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Lin R, Li H, Wu H, Ren H, Kong X, Lu Z. Resting for viability: Gordonia polyisoprenivorans ZM27, a robust generalist for petroleum bioremediation under hypersaline stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124618. [PMID: 39067736 DOI: 10.1016/j.envpol.2024.124618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
The intrinsic issue associated with the application of microbes for practical pollution remediation involves maintaining the expected activity of engaged strains or consortiums as effectively as that noted under laboratory conditions. Faced with various stress factors, degraders with dormancy ability are more likely to survive and exhibit degradation activity. In this study, a hydrocarbonoclastic and halotolerant strain, Gordonia polyisoprenivorans ZM27, was isolated via stimulation with resuscitation-promoting factor (Rpf). Long-term exposure to dual stresses of 10% NaCl and starvation induced ZM27 to enter a viable but nonculturable (VBNC)-like state, and ZM27 cells could be resuscitated upon Rpf stimulation. Notable changes in both morphological and physiological characteristics between VBNC-like ZM27 cells and resuscitated cells confirmed the response to Rpf and their robust resistance against harsh environments. Whole-genome sequencing and analysis indicated ZM27 could be a generalist degrader with dormancy ability. Subsequently, VBNC-like ZM27 was applied in a soil microcosm experiment to investigate the practical application potential under harsh conditions. VBNC-like ZM27 combined with Rpf stimulation exhibited the most effective biodegradation performance, and the initial n-hexadecane content (1000 mg kg-1) decreased by 63.29% after 14-day incubation. Based on 16S rRNA amplicon sequencing and analysis, Gordonia exhibited a positive response to Rpf stimulation. The relative abundance of genus Gordonia was negatively correlated with that of Alcanivorax, a genus of obligate hydrocarbon degrader with the greatest abundance during soil incubation. Based on the degradation profile and community analysis, generalist Gordonia may be more efficient in hydrocarbon degradation than specialist Alcanivorax under harsh conditions. The characteristics of ZM27, including its sustainable culturability under long-term stress, response to Rpf and robust performance in soil microcosms, are valuable for the remediation of petroleum pollution under stressful conditions. Our work validated the importance of dormancy and highlighted the underestimated role of low-activity degraders in petroleum remediation.
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Affiliation(s)
- Renzhang Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Li
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
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Suphannarot A, Butdee W, Suriyachadkun C, Duangmal K, Mingma R. Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov., two novel actinobacteria isolated from mangrove sediments and leaves of halophyte Sesuvium portulacastrum in Thailand. Int J Syst Evol Microbiol 2024; 74. [PMID: 38805028 DOI: 10.1099/ijsem.0.006401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1 ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.
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Affiliation(s)
- Aekasit Suphannarot
- Division of Microbiology, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Waranya Butdee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Chanwit Suriyachadkun
- BIOTEC Culture Collection, Biodiversity and Biotechnological Resource Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Kannika Duangmal
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Ratchanee Mingma
- Division of Microbiology, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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Sun CS, Zhou LY, Liang QY, Wang XM, Lei YX, Xu ZX, Wang FQ, Chen GJ, Du ZJ, Mu DS. Short-chain fatty acids (SCFAs) as potential resuscitation factors that promote the isolation and culture of uncultured bacteria in marine sediments. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:400-414. [PMID: 37637259 PMCID: PMC10449756 DOI: 10.1007/s42995-023-00187-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/20/2023] [Indexed: 08/29/2023]
Abstract
Many marine bacteria are difficult to culture because they are dormant, rare or found in low-abundances. Enrichment culturing has been widely tested as an important strategy to isolate rare or dormant microbes. However, many more mechanisms remain uncertain. Here, based on 16S rRNA gene high-throughput sequencing and metabolomics technology, it was found that the short-chain fatty acids (SCFAs) in metabolites were significantly correlated with uncultured bacterial groups during enrichment cultures. A pure culture analysis showed that the addition of SCFAs to media also resulted in high efficiency for the isolation of uncultured strains from marine sediments. As a result, 238 strains belonging to 10 phyla, 26 families and 82 species were successfully isolated. Some uncultured rare taxa within Chlorobi and Kiritimatiellaeota were successfully cultured. Amongst the newly isolated uncultured microbes, most genomes, e.g. bacteria, possess SCFA oxidative degradation genes, and these features might aid these microbes in better adapting to the culture media. A further resuscitation analysis of a viable but non-culturable (VBNC) Marinilabiliales strain verified that the addition of SCFAs could break the dormancy of Marinilabiliales in 5 days, and the growth curve test showed that the SCFAs could shorten the lag phase and increase the growth rate. Overall, this study provides new insights into SCFAs, which were first studied as resuscitation factors in uncultured marine bacteria. Thus, this study can help improve the utilisation and excavation of marine microbial resources, especially for the most-wanted or key players. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00187-w.
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Affiliation(s)
- Chun-Shui Sun
- Marine College, Shandong University, Weihai, 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209 China
| | - Liu-Yan Zhou
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000 China
| | - Qi-Yun Liang
- Marine College, Shandong University, Weihai, 264209 China
| | - Xiao-Man Wang
- Tancheng County Inspection and Testing Center, Tancheng, 276100 China
| | - Yi-Xuan Lei
- Marine College, Shandong University, Weihai, 264209 China
| | - Zhen-Xing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657 Japan
| | - Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai, 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209 China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209 China
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Frantsuzova E, Bogun A, Vetrova A, Delegan Y. Methods of Identifying Gordonia Strains in Clinical Samples. Pathogens 2022; 11:pathogens11121496. [PMID: 36558832 PMCID: PMC9786905 DOI: 10.3390/pathogens11121496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Gordonia spp. are members of the family Gordoniacea in the suborder Corynebacteriales; their habitat, in most cases, is soil. Many representatives of this genus are human or veterinary pathogens. The main cause of the lack of a standardized approach to dealing with infections caused by Gordonia is their erroneous identification and little information regarding their susceptibility to antimicrobial drugs. This review presents the most common methods for identifying Gordonia strains, including modern approaches for identifying a species. The main prospects and future directions of this field of knowledge are briefly presented.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Correspondence:
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Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13030031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.
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Fu H, Ding L, Zhai J, Wang X. Purification effect evaluation of the designed new volcanic soil adsorption material containing bioreactor for eutrophic water treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:59821-59833. [PMID: 34148168 DOI: 10.1007/s11356-021-14924-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/11/2021] [Indexed: 06/12/2023]
Abstract
The purpose of this study was to investigate the purification effect of a new adsorption material containing bioreactor and the critical role of viable but non-culturable (VBNC) bacteria in a eutrophication ecosystem. Major water quality parameters of the prepared eutrophic water were determined, and the microbial community was analyzed during 2 years. The results showed that removal rates of total phosphorus (TP), total nitrogen (TN), chlorophyll-a (Chl-a), and chemical oxygen demand (COD) were 90.7-95.9%, 84.5-92.4%, 87.9-95.8%, and 68.3-82.7%, respectively, indicating the high efficiency of the bioreactor in the eutrophic water treatment. Although the bioreactor had been operated for 2 years, water from the treatment group was much clearer and odorless than from the control group, exhibiting the long service life of the bioreactor. Stopping operation in August caused significant decrease of the removal rates of major water quality parameters (p < 0.05). This operational stop event and high temperature in summer exerted a dual effect on the bioreactor, whereas the impact could be minimized when the bioreactor was running. Moreover, the total bacteria under +Rpf (active resuscitation-promoting factor) treatment were higher than under -Rpf (inactive resuscitation-promoting factor) treatment, implying that Rpf could resuscitate VBNC bacteria in the eutrophication ecosystem. Nine strains of VBNC bacteria were isolated based on the BLAST results of the 16S rRNA gene. Also, these bacteria might contribute to the eutrophic water treatment based on their functions of phosphorus collecting and denitrification. These results provided new insights for engineering technology innovations, and consequently these findings had benefits in eutrophic water treatment.
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Affiliation(s)
- Huiling Fu
- School of Safety and Environment Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Linxian Ding
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Jingyu Zhai
- Ecological Environment Monitoring Station of Yuxi city, Department of Ecology and Environment of Yunnan Province, Yuxi, 653100, China
| | - Xuesong Wang
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 510070, China.
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Welz P, Swanepoel G, Weels S, Le Roes-Hill M. Wastewater from the Edible Oil Industry as a Potential Source of Lipase- and Surfactant-Producing Actinobacteria. Microorganisms 2021; 9:microorganisms9091987. [PMID: 34576882 PMCID: PMC8465459 DOI: 10.3390/microorganisms9091987] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
Wastewaters generated from various stages of edible oil production in a canola processing facility were collected with the aim of determining the presence of lipase-producing actinobacteria of potential industrial significance. The high chemical oxygen demand (COD) readings (up to 86,700 mg L−1 in some samples) indicated that the wastewater exhibited the nutritional potential to support bacterial growth. A novel approach was developed for the isolation of metagenomic DNA from the oil-rich wastewater samples. Microbiota analysis of the buffer tank and refinery condensate tank wastewater samples showed a dominance of Cutibacterium acnes subsp. defendens, followed by a limited number of other actinobacterial genera, indicating the presence of a highly specialized actinobacterial population. Cultured isolates with typical actinobacterial morphology were analyzed for their ability to produce lipases and biosurfactants. Two strains, designated as BT3 and BT4, exhibited the highest lipase production levels when grown in the presence of tributyrin and olive oil (1.39 U mg−1 crude protein and 0.8 U mg−1 crude protein, respectively) and were subsequently definitively identified by genome sequencing to be related to Streptomyces albidoflavus. Cultivation of the strains in media containing different types of oils did not markedly increase the level of enzyme production, with the exception of strain BT4 (1.0 U mg−1 crude protein in the presence of peanut oil). Genome sequencing of the two strains, BT3 and BT4, revealed the presence of a range of lipase and esterase genes that may be involved in the production of the enzymes detected in this study. The presence of gene clusters involved in the production of biosurfactants were also detected, notably moreso in strain BT3 than BT4.
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Wang Y, Shi J, Tang L, Zhang Y, Zhang Y, Wang X, Zhang X. Evaluation of Rpf protein of Micrococcus luteus for cultivation of soil actinobacteria. Syst Appl Microbiol 2021; 44:126234. [PMID: 34343788 DOI: 10.1016/j.syapm.2021.126234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022]
Abstract
Rpf protein, a kind of resuscitation promoting factor, was first found in the culture supernatant of Micrococcus luteus. It can resuscitate the growth of M. luteus in "viable but non-culture, VBNC" state and promote the growth of Gram-positive bacteria with high G + C content. This paper investigates the resuscitating activity of M. luteus ACCC 41016T Rpf protein, which was heterologously expressed in E. coli, to cells of M. luteus ACCC 41016T and Rhodococcus marinonascens HBUM200062 in VBNC state, and examines the effect on the cultivation of actinobacteria in soil. The results showed that the recombinant Rpf protein had resuscitation effect on M. luteus ACCC 41016T and R. marinonascens HBUM200062 in VBNC state. 83 strains of actinobacteria, which were distributed in 9 families and 12 genera, were isolated from the experimental group with recombinant Rpf protein in the culture medium. A total of 41 strains of bacteria, which were distributed in 8 families and 9 genera, were isolated from the control group without Rpf protein. The experimental group showed richer species diversity than the control group. Two rare actinobacteria, namely HBUM206391T and HBUM206404T, were obtained in the experimental group supplemented with Rpf protein. Both may be potential new species of Actinomadura and Actinokineospora, indicating that the recombinant expression of M. luteus ACCC 41016T Rpf protein can effectively promote the isolation and culture of actinobacteria in soil.
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Affiliation(s)
- Yuhui Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding 071002, PR China
| | - Jiangli Shi
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding 071002, PR China
| | - Lingjie Tang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding 071002, PR China
| | - Yufan Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding 071002, PR China
| | - Yujia Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding 071002, PR China
| | - Xinyu Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding 071002, PR China
| | - Xiumin Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding 071002, PR China.
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Muangham S, Lipun K, Thamchaipenet A, Matsumoto A, Duangmal K. Gordonia oryzae sp. nov., isolated from rice plant stems (Oryza sativa L.). Int J Syst Evol Microbiol 2019; 69:1621-1627. [DOI: 10.1099/ijsem.0.003368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Supattra Muangham
- 1Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Kenika Lipun
- 1Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Arinthip Thamchaipenet
- 2Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Atsuko Matsumoto
- 3Kitasato Institute for Life Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Kannika Duangmal
- 1Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
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Yu XY, Zhai JY, Wu C, Zhang CY, Shi JY, Ding LX, Wu M. Pseudomonas pharmafabricae sp. nov., Isolated From Pharmaceutical Wastewater. Curr Microbiol 2018; 75:1119-1125. [PMID: 29725767 DOI: 10.1007/s00284-018-1495-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/17/2018] [Indexed: 11/25/2022]
Abstract
A Gram-stain-negative, aerobic, rod-shaped bacterial strain, designated ZYSR67-ZT, was isolated from a pharmaceutical wastewater sample collected from a chemical factory in Zhejiang, China. The strain was motile by a single polar flagellum and grew at 4-42 °C (optimum, 35 °C), pH 5.0-9.0 (optimum, 6.0) and 0-5.0% (w/v) NaCl (optimum, 2.0%). Based on multilocus sequence analysis using 16S rRNA, gyrB, rpoB and rpoD, the strain ZYSR67-ZT formed a distinct phylogenetic group in the genus Pseudomonas. The average nucleotide identity values between strain ZYSR67-ZT and the closely related 10 type strains of the Pseudomonas species were 75.8-78.6%. The in silico DNA-DNA hybridization values indicated that strain ZYSR67-ZT and the type strains of the Pseudomonas shared 21.4-23.1% DNA relatedness. The predominant isoprenoid quinone system was ubiquinone-9 while ubiquinone-8 was present in trace amounts. The major fatty acids (> 10%) identified were C12:0, C16:0, C18:1 ω7c and summed features 3 (C16:1 ω7c and/or iso-C15:0 2OH). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 62.6 mol%. On the basis of morphological, physiological and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain ZYSR67-ZT was proposed to represent a novel species of the genus Pseudomonas, named Pseudomonas pharmafabricae sp. nov.. The type strain is ZYSR67-ZT (= CGMCC 1.15498T = JCM 31306T).
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Affiliation(s)
- Xiao-Yun Yu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jing-Yu Zhai
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Chen Wu
- Zhejiang University of Water Resources and Electric Power, Hangzhou, 310018, People's Republic of China
| | - Chong-Ya Zhang
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China
| | - Jie-Ying Shi
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Lin-Xian Ding
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China.
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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Frikha Dammak D, Zarai Z, Najah S, Abdennabi R, Belbahri L, Rateb ME, Mejdoub H, Maalej S. Antagonistic Properties of Some Halophilic Thermoactinomycetes Isolated from Superficial Sediment of a Solar Saltern and Production of Cyclic Antimicrobial Peptides by the Novel Isolate Paludifilum halophilum. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1205258. [PMID: 28819625 PMCID: PMC5551467 DOI: 10.1155/2017/1205258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/18/2017] [Indexed: 02/07/2023]
Abstract
This study has focused on the isolation of twenty-three halophilic actinomycetes from two ponds of different salinity and the evaluation of their ability to exert an antimicrobial activity against both their competitors and several other pathogens. From the 23 isolates, 18 strains showed antagonistic activity, while 19 showed activities against one or more of the seven pathogen strains tested. Six strains exhibited consistent antibacterial activity against Gram-negative and Gram-positive pathogens characterized at the physiological and molecular levels. These strains shared only 94-95% 16S rRNA sequence identity with the closely related species of the Thermoactinomycetaceae family. Among them, the potent strain SMBg3 was further characterized and assigned to a new genus in the family for which the name Paludifilum halophilum (DSM 102817T) is proposed. Sequential extraction of the antimicrobial compounds with ethyl acetate revealed that the crude extract from SMBg3 strain had inhibitory effect on the growth of the plant pathogen Agrobacterium tumefaciens and the human pathogens Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa. Based on the HRESI-MS spectral data, the cyclic lipopeptide Gramicidin S and four cyclic dipeptides (CDPs) named cyclo(L-4-OH-Pro-L-Leu), cyclo(L-Tyr-L-Pro), cyclo(L-Phe-L-Pro), and cyclo(L-Leu-L-Pro) were detected in the fermentation broth of Paludifilum halophilum. To our knowledge, this is the first report on the isolation of these compounds from members of the Thermoactinomycetaceae family.
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Affiliation(s)
- Donyez Frikha Dammak
- Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES/72), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Ziad Zarai
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS, BPW, 1173 Sfax, Tunisia
| | - Soumaya Najah
- Institut de Biologie Integrative, UMR 9198, Université Paris-Sud, Bat 400, 91405 Orsay Cedex, France
| | - Rayed Abdennabi
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000 Neuchatel, Switzerland
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000 Neuchatel, Switzerland
| | - Mostafa E. Rateb
- School of Science & Sport, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Hafedh Mejdoub
- Laboratoire des Biotechnologies Végétales Appliquées à l'Amélioration des Cultures, FSS, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Sami Maalej
- Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES/72), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
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12
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Gordonia: isolation and identification in clinical samples and role in biotechnology. Folia Microbiol (Praha) 2017; 62:245-252. [DOI: 10.1007/s12223-017-0491-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 01/01/2017] [Indexed: 10/20/2022]
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13
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Delegan YA, Vetrova AA, Akimov VN, Titok MA, Filonov AE, Boronin AM. Thermotolerant oil-degrading bacteria isolated from soil and water of geographically distant regions. APPL BIOCHEM MICRO+ 2016. [DOI: 10.1134/s0003683816040025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Tsang CC, Xiong L, Poon RWS, Chen JHK, Leung KW, Lam JYW, Wu AKL, Chan JFW, Lau SKP, Woo PCY. Gordonia hongkongensis sp. nov., isolated from blood culture and peritoneal dialysis effluent of patients in Hong Kong. Int J Syst Evol Microbiol 2016; 66:3942-3950. [PMID: 27406710 DOI: 10.1099/ijsem.0.001292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Two bacterial strains, HKU50T and HKU46, were isolated in Hong Kong from the blood culture and the peritoneal dialysis effluent of two patients. The strains are Gram-stain-positive, acid-fast, non-motile, non-sporulating bacilli. They grow on Columbia agar with 5 % defibrinated sheep blood and brain-heart infusion agar under aerobic conditions with 5 % CO2 at 37 °C as pink-to-orange, non-haemolytic colonies. The strains are catalase-positive and oxidase-negative, and have a unique biochemical profile distinguishable from other closely related species. DNA sequencing revealed that both isolates possessed multiple intra-genomic 16S rRNA gene copies (99.8-100 % sequence identities to Gordonia lacunae NRRL B-24551T and Gordonia terrae NRRL B-16283T). Phylogenetic analysis of the 16S rRNA gene, secA1 and gyrB showed that the two isolates formed a distinct branch within the genus Gordonia and were most closely related to G. lacunae and G. terrae. DNA-DNA hybridization demonstrated ≤53.7 % and ≤49.4 % DNA relatedness between the two isolates and G. lacunae, and between the two isolates and G. terrae, respectively. Hierarchical cluster analysis of MALDI-TOF MS main spectrum profiles showed that strains HKU50T and HKU46 were closely related to each other, but were distinct from G. lacunae, G. terrae, or any other species of the genus Gordonia in the Bruker database. The chemotaxonomic traits of the two strains were highly similar, and the major fatty acids were summed feature 4 (iso-C15 : 0 2-OH/C16 : 1trans-9), C16 : 0, C18 : 1cis-9, and tuberculostearic acid. A novel species named Gordonia hongkongensis sp. nov. is proposed to accommodate strains HKU50T and HKU46, with strain HKU50T (=CCOS 955T=CIP 111027T=NBRC 111234T=NCCP 16210T) as the type strain.
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Affiliation(s)
- Chi-Ching Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong, SAR
| | - Lifeng Xiong
- Department of Microbiology, The University of Hong Kong, Hong Kong, SAR
| | - Rosana W S Poon
- Department of Microbiology, The University of Hong Kong, Hong Kong, SAR
| | - Jonathan H K Chen
- Department of Microbiology, The University of Hong Kong, Hong Kong, SAR
| | - Kit-Wah Leung
- Department of Microbiology, The University of Hong Kong, Hong Kong, SAR
| | - Jimmy Y W Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, SAR
| | - Alan K L Wu
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, SAR
| | - Jasper F W Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, SAR.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, SAR.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, SAR.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, SAR
| | - Susanna K P Lau
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, SAR.,Department of Microbiology, The University of Hong Kong, Hong Kong, SAR.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, SAR.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, SAR
| | - Patrick C Y Woo
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, SAR.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, SAR.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, SAR.,Department of Microbiology, The University of Hong Kong, Hong Kong, SAR
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Yu XY, Zhang L, Ren B, Yang N, Liu M, Liu XT, Zhang LX, Ding LX. Arthrobacter liuii sp. nov., resuscitated from Xinjiang desert soil. Int J Syst Evol Microbiol 2014; 65:896-901. [PMID: 25525122 DOI: 10.1099/ijs.0.000037] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain positive, aerobic, non-motile actinobacterium, designated DSXY973(T), was isolated from soil samples collected from Xinjiang desert using medium supplemented with resuscitation-promoting factor, and subjected to a polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that DSXY973(T) belonged to the genus Arthrobacter and was most closely related to Arthrobacter oryzae JCM 15922(T) with 97.1 % similarity. The DNA G+C content was 67.6 %. Cells of strain DSXY973(T) mainly contained MK-9(H2), and the cell wall contained l-lysine as the primary diamino acid. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. Strain DSXY973(T) was positive for catalase and negative for oxidase activity. On the basis of its phylogenetic position and phenotypic properties, strain DSXY973(T) represents a novel species of the genus Arthrobacter, for which the name Arthrobacter liuii sp. nov. is proposed. The type strain is DSXY973(T) ( = CGMCC1.12778(T) = JCM 19864(T)).
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Affiliation(s)
- Xiao-Yun Yu
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, PR China
| | - Li Zhang
- University of Chinese Academy of Sciences, Beijing 100101 PR China.,Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Biao Ren
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Na Yang
- University of Chinese Academy of Sciences, Beijing 100101 PR China.,Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Mei Liu
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xue-Ting Liu
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Li-Xin Zhang
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lin-Xian Ding
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, PR China.,College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, PR China
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Li SH, Yu XY, Park DJ, Hozzein WN, Kim CJ, Shu WS, Wadaan MAM, Ding LX, Li WJ. Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique. Antonie van Leeuwenhoek 2014; 107:357-66. [PMID: 25417053 DOI: 10.1007/s10482-014-0334-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
Abstract
A Gram-positive, aerobic, non-motile, non-spore forming strain, designated DSD51W(T), was isolated using a resuscitative technique from a soil sample collected from Kyoto park, Japan, and characterized by using a polyphasic approach. The morphological and chemotaxonomic properties of the isolate were typical of those of members of the genus Rhodococcus. Strain DSD51W(T) was found to form a coherent cluster with Rhodococcus hoagii ATCC 7005(T), Rhodococcus equi NBRC 101255(T), Rhodococcus defluvii Call(T) and Rhodococcus kunmingensis YIM 45607(T) as its closest phylogenetic neighbours in 16S rRNA gene sequence analysis. However, the DNA-DNA hybridization values with the above strains were 58.2 ± 2.2, 58.4 ± 1.9, 45.1 ± 1.4 and 40.3 ± 4.7 %, respectively. In combination with differences in physiological and biochemical properties, strain DSD51W(T) can be concluded to represent a novel species of the genus Rhodococcus, for which the name Rhodococcus soli sp. nov. is proposed, with the type strain DSD51W(T) (=KCTC 29259(T) = JCM 19627(T) = DSM 46662(T) = KACC 17838(T)).
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Affiliation(s)
- Shan-Hui Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
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17
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2014. [DOI: 10.1099/ijs.0.070847-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Su X, Liu Y, Hashmi MZ, Hu J, Ding L, Wu M, Shen C. Rhodococcus biphenylivorans sp. nov., a polychlorinated biphenyl-degrading bacterium. Antonie van Leeuwenhoek 2014; 107:55-63. [DOI: 10.1007/s10482-014-0303-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/07/2014] [Indexed: 11/30/2022]
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Fu H, Wei Y, Zou Y, Li M, Wang F, Chen J, Zhang L, Liu Z, Ding L. Research Progress on the <i>Actinomyces arthrobacter</i>. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/aim.2014.412081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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