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Ning S, Hou Q, Yang J, Ma C, Chen Y, Liu Y, Zhou H, Ma J, Huang Y, Cao L, Liu X, Pu J, Jin D, Lu S, Xu J. Planococcus shenhongbingii sp. nov., Planococcus shixiaomingii sp. nov. and Planococcus liqunii sp. nov., isolated from soil of the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2024; 74. [PMID: 39042107 DOI: 10.1099/ijsem.0.006465] [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: 07/24/2024] Open
Abstract
Six novel bacterial strains, designated N016T, N017, N022T, N028, N056T, and N064, were isolated from soil sampled on the Qinghai-Tibet Plateau. Cells were aerobic, orange or yellow, globular or rod-shaped, non-motile, non-spore-forming, Gram-stain-positive, catalase-positive and oxidase-negative. All the isolates were salt-tolerant and could grow in the range of 4-42 °C. Results of phylogenomic analyses based on 16S rRNA gene sequences and core genomic genes showed that the three pairs of strains (N016T/N017, N022T/N028, and N056T/N064) were closely related to the members of the genus Planococcus, and clustered with Planococcus ruber, Planococcus glaciei, and Planococcus chinensis. The digital DNA-DNA hybridization and average nucleotide identity values of the six novel strains with other members of the genus Planococcus were within the ranges of 18.7-53 % and 70.58-93.49 %, respectively, all below the respective recommended thresholds of 70.0 % and 95-96 %. The genomic DNA G+C content of the six strains ranged from 43.5 to 46.0 mol%. The major fatty acids of the six strains were anteiso-C15 : 0, iso-C14 : 0, and C16 : 1 ω7c alcohol. The predominant polar lipids of strains N016T, N022T, and N056T were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Menaquinones 7 and 8 were the respiratory quinones. The results of the above analyses indicated that the six strains represent three novel species of the genus Planococcus, for which the names Planococcus shenhongbingii sp. nov. (type strain N016T=GDMCC 1.4062T=JCM 36224T), Planococcus shixiaomingii sp. nov. (type strain N022T=GDMCC 1.4063T=JCM 36225T), and Planococcus liqunii sp. nov. (type strain N056T=GDMCC 1.4064T=JCM 36226T) are proposed.
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Affiliation(s)
- Shuo Ning
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Qiang Hou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Academy of Medical Sciences, Shanxi Medical University, Taiyuan 030001, PR China
| | - Jing Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Caiyun Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yulu Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yue Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Huimin Zhou
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jiajia Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Academy of Medical Sciences, Shanxi Medical University, Taiyuan 030001, PR China
| | - Yuyuan Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, Nanning 530021, PR China
| | - Linglin Cao
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaorui Liu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Shan Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Academy of Medical Sciences, Shanxi Medical University, Taiyuan 030001, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
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Huang Y, Jiao Y, Zhang S, Tao Y, Zhang S, Jin D, Pu J, Liu L, Yang J, Lu S. Description of Ornithinimicrobium cryptoxanthini sp. nov., a Novel Actinomycete Producing β-cryptoxanthin Isolated from the Tongtian River Sediments. J Microbiol 2023; 61:379-388. [PMID: 36929341 DOI: 10.1007/s12275-023-00029-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023]
Abstract
Two novel Gram-stain-positive, aerobic, non-motile, and yellow-pigmented, irregular rod-shaped bacteria (JY.X269 and JY.X270T) were isolated from the near-surface sediments of river in Qinghai Province, P. R. China (32°37'13″N, 96°05'37″E) in July 2019. Both strains were shown to grow at 15-35 °C and pH 7.0-10.0, and in the presence of 0-6.0% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that the isolates were closely related to Ornithinimicrobium cavernae CFH 30183 T (98.6-98.8% 16S rRNA gene sequence similarity), O. ciconiae H23M54T (98.5-98.6%) and O. murale 01-Gi-040T (98.3-98.5%). The phylogenetic and phylogenomic trees based on the 16S rRNA gene and 537 core gene sequences, respectively, revealed that the two strains formed a distinct cluster with the above three species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between our two isolates (JY.X269 and JY.X270T) and other Ornithinimicrobium species were within the ranges of 19.0-23.9% and 70.8-80.4%, respectively, all below the respective recommended 70.0% and 95-96% cutoff point. Furthermore, the major cellular fatty acids (> 10.0%) of strains JY.X269 and JY.X270T were iso-C15:0, iso-C16:0, and summed feature 9. Strain JY.X270T contained MK-8(H4) and ornithine as the predominant menaquinone and diagnostic diamino acid component within the cell wall teichoic acids. β-cryptoxanthin (C40H56O) can be extracted from strain JY.X270T, and its content is 6.3 µg/ml. Based on results from the phylogenetic, chemotaxonomic, and phenotypic analyses, the two strains could be classified as a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium cryptoxanthini sp. nov. is proposed (type strain JY.X270T = CGMCC 1.19147T = JCM 34882T).
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Affiliation(s)
- Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Yifan Jiao
- Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, 030009, People's Republic of China
| | - Sihui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China.,Peking University School of Public Health, Beijing, 100083, People's Republic of China
| | - Yuanmeihui Tao
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Suping Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, People's Republic of China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China. .,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, People's Republic of China.
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, People's Republic of China. .,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, People's Republic of China.
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3
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Huang Y, Zhang S, Tao Y, Yang J, Lu S, Jin D, Pu J, Luo W, Zheng H, Liu L, Jiang JF, Xu J. Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces ( Rousettus leschenaultia and Taphozous perforates). Front Cell Infect Microbiol 2023; 13:1093407. [PMID: 36864884 PMCID: PMC9973731 DOI: 10.3389/fcimb.2023.1093407] [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: 11/09/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
Four Gram-staining-positive, aerobic, non-motile, circle-shaped bacteria were isolated from the faeces of bats (Rousettus leschenaultia and Taphozous perforates) collected from Guangxi autonomous region (E106°49'20″, N22°20'54″) and Yunnan province (E102°04'39″, N25°09'10″) of South China. Strains HY006T and HY008 shared highly 16S rRNA gene sequence similarity to those of Ornithinimicrobium pratense W204T (99.3%) and O. flavum CPCC 203535T (97.3%), while the strains HY1745 and HY1793T were closest to the type strains O. ciconiae H23M54T (98.7%), O. cavernae CFH 30183T (98.3%), and O. murale 01-Gi-040T (98.1%). Furthermore, when compared to the other members of the genus Ornithinimicrobium, the digital DNA-DNA hybridization and average nucleotide identity values of the four novel strains were within the ranges of 19.6-33.7% and 70.6-87.4%, respectively, both of which were below the respective recommended cutoff values of 70.0% and 95-96%. Significantly, strain HY006T was resistant to chloramphenicol and linezolid whereas strain HY1793T was resistant to erythromycin, clindamycin (intermediately), and levofloxacin (intermediately). The main cellular fatty acids (>20.0%) of our isolates were iso-C15:0 and iso-C16:0. Strains HY006T and HY1793T contained ornithine as the diagnostic diamino acid, also along with the alanine, glycine and glutamic acid in their cell wall. Based on phylogenetic, chemotaxonomic and phenotypic analyses, these four strains could be classified as two novel species of the genus Ornithinimicrobium, for which the names Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. are proposed. The type strains are HY006T (=CGMCC 1.16565T =JCM 33397T) and HY1793T (=CGMCC 1.19143T =JCM 34881T), respectively.
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Affiliation(s)
- Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Suping Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuanmeihui Tao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jia-fu Jiang
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China,*Correspondence: Jianguo Xu, ; Jia-fu Jiang,
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China,Research Institute of Public Health, Nankai University, Tianjin, China,*Correspondence: Jianguo Xu, ; Jia-fu Jiang,
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4
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Huang Y, Sun Y, Huang Q, Lv X, Pu J, Zhu W, Lu S, Jin D, Liu L, Shi Z, Yang J, Xu J. The Threat of Potentially Pathogenic Bacteria in the Feces of Bats. Microbiol Spectr 2022; 10:e0180222. [PMID: 36287057 PMCID: PMC9769573 DOI: 10.1128/spectrum.01802-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/23/2022] [Indexed: 01/05/2023] Open
Abstract
Bats have attracted global attention because of their zoonotic association with severe acute respiratory syndrome coronavirus (SARS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Previous and ongoing studies have predominantly focused on bat-borne viruses; however, the prevalence or abundance of bat-borne pathogenic bacteria and their potential public health significance have largely been neglected. For the first time, this study used both metataxonomics (16S rRNA marker gene sequencing) and culturomics (traditional culture methods) to systematically evaluate the potential public health significance of bat fecal pathogenic bacteria. To this end, fecal samples were obtained from five bat species across different locations in China, and their microbiota composition was analyzed. The results revealed that the bat microbiome was most commonly dominated by Proteobacteria, while the strictly anaerobic phylum Bacteroidetes occupied 35.3% of the relative abundance in Rousettus spp. and 36.3% in Hipposideros spp., but less than 2.7% in the other three bat species (Taphozous spp., Rhinolophus spp., and Myotis spp.). We detected 480 species-level phylotypes (SLPs) with PacBio sequencing, including 89 known species, 330 potentially new species, and 61 potentially higher taxa. In addition, a total of 325 species were identified by culturomics, and these were classified into 242 named species and 83 potentially novel species. Of note, 32 of the 89 (36.0%) known species revealed by PacBio sequencing were found to be pathogenic bacteria, and 69 of the 242 (28.5%) known species isolated by culturomics were harmful to people, animals, or plants. Additionally, nearly 40 potential novel species which may be potential bacterial pathogens were identified. IMPORTANCE Bats are one of the most diverse and widely distributed groups of mammals living in close proximity to humans. In recent years, bat-borne viruses and the viral zoonotic diseases associated with bats have been studied in great detail. However, the prevalence and abundance of pathogenic bacteria in bats have been largely ignored. This study used high-throughput sequencing techniques (metataxonomics) in combination with traditional culture methods (culturomics) to analyze the bacterial flora in bat feces from different species of bats in China, revealing that bats are natural hosts of pathogenic bacteria and carry many unknown bacteria. The results of this study can be used as guidance for future investigations of bacterial pathogens in bats.
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Affiliation(s)
- Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yamin Sun
- Research Institute of Public Health, Nankai University, Tianjin, People’s Republic of China
- Research Center for Functional Genomics and Biochip, Tianjin, People’s Republic of China
| | - Qianni Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Xianglian Lv
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zhengli Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Research Institute of Public Health, Nankai University, Tianjin, People’s Republic of China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Peking University School of Public Health, Beijing, People’s Republic of China
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Huang Y, Gong J, Dong L, Yang J, Lu S, Lai XH, Pu J, Jin D, Xu J. Gordonia zhenghanii sp. nov. and Gordonia liuliyuniae sp. nov., isolated from bat faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Four mesophilic actinobacteria (HY002T, HY442, HY366T and HY285) isolated from the faeces of bats collected in southern China were found to be strictly aerobic, non-motile, rod-shaped, oxidase-negative, Gram-stain-positive and catalase-positive. Strains HY002T and HY366T contained meso-diaminopimelic acid as the diagnostic diamino acid and MK-9(H2) the sole respiratory quinone. Arabinose, galactose and ribose were detected in the whole-cell hydrolysates of both type strains. The main cellular fatty acids (> 10.0%) of all strains were C16 : 0, C18 : 1
ω9c, 10-methyl-C18 : 0 and summed feature 3. Strains HY002T and HY366T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidyl inositol mannosides as the major polar lipids. The phylogenetic/phylogenomic analyses based on 16S rRNA gene and genomic sequence comparison revealed that the four strains belong to the genus
Gordonia
, most closely related to
G. neofelifaecis
NRRL B-59395T(98.2–98.3% sequence similarity) on the EzBioCloud database. The G+C contents of strains HY002T and HY366T based on genomic DNA were 66.5 and 66.9%, respectively. The DNA–DNA relatedness values between the two types strains and members of the genus
Gordonia
were far below 70 % (18.6–23.1 %). All genotypic and phenotypic data indicated that the four strains are representatives of two novel separate species, for which the names Gordonia zhenghanii sp. nov. and Gordonia liuliyuniae sp. nov. are proposed, with HY002T (=CGMCC 4 7757T=JCM 34 878T) and HY366T (=CGMCC 1 19146T=JCM 34 879T) as the respective type strains.
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Affiliation(s)
- Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jian Gong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lingzhi Dong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, 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 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Peking University School of Public Health, Beijing 100083, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Research Institute of Public Health, Nankai University, Tianjin 300350, PR China
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6
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Huang Y, Dong L, Gong J, Yang J, Lu S, Lai XH, Jin D, Huang Q, Pu J, Liu L, Xu J. Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces. J Microbiol 2022; 60:977-985. [PMID: 35984616 PMCID: PMC9390107 DOI: 10.1007/s12275-022-2134-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022]
Abstract
Two strictly aerobic, Gram-staining-positive, non-spore-forming, regular rod-shaped (approximately 0.7 × 1.9 mm) bacteria (HY170T and HY001) were isolated from bat feces collected from Chongzuo city, Guangxi province (22°20′54″N, 106°49′20″E, July 2011) and Chuxiong Yi Autonomous Prefecture, Yunnan province (25°09′10″N, 102°04′39″E, October 2013) of South China, respectively. Optimal growth is obtained at 25–28°C (range, 4–32°C) on BHI-5% sheep blood plate with pH 7.5 (range, 5.0–10.0) in the presence of 0.5–1.0% NaCl (w/v) (range, 0–15% NaCl [w/v]). The phylogenetic and phylogenomic trees based respectively on the 16S rRNA gene and 845 core gene sequences revealed that the two strains formed a distinct lineage within the genus Brevibacterium, most closely related to B. aurantiacum NCDO 739T (16S rRNA similarity, both 98.5%; dDDH, 46.7–46.8%; ANI, 91.9–92.1%). Strain HY170T contained MK-8(H2), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), galactose and ribose as the predominant menaquinone, major polar lipids, and main sugars in the cell wall teichoic acids, respectively. The meso-diaminopimelic acid (meso-DAP) was the diagnostic diamino acid of the peptidoglycan found in strain HY170T. Anteiso-C15:0 and anteiso-C17:0 were the major fatty acids (> 10%) of strains HY170T and HY001, with anteiso-C17:1A predominant in strain HY170T but absent in strain HY001. Mining the genomes revealed the presence of secondary metabolite biosynthesis gene clusters encoding for non-alpha poly-amino acids (NAPAA), ectoine, siderophore, and terpene. Based on results from the phylogenetic, chemotaxonomic and phenotypic analyses, the two strains could be classified as a novel species of the genus Brevibacterium, for which the name Brevibacterium zhoupengii sp. nov. is proposed (type strain HY170T = CGMCC 1.18600T = JCM 34230T).
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Affiliation(s)
- Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Lingzhi Dong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
| | - Jian Gong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, China
| | - Qianni Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, 030001, China.
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 102206, China.
- Research Institute of Public Health, Nankai University, Tianjin, 300350, China.
- Peking University School of Public Health, Beijing, 100083, China.
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