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Xu Y, Chen L, Yang L, Pan L, Zheng M, Shen N, Yang D. Chitinibacter mangrovi sp. nov., a Novel Chitin-Degrading Bacterium Isolated from Mangrove Sediment. Curr Microbiol 2025; 82:299. [PMID: 40397172 DOI: 10.1007/s00284-025-04281-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Accepted: 05/05/2025] [Indexed: 05/22/2025]
Abstract
A bacterial strain with chitin-degrading ability, designated FCG-7T, was isolated from a mangrove sediment in Guangxi, PR China, and characterized using a polyphasic taxonomy approach. Cells of strain FCG-7T were Gram-stain-negative, aerobic, rod-shaped and formed milky-white colonies. Growth occurred at 15-37 °C (optimum, 30 °C), at pH 7-9 (optimum, pH 7-8) and with 0-1% NaCl (optimum, 0.5%). The major isoprenoid quinone was ubiquinone-8 (Q-8). The predominant fatty acids were summed feature 3 (C16:1 ω6c and/or C16:1ω7c) and C16:0. The polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, five unidentified phospholipids and two unidentified aminophospholipids. The G + C content of the genomic DNA was 53.8%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FCG-7T belonged to the genus Chitinibacter and was closely related to Chitinibacter bivalviorum 2T18T (similarity 99.29%) and Chitinibacter fontanus STM-7T (similarity 98.85%). The average nucleotide identity (ANI) values of FCG-7T and the above two type strains were 81.4-83.1%, and the digital DNA-DNA hybridization (dDDH) values were 22.9-24.3%. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, strain FCG-7T represents a novel species of the genus Chitinibacter, for which the name Chitinibacter mangrovi sp. nov. is proposed. The type strain is FCG-7T (= KCTC 8742T = GDMCC 1.4868T).
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Affiliation(s)
- Yong Xu
- National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Academy of Sciences, Nanning, 530007, China
- Guangxi PFomic Information Technology Co., Ltd., Nanning, 530006, China
| | - Longzhi Chen
- National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Academy of Sciences, Nanning, 530007, China
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Liyan Yang
- National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Lixia Pan
- National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Mengting Zheng
- National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Naikun Shen
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, 530008, China
| | - Dengfeng Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, No.98 Daling Road, Nanning, 530007, China.
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Liu M, Sun C, Zhou Q, Xu P, Wang A, Zheng X, Liu B. Supplementation of Yupingfeng polysaccharides in low fishmeal diets enhances intestinal health through influencing the intestinal barrier, immunity, and microflora in Macrobrachium rosenbergii. Front Immunol 2024; 15:1480897. [PMID: 39660141 PMCID: PMC11628508 DOI: 10.3389/fimmu.2024.1480897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 11/04/2024] [Indexed: 12/12/2024] Open
Abstract
Introduction This study aimed to investigate the effects of a low-fishmeal diet (LF, substituting soybean meal for 40% fish meal) and the supplementation of 500 mg/kg and 1000 mg/kg Yu Ping Feng (YPF) polysaccharides on the growth performance, antioxidant enzyme activities, intestinal ultrastructure, non-specific immunity, and microbiota of Macrobrachium rosenbergii. Methods The study involved the administration of different diets to M. rosenbergii, including a control diet, a low-fishmeal diet (LF), and LF diets supplemented with 500 mg/kg and 1000 mg/kg YPF polysaccharides. Growth performance, antioxidant enzyme activities, intestinal ultrastructure, non-specific immunity, and microbiota were assessed. Results The LF diet significantly reduced growth performance parameters compared to the control group. However, YPF supplementation notably improved these parameters, with the greatest improvement observed at a 1000 mg/kg dosage. Antioxidant enzyme activities (SOD, GSH-PX) were diminished in the LF group, accompanied by elevated MDA levels, whereas YPF supplementation restored these activities and reduced MDA levels. Ultrastructural analysis revealed that the LF diet caused intestinal villi detachment and peritrophic matrix (PM) shedding, which were alleviated by YPF. Gene expression related to PM formation (GS, CHS, EcPT) was downregulated in the LF group but significantly upregulated in the 1000P group. Non-specific immune gene expressions (IMD, Relish, IκBα) and enzyme activities (NO, iNOS) were suppressed in the LF group but enhanced by YPF supplementation. Microbial community analysis showed reduced diversity and altered composition in the LF group, with increased Proteobacteria and decreased Firmicutes, which were partially restored by YPF. Correlation analysis revealed that Lactobacillus and Chitinibacter play pivotal roles in regulating intestinal health. Lactobacillus exhibited a positive relationship with the intestinal PM and immune-related indicators, whereas Chitinibacter was negatively associated with these factors. Discussion These results highlight the adverse impacts of a low-fishmeal diet on the intestinal health of M. rosenbergii and demonstrate the beneficial effects of YPF polysaccharides in alleviating these negative consequences through various mechanisms, including improved growth performance, enhanced antioxidant enzyme activities, restored intestinal ultrastructure, and modulated immune responses. The findings suggest that YPF supplementation could be a valuable strategy for mitigating the negative effects of low-fishmeal diets in aaquaculture.
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Affiliation(s)
- Mingyang Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Cunxin Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Qunlan Zhou
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Aimin Wang
- College of Marine and Biology Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Xiaochuan Zheng
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Bo Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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Liou JS, Zhang WL, Hsu LW, Chen CC, Wang YT, Mori K, Hidaka K, Hamada M, Huang L, Watanabe K, Huang CH. Faecalibacterium taiwanense sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2024; 74:006413. [PMID: 38848117 PMCID: PMC11261667 DOI: 10.1099/ijsem.0.006413] [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: 02/23/2024] [Accepted: 05/26/2024] [Indexed: 06/09/2024] Open
Abstract
Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21T(98.3-98.1 % and 79.0-79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8-97.9 % and 70.9-80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1-97.3 % and 80.3-80.5 %), Faecalibacterium longum CM04-06T(97.8-98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3-97.4 % and 82.7-82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA-DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T and its closest neighbours were below the species delineation thresholds of 77.6-85.1 %, 71.4-85.2 % and 28.3-30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C18 : 1 ω7c and lacked C15 : 0 and C17 : 1 ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78T (=BCRC 81397T=NBRC 116372T).
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Affiliation(s)
- Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Wei-Ling Zhang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Li-Wen Hsu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 11561, Taiwan, ROC
| | - Koji Mori
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kohei Hidaka
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec 3, Keelung Rd., Taipei 10673, Taiwan, ROC
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
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Wang YT, Lin YC, Hsieh YH, Lin YT, Hamada M, Chen CC, Liou JS, Lee AY, Zhang WL, Chen YT, Huang CH. Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk. Pathogens 2024; 13:343. [PMID: 38668298 PMCID: PMC11055063 DOI: 10.3390/pathogens13040343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
A novel coagulase-negative Staphylococcus strain (H164T) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164T strain is a member of the genus Staphylococcus. We used multilocus sequence analysis (MLSA) and phylogenomic analyses to demonstrate that the novel strain was closely related to Staphylococcus gallinarum, Staphylococcus nepalensis, Staphylococcus cohnii, and Staphylococcus urealyuticus. The average nucleotide identity and digital DNA-DNA hybridization values between H164T and its closest relatives were <95% and <70%, respectively. The H164T strain could also be distinguished from its closest relatives by the fermentation of d-fructose, d-maltose, d-trehalose, and d-mannitol, as well as by the activities of α-glucosidase and alkaline phosphatase. The major cellular fatty acids were C15:0 iso and C15:0 anteiso, and the predominant menaquinones were MK-7 and MK-8, respectively. The major cellular fatty acids and predominant menaquinones were C15:0 iso and C15:0 anteiso and MK-7 and MK-8, respectively. In conclusion, this strain represents a novel species, named Staphylococcus hsinchuensis sp. nov., with the type strain H164T (=BCRC 81404T = NBRC 116174T).
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Affiliation(s)
- Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 115021, Taiwan;
| | - Yu-Chun Lin
- Taiwan Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (Y.-C.L.)
- Fisheries Research Institute, Ministry of Agriculture, Keelung 202008, Taiwan
| | - Yi-Huei Hsieh
- Taiwan Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (Y.-C.L.)
| | - Yu-Tzu Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404328, Taiwan;
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Chiba, Japan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Ai-Yun Lee
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Wei-Ling Zhang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Yung-Tsung Chen
- Department of Food Science, National Taiwan Ocean University, Keelung 202301, Taiwan;
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
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Das S, Chowdhury C, Kumar SP, Roy D, Gosavi SW, Sen R. Microbial production of N-acetyl-D-glucosamine (GlcNAc) for versatile applications: Biotechnological strategies for green process development. Carbohydr Res 2024; 536:109039. [PMID: 38277719 DOI: 10.1016/j.carres.2024.109039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 12/07/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
N-acetyl-d-glucosamine (GlcNAc) is a commercially important amino sugar for its wide range of applications in pharmaceutical, food, cosmetics and biofuel industries. In nature, GlcNAc is polymerised into chitin biopolymer, which is one of the major constituents of fungal cell wall and outer shells of crustaceans. Sea food processing industries generate a large volume of chitin as biopolymeric waste. Because of its high abundance, chitinaceous shellfish wastes have been exploited as one of the major precursor substrates of GlcNAc production, both in chemical and enzymatic means. Nevertheless, the current process of GlcNAc extraction from shellfish wastes generates poor turnover and attracts environmental hazards. Moreover, GlcNAc isolated from shellfish could not be prescribed to certain groups of people because of the allergic nature of shell components. Therefore, an alternative route of GlcNAc production is advocated. With the advancement of metabolic construction and synthetic biology, microbial synthesis of GlcNAc is gaining much attention nowadays. Several new and cutting-edge technologies like substrate co-utilization strategy, promoter engineering, and CRISPR interference system were proposed in this fascinating area. The study would put forward the potential application of microbial engineering in the production of important pharmaceuticals. Very recently, autotrophic fermentation of GlcNAc synthesis has been proposed. The metabolic engineering approaches would offer great promise to mitigate the issues of low yield and high production cost, which are major challenges in microbial bio-processes industries. Further process optimization, optimising metabolic flux, and efficient recovery of GlcNAc from culture broth, should be investigated in order to achieve a high product titer. The current study presents a comprehensive review on microbe-based eco-friendly green methods that would pave the way towards the development of future research directions in this field for the designing of a cost-effective fermentation process on an industrial setup.
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Affiliation(s)
- Sancharini Das
- Department of Environmental Science, Savitribai Phule Pune University, Pune, MH, 411007, India; Department of Biotechnology, Indian Institute of Technology Kharagpur, WB, 721302, India.
| | - Chiranjit Chowdhury
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH, 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - S Pavan Kumar
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, TN, 600 036, India
| | - Debasis Roy
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, WB, 721302, India
| | - Suresh W Gosavi
- Department of Environmental Science, Savitribai Phule Pune University, Pune, MH, 411007, India
| | - Ramkrishna Sen
- Department of Biotechnology, Indian Institute of Technology Kharagpur, WB, 721302, India
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Deng H, Li Q, Li M, Sun L, Li B, Wang Y, Wu QL, Zeng J. Epiphytic microorganisms of submerged macrophytes effectively contribute to nitrogen removal. ENVIRONMENTAL RESEARCH 2024; 242:117754. [PMID: 38016497 DOI: 10.1016/j.envres.2023.117754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023]
Abstract
Submerged macrophytes play important roles in nutrient cycling and are widely used in ecological restoration to alleviate eutrophication and improve water quality in lakes. Epiphytic microbial communities on leaves of submerged macrophytes might promote nitrogen cycling, but the mechanisms and quantification of their contributions remain unclear. Here, four types of field zones with different nutrient levels and submerged macrophytes, eutrophic + Vallisneria natans (EV), eutrophic + V. natans + Hydrilla verticillata, mesotrophic + V. natans + H. verticillata, and eutrophic without macrophytes were selected to investigate the microbial communities that involved in nitrification and denitrification. The alpha diversity of bacterial community was higher in the phyllosphere than in the water, and that of H. verticillata was higher compared to V. natans. Bacterial community structures differed significantly between the four zones. The highest relative abundance of dominant bacterioplankton genera involved in nitrification and denitrification was observed in the EV zone. Similarly, the alpha diversity of the epiphytic ammonia-oxidizing archaea and nosZI-type denitrifiers were highest in the EV zone. Consist with the diversity patterns, the potential denitrification rates were higher in the phyllosphere than those in the water. Higher potential denitrification rates in the phyllosphere were also found in H. verticillata than those in V. natans. Anammox was not detected in all samples. Nutrient loads, especially nitrogen concentrations were important factors influencing potential nitrification, denitrification rates, and bacterial communities, especially for the epiphytic nosZI-type taxa. Overall, we observed that the phyllosphere harbors more microbes and promotes higher denitrification rates compared to water, and epiphytic bacterial communities are shaped by nitrogen nutrients and macrophyte species, indicating that epiphytic microorganisms of submerged macrophytes can effectively contribute to the N removal in shallow lakes.
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Affiliation(s)
- Hongyang Deng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qisheng Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengyuan Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Lijie Sun
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210024, China
| | - Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yujing Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang, 332899, China.
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Lee AY, Chen CH, Liou JS, Lin YC, Hamada M, Wang YT, Peng LL, Chang SC, Chen CC, Lin CF, Huang L, Huang CH. Micrococcus porci sp. nov., Isolated from Feces of Black Pig ( Sus scrofa). Life (Basel) 2022; 12:1749. [PMID: 36362904 PMCID: PMC9697426 DOI: 10.3390/life12111749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
An aerobic bacterium, designated as strain KD337-16T, was isolated from the fecal samples of a black pig. It exhibited spherical, non-motile and non−spore-forming, Gram-positive cells. KD337-16T was identified as a member of the genus Micrococcus through 16S rRNA gene sequencing, and its closest relatives were found to be Micrococcus endophyticus YIM 56238T (99.5% similarity), Micrococcus luteus NCTC 2665T (99.1%), Micrococcus yunnanensis YIM 65004T (99.1%), Micrococcus aloeverae AE-6T (99.1%), Micrococcus antarcticus T2T (98.9%), and Micrococcus flavus LW4T (98.7%). Phylogenomic trees were constructed, and strain KD337-16T was found to form its own cluster as an independent lineage of M. flavus LW4T. Between KD337-16T and its close relatives, the average nucleotide identity, average amino acid identity, and digital DNA−DNA hybridization were below the respective species delineation thresholds at 82.1−86.6%, 78.1−86.1%, and 24.4−34.9%. The major cellular fatty acids and polar lipids were anteiso-C15:0 and iso-C15:0, and DPG and PG, respectively. The predominant menaquinone was MK-8(H2). Taken together, the results indicate that strain KD337-16T is a novel species of the genus Micrococcus, for which the name Micrococcus porci sp. nov. is proposed. The type strain is KD337-16T (=BCRC 81318T = NBRC 115578T).
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Affiliation(s)
- Ai-Yun Lee
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 11561, Taiwan
| | - Lin-Liang Peng
- Kaohsiung Animal Propagation Station, COA-LRI, Pingtung 91247, Taiwan
| | - Shen-Chang Chang
- Kaohsiung Animal Propagation Station, COA-LRI, Pingtung 91247, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Chuen-Fu Lin
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
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Chen S, Rudra B, Gupta RS. Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov. Syst Appl Microbiol 2021; 44:126251. [PMID: 34600238 DOI: 10.1016/j.syapm.2021.126251] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/22/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
The order Neisseriales contains 37 genera harboring 122 species with validly published names, which are placed into two families, Neisseriaceae and Chromobacteriaceae. Genome sequences are now available for 35 of the 37 Neisseriales genera for reliably determining their evolutionary relationships and taxonomy. We report here comprehensive phylogenomic and comparative analyses on protein sequences from 110 Neisseriales genomes plus 3 Chitinimonas genomes using multiple approaches. In a phylogenomic tree based on 596 core proteins, Neisseriales species formed 5 strongly supported clades. In addition to the clades for Neisseriaceae and Chromobacteriaceae families, three novel species clades designated as the "Chitinibacteraceae", "Aquaspirillaceae", and "Leeiaceae" were observed. The genus Chitinimonas grouped reliably with members of the "Chitinibacteraceae" clade. The major clades within the order Neisseriales can also be distinguished based on average amino acid identity analysis. In parallel, our comparative genomic studies have identified 30 conserved signature indels (CSIs) that are specific for members of the order Neisseriales or its five main clades. One of these CSIs is uniquely shared by all Neisseriales, whereas 8, 4, 9, 3 and 5 CSIs are distinctive characteristics of the Neisseriaceae, Chromobacteriaceae, "Chitinibacteraceae", "Aquaspirillaceae" and "Leeiaceae" clades, respectively. Based on the strong phylogenetic and molecular evidence presented here, we are proposing that the three newly identified clades should be recognized as novel families (Chitinibacteraceae fam. nov., Aquaspirillaceae fam. nov. and Leeiaceae fam. nov.) within the order Neisseriales. In addition, we are also emending descriptions of the families Neisseriaceae and Chromobacteriaceae regarding their constituent genera and other distinguishing characteristics.
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Affiliation(s)
- Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
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9
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Choi JW, Lee JY, Hyun DW, Lee JY, Kim PS, Han JE, Jeong YS, Lee SY, Sung H, Tak EJ, Kim HS, Bae JW. Chitinibacter bivalviorum sp. nov., isolated from the gut of the freshwater mussel Anodonta arcaeformis. Int J Syst Evol Microbiol 2021; 71. [PMID: 34296988 DOI: 10.1099/ijsem.0.004909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, rod-shaped bacterium with a single polar flagellum, designated strain 2T18T, was isolated from the gut of the freshwater mussel Anodonta arcaeformis collected in the Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter. Strain 2T18T formed a monophyletic clade with Chitinibacter fontanus KCTC 42982T, C. tainanensis KACC 11706T and C. alvei KCTC 23839T, with sequence similarities of 98.5, 98.4 and 95.9 %, respectively. Strain 2T18T exhibited optimal growth at 30 °C, at pH 8 and with 0.5 % (w/v) NaCl. The major isoprenoid quinone was ubiquinone-8 (Q-8). The predominant fatty acids were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and two unidentified aminophospholipids. The G+C content of the genomic DNA was 50.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strains 2T18T and C. fontanus KCTC 42982T were below the thresholds used for the delineation of a novel species. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, strain 2T18T represents a novel species of the genus Chitinibacter, for which the name Chitinibacter bivalviorum sp. nov. is proposed. The type strain is 2T18T (=KCTC 72821T=CCUG 74764T).
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Affiliation(s)
- Jee-Won Choi
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Jae-Yun Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - June-Young Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Jeong Eun Han
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Yun-Seok Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - So-Yeon Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Hojun Sung
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Euon Jung Tak
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Hyun Sik Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
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10
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Huang CH, Chen CC, Lin YC, Chen CH, Lee AY, Liou JS, Gu CT, Huang L. The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa. Microorganisms 2021; 9:microorganisms9081570. [PMID: 34442649 PMCID: PMC8399863 DOI: 10.3390/microorganisms9081570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022] Open
Abstract
The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
- Correspondence:
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Chun-Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China;
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
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11
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Ndongo S, Maaloum M, Richez M, Saile R, Fournier PE, Lagier JC, Raoult D, Khelaifia S. Vitreoscilla massiliensis sp. nov., Isolated From the Stool of an Amazonian Patient. Curr Microbiol 2021; 78:3313-3320. [PMID: 34165609 PMCID: PMC8289809 DOI: 10.1007/s00284-021-02577-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 06/15/2021] [Indexed: 11/30/2022]
Abstract
Strain SN6T is a non-motile and non-spore-forming gram-negative bacterium which was isolated from the stool sample of an Amazonian patient. The optimum growth was observed at 37 °C, pH 7, and 0–5 g/l of NaCl. Based on the 16S rRNA gene sequence similarity, the strain SN6T exhibited 97.5% identity with Vitreoscilla stercoraria strain ATCC_15218 (L06174), the phylogenetically closest species with standing in nomenclature. The predominant fatty acid was hexadecenoic acid (31%). The genomic DNA G + C content of the strain SN6T was 49.4 mol %. After analysis of taxonogenomic data, phenotypic and biochemical characteristics, we concluded that strain SN6T represents a new species of the genus Vitreoscilla for which the name Vitreoscilla massiliensis sp.nov is proposed. The type strain is SN6T (=CSUR P2036 = LN870312 = DSM 100958).
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Affiliation(s)
- Sokhna Ndongo
- IHU-Méditerranée Infection, Marseille, France.,IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Mossaab Maaloum
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Aix Marseille Univ, Marseille, France.,Laboratory of Biology and Health, Faculty of Sciences Ben M'sik, Hassan II University, Casablanca, Morocco
| | | | - Rachid Saile
- Laboratory of Biology and Health, Faculty of Sciences Ben M'sik, Hassan II University, Casablanca, Morocco
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Aix Marseille Univ, Marseille, France
| | - Jean Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France.,IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Saber Khelaifia
- IHU-Méditerranée Infection, Marseille, France. .,IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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12
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Recent advances in the bioprospection and applications of chitinolytic bacteria for valorization of waste chitin. Arch Microbiol 2021; 203:1953-1969. [PMID: 33710379 DOI: 10.1007/s00203-021-02234-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/12/2021] [Accepted: 02/11/2021] [Indexed: 10/21/2022]
Abstract
One of the most abundant natural polymers on earth, chitin is a fibrous and structural polysaccharide, composed of N-acetyl-D-glucosamine. The biopolymer is the major structural constituent of fungi, arthropods, mollusks, nematodes, and some algae. The biodegradation of chitin is largely manifested by chitinolytic enzyme secreting organisms including bacteria, insects, and plants. Among them, bacterial chitinases represent the most promising, inexpensive, and sustainable source of proteins that can be employed for industrial-scale applications. To this end, the presented review comes at a timely moment to highlight the major sources of chitinolytic bacteria. It also discusses the potential pros and cons of prospecting bacterial chitinases that can be easily manipulated through genetic engineering. Additionally, we have elaborated the recent applications of the chitin thereby branding chitinases as potential candidates for biorefinery and biomedical research for eco-friendly and sustainable management of chitin waste in the environment.
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13
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Exploring Simplified Methods for Insect Chitin Extraction and Application as a Potential Alternative Bioethanol Resource. INSECTS 2020; 11:insects11110788. [PMID: 33198072 PMCID: PMC7696517 DOI: 10.3390/insects11110788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary The studies on chitin utilization as a source for bioethanol production are still very few. The present study explores some simple methods for insect chitin extraction and application in bioethanol production. Using insect chitin in bioethanol production, may help decreasing the dependence on energy crops as a carbon source for bioethanol. Fungal strains of Mucor circinelloides were reported previously to bio-convert chitin directly to ethanol in submerged fermentation systems. In our study, we explored the bioconversion of insect chitin to bioethanol using two different strains of Mucor circinelloides in submerged fermentation systems. An insect-isolated M. circinelloides strain was found to bio-convert the extracted chitin directly to ethanol in submerged fermentation system. The source of strain isolation and the pH of the production medium were showed to influence the chitin bioconversion directly to bioethanol. All fermentation processes can be conducted easily, using the whole growing microorganism instead of using purified enzymes. These results highlight the insect biomass as a potential new, cheap and renewable source for bioethanol production simply, using a potent insect-isolated M. circinelloides strain. Abstract Chitin, the second most plentiful biopolymer in nature, is a major component of insect cuticle. In searching for alternative resources for fossil fuels, some fungal strains of Mucor circinelloides from an insect-source were found to produce bioethanol directly using insect chitin as a substrate. Herein, simplified methods for insect chitin extraction and application as a substrate in submerged fermentation for bioethanol production were explored. Chitin of the American cockroach (Periplaneta americana (L.)) was isolated by refluxing the cockroaches dried exoskeletons with 4% NaOH. The purity of the extracted chitin was assessed to be high when the physicochemical properties of the extracted chitin matched these of commercially available crab and shrimp samples. The extracted chitin was employed as a substrate in submerged fermentation using two strains of M. circinelloides. One of these, strains M. circinelloides 6017 showed immense potential for bioethanol production directly. It could to bio-transform 15 g/L of colloidal chitin directly to 11.22 ± 0.312 g/L of bioethanol (74% of the initial chitin mass) after 6 days of incubation. These results confirm the possibility of using insect biomass as a potential alternative resource for bioethanol production in a simple manner thus contributing to the creation of an alternate energy source.
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14
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Zhang A, Mo X, Zhou N, Wang Y, Wei G, Hao Z, Chen K. Identification of Chitinolytic Enzymes in Chitinolyticbacter meiyuanensis and Mechanism of Efficiently Hydrolyzing Chitin to N-Acetyl Glucosamine. Front Microbiol 2020; 11:572053. [PMID: 33193169 PMCID: PMC7641034 DOI: 10.3389/fmicb.2020.572053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/28/2020] [Indexed: 01/20/2023] Open
Abstract
Chitinolyticbacter meiyuanensis SYBC-H1, a bacterium capable of hydrolyzing chitin and shrimp shell to N-acetyl glucosamine (GlcNAc) as the only product, was isolated previously. Here, the hydrolysis mechanism of this novel strain toward chitin was investigated. Sequencing and analysis of the complete genome of SYBC-H1 showed that it encodes 32 putatively chitinolytic enzymes including 30 chitinases affiliated with the glycoside hydrolase (GH) families 18 (26) and 19 (4), one GH family 20 β-N-acetylglucosaminidase (NAGase), and one Auxiliary Activities (AA) family 10 lytic polysaccharide monooxygenase (LPMO). However, only eight GH18 chitinases, one AA10 LPMO, and one GH20 NAGase were detected in the culture broth of the strain, according to peptide mass fingerprinting (PMF). Of these, genes encoding chitinolytic enzymes including five GH18 chitinases (Cm711, Cm3636, Cm3638, Cm3639, and Cm3769) and one GH20 NAGase (Cm3245) were successfully expressed in active form in Escherichia coli. The hydrolysis of chitinous substrates showed that Cm711, Cm3636, Cm3638, and Cm3769 were endo-chitinases and Cm3639 was exo-chitinase. Moreover, Cm3639 and Cm3769 can convert the GlcNAc dimer and colloidal chitin (CC) into GlcNAc, which showed that they also possess NAGase activity. In addition, NAGase Cm3245 possesses a very high exo-acting activity of hydrolyzing GlcNAc dimer. These results suggest that chitinases and NAGase from SYBC-H1 both play important roles in conversion of N-acetyl chitooligosaccharides to GlcNAc, resulting in the accumulation of the final product GlcNAc. To our knowledge, this is the first report of the complete genome sequence and chitinolytic enzyme genes discovery of this strain.
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Affiliation(s)
- Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xiaofang Mo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Ning Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Guoguang Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Zhikui Hao
- Taizhou Vocational and Technical College, Taizhou, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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15
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Zhang A, Mo X, Wei G, Zhou N, Yang S, Chen J, Wang Y, Chen K, Ouyang P. The Draft Genome Sequence and Analysis of an Efficiently Chitinolytic Bacterium Chitinibacter sp. Strain GC72. Curr Microbiol 2020; 77:3903-3908. [PMID: 32980915 DOI: 10.1007/s00284-020-02215-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 09/15/2020] [Indexed: 11/25/2022]
Abstract
A novel chitinolytic bacterium Chitinibacter sp. GC72, which produces an enzyme capable of efficiently converting chitin only into N-acetyl-D-glucosamine (GlcNAc), was successfully sequenced and analyzed. The assembled draft genome of strain GC72 is 3,455,373 bp, containing 3346 encoded protein sequences with G + C content of 53.90%. Among these annotated genes, 17 chitinolytic enzymes including 12 glycoside hydrolase family 18 chitinases, three family 19 chitinases, one family 20 β-hexosaminidase, and one auxiliary activity family 10 lytic polysaccharide monooxygenase, were found to be essential in the production of GlcNAc from chitin. The genomic information of strain GC72 provides a reference genome for Chitinibacter bacteria and abundant novel chitinolytic enzyme resources, and allows researchers to explore potential applications in GlcNAc enzymatic production.
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Affiliation(s)
- Alei Zhang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Xiaofang Mo
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Guoguang Wei
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Ning Zhou
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Sai Yang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Jie Chen
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Yingying Wang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Kequan Chen
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Pingkai Ouyang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People's Republic of China
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16
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Modesto M, Satti M, Watanabe K, Scarafile D, Huang CH, Liou JS, Tamura T, Saito S, Watanabe M, Mori K, Huang L, Sandri C, Spiezio C, Arita M, Mattarelli P. Phylogenetic characterization of two novel species of the genus Bifidobacterium: Bifidobacterium saimiriisciurei sp. nov. and Bifidobacterium platyrrhinorum sp. nov. Syst Appl Microbiol 2020; 43:126111. [PMID: 32847786 DOI: 10.1016/j.syapm.2020.126111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
Three bifidobacterial Gram-stain-positive, non-spore forming and fructose-6-phosphate phosphoketolase-positive strains, SMA1T, SMB2 and SMA15T were isolated from the faeces of two adult males of the squirrel monkey (Saimiri sciureus). On the basis of 16S rRNA gene sequence similarities, the type strain of Bifidobacterium primatium DSM 100687T (99.3%; similarity) was the closest neighbour to strains SMA1T and SMB2, whereas the type strain of Bifidobacterium stellenboschense DSM 23968T (96.5%) was the closest neighbour to strain SMA15T. The average nucleotide identity (ANI) values of SMA1T and SAM15T with the closely related type strains were 93.7% and 88.1%, respectively. The in silico DNA‒DNA hybridization values with the closest neighbours were 53.1% and 36.9%, respectively. GC contents of strains SMA1T and SMA15T were 63.6 and 66.4 mol%, respectively. Based on the phylogenetic, genotypic and phenotypic data obtained, the strains SMA1T and SMA15T clearly represent two novel taxa within the genus Bifidobacterium for which the names Bifidobacterium saimiriisciurei sp. nov. (type strain SMA1T = BCRC 81223T = NBRC 114049T = DSM 106020T) and Bifidobacterium platyrrhinorum sp. nov. (type strain SMA15T = BCRC 81224T = NBRC 114051T = DSM 106029T) are proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Mizuki Watanabe
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Masanori Arita
- RIKEN Centerfor Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 2230-0045, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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17
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Liou JS, Huang CH, Ikeyama N, Lee AY, Chen IC, Blom J, Chen CC, Chen CH, Lin YC, Hsieh SY, Huang L, Ohkuma M, Watanabe K, Sakamoto M. Prevotella hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2020; 70:4767-4773. [PMID: 32697186 DOI: 10.1099/ijsem.0.004342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A strictly anaerobic predominant bacterium, designated as strain gm001T, was isolated from a freshly voided faecal sample collected from a healthy Taiwanese adult. Cells were Gram-stain-negative rods, non-motile and non-spore-forming. Strain gm001T was identified as a member of the genus Prevotella, and a comparison of 16S rRNA and hsp60 gene sequences revealed sequence similarities of 98.5 and 93.3 %, respectively, demonstrating that it was most closely related to the type strain of Prevotella copri. Phylogenomic tree analysis indicated that the gm001T cluster is an independent lineage of P. copri DSM 18205T. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between strain gm001T and P. copri DSM 18205T were 80.9, 28.6 and 83.8 %, respectively, which were clearly lower than the species delineation thresholds. The species-specific genes of this novel species were also identified on the basis of pan-genomic analysis. The predominant menaquinones were MK-11 and MK-12, and the predominant fatty acids were anteiso-C15 : 0, C15 : 0 and iso-C15 : 0. Acetate and succinate were produced from glucose as metabolic end products. Taken together, the results indicate that strain gm001T represents a novel species of the genus Prevotella, for which the name Prevotella hominis sp. nov. is proposed. The type strain is gm001T (=BCRC 81118T=JCM 33280T).
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Affiliation(s)
- Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - I-Ching Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Chih-Chieh Chen
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan, ROC
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan, ROC
| | - Sung-Yuan Hsieh
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Koichi Watanabe
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10673, Taiwan, ROC
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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18
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Huang CH, Chen CC, Liou JS, Lee AY, Blom J, Lin YC, Huang L, Watanabe K. Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae. Int J Syst Evol Microbiol 2020; 70:3755-3762. [DOI: 10.1099/ijsem.0.003969] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Taxonomic relationships between
Lactobacillus casei
,
Lactobacillus paracasei
and
Lactobacillus zeae
have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains
L. casei
ATCC 393T and
L. zeae
ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that
L. casei
could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the
L. zeae
strains, and supported an emended the description of the name of
Lactobacillus zeae
(ex Kuznetsov 1956) Dicks et al. 1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
- General Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, ROC
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan, Taiwan, ROC
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10673, Taiwan, ROC
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19
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Huang CH, Wang CL, Liou JS, Lee AY, Blom J, Huang L, Watanabe K. Reclassification of Micrococcus aloeverae and Micrococcus yunnanensis as later heterotypic synonyms of Micrococcus luteus. Int J Syst Evol Microbiol 2019; 69:3512-3518. [DOI: 10.1099/ijsem.0.003654] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Chun-Lin Wang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Jong-Shian Liou
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Ai-Yun Lee
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Lina Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, No. 50, Ln. 155, Sec. 3, Keelung Rd., Taipei 10673, Taiwan, ROC
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20
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Liou JS, Huang CH, Wang CL, Lee AY, Mori K, Tamura T, Watanabe M, Blom J, Huang L, Watanabe K. Lactobacillus suantsaii sp. nov., isolated from suan-tsai, a traditional Taiwanese fermented mustard green. Int J Syst Evol Microbiol 2019; 69:1484-1489. [DOI: 10.1099/ijsem.0.003346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Jong-Shian Liou
- 1Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chien-Hsun Huang
- 1Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chun-Lin Wang
- 1Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Ai-Yun Lee
- 1Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koji Mori
- 2Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- 2Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Mizuki Watanabe
- 2Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Jochen Blom
- 3Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Lina Huang
- 1Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- 4Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, No. 50, Ln. 155, Sec. 3, Keelung Rd., Taipei 10673, Taiwan, ROC
- 1Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
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21
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Huang CH, Liou JS, Lee AY, Tseng M, Miyashita M, Huang L, Watanabe K. Polyphasic characterization of a novel species in the Lactobacillus casei group from cow manure of Taiwan: Description of L. chiayiensis sp. nov. Syst Appl Microbiol 2018; 41:270-278. [DOI: 10.1016/j.syapm.2018.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 10/18/2022]
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22
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Piao C, Jin L, Zhao J, Liu C, Zhao Y, Wang X, Xiang W. Longispora urticae sp. nov., isolated from rhizosphere soil of Urtica urens L., and emended descriptions of the species Longispora albida and Longispora fulva. Int J Syst Evol Microbiol 2017; 67:4228-4234. [DOI: 10.1099/ijsem.0.002288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chenyu Piao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Liying Jin
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Chongxi Liu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yue Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
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23
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Sheu SY, Li YS, Young CC, Chen WM. Chitinibacter fontanus sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2016; 66:4262-4268. [DOI: 10.1099/ijsem.0.001345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Yi-Shu Li
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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24
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Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2015; 65:214-219. [DOI: 10.1099/ijs.0.060996-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A slightly thermophilic, Gram-staining-negative and strictly aerobic bacteria, designated strain YIM 78141T, was isolated from a sediment sample collected at Hehua hot spring, Tengchong, Yunnan province, south-west China. Cells of the strain were short-rod-shaped and colonies were yellowish and circular. The strain grew at pH 6.0–10.0 (optimum, pH 8.0–9.0) and 10–55 °C (optimum, 40–50 °C). Phylogenetic analyses based on 16S rRNA gene sequence comparison demonstrated that strain YIM 78141T belongs to the family
Neisseriaceae
, and strain YIM 78141T also showed low levels of 16S rRNA gene sequence similarity (below 93.4 %) with all other genera in this family. The only quinone was ubiquinone 8 and the genomic DNA G+C content was 67.3 mol%. Major fatty acids (>5 %) were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phospholipids of unknown structure containing aminoglycophospholipid and three unidentified polar lipids. On the basis of the morphological, physiological and biochemical characteristics as well as genotypic data, this strain should be classified as a representative of a novel genus and species of the family
Neisseriaceae
, for which the name Crenobacter luteus gen. nov., sp. nov. is proposed. The type strain is YIM 78141T ( = BCRC 80650T = KCTC 32558T = DSM 27258T).
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25
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Sheu SY, Chen JC, Young CC, Chen WM. Rivicola pingtungensis gen. nov., sp. nov., a new member of the family Neisseriaceae isolated from a freshwater river. Int J Syst Evol Microbiol 2014; 64:2009-2016. [PMID: 24639240 DOI: 10.1099/ijs.0.055285-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated Npb-03(T), was isolated from a freshwater river in Taiwan and was characterized using a polyphasic taxonomic approach. The cells were Gram-reaction-negative, straight rod-shaped, non-motile, non-spore-forming and facultatively anaerobic. Growth occurred at 10-37 °C (optimum, 30-35 °C), at pH 6.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.0% NaCl (optimum, 0%). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8 and the DNA G+C content was 64.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and three uncharacterized phospholipids. The major polyamines were putrescine, 2-hydroxyputrescine, cadaverine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-03(T) forms a distinct lineage with respect to closely related genera within the family Neisseriaceae of the class Betaproteobacteria, most closely related to the genera Aquaspirillum, Laribacter, Leeia and Microvirgula, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93%. On the basis of the genotypic and phenotypic data, strain Npb-03(T) represents a novel genus and species of the family Neisseriaceae, for which the name Rivicola pingtungensis gen. nov., sp. nov. is proposed. The type strain is Npb-03(T) ( = BCRC 80376(T) = LMG 26668(T) = KCTC 23712(T)).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Jhen-Ci Chen
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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26
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Chavan SB, Deshpande MV. Chitinolytic enzymes: An appraisal as a product of commercial potential. Biotechnol Prog 2013; 29:833-46. [DOI: 10.1002/btpr.1732] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 02/03/2013] [Indexed: 11/10/2022]
Affiliation(s)
- S. B. Chavan
- Jay Biotech; 111, Matrix, World Trade Centre, Kharadi, Pune 411014 India
| | - M. V. Deshpande
- Biochemical Sciences Division; National Chemical Laboratory; Pune 411008 India
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27
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Adeolu M, Gupta RS. Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov. Antonie Van Leeuwenhoek 2013; 104:1-24. [PMID: 23575986 DOI: 10.1007/s10482-013-9920-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/01/2013] [Indexed: 11/29/2022]
Abstract
The species from the order Neisseriales are currently distinguished from other bacteria on the basis of branching in 16S rRNA gene trees. For this order containing a single family, Neisseriaceae, no distinctive molecular, biochemical, or phenotypic characters are presently known. We report here detailed phylogenetic and comparative analyses on the 27 genome sequenced species of the order Neisseriales. Our comparative genomic analyses have identified 54 conserved signature indels (CSIs) in widely distributed proteins that are specific for either all of the sequenced Neisseriales species or a number of clades within this order that are also supported by phylogenetic analyses. Of these CSIs, 11 are specifically present in all of the sequenced species from this order, but are not found in homologous proteins from any other bacteria. These CSIs provide novel molecular markers specific for, and delimiting, this order. Twenty-one CSIs in diverse proteins are specific for a group comprised of the genera Neisseria, Eikenella, Kingella, and Simonsiella (Clade I), which are obligate host-associated organisms, lacking flagella and exhibiting varied morphology. The species from these genera also formed a strongly supported clade in phylogenetic trees based upon concatenated protein sequences; a monophyletic grouping of these genera and other genera displaying similar morphological characteristics was also observed in the 16S rRNA gene tree. A second clade (Clade II), supported by seven of the identified CSIs and phylogenetic trees based upon concatenated protein sequences, grouped together species from the genera Chromobacterium, Laribacter, and Pseudogulbenkiania that are rod-shaped bacteria, which display flagella-based motility and are capable of free living. The remainder of the CSIs were uniquely shared by smaller groups within these two main clades. Our analyses also provide novel insights into the evolutionary history of the Neisseriales and suggest that the CSIs that are specific for the Clade I species may play an important role in the evolution of obligate host-association within this order. On the basis of phylogenetic analysis, the identified CSIs, and conserved phenotypic characteristics of different Neisseriales genera, we propose a division of this order into two families: an emended family Neisseriaceae (corresponding to Clade I) containing the genera Alysiella, Bergeriella, Conchiformibius, Eikenella, Kingella, Neisseria, Simonsiella, Stenoxybacter, Uruburuella and Vitreoscilla and a new family, Chromobacteriaceae fam. nov., harboring the remainder of the genera from this order (viz. Andreprevotia, Aquaspirillum, Aquitalea, Chitinibacter, Chitinilyticum, Chitiniphilus, Chromobacterium, Deefgea, Formivibrio, Gulbenkiania, Iodobacter, Jeongeupia, Laribacter, Leeia, Microvirgula, Paludibacterium, Pseudogulbenkiania, Silvimonas, and Vogesella).
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Affiliation(s)
- Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
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28
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Kim SK, Kim YH, Jeong YS, Na HB, Kim J, Baik KS, Yun HD, Lee JK, Kim H. Chitinibacter suncheonensis sp. nov., a chitinolytic bacterium from a mud flat in Suncheon Bay. J Microbiol 2012; 50:1058-62. [DOI: 10.1007/s12275-012-2333-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 08/01/2012] [Indexed: 11/29/2022]
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29
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Hao Z, Cai Y, Liao X, Liang X, Liu J, Fang Z, Hu M, Zhang D. Chitinolyticbacter meiyuanensis SYBC-H1T, gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil. Curr Microbiol 2011; 62:1732-8. [PMID: 21431834 DOI: 10.1007/s00284-011-9921-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 03/10/2011] [Indexed: 11/25/2022]
Abstract
A novel aerobic mesophilic bacterial strain SYBC-H1(T) capable of degrading chitin was isolated and classified in this study. The strain exhibited strong chitinolytic activity and was a Gram-negative, curved, rod-shaped, and motile bacterium. Growth of this strain was observed between 10 and 41°C and between pH 3.5 and 9.5. The DNA G + C content of strain SYBC-H1(T) was 53.25 mol%. The cellular fatty acids (>5%) were 12:0 iso 3-OH (5.87%), 16:0 (28.16%), and 18:1ω7c (20.48%). Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain SYBC-H1(T) belonged to the family Neisseriaceae, and was distantly related (95.0% similarity) to the genus Chitiniphilus. Its phenotype was unique and genetic and phylogenetic analysis experiments suggested that strain SYBC-H1(T) represented the type strain (CGMCC 3438(T), ATCC BAA-2140(T)) of a novel genus, for which the name Chitinolyticbacter meiyuanensis SYBC-H1(T) gen. nov., sp. nov. was proposed. The highest enzymatic activity of chitinase (9.6 U/ml) was obtained at 72 h in 250 ml shake flasks. The 16S rRNA gene sequence of SYBC-H1(T) has been deposited in GenBank under the accession number GQ981314.
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Affiliation(s)
- Zhikui Hao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
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30
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Jung A, Jung-Schroers V. Detection of Deefgea chitinilytica in freshwater ornamental fish. Lett Appl Microbiol 2011; 52:497-500. [PMID: 21323934 DOI: 10.1111/j.1472-765x.2011.03030.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM To identify and characterize six chitinolytic bacterial strains isolated from ornamental fish. METHODS AND RESULTS Six different isolates of Deefgea chitinilytica were detected in healthy as well as diseased ornamental fish in Germany over a period of 2 years. Bacterial strains were identified using 16S rRNA partial gene sequencing and further characterized using different biochemical microtest systems and additional standard biochemical tests. CONCLUSION We show that commercially available biochemical microtest systems are useful for identification of D. chitinilytica, supplemented by 16S rRNA partial gene sequencing. Furthermore, this study provides new information about the occurrence of D. chitinilytica, as this is the first isolation of D. chitinilytica from animals and first described isolation in Europe. SIGNIFICANCE AND IMPACT OF THE STUDY Deefgea chitinilytica may be isolated regularly in fish diagnostic laboratories. Therefore, accurate identification of this bacterial species is important. Involvement of D. chitinilytica in opportunistic infections of aquatic organisms cannot be excluded and has to be further investigated.
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Affiliation(s)
- A Jung
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany.
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31
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N-acetyl glucosamine obtained from chitin by chitin degrading factors in Chitinbacter tainanesis. Int J Mol Sci 2011; 12:1187-95. [PMID: 21541052 PMCID: PMC3083699 DOI: 10.3390/ijms12021187] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 02/15/2011] [Accepted: 02/15/2011] [Indexed: 12/02/2022] Open
Abstract
A novel chitin-degrading aerobe, Chitinibacter tainanensis, was isolated from a soil sample from southern Taiwan, and was proved to produce N-acetyl glucosamine (NAG). Chitin degrading factors (CDFs) were proposed to be the critical factors to degrade chitin in this work. When C. tainanensis was incubated with chitin, CDFs were induced and chitin was converted to NAG. CDFs were found to be located on the surface of C. tainanensis. N-Acetylglucosaminidase (NAGase) and endochitinase activities were found in the debris, and the activity of NAGase was much higher than that of endochitinase. The optimum pH of the enzymatic activity was about 7.0, while that of NAG production by the debris was 5.3. These results suggested that some factors in the debris, in addition to NAGase and endochitinase, were crucial for chitin degradation.
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32
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Chen JK, Shen CR, Liu CL. N-acetylglucosamine: production and applications. Mar Drugs 2010; 8:2493-516. [PMID: 20948902 PMCID: PMC2953398 DOI: 10.3390/md8092493] [Citation(s) in RCA: 244] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 04/19/2010] [Accepted: 04/23/2010] [Indexed: 12/21/2022] Open
Abstract
N-Acetylglucosamine (GlcNAc) is a monosaccharide that usually polymerizes linearly through (1,4)-β-linkages. GlcNAc is the monomeric unit of the polymer chitin, the second most abundant carbohydrate after cellulose. In addition to serving as a component of this homogeneous polysaccharide, GlcNAc is also a basic component of hyaluronic acid and keratin sulfate on the cell surface. In this review, we discuss the industrial production of GlcNAc, using chitin as a substrate, by chemical, enzymatic and biotransformation methods. Also, newly developed methods to obtain GlcNAc using glucose as a substrate in genetically modified microorganisms are introduced. Moreover, GlcNAc has generated interest not only as an underutilized resource but also as a new functional material with high potential in various fields. Here we also take a closer look at the current applications of GlcNAc, and several new and cutting edge approaches in this fascinating area are thoroughly discussed.
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Affiliation(s)
- Jeen-Kuan Chen
- Department of Environment and Biotechnology, Refining & Manufacturing Research Institute, CPC Corporation, 217 Min-Sheng S. Rd, Chiayi, Taiwan; E-Mail: (J.-K.C.)
| | - Chia-Rui Shen
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Kweishan, Taoyuan, 259 Wen-Hwa 1st Road, Kweishan, Taoyuan, Taiwan; E-Mail: (C.-R.S.)
| | - Chao-Lin Liu
- Graduate School of Biochemical Engineering and Department of Chemical Engineering, Ming Chi University of Technology, Taishan, Taipei, 84 Gung-Juan Road, Taishan, Taipei, Taiwan
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Yang CS, Sheu SY, Young CC, Arun AB, Cheng CY, Chen WM. Chitinibacter alvei sp. nov., isolated from stream water. Int J Syst Evol Microbiol 2010; 60:1760-1764. [DOI: 10.1099/ijs.0.016170-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic bacterium, designated strain TNR-14T, was isolated from water of a stream located in southern Taiwan. Cells were rod-shaped and motile by means of a polar flagellum. The isolate exhibited optimum growth at 20 °C, at pH 7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter and was related most closely to the type strain of Chitinibacter tainanensis (96.0 % similarity). The predominant cellular fatty acids were summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c; 54.03 %) and C16 : 0 (27.22 %). The DNA G+C content of strain TNR-14T was 57.5 mol%. The results of physiological and biochemical tests and chemotaxonomic data allowed the clear phenotypic differentiation of the new isolate from Chitinibacter tainanensis. Strain TNR-14T is therefore considered to represent a novel species of the genus Chitinibacter, for which the name Chitinibacter alvei sp. nov. is proposed. The type strain is TNR-14T (=LMG 25206T =DSM 22217T =BCRC 17968T).
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Affiliation(s)
- Cho-Song Yang
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil Environmental Science, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - A. B. Arun
- Yenepoya Research Center, Yenepoya University, University Road, Deralakatte, Mangalore, Karnataka, India
| | - Chih-Yu Cheng
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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Sato K, Kato Y, Taguchi G, Nogawa M, Yokota A, Shimosaka M. Chitiniphilus shinanonensis gen. nov., sp. nov., a novel chitin-degrading bacterium belonging to Betaproteobacteria. J GEN APPL MICROBIOL 2009; 55:147-53. [PMID: 19436131 DOI: 10.2323/jgam.55.147] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A bacterial strain capable of degrading chitin, strain SAY3T, was isolated from moat water of Ueda Castle in Nagano Prefecture, Japan. The strain was gram-negative, curved rod-shaped, facultatively anaerobic, and motile with a single polar flagellum. It grew well with chitin as a sole carbon source. The cellular fatty acids profiles showed the presence of C16:1 omega7c and C16:0 as the major components. The G+C content of DNA was 67.6 mol% and Q-8 was the major respiratory quinone. A 16S rRNA gene sequence-based phylogenetic analysis showed the strain belonged to the family Neisseriaceae but was distantly related (94% identity) to any previously known species. Since the strain was clearly distinct from closely related genera in phenotypic and chemotaxonomic characteristics, it should be classified under a new genus and a new species. We propose the name Chitiniphilus shinanonensis gen. nov., sp. nov. The type strain is SAY3T (=NBRC 104970T=NICMB 14509T).
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Affiliation(s)
- Kazuaki Sato
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Nagano, Japan
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35
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Chitinilyticum litopenaei sp. nov., isolated from a freshwater shrimp pond, and emended description of the genus Chitinilyticum. Int J Syst Evol Microbiol 2009; 59:2651-5. [DOI: 10.1099/ijs.0.005090-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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36
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Szoboszlay S, Atzél B, Kukolya J, Tóth EM, Márialigeti K, Schumann P, Kriszt B. Chryseobacterium hungaricum sp. nov., isolated from hydrocarbon-contaminated soil. Int J Syst Evol Microbiol 2009; 58:2748-54. [PMID: 19060052 DOI: 10.1099/ijs.0.65847-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a strain isolated from kerosene-contaminated soil in Hungary and formerly misidentified as Brevundimonas vesicularis was examined using a polyphasic approach. The isolate, designated CHB-20p(T), could be clearly assigned to the genus Chryseobacterium (family Flavobacteriaceae) on the basis of 16S rRNA gene sequence similarity. Strain CHB-20p(T), a moderate oil degrader, was a Gram-negative, aerobic, mesophilic microbe with a temperature optimum of 28-30 degrees C. Predominant fatty acids were iso-C(15 : 0), summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH) and iso-C(17 : 0) 3-OH. Menaquinone-6 (MK-6) was the predominant respiratory quinone; MK-5 was present as a minor component. The almost complete 16S rRNA gene sequence of strain CHB-20p(T) shared 94-97 % similarity with sequences of the type strains of species of the genus Chryseobacterium. DNA-DNA relatedness between strain CHB-20p(T) and its closest relative, Chryseobacterium caeni, was lower than 46 %. Moreover, several diagnostic phenotypic properties distinguished strain CHB-20p(T) from C. caeni. On the basis of biochemical, chemotaxonomic and genotypic data, isolate CHB-20p(T) represents a novel species within the genus Chryseobacterium, Chryseobacterium hungaricum sp. nov.; the type strain is CHB-20p(T) (=NCAIM B2269(T)=DSM 19684(T)).
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Affiliation(s)
- Sándor Szoboszlay
- Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllo, Hungary
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37
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Lee FL, Tien CJ, Tai CJ, Wang LT, Liu YC, Chern LL. Paenibacillus taichungensis sp. nov., from soil in Taiwan. Int J Syst Evol Microbiol 2008; 58:2640-5. [DOI: 10.1099/ijs.0.65776-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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38
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Chang SC, Chen WM, Wang JT, Wu MC. Chitinilyticum aquatile gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater pond used for Pacific white shrimp culture. Int J Syst Evol Microbiol 2007; 57:2854-2860. [DOI: 10.1099/ijs.0.65168-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain c14T, originally isolated from surface water of a freshwater pond located in Pingtung (southern Taiwan) used for culture of Pacific white shrimp (Litopenaeus vannamei), was subjected to a polyphasic taxonomic approach. The strain exhibited strong chitinolytic activity and was able to grow under aerobic and anaerobic conditions by utilizing chitin exclusively as the carbon, nitrogen and energy source. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation of the proposed bacterium to the Betaproteobacteria, most closely related to Chitinibacter tainanensis S1T, Deefgea rivuli WB 3.4-79T and Silvimonas terrae KM-45T, with 94.6, 93.6 and 92.9 % 16S rRNA gene sequence similarity, respectively. The predominant fatty acids detected in cells of strain c14T were C16 : 0, C18 : 1
ω7c and summed feature 3 (C16 : 1
ω7c and/or C15 : 0 iso 2-OH). The G+C content of the genomic DNA was 69.5 (±1.0) mol%. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain c14T could not be assigned to any known genus of the Betaproteobacteria. Therefore, strain c14T is classified within a novel genus and species, for which the name Chitinilyticum aquatile gen. nov., sp. nov. is proposed. The type strain of Chitinilyticum aquatile is c14T (=LMG 23346T =BCRC 17533T).
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Affiliation(s)
- Shu-Chen Chang
- Department of Food Science, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
- Department of Food Science and Technology, Tajen University, 20 Weishin Rd, YanPu Shiang, Pingtung City 907, Taiwan, ROC
| | - Wen-Ming Chen
- Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan, ROC
| | - Jih-Terng Wang
- Department of Biotechnology, Tajen University, Pingtung, Taiwan, ROC
| | - Ming-Chang Wu
- Department of Food Science, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
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39
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Wang LT, Lee FL, Tai CJ, Kasai H. Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. Int J Syst Evol Microbiol 2007; 57:1846-1850. [PMID: 17684269 DOI: 10.1099/ijs.0.64685-0] [Citation(s) in RCA: 188] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA-DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4-95.0 % and 88.5-99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1-99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA-DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.
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Affiliation(s)
- Li-Ting Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Fwu-Ling Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Chun-Ju Tai
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Hiroaki Kasai
- Marine Biotechnology Institute, Heita, Kamaishi, Iwate, 026-0001, Japan
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40
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Lee FL, Kuo HP, Tai CJ, Yokota A, Lo CC. Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan. Int J Syst Evol Microbiol 2007; 57:1351-1354. [PMID: 17551057 DOI: 10.1099/ijs.0.64764-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile and endospore-forming bacterial strain, designated G-soil-2-3(T), was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequence analysis, DNA-DNA hybridization experiments, fatty acid analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belongs within the genus Paenibacillus. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C(15 : 0) (40.5 %), iso-C(15 : 0) (13.1 %), iso-C(16 : 0) (10.8 %) and anteiso-C(17 : 0) (7.3 %) as the major fatty acids. Phylogenetically, the closest relatives of strain G-soil-2-3(T) were the type strains of Paenibacillus assamensis, Paenibacillus alvei and Paenibacillus apiarius, with 16S rRNA gene sequence similarity of 95.7, 95 and 95.2 %, respectively. DNA-DNA hybridization experiments showed levels of relatedness of 2.8-9.0 % of strain G-soil-2-3(T) with these strains. The G+C content of the DNA was 44.6 mol%. Strain G-soil-2-3(T) was clearly distinguishable from P. assamensis, P. alvei and P. apiarius and thus represents a novel species of the genus Paenibacillus, for which the name Paenibacillus taiwanensis sp. nov. is proposed. The type strain is G-soil-2-3(T) (=BCRC 17411(T)=IAM 15414(T)=LMG 23799(T)=DSM 18679(T)).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Gram-Positive Endospore-Forming Rods/chemistry
- Gram-Positive Endospore-Forming Rods/classification
- Gram-Positive Endospore-Forming Rods/isolation & purification
- Gram-Positive Endospore-Forming Rods/physiology
- Locomotion
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Taiwan
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Affiliation(s)
- Fwu-Ling Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Hsiao-Ping Kuo
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Chun-Ju Tai
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Chi-Chu Lo
- Division of Bio-Pesticide, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Wufong, Taichung 41358, Taiwan
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41
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Wang LT, Lee FL, Tai CJ, Yokota A, Kuo HP. Reclassification of Bacillus axarquiensis Ruiz-García et al. 2005 and Bacillus malacitensis Ruiz-García et al. 2005 as later heterotypic synonyms of Bacillus mojavensis Roberts et al. 1994. Int J Syst Evol Microbiol 2007; 57:1663-1667. [PMID: 17625213 DOI: 10.1099/ijs.0.64808-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Bacillus subtilis group encompasses the taxa Bacillus subtilis subsp. subtilis, B. licheniformis, B. amyloliquefaciens, B. atrophaeus, B. mojavensis, B. vallismortis, B. subtilis subsp. spizizenii, B. sonorensis, B. velezensis, B. axarquiensis and B. malacitensis. In this study, the taxonomic relatedness between the species B. axarquiensis, B. malacitensis and B. mojavensis was investigated. Sequence analysis of the 16S rRNA gene and the gene for DNA gyrase subunit B (gyrB) confirmed the very high similarities between these three type strains and a reference strain of B. mojavensis (>99 and >97 %, respectively). DNA–DNA hybridization experiments revealed high relatedness values between the type strains of B. axarquiensis, B. malacitensis and B. mojavensis and between these strains and a reference strain of B. mojavensis (83–98 %). Based on these molecular taxonomic data and the lack of phenotypic distinctive characteristics, Bacillus axarquiensis and Bacillus malacitensis should be reclassified as later heterotypic synonyms of Bacillus mojavensis.
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MESH Headings
- Bacillus/classification
- Bacillus/genetics
- DNA Gyrase/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Li-Ting Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Fwu-Ling Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Chun-Ju Tai
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Hsiao-Ping Kuo
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30099, Taiwan
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42
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Weon HY, Kim BY, Yoo SH, Joa JH, Kwon SW, Kim WG. Andreprevotia chitinilytica gen. nov., sp. nov., isolated from forest soil from Halla Mountain, Jeju Island, Korea. Int J Syst Evol Microbiol 2007; 57:1572-1575. [PMID: 17625196 DOI: 10.1099/ijs.0.64694-0] [Citation(s) in RCA: 13] [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 motile, Gram-negative, rod-shaped bacterium, designated strain JS11-7T, was isolated from forest soil from Halla Mountain, Jeju Island, Korea. It grew optimally at 28 °C, pH 6–7 and in the presence of 0–2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JS11-7T belongs to the family Neisseriaceae, with Silvimonas terrae as its closest relative (95.0 % similarity). It contained Q-8 as the predominant quinone and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1
ω6c), C16 : 0 and C18 : 1
ω7c as the major fatty acids. The DNA G+C content was 62 mol%. On the basis of phenotypic and genotypic characteristics and the results of 16S rRNA gene sequence analysis, strain JS11-7T represents a novel genus and species, for which the name Andreprevotia chitinilytica gen. nov., sp. nov. is proposed. The type species is Andreprevotia chitinilytica and the type strain is JS11-7T (=KACC 11608T=DSM 18519T).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Hydrogen-Ion Concentration
- Korea
- Molecular Sequence Data
- Neisseriaceae/chemistry
- Neisseriaceae/classification
- Neisseriaceae/genetics
- Neisseriaceae/isolation & purification
- Phylogeny
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Soil Microbiology
- Temperature
- Trees
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Affiliation(s)
- Hang-Yeon Weon
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Byung-Yong Kim
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Seung-Hee Yoo
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Jae-Ho Joa
- National Institute of Subtropical Agriculture, Rural Development Administration, Jeju 690-150, Republic of Korea
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Wan-Gyu Kim
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, Rural Development Administration, Suwon 441-707, Republic of Korea
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Stackebrandt E, Lang E, Cousin S, Päuker O, Brambilla E, Kroppenstedt R, Lünsdorf H. Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria. Int J Syst Evol Microbiol 2007; 57:639-645. [PMID: 17329799 DOI: 10.1099/ijs.0.64771-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains, designated WB 3.4-79(T) and WB 3.3-25, were isolated from a hard-water sample collected from the Westerhöfer Bach, Lower Saxony, Germany. The strains shared 100 % DNA-DNA relatedness, indicating membership of the same genospecies. This close relationship was supported by identical 16S rRNA gene sequences and high similarities in fatty acid composition and biochemical characteristics. The G+C content of the genomic DNA of strain WB 3.4-79(T) was 48.5 mol% and the predominant ubiquinone was Q-8. Major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Major fatty acids (>10 %) were C(16 : 0) and C(16 : 1)omega7c. Polyhydroxybutyrate and polyphosphate granules as well as unidentified enterosomes and a polar organelle are visible by electron microscopy. Comparative 16S rRNA gene sequence analysis indicated that the isolates were placed within the class Betaproteobacteria, remotely related to Chitinibacter tainanensis DSM 15459(T), Silvimonas terrae KCTC 12358(T), Formivibrio citricus DSM 6150(T) and Iodobacter fluviatilis DSM 3764(T). On the basis of phylogenetic and phenotypic distinctness, we propose a novel genus, Deefgea gen. nov., with Deefgea rivuli sp. nov. as the type species. The type strain of Deefgea rivuli is strain WB 3.4-79(T) (=DSM 18356(T)=CIP 109326(T)).
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Affiliation(s)
- Erko Stackebrandt
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7b, 38124 Braunschweig, Germany
| | - Elke Lang
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7b, 38124 Braunschweig, Germany
| | - Sylvie Cousin
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7b, 38124 Braunschweig, Germany
| | - Orsola Päuker
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7b, 38124 Braunschweig, Germany
| | - Evelyne Brambilla
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7b, 38124 Braunschweig, Germany
| | - Reiner Kroppenstedt
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7b, 38124 Braunschweig, Germany
| | - Heinrich Lünsdorf
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
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Vaz-Moreira I, Nobre MF, Nunes OC, Manaia CM. Gulbenkiania mobilis gen. nov., sp. nov., isolated from treated municipal wastewater. Int J Syst Evol Microbiol 2007; 57:1108-1112. [PMID: 17473267 DOI: 10.1099/ijs.0.64726-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain (E4FC31T) isolated from treated municipal wastewater was characterized phenotypically and phylogenetically. Cells were Gram-negative, curved rods with a polar flagellum. The isolate was catalase-, oxidase- and arginine dihydrolase-positive, and able to grow between 15 and 45 °C and between pH 5.5 and 9.0. The predominant fatty acids were C16 : 1/iso-C15 : 02-OH and C16 : 0, the major respiratory quinone was ubiquinone 8 and the G+C content of the genomic DNA was 63 mol%. 16S rRNA gene sequence analysis indicated that strain E4FC31Tbelonged to the classBetaproteobacteriaand was a member of the familyNeisseriaceae. Its closest phylogenetic neighbours wereAquitalea magnusoniiandChromobacterium violaceum(<94 % 16S rRNA gene sequence similarity). Phylogenetic analysis and phenotypic characteristics of strain E4FC31Tsuggest that it represents a novel species of a new genus, for which the nameGulbenkiania mobilisgen. nov., sp. nov. is proposed. The type strain ofGulbenkiania mobilisis E4FC31T(=DSM 18507T=LMG 23770T).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- Catalase/biosynthesis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Hydrogen-Ion Concentration
- Hydrolases/biosynthesis
- Molecular Sequence Data
- Neisseriaceae/classification
- Neisseriaceae/cytology
- Neisseriaceae/isolation & purification
- Neisseriaceae/physiology
- Oxidoreductases/biosynthesis
- Phylogeny
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Temperature
- Water Microbiology
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Affiliation(s)
- Ivone Vaz-Moreira
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4200-072 Porto, Portugal
| | - M Fernanda Nobre
- Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Olga C Nunes
- LEPAE - Departamento de Engenharia Química, Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
| | - Célia M Manaia
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4200-072 Porto, Portugal
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45
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Tai CJ, Kuo HP, Lee FL, Chen HK, Yokota A, Lo CC. Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan. Int J Syst Evol Microbiol 2006; 56:1771-1776. [PMID: 16902006 DOI: 10.1099/ijs.0.64294-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among a large collection of Taiwanese soil isolates, a novel Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterial strain, Soil-3-27T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequencing, DNA–DNA hybridization, fatty acid analysis and comparative phenotypic characterization. The 16S rRNA gene sequence analysis indicated that the organism belongs to the genus Chryseobacterium. The organism contains menaquinone MK-6 as the predominant isoprenoid quinone and 15 : 0 iso (43 %), 17 : 1 isoω9c (17.5 %) and 17 : 0 iso 3-OH (16.6 %) as the major fatty acids. Phylogenetically, the closest relatives of strain Soil-3-27T are Chryseobacterium daecheongense, Chryseobacterium defluvii and Chryseobacterium taichungense with 96.7–97.2 % sequence similarity. DNA–DNA hybridization showed relatedness values of 8.5–24.2 % with these species. The DNA G+C content is 36.8 mol%. Strain Soil-3-27T is clearly distinguishable from other Chryseobacterium species and represents a novel species, for which the name Chryseobacterium taiwanense sp. nov. is proposed. The type strain is strain Soil-3-27T (=BCRC 17412T=IAM 15317T=LMG 23355T).
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Affiliation(s)
- Chun-Ju Tai
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30062, Taiwan
| | - Hsiao-Ping Kuo
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30062, Taiwan
| | - Fwu-Ling Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30062, Taiwan
| | - Han-Ken Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, PO Box 246, Hsinchu 30062, Taiwan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Chi-Chu Lo
- Division of Bio-Pesticide, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taiwan
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Yang HC, Im WT, An DS, Park WS, Kim IS, Lee ST. Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the ‘Betaproteobacteria’. Int J Syst Evol Microbiol 2005; 55:2329-2332. [PMID: 16280491 DOI: 10.1099/ijs.0.63837-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on a bacterial strain, designated KM-45T, isolated from forest soil collected near Daejeon, South Korea. Comparative 16S rRNA gene sequence analysis indicated a clear affiliation of this bacterium to the ‘Betaproteobacteria’ and that it was related most closely to Chitinibacter tainanensis BCRC 17254T, Formivibrio citricus DSM 6150T and Iodobacter fluviatilis ATCC 33051T (92·4, 91·2 and 88·9 % 16S rRNA gene sequence similarity, respectively). Cells were Gram-negative, facultatively anaerobic, motile and rod-shaped. The strain grew well on R2A medium and utilized a broad spectrum of carbon sources. The G+C content of the genomic DNA was 58 mol% and the predominant ubiquinone was Q-8. Major fatty acids were C16 : 0, C16 : 1
ω7c/iso-C15 : 0 2-OH, C18 : 1
ω7c/ω9t/ω12t and C17 : 0 cyclo. On the basis of the evidence presented, it is proposed that strain KM-45T should be placed in a novel genus and species, for which the name Silvimonas terrae gen. nov., sp. nov. is proposed. The type strain is KM-45T (=KCTC 12358T=NBRC 100961T).
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MESH Headings
- Bacteria, Anaerobic
- Base Composition
- Biodegradation, Environmental
- Chitin/metabolism
- DNA, Bacterial/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/analysis
- DNA, Ribosomal/chemistry
- Molecular Sequence Data
- Neisseriaceae/classification
- Neisseriaceae/genetics
- Neisseriaceae/metabolism
- Neisseriaceae/ultrastructure
- Phylogeny
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Hee-Chan Yang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
| | - Wan-Taek Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
| | - Dong-Shan An
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
| | - Woo-Shin Park
- Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology, 1 Oryong-dong, Buk-gu, Gwangju 500-712, South Korea
| | - In S Kim
- Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology, 1 Oryong-dong, Buk-gu, Gwangju 500-712, South Korea
| | - Sung-Taik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
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