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Lee SD, Yang HL, Kim IS. Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium. Front Microbiol 2023; 14:1299950. [PMID: 38164402 PMCID: PMC10757982 DOI: 10.3389/fmicb.2023.1299950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the "Microbacterium agarici clade", with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.
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Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - Hong Lim Yang
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon, Republic of Korea
- BioPS Co., Ltd., Daejeon, Republic of Korea
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Lei RF, Ma Q, Li YQ, Abudourousuli D, Wang S, Rouzi Z, Aosiman M, An DD, Li WJ. Bacillus suaedae sp. nov., isolated from the stem of Suaeda aralocaspica in north-west China. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated YZJH907-2T, was isolated from the stem of Suaeda aralocaspica, collected from the southern edge of the Gurbantunggut desert, Xinjiang, PR China. Cells of strain YZJH907-2T were Gram-stain-positive, aerobic and rod-shaped. They formed white or colourless circular colonies with smooth convex surfaces. Strain YZJH907-2T grew at 4–50 °C (optimum, 28–30 °C), pH 7.0–10.0 (optimum, pH 8.0–9.0) and with 0–10 % (w/v) NaCl (optimum, 3–7 %). The genomic DNA G+C content of strain YZJH907-2T was 38.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that the strain was most closely related to
Bacillus alcalophilus
DSM 485T (97.37 %),
Bacillus kiskunsagensis
B16-24T (96.87 %) and
Bacillus bogoriensis
LBB3T (96.71 %). Average nucleotide identity values between YZJH907-2T and
B. alcalophilus
DSM 485Tand
B. bogoriensis
LBB3T were 69.2 and 69.0 %, respectively. Digital DNA–DNA hybridization values of YZJH907-2T with
B. alcalophilus
DSM 485T and
B. bogoriensis
LBB3T were 19.6 and 20.4 %, respectively. The cell wall of strain YZJH907-2T contained meso-diaminopimelic acid, and the major and secondary isoprenoid quinones were MK-7 and MK-5, respectively. Results of fatty acids showed that anteiso-C15 : 0, iso-C15 : 0 and C16 : 0 were the predominant cellular fatty acids. Two-dimensional thin-layer chromatography analysis indicated that the polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. Based on the genomic, phylogenetic and phenotypic analyses, strain YZJH907-2T represented a novel species of the genus
Bacillus
, and thus the name Bacillus suaedae sp. nov. is proposed. The type strain is YZJH907-2T (=CGMCC 1.18763T=KCTC 43335T).
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Affiliation(s)
- Rui-Feng Lei
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, 830054, PR China
| | - Qin Ma
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, 830054, PR China
| | - Yu-Qian Li
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 511458, PR China
| | - Dilireba Abudourousuli
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, 830054, PR China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation & Utilization, Heilongjiang Academy of Agricultural Sciences, Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Harbin, 150086, PR China
| | - Zulihumaer Rouzi
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, 830054, PR China
| | - Muyesaier Aosiman
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, 830054, PR China
| | - Deng-Di An
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, 830054, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
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Xie F, Pathom-aree W. Actinobacteria From Desert: Diversity and Biotechnological Applications. Front Microbiol 2021; 12:765531. [PMID: 34956128 PMCID: PMC8696123 DOI: 10.3389/fmicb.2021.765531] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.
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Affiliation(s)
- Feiyang Xie
- Doctor of Philosophy Program in Applied Microbiology (International Program), Faculty of Science, Chiang Mai University, under the CMU Presidential Scholarship, Chiang Mai, Thailand
| | - Wasu Pathom-aree
- Research Center of Microbial Diversity and Sustainable Utilization, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
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Zhu QH, Yang CL, Luo XX, Zhang LL, Xia ZF. Microbacterium karelineae sp. nov. isolated from a halophyte plant in the Taklamakan desert. Int J Syst Evol Microbiol 2021; 71. [PMID: 33480836 DOI: 10.1099/ijsem.0.004629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated TRM 80801T, was isolated from the Karelinea in Taklamakan desert, Xinjiang Uygur Autonomous Region, north-west China. Cells were Gram-stain-positive, aerobic, non-motile, short rods. Strain TRM 80801T grew at 4-50 °C, with optimum growth at 28 °C, and grew at pH 6.0-11.0 and 1-15 % (w/v) NaCl. Phylogenetic analyses of the 16S rRNA gene sequences placed strain TRM 80801T within the genus Microbacterium with the highest similarities to Microbacterium suaedae YZYP 306T (98.97 %) and Microbacterium indicum BBH6T (98.17 %), respectively. The DNA G+C content of TRM 80801T is 69.38 mol%. The cell-wall peptidoglycan contained the amino acids ornithine, glutamic acid, glycine and alanine, the diagnostic diamino acid was ornithine. The acyl type of the peptidoglycan was glycolyl. Whole-cell sugars were ribose, mannose, glucose, rhamnose and galactose. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The predominant menaquinones were MK-10, MK-11 and MK-12. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol. The whole-genome average nucleotide identity (ANI) value between strain TRM 80801T and Microbacterium suaedae YZYP 306T is 70.2 %. On the basis of the evidence presented in this study, strain TRM 80801T is representative of a novel species in the genus Microbacterium, for which the name Microbacterium karelineae sp. nov. is proposed. The type strain is TRM 80801T (=CCTCC AB 2019248T=KCTC 49357T).
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Affiliation(s)
- Qi-Hui Zhu
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar 843300, PR China
| | - Cai-Ling Yang
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar 843300, PR China
| | - Xiao-Xia Luo
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar 843300, PR China
| | | | - Zhan-Feng Xia
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar 843300, PR China
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Dong K, Yang J, Lu S, Pu J, Lai XH, Jin D, Li J, Zhang G, Wang X, Zhang S, Lei W, Ren Z, Wu X, Huang Y, Wang S, Xu J. Microbacterium wangchenii sp. nov., isolated from faeces of Tibetan gazelles ( Procapra picticaudata) on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2020; 70:1307-1314. [PMID: 31829917 DOI: 10.1099/ijsem.0.003912] [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
Two strains of Gram-stain-positive, aerobic, non-spore-forming, non-motile, rod-shaped bacteria (designated dk512T and dk508) were isolated from the faeces of Tibetan gazelle (Procapra picticaudata) collected from the Qinghai-Tibet Plateau, PR China. The 16S rRNA gene sequences of the strains showed the highest identity to Microbacterium saccharophilum K-1T (98.0 and 97.9 % similarity, respectively). The phylogenetic analysis based on 16S rRNA gene sequences revealed that dk512T and dk508 were members of the genus Microbacterium, and most closely related to strains Microbacterium mitrae M4-8T and Microbacterium hatanonis FCC-01T. The strains grew optimally on brain-heart infusion (BHI) agar with 5.0 % (v/v) sheep blood at 30 °C, pH 7.0 and with 1.0 % (w/v) NaCl. The genome of type strain dk512T was 3.8 Mb with a G+C content of 70.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain dk512T and previously characterized Microbacterium species were <95 and <70 %, respectively. In strain dk512T, the detected primary cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0, the main respiratory quinones were MK-9 (37.9 %) and MK-10 (35.7 %), and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. The major cell-wall sugars were rhamnose, ribose and galactose. Alanine, glutamic acid, glycine and ornithine were in the cell-wall peptidoglycan. Based on phenotypic data and phylogenetic inference, these two strains represent a novel species of the genus Microbacterium, named here as Microbacterium wangchenii sp. nov, where dk512T is designated the type strain (=CGMCC 1.16590T=JCM 33494T=KCTC 49313T).
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Affiliation(s)
- Kui Dong
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan Province, 476000, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Junqin Li
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaoxia Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Sihui Zhang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Wenjing Lei
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Zhihong Ren
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaomin Wu
- Shaanxi Institute of Zoology, Xi'an 710032, Shaanxi Province, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Suping Wang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Jianguo Xu
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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