formosa University, Yunlin, Taiwan, ROC
| | - Li-Sen Young
- Department of Biotechnology, College of Applied Arts and Sciences, National Formosa University, Yunlin, Taiwan, ROC
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Edlefsen PT, Birkmann A, Huang ML, Magaret CA, Kee JJ, Diem K, Goldner T, Timmler B, Stoelben S, Ruebsamen-Schaeff H, Zimmermann H, Warren T, Wald A, Corey L. No Evidence of Pritelivir Resistance Among Herpes Simplex Virus Type 2 Isolates After 4 Weeks of Daily Therapy. J Infect Dis 2016; 214:258-64. [PMID: 27056950 PMCID: PMC4918824 DOI: 10.1093/infdis/jiw129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/24/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Pritelivir is a novel helicase-primase inhibitor in clinical development for treatment of herpes simplex virus type 2 (HSV-2) infections. In preclinical work, resistance-mediating mutations were identified in the HSV-2 genome at 3 loci in the UL5 gene and 1 locus in UL52. METHODS To evaluate whether daily pritelivir treatment results in emergence of resistance-mediating mutations, we analyzed HSV-2 strains detected in genital swab specimens from trial participants who were randomly assigned to receive different dosages of pritelivir. We sequenced resistance regions from 87 participants' samples, the UL5 gene in 73 samples from 44 participants, and the UL52 gene in 71 samples from 43 participants. RESULTS We found no evidence that pritelivir induced known resistance-mediating mutations or for amino acid variation at other loci. In one participant's HSV-2 isolate, we found a previously unidentified mutation close to the putative resistance-mediating region in UL5 and subsequently determined in vitro susceptibility to pritelivir. We characterized mutations from 32 cultivated HSV-2 isolates previously found to be susceptible to pritelivir in vitro and identified several novel mutations that most likely reflect preexisting variation in circulating HSV-2. CONCLUSIONS This study demonstrates evidence of retained susceptibility of HSV-2 to pritelivir in immunocompetent persons following daily therapy for up to 28 days.
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Affiliation(s)
- Paul T Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Biostatistics
| | | | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Laboratory Medicine
| | - Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Jia Jin Kee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Biostatistics
| | - Kurt Diem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Laboratory Medicine
| | | | | | | | | | | | | | - Anna Wald
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Laboratory Medicine Department of Epidemiology Department of Medicine, University of Washington, Seattle
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Laboratory Medicine Department of Medicine, University of Washington, Seattle
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Lin SY, Liu YC, Hameed A, Hsu YH, Huang HI, Lai WA, Young CC. Azospirillum agricola sp. nov., a nitrogen-fixing species isolated from cultivated soil. Int J Syst Evol Microbiol 2016; 66:1453-1458. [DOI: 10.1099/ijsem.0.000904] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Hsin-I Huang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Shen FT, Young CC. Azospirillum soli sp. nov., a nitrogen-fixing species isolated from agricultural soil. Int J Syst Evol Microbiol 2015; 65:4601-4607. [DOI: 10.1099/ijsem.0.000618] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, rod or spiral-shaped diazotrophic bacterium (designated strain CC-LY788T), was isolated from agricultural soil in Taiwan. Strain CC-LY788T was able to grow at 25–40 °C, pH 6.0–8.0 and tolerated NaCl to 2.0% (w/v). Positive for nitrogen fixation with the activity recorded as 6.5 nmol ethylene h− 1. Strain CC-LY788T showed highest 16S rRNA gene sequence similarity to Azospirillum picis DSM 19922T (97.2%) and Azospirillum rugosum DSM 19657T (97.1%) and lower sequence similarities ( < 96.6%) to all other species of the genus Azospirillum. According to the DNA–DNA hybridization, the relatedness values of strain CC-LY788T with A. picis DSM 19922T and A. rugosum DSM 19657T were 51.1 ± 5.5% and 46.8 ± 2.1%, respectively. Strain CC-LY788T was positive for the rapid identification of the genus-specific primer set. The respiratory quinone system was ubiquinone (Q-10) and the DNA G+C content was 69.8 mol%. The major fatty acids found in strain CC-LY788T were C16 : 0, C18 : 1 2-OH, C14 : 0 3-OH/C16 : 1 iso I (summed feature 2), C16 : 1ω7c/C16 : 1ω6c (summed feature 3), C18 : 0 ante/C18 : 2ω6,9c (summed feature 5) and C18 : 1ω7c/C18 : 1ω6c (summed feature 8). Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY788T represents a novel species of the genus Azospirillum, for which the name Azospirillum soli sp. nov. is proposed. The type strain is CC-LY788T ( = BCRC 80569T = JCM 18820T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, , Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, , Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, , Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, , Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, , Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Fo-Ting Shen
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, , Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, , Taichung, Taiwan, ROC
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Lai WA, Lin SY, Hameed A, Hsu YH, Liu YC, Huang HR, Shen FT, Young CC. Leucobacter zeae sp. nov., isolated from the rhizosphere of maize (Zea mays L.). Int J Syst Evol Microbiol 2015; 65:4734-4742. [DOI: 10.1099/ijsem.0.000640] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel yellow-pigmented, aerobic, rod-shaped, non-motile bacterium, designated strain CC-MF41T, was isolated from rhizosphere soil of maize (Zea mays) collected in Wufeng District, Taichung, Taiwan. Strain CC-MF41T exhibited 16S rRNA gene sequence similarity of 97.5, 97.3, 97.2 and 97.1 % to Leucobacter chironomi MM2LBT (and ‘Leucobacter kyeonggiensis’ F3-P9 and ‘L. humi’ Re-6, the names of which have not been validly published), Leucobacter tardus K70/01T, L. komagatae IFO 15245T and ‘Leucobacter margaritiformis’ A23. However, CC-MF41T and ‘L. margaritiformis’ A23 formed a loosely bound phylogenetic lineage (with a low bootstrap value) associated with species of the genus Leucobacter. In DNA–DNA reassociation experiments, the relatedness of strain CC-MF41T to L. chironomi DSM 19883T was 57.1 % (reciprocal value 29.1 %). The DNA G+C content of strain CC-MF41T was 72.1 mol% and the cell-wall peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine, glutamic acid and threonine. The major menaquinone was MK-11 and the predominant fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipid profile of strain CC-MF41T contained major amounts of diphosphatidylglycerol followed by an unidentified glycolipid, phosphatidylglycerol and an unknown phospholipid. Based on its phylogenetic, phenotypic and chemotaxonomic distinctiveness, strain CC-MF41T represents a novel species of Leucobacter, for which the name Leucobacter zeae sp. nov. is proposed. The type strain is CC-MF41T ( = BCRC 80515T = LMG 27265T).
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Affiliation(s)
- Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Hsuan-Ru Huang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Fo-Ting Shen
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan ROC
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Hameed A, Pi HW, Lin SY, Lai WA, Young LS, Liu YC, Shen FT, Young CC. Direct Electrochemical Sensing of Phenazine-1-carboxylic Acid Secreted byPseudomonas chlororaphissubsp.aureofaciensBCRC 11057TUsing Disposable Screen-printed Carbon Electrode. ELECTROANAL 2015. [DOI: 10.1002/elan.201500278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Global Changes in Mycoplasma gallisepticum Phase-Variable Lipoprotein Gene vlhA Expression during In Vivo Infection of the Natural Chicken Host. Infect Immun 2015; 84:351-5. [PMID: 26553465 DOI: 10.1128/iai.01092-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/02/2015] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma gallisepticum is the primary etiologic agent of chronic respiratory disease in poultry, a disease largely affecting the respiratory tract and causing significant economic losses worldwide. Immunodominant proteins encoded by members of the variable lipoprotein and hemagglutinin (vlhA) gene family are thought to be important for mechanisms of M. gallisepticum-host interaction, pathogenesis, and immune evasion, but their exact role and the overall nature of their phase variation are unknown. To better understand these mechanisms, we assessed global transcriptomic vlhA gene expression directly from M. gallisepticum populations present on tracheal mucosae during a 7-day experimental infection in the natural chicken host. Here we report differences in both dominant and minor vlhA gene expression levels throughout the first week of infection and starting as early as day 1 postinfection, consistent with a functional role not dependent on adaptive immunity for driving phase variation. Notably, data indicated that, at given time points, specific vlhA genes were similarly dominant in multiple independent hosts, suggesting a nonstochastic temporal progression of dominant vlhA gene expression in the colonizing bacterial population. The dominant expression of a given vlhA gene was not dependent on the presence of 12-copy GAA trinucleotide repeats in the promoter region and did not revert to the predominate vlhA gene when no longer faced with host pressures. Overall, these data indicate that vlhA phase variation is dynamic throughout the earliest stages of infection and that the pattern of dominant vlhA expression may be nonrandom and regulated by previously unrecognized mechanisms.
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Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Yen WS, Young CC. Bacillus formosensis sp. nov., isolated from pesticide wastewater. Int J Syst Evol Microbiol 2015; 65:3800-3805. [PMID: 28875914 DOI: 10.1099/ijsem.0.000497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
A Gram-stain-positive, endospore-forming rod (designated strain CC-LY275T) was isolated from a pesticide wastewater sample. The isolate grew at a temperature 20-45 °C, at pH 7.0-8.0 and tolerated NaCl 6 % (w/v). The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus horneckiae (97.1 %) and Bacillus oceanisediminis (96.8 %), respectively. The G+C content of the genomic DNA was 37.9 mol%. Strain CC-LY275T was determined to possess iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0 as predominant fatty acids. The major polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Cell-wall peptidoglycan contained meso-diaminopimelic acid; menaquinone (MK-7) was the predominant respiratory quinone. According to the distinct phylogenetic, phenotypic and chemotaxonomic properties, the name Bacillus formosensis sp. nov. (type strain CC-LY275T = BCRC 80443T = JCM 18448T) is proposed.
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wen-Shao Yen
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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Lai WA, Hameed A, Lin SY, Hung MH, Hsu YH, Liu YC, Shahina M, Shen FT, Young CC. Paenibacillus medicaginis sp. nov. a chitinolytic endophyte isolated from a root nodule of alfalfa (Medicago sativa L.). Int J Syst Evol Microbiol 2015; 65:3853-3860. [PMID: 28875919 DOI: 10.1099/ijsem.0.000505] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-variable, short-rod-shaped, endospore-forming, strictly aerobic, non-motile, chitinolytic and endophytic bacterium, designated strain CC-Alfalfa-19T, exhibiting unusual bipolar appendages was isolated from a root nodule of alfalfa (Medicago sativa L.) in Taiwan and subjected to a polyphasic taxonomic study. Based on 16S rRNA gene sequence analysis, strain CC-Alfalfa-19T was found to be most closely related to Paenibacillus puldeungensis CAU 9324T (95.2 %), whereas other species of the genus Paenibacillus shared ≤ 95.0 % sequence similarity. The phylogenetic analysis revealed a distinct phyletic lineage established by strain CC-Alfalfa-19T with respect to other species of the genus Paenibacillus. Fatty acids comprised predominantly anteiso-C15 : 0, C16 : 0, anteiso-C17 : 0 and iso-C16 : 0. Menaquinone 7 (MK-7) was identified as the sole respiratory quinone and the genomic DNA G+C content was 42.7 mol%. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on the polyphasic taxonomic evidence that was in line with the genus Paenibacillus and additional distinguishing characteristics, strain CC-Alfalfa-19T is considered to represent a novel species, for which the name Paenibacillus medicaginis sp. nov. (type strain CC-Alfalfa-19T = BCRC 80441T = JCM 18446T) is proposed.
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Affiliation(s)
- Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Mariyan Shahina
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Fo-Ting Shen
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung City 402, Taiwan, ROC
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Lin SY, Hameed A, Liu YC, Wen CZ, Lai WA, Hsu YH, Young CC. Bacillus lycopersici sp. nov., isolated from a tomato plant (Solanum lycopersicum L.). Int J Syst Evol Microbiol 2015; 65:2085-2090. [DOI: 10.1099/ijs.0.000223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, endospore-forming bacterium (designated strain CC-Bw-5T) was isolated from chopped tomato stems. The isolate grew at 20–40 °C, pH 6.0–8.0 and tolerated 6 % (w/v) NaCl. The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus isabeliae (95.3 %) and Bacillus oleronius (95.3 %). The G+C content of the genomic DNA was 37.2 ± 3.6 mol%. Strain CC-Bw-5T was determined to possess C16 : 0, iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as predominant fatty acids. The polar lipid profile consisted of predominant amounts of diphosphatidylglycerol, and moderate-to-trace amounts of phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified phosphoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid; menaquinone (MK-7) was the predominant respiratory quinone. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-Bw-5T is proposed to represent a novel species within the genus Bacillus for which the name Bacillus lycopersici sp. nov. is proposed. The type strain is CC-Bw-5T ( = BCRC 80623T = JCM 19140T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Cheng-Zhe Wen
- Bachelor Program of Bio-Industry Management, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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Lin SY, Hameed A, Wen CZ, Liu YC, Hsu YH, Lai WA, Young CC. Lysobacter lycopersici sp. nov., isolated from tomato plant Solanum lycopersicum. Antonie van Leeuwenhoek 2015; 107:1261-70. [PMID: 25750064 DOI: 10.1007/s10482-015-0419-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/26/2015] [Indexed: 11/28/2022]
Abstract
A Gram-stain negative, aerobic, rod-shaped and non-spore-forming bacterium, CC-Bw-6(T) was isolated from chopped tomato stems. Analysis of the 16S rRNA gene sequence of the strain CC-Bw-6(T) showed its affiliation with the genus Lysobacter within the class Gammaproteobacteria. Strain CC-Bw-6(T) was found to be most closely related to Lysobacter panaciterrae KCTC 12601(T) (97.0%) and Lysobacter daecheongensis KCTC 12600(T) (96.8%), and showed lower similarity (<96.5%) to other Lysobacter species. DNA-DNA relatedness between strain CC-Bw-6(T) and L. panaciterrae KCTC 12601(T) was 10.8%, the G+C content of the genomic DNA is 69.9 mol%. Strain CC-Bw-6(T) was determined to possess C(11:0) iso, C(11:0) iso 3OH, C(14:0) iso, C(15:0) anteiso, C(15:1) ω5c, C(16:1) ω5c, C(16:0), C(15:0) iso, C(16:0) iso, C(17:0) iso and C(16:0) 10-methyl/C(17:1) iso ω9c as predominant fatty acids. The major polar lipid profile consists of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipids. The predominant polyamine is spermidine, and ubiquinone-8 is the predominant respiratory quinone. Analysis of phenotypic, geno- and phylogenetic characteristics revealed a distinct taxonomic position of strain CC-Bw-6(T) with respect to other Lysobacter species. Based on the phylogenetic, chemotaxonomic and phenotypic data presented here, we propose a novel species with the name Lysobacter lycopersici sp. nov. The type strain is CC-Bw-6(T) (=BCRC 80612(T) = JCM 19164(T)).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung, 402, Taiwan
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Lin SY, Hameed A, Hung MH, Liu YC, Hsu YH, Young LS, Young CC. Pseudomonas matsuisoli sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2015; 65:902-909. [DOI: 10.1099/ijs.0.000035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, rod-shaped and polar-flagellated bacterium, designated strain CC-MHH0089T, was isolated from a soil sample taken on Matsu Island (Taiwan). Strain CC-MHH0089T grew at 15–30 °C and pH 5.0–10.0 and tolerated ≤8 % (w/v) NaCl. 16S rRNA gene sequence analysis showed high pairwise sequence similarity to
Pseudomonas azotifigens
6H33bT (97.3 %) and
Pseudomonas balearica
SP1402T (96.7 %) and lower sequence similarity to other strains (<96.0 %). In DNA–DNA reassociation experiments, the relatedness of strain CC-MHH0089T to
P. azotifigens
JCM 12708T was 38.3 % (reciprocal value 19.5 %). Evolutionary trees reconstructed on the basis of 16S rRNA, gyrB and rpoB gene sequences revealed a varying phylogenetic neighbourhood of strain CC-MHH0089T with regard to the most closely related type strains. The predominant quinone system was ubiquinone 9 (Q-9) and the DNA G+C content was 63.6 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0, C19 : 0 cyclo ω8c and summed features 2 (C14 : 0 3-OH/iso-C16 : 1 I), 3 (C16 : 1ω7c/C16 : 1ω6c) and 8 (C18 : 1ω7c/C18 : 1ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. According to its distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-MHH0089T is proposed to represent a novel species within the genus
Pseudomonas
, for which the name Pseudomonas matsuisoli sp. nov. is proposed. The type strain is CC-MHH0089T ( = BCRC 80771T = JCM 30078T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Li-Sen Young
- Department of Biotechnology, College of Applied Arts and Sciences, National Formosa University, Yunlin, Taiwan
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
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Hanstruepera neustonica gen. nov., sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from estuarine water, and emendation of Sediminibacter
furfurosus Khan et al. 2007 emend. Kwon et al. 2014, Mangrovimonas yunxiaonensis Li et al. 2013, Antarcticimonas flava Yang et al. 2009 and Hoppeia youngheungensis Kwon et al. 2014. Int J Syst Evol Microbiol 2015; 65:336-345. [DOI: 10.1099/ijs.0.066852-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A Gram-staining-negative, strictly aerobic, yellowish-orange, flexirubin-positive, rod-shaped, non-flagellated, non-spore-forming and non-gliding marine bacterium, designated strain CC-PY-50T, was isolated from estuarine water off Pingtung, Taiwan. The strain produced zeaxanthin as a major carotenoid pigment, and showed highest pairwise 16S rRNA gene sequence similarity to
Bizionia hallyeonensis
T-y7T (93.9 %) followed by
Corallibacter vietnamensis
KMM 6217T (93.8 %),
Geojedonia litorea
YCS-16T (93.7 %) and other members of the family
Flavobacteriaceae
(<93.7 %). Strain CC-PY-50T established a distinct phyletic lineage associated with
Mangrovimonas yunxiaonensis
LYYY01T (93.1 % sequence similarity) with poor bootstrap support during neighbour-joining and maximum-likelihood phylogenetic analyses (37 % for each). The polar lipid profile of strain CC-PY-50T was determined to accommodate large numbers of unknown lipids including major amounts of three unidentified aminolipids and two unidentified lipids, and moderate amounts of an unidentified phospholipid, an unidentified glycolipid and an unidentified lipid. In addition, phosphatidylethanolamine was also detected in significant amounts. The major (>5 % of total) fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, C16 : 0 and C16 : 1ω6c and/or C16 : 1ω7c. The DNA G+C content was 37.1 mol% and menaquinone-6 (MK-6) was the sole respiratory quinone. Based on the phylogenetic evidence and several distinguishing phenotypic and chemotaxonomic features, strain CC-PY-50T is proposed to represent a novel genus and species of the family
Flavobacteriaceae
, for which the name Hanstruepera neustonica gen. nov., sp. nov. is proposed. The type strain of the type species Hanstruepera neustonica gen. nov., sp. nov. is CC-PY-50T ( = JCM 19743T = BCRC 80747T). Emended descriptions of the species
Sediminibacter furfurosus
,
Mangrovimonas yunxiaonensis
,
Antarcticimonas flava
and
Hoppeia youngheungensis
are also proposed.
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Hameed A, Shahina M, Lai WA, Lin SY, Young LS, Liu YC, Hsu YH, Young CC. Oricola cellulosilytica gen. nov., sp. nov., a cellulose-degrading bacterium of the family Phyllobacteriaceae isolated from surface seashore water, and emended descriptions of Mesorhizobium loti and Phyllobacterium myrsinacearum. Antonie van Leeuwenhoek 2015; 107:759-71. [PMID: 25566955 DOI: 10.1007/s10482-014-0370-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
Abstract
A Gram-stain negative, strictly aerobic, rod-shaped, non-spore-forming, motile cellulolytic bacterium, designated strain CC-AMH-0(T), was isolated from surface seashore water of Hualien, Taiwan and subjected to polyphasic taxonomy. Strain CC-AMH-0(T) exhibited enzymatic saccharification of cellulose and active growth particularly during log-phase under nutrient-limited conditions, whereas enhanced saccharification was found in the declining growth phase under copiotrophic conditions. The novel strain shared high pairwise 16S rRNA gene sequence similarities to Mesorhizobium loti USDA 3471(T) (96.2 %), Phyllobacterium myrsinacearum IAM 13584(T) (95.9 %), Hoeflea marina LMG 128(T) (94.0 %) and other Phyllobacteriaceae members. However, phylogenetic analyses based on 16S rRNA, atpD and recA gene sequences clearly distinguished strain CC-AMH-0(T) from other representatives of related genera. In addition, strain CC-AMH-0(T) was distinguished from the above mentioned species by significantly lacking phosphatidylcholine besides accommodating major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine and sulfoquinovosyldiacylglycerol; moderate amounts of phosphatidylethanolamine and trace amounts of an unidentified phospholipid, an unidentified aminolipid and an unidentified phosphoglycolipid. Strain CC-AMH-0(T) possessed C18:1 ω7c and/or C18:1 ω6c (summed feature 8) as predominant fatty acids, 63.3 mol% DNA G+C content and ubiquinone-10 (Q-10) as the sole respiratory quinone. On the basis of polyphasic taxonomic evidences, strain CC-AMH-0(T) is proposed to represent a novel genus and species of the family Phyllobacteriaceae, for which the name Oricola cellulosilytica gen. nov., sp. nov. is proposed. The type strain of the type species is CC-AMH-0(T) (=JCM 19534(T) =BCRC 80694(T)). Emended descriptions of M. loti and P. myrsinacearum are also proposed.
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Affiliation(s)
- Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan
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Lin SY, Hung MH, Hameed A, Liu YC, Hsu YH, Wen CZ, Arun AB, Busse HJ, Glaeser SP, Kämpfer P, Young CC. Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant. Antonie van Leeuwenhoek 2015; 107:773-84. [PMID: 25555455 DOI: 10.1007/s10482-014-0371-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
Abstract
A novel, Gram-staining-negative, rod-shaped, aerobic and motile bacterium, designated strain CC-SKC2(T), was isolated from the root tumor of a green bell pepper (Capsicum annuum var. grossum) plant in Taiwan. Cells were positive for oxidase and catalase activities and exhibited growth at 25-37 °C, pH 4.0-9.0 and tolerated NaCl concentrations up to 4.0 % (w/v). Strain CC-SKC2(T) is able to trigger nodulation in soybean (Glycine max Merr.), but not in Capsicum annuum var. grossum, red bean (Vigna angularis), sesbania (Sesbania roxburghii Merr.) or alfalfa (Medicago varia Martin.). The novel strain shared highest 16S rRNA gene sequence similarity to Rhizobium rhizoryzae KCTC 23652(T) and Rhizobium straminoryzae CC-LY845(T) (both 97.5 %) followed by Rhizobium lemnae L6-16(T) (97.3 %), Rhizobium pseudoryzae KCTC 23294(T) (97.1 %), and Rhizobium paknamense NBRC 109338(T) (97.0 %), whereas other Rhizobium species shared <96.7 % similarity. The DNA-DNA relatedness values of strain CC-SKC2(T) with R. rhizoryzae KCTC 23652(T), R. pseudoryzae KCTC 23294(T) and R. paknamense NBRC 109338(T) were 11.4, 17.2 and 17.0 %, respectively (reciprocal values were 11.1, 28.3 and 24.0 %, respectively). Phylogenetic analysis based on 16S rRNA, atpD and recA genes revealed a distinct taxonomic position attained by strain CC-SKC2(T) with respect to other Rhizobium species. The major fatty acids in strain CC-SKC2(T) were C16:0, C19:0 cyclo ω8c, C14:0 3-OH and/or C16:1 iso I and C18:1 ω7c and/or C18:1 ω6c. The polyamine pattern showed predominance of spermidine and moderate amounts of sym-homospermidine. The predominant quinone system was ubiquinone (Q-10) and the DNA G+C content was 60.5 mol%. On the basis of polyphasic taxonomic evidence presented here, strain CC-SKC2(T) is proposed to represent a novel species within the genus Rhizobium, for which the name Rhizobium capsici sp. nov. is proposed. The type strain is CC-SKC2(T) (=BCRC 80699(T) = JCM 19535(T)).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung, 402, Taiwan
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Description of Algoriphagus taiwanensis sp. nov., a xylanolytic bacterium isolated from surface seawater, and emended descriptions of Algoriphagus mannitolivorans, Algoriphagus olei, Algoriphagus aquatilis and Algoriphagus ratkowskyi. Antonie van Leeuwenhoek 2014; 106:1031-40. [DOI: 10.1007/s10482-014-0272-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/26/2014] [Indexed: 10/24/2022]
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Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC. Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014. Int J Syst Evol Microbiol 2014; 64:3897-3903. [PMID: 25180090 DOI: 10.1099/ijs.0.066142-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, rod- or oval-shaped, motile, non-spore-forming bacterium, designated strain CC-AMHB-3(T), was isolated from coastal surface seawater off Hualien, Taiwan. The novel strain showed high pairwise 16S rRNA gene sequence similarities to Ruegeria mobilis NBRC 101030(T) (96.5%), Ruegeria scottomollicae LMG 24367(T) (96.4%), Phaeobacter aquaemixtae SSK6-1(T) (96.2%), Phaeobacter daeponensis TF-218(T) (96.2%), Cribrihabitans marinus CZ-AM5(T) (96.1%) and other species of the family Rhodobacteraceae (≤ 95.9%). However, strain CC-AMHB-3(T) formed a distinct phyletic lineage associated with C. marinus CZ-AM5(T) during phylogenetic analyses. The polar lipid profile of strain CC-AMHB-3(T) included major amounts of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine; moderate amounts of phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid; and trace amounts of an unidentified lipid and an unidentified phospholipid, which was qualitatively almost in line with that of C. marinus CZ-AM5(T) but remarkably distinct as compared with the type species of the genera Ruegeria (Ruegeria atlantica JCM 21234(T)) and Phaeobacter (Phaeobacter gallaeciensis JCM 21319(T)). In line with the fatty acid profile of C. marinus CZ-AM5(T), the major (>5% of total) fatty acids of strain CC-AMHB-3(T) were C(18:1)ω7c and/or C(18:1)ω6c (summed feature 8), 11-methyl C(18:1)ω7c and C(16:0). The DNA G+C content was 66.7 mol%. Ubiquinone-10 (Q-10) was the sole respiratory quinone. Thus, based on the results of the polyphasic study presented here, strain CC-AMHB-3(T) is considered to represent a novel species of the genus Cribrihabitans, for which the name Cribrihabitans neustonicus sp. nov. is proposed; the type strain is CC-AMHB-3(T) ( = JCM 19537(T) =BCRC 80695(T)). In addition, an emended description of the genus Cribrihabitans is also proposed.
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Affiliation(s)
- Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
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