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Wang C, Wang S, Jing S, Zeng Y, Yang L, Mu Y, Ding Z, Song Y, Sun Y, Zhang G, Wei D, Li M, Ma Y, Zhou H, Wu L, Feng J. Data-Driven Engineering of Phages with Tunable Capsule Tropism for Klebsiella pneumoniae. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309972. [PMID: 38937990 DOI: 10.1002/advs.202309972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/26/2024] [Indexed: 06/29/2024]
Abstract
Klebsiella pneumoniae, a major clinical pathogen known for causing severe infections, is attracting heightened attention due to its escalating antibiotic resistance. Phages are emerging as a promising alternative to antibiotics; however, their specificity to particular hosts often restricts their use. In this study, a collection of 114 phages is obtained and subjected to analysis against 238 clinical K. pneumoniae strains, revealing a spectrum of lytic behaviors. A correlation between putative tail protein clusters and lysis patterns leads to the discovery of six receptor-binding protein (RBP) clusters that determine host capsule tropism. Significantly, RBPs with cross-capsular lysis capabilities are identified. The newly-identified RBPs provide a toolbox for customizing phages to target diverse capsular types. Building on the toolbox, the engineered phages with altered RBPs successfully shifted and broadened their host capsule tropism, setting the stage for tunable phage that offer a precise and flexible solution to combat K. pneumoniae infections.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Shisong Jing
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Zeng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lili Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Yongqi Mu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zixuan Ding
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dawei Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingfei Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Linhuan Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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2
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Boutroux M, Chiarelli A, Ferrari ML, Chesneau O, Clermont D, Betsou F. A Ranking Tool for "Category Killer" Microbial Biobanks. Biopreserv Biobank 2024. [PMID: 38923919 DOI: 10.1089/bio.2024.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024] Open
Abstract
Microbial biobanks preserve and provide microbial bioresources for research, training, and quality control purposes. They ensure the conservation of biodiversity, contribute to taxonomical research, and support scientific advancements. Microbial biobanks can cover a wide range of phylogenetic and metabolic diversity ("category killers") or focus on specific taxonomic, thematic, or disease areas. The strategic decisions about strain selection for certain applications or for the biobank culling necessitate a method to support prioritization and selection. Here, we propose an unbiased scoring approach based on objective parameters to assess, categorize, and assign priorities among samples in stock in a microbial biobank. We describe the concept of this ranking tool and its application to identify high-priority strains for whole genome sequencing with two main goals: (i) genomic characterization of quality control, reference, and type strains; (ii) genome mining for the discovery of natural products, bioactive and antimicrobial molecules, with focus on human diseases. The general concept of the tool can be useful to any biobank and for any ranking or culling needs.
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Affiliation(s)
- Martin Boutroux
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur - Project Management Office, Paris, France
| | - Adriana Chiarelli
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur - Project Management Office, Paris, France
| | - Mariana L Ferrari
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur - Project Management Office, Paris, France
| | - Olivier Chesneau
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur - Collection de l'Institut Pasteur, Paris, France
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur - Collection de l'Institut Pasteur, Paris, France
| | - Fay Betsou
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur - Project Management Office, Paris, France
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3
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Goussarov G, Mysara M, Cleenwerck I, Claesen J, Leys N, Vandamme P, Van Houdt R. Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 38916949 DOI: 10.1099/mic.0.001469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Metagenome community analyses, driven by the continued development in sequencing technology, is rapidly providing insights in many aspects of microbiology and becoming a cornerstone tool. Illumina, Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) are the leading technologies, each with their own advantages and drawbacks. Illumina provides accurate reads at a low cost, but their length is too short to close bacterial genomes. Long reads overcome this limitation, but these technologies produce reads with lower accuracy (ONT) or with lower throughput (PacBio high-fidelity reads). In a critical first analysis step, reads are assembled to reconstruct genomes or individual genes within the community. However, to date, the performance of existing assemblers has never been challenged with a complex mock metagenome. Here, we evaluate the performance of current assemblers that use short, long or both read types on a complex mock metagenome consisting of 227 bacterial strains with varying degrees of relatedness. We show that many of the current assemblers are not suited to handle such a complex metagenome. In addition, hybrid assemblies do not fulfil their potential. We conclude that ONT reads assembled with CANU and Illumina reads assembled with SPAdes offer the best value for reconstructing genomes and individual genes of complex metagenomes, respectively.
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Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Bioinformatics group, Information Technology & Computer Science, Nile University, Giza, Egypt
| | - Ilse Cleenwerck
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Jürgen Claesen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Present address: Department of Epidemiology & Biostatistics, Amsterdam UMC, VU University, Amsterdam, Netherlands
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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Chen LB, OuYang YT, Liu L, Jin PJ, Huang RR, Pan WY, Wang Y, Xing JY, She TT, Jiao JY, Wang S, Li WJ. Methylobacterium nigriterrae sp. nov., isolated from black soil. Antonie Van Leeuwenhoek 2024; 117:83. [PMID: 38806744 DOI: 10.1007/s10482-024-01981-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/18/2024] [Indexed: 05/30/2024]
Abstract
An aerobic, Gram-stain-negative, motile rod bacterium, designated as SYSU BS000021T, was isolated from a black soil sample in Harbin, Heilongjiang province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Methylobacterium, and showed the highest sequence similarity to Methylobacterium segetis KCTC 62267 T (98.51%) and Methylobacterium oxalidis DSM 24028 T (97.79%). Growth occurred at 20-37℃ (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0% (w/v) NaCl. Polar lipids comprised of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified polar lipid. The major cellular fatty acids (> 5%) were C18:0 and C18:1 ω7c and/or C18:1 ω6c. The predominant respiratory quinone was Q-10. The genomic G + C content was 68.36% based on the whole genome analysis. The average nucleotide identity (≤ 83.5%) and digital DNA-DNA hybridization (≤ 27.3%) values between strain SYSU BS000021T and other members of the genus Methylobacterium were all lower than the threshold values recommended for distinguishing novel prokaryotic species. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain SYSU BS000021T represents a novel species of the genus Methylobacterium, for which the name Methylobacterium nigriterrae sp. nov. is proposed. The type strain of the proposed novel species is SYSU BS000021T (= GDMCC 1.3814 T = KCTC 8051 T).
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Affiliation(s)
- Le-Bin Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu-Ting OuYang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Pin-Jiao Jin
- Heilongjiang Academy of Black Soil Conservation & Utilization/Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin, 150086, People's Republic of China
| | - Rong-Rong Huang
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Wen-Yi Pan
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Ying Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Ying Xing
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ting-Ting She
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation & Utilization/Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin, 150086, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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5
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Chebotar VK, Gancheva MS, Chizhevskaya EP, Keleinikova OV, Baganova ME, Zaplatkin AN, Husainov KA. Whole-genome sequence of Kosakonia cowanii strain W006, isolated from seeds of Triticum aestivum L. Microbiol Resour Announc 2024; 13:e0118123. [PMID: 38488373 PMCID: PMC11008199 DOI: 10.1128/mra.01181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/04/2024] [Indexed: 04/12/2024] Open
Abstract
In this study, we sequence, assemble, and annotate Kosakonia cowanii strain W006, isolated from seeds of Triticum aestivum L. W006 has a single circular chromosome of 4,788,099 bp and 4,466 genes, with a mean G +C content of 56.1%.
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Affiliation(s)
- Vladimir K. Chebotar
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Maria S. Gancheva
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, St. Petersburg, Russia
| | | | | | - Maria E. Baganova
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
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6
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Huq MA, Rahman MS, Rahman MM. Aquincola agrisoli sp. nov., isolated from rhizospheric soil of eggplant and in silico genome mining for the prediction of biosynthetic gene clusters. Int J Syst Evol Microbiol 2024; 74. [PMID: 38683662 DOI: 10.1099/ijsem.0.006355] [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: 05/01/2024] Open
Abstract
A Gram-stain negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-54T, was isolated from the rhizospheric soil of eggplant. The colonies were observed to be light pink coloured, smooth, spherical and 0.2-0.6 mm in diameter when grown on R2A agar medium for 2 days. MAHUQ-54T was able to grow at 15-40 °C, at pH 5.5-9.0 and in the presence of 0-0.5 % NaCl (w/v). The strain gave positive results for both catalase and oxidase tests. The strain was positive for hydrolysis of l-tyrosine, urea, Tween 20 and Tween 80. On the basis of the results of 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Aquincola and is closely related to Aquincola tertiaricarbonis L10T (98.8 % sequence similarity) and Leptothrix mobilis Feox-1T (98.2 %). MAHUQ-54T has a draft genome size of 5 994 516 bp (60 contigs), annotated with 5348 protein-coding genes, 45 tRNA and 5 rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between MAHUQ-54T and its closest phylogenetic neighbours were 75.8-83.3 and 20.8-25.3 %, respectively. In silico genome mining revealed that MAHUQ-54T has a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 70.4 %. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). On the basis of dDDH, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAHUQ-54T represents a novel species within the genus Aquincola, for which the name Aquincola agrisoli sp. nov. is proposed, with MAHUQ-54T (=KACC 22001T = CGMCC 1.18515T) as the type strain.
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
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7
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Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38512750 DOI: 10.1099/ijsem.0.006300] [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: 03/23/2024] Open
Abstract
The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics limited the comprehensive understanding of microbial diversity and evolution. The introduction of molecular techniques, particularly DNA sequencing and genomics, has transformed our perception of prokaryotic diversity. In the past two decades, advancements in genome sequencing have transitioned from traditional methods to a genome-based taxonomic framework, not only to define species, but also higher taxonomic ranks. As technology and databases rapidly expand, maintaining updated standards is crucial. This work seeks to revise the 2018 guidelines for applying genome sequencing data in microbial taxonomy, adapting minimal standards and recommendations to reflect technological progress during this period.
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Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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Li X, Li M, Shi W, Li X, Xiang Z, Su L. Clostridium lamae sp. nov., a novel bacterium isolated from the fresh feces of alpaca. Antonie Van Leeuwenhoek 2024; 117:36. [PMID: 38367205 DOI: 10.1007/s10482-024-01931-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/21/2024] [Indexed: 02/19/2024]
Abstract
A novel Gram-positive, anaerobic, nonspore-forming, rod-shaped bacterium, designated strain NGMCC 1.200840 T, was isolated from the alpacas fresh feces. The taxonomic position of the novel strain was determined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed strain NGMCC 1.200840 T was a member of the genus Clostridium and closely related to Clostridium tertium DSM 2485 T (98.16% sequence similarity). Between strains NGMCC 1.200840 T and C. tertium DSM 2485 T, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 79.91% and 23.50%, respectively. Genomic DNA G + C content is 28.44 mol%. The strain can utilise D-glucose, D-mannitol, D-lactose, D-saccharose, D-maltose, D-xylose, L-arabinose, D-cellobiose, D-mannose, D-melezitose, D-raffinose, D-sorbitol, L-rhamnose, D-trehalose, D-galactose and Arbutin to produce acid. The optimal growth pH was 7, the temperature was 37 °C, and the salt concentration was 0-0.5% (w/v). The major cellular fatty acids (> 10%) included iso-C15:0, anteiso-C15:0 and iso-C17:0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two unidentified aminolipids. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, NGMCC 1.200840 T represents a novel species within the genus Clostridium, for which the named Clostridium lamae sp. nov. is proposed. The type strain is NGMCC 1.200840 T (= CGMCC 1.18014 T = JCM 35704 T).
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Affiliation(s)
- Xue Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Ming Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Technology Support Platform, Beijing, 100193, China
| | - Weixiong Shi
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Xia Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Zhiguang Xiang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China.
- Changping National Laboratory (CPNL), Beijing, 102299, China.
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9
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Guo C, Chen Q, Fan G, Sun Y, Nie J, Shen Z, Meng Z, Zhou Y, Li S, Wang S, Ma J, Sun Q, Wu L. gcPathogen: a comprehensive genomic resource of human pathogens for public health. Nucleic Acids Res 2024; 52:D714-D723. [PMID: 37850635 PMCID: PMC10767814 DOI: 10.1093/nar/gkad875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration and monitoring of antibiotic resistance features and virulence factors. The catalogue seamlessly integrates and analyzes genomic data and associated metadata for human pathogens isolated from infected patients, animal hosts, food and the environment. The pathogen list is supported by evidence from medical or government pathogenic lists and publications. The current version of gcPathogen boasts an impressive collection of 1 164 974 assemblies comprising 986 044 strains from 497 bacterial taxa, 4794 assemblies encompassing 4319 strains from 265 fungal taxa, 89 965 assemblies featuring 13 687 strains from 222 viral taxa, and 646 assemblies including 387 strains from 159 parasitic taxa. Through this database, researchers gain access to a comprehensive 'one-stop shop' that facilitates global, long-term public health surveillance while enabling in-depth analysis of genomes, sequence types, antibiotic resistance genes, virulence factors and mobile genetic elements across different countries, diseases and hosts. To access and explore the data and statistics, an interactive web interface has been developed, which can be accessed at https://nmdc.cn/gcpathogen/. This user-friendly platform allows seamless querying and exploration of the extensive information housed within the gcPathogen database.
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Affiliation(s)
- Chongye Guo
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Qi Chen
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Guomei Fan
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Yan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Jingyi Nie
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Zhihong Shen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhen Meng
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuanchun Zhou
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Shiwen Li
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Shuai Wang
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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10
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de la Haba RR, Arahal DR, Sánchez-Porro C, Chuvochina M, Wittouck S, Hugenholtz P, Ventosa A. A long-awaited taxogenomic investigation of the family Halomonadaceae. Front Microbiol 2023; 14:1293707. [PMID: 38045027 PMCID: PMC10690426 DOI: 10.3389/fmicb.2023.1293707] [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: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 12/05/2023] Open
Abstract
The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - David R. Arahal
- Departament of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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11
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Huq MA, Rahman MS, Rahman MM, Akter S. Isolation and characterization of Pinibacter soli sp. nov., and in silico genome mining of Pinibacter for biosynthetic gene cluster prediction. Int J Syst Evol Microbiol 2023; 73. [PMID: 37937829 DOI: 10.1099/ijsem.0.006136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, non-motile and non-flagellated novel bacterial strain, designated MAH-24T, was isolated from the rhizospheric soil of a pine garden. The colonies were observed to be orange-coloured, smooth, spherical and 0.4-0.8 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAH-24T was found to be able to grow at 10-35 °C, at pH 6.0-9.0 and in the presence of 0-1.0 % NaCl (w/v). The strain was found to be positive for the catalase and oxidase tests. The strain was positive for hydrolysis of aesculin and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pinibacter and to be closely related to Pinibacter aurantiacus MAH-26T (99.2 % sequence similarity). The novel strain MAH-24T has a draft genome size of 5 918 133 bp (13 contigs), annotated with 4613 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-24T and the closest type strain P. aurantiacus MAH-26T were in the range of 85.3 and 29.9 %, respectively. In silico genome mining revealed that both novel strain MAH-24T and P. aurantiacus MAH-26T have a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 41.0 mol%. The predominant isoprenoid quinone was menaquinone-7. The major fatty acids were identified as C15:0 iso, C15:1 iso G and C17:0 iso 3OH. On the basis of dDDH, ANI, genotypic, chemotaxonomic and physiological data, strain MAH-24T represents a novel species within the genus Pinibacter, for which the name Pinibacter soli sp. nov. is proposed, with MAH-24T (=KACC 19747T=CGMCC 1.13659T) as the type strain.
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
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12
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Takahashi K, Kuwahara H, Horikawa Y, Izawa K, Kato D, Inagaki T, Yuki M, Ohkuma M, Hongoh Y. Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade. THE ISME JOURNAL 2023; 17:1895-1906. [PMID: 37653056 PMCID: PMC10579323 DOI: 10.1038/s41396-023-01502-0] [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: 03/26/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute to the animal host. Here, we discovered clostridial endosymbionts of cellulolytic protists in termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences of three endosymbiotic Clostridia, each associated with a different parabasalid protist species with various infection rates: Trichonympha agilis, Pseudotrichonympha grassii, and Devescovina sp. All these protists are previously known to harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. The genomes of the endosymbiotic Clostridia were small in size (1.0-1.3 Mbp) and exhibited signatures of an obligately-intracellular parasite, such as an extremely limited capability to synthesize amino acids, cofactors, and nucleotides and a disrupted glycolytic pathway with no known net ATP-generating system. Instead, the genomes encoded ATP/ADP translocase and, interestingly, regulatory proteins that are unique to eukaryotes in general and are possibly used to interfere with host cellular processes. These three genomes formed a clade with metagenome-assembled genomes (MAGs) derived from the guts of other animals, including human and ruminants, and the MAGs shared the characteristics of parasites. Gene flux analysis suggested that the acquisition of the ATP/ADP translocase gene in a common ancestor was probably key to the emergence of this parasitic clade. Taken together, we provide novel insights into the multilayered symbiotic system in the termite gut by adding the presence of parasitism and present an example of the emergence of putative energy parasites from a dominant gut bacterial clade.
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Affiliation(s)
- Kazuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
| | - Hirokazu Kuwahara
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Yutaro Horikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kazuki Izawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Daiki Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Tatsuya Inagaki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan.
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13
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Chebotar VK, Gancheva MS, Chizhevskaya EP, Keleinikova OV, Baganova ME, Zaplatkin AN, Husainov KA. Whole-genome sequence of Paenibacillus amylolyticus strain W018, isolated from Triticum aestivum L. seeds, obtained using nanopore sequencing. Microbiol Resour Announc 2023; 12:e0068723. [PMID: 37747250 PMCID: PMC10586160 DOI: 10.1128/mra.00687-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
In this study, we performed nanopore sequencing of the genome of Paenibacillus amylolyticus strain W018, isolated from the seeds of winter wheat, cv. Bezostaya 100. The genome size is 7.07 Mb, with a GC content of 45.8%, and contains 8,190 genes.
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Affiliation(s)
- Vladimir K. Chebotar
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Maria S. Gancheva
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, St. Petersburg, Russia
| | - Elena P. Chizhevskaya
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Oksana V. Keleinikova
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Maria E. Baganova
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Alexander N. Zaplatkin
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Kharon A. Husainov
- Laboratory of Generic and Selection of Microorganisms, Chechen Research Institute of Agriculture, Chechen Republic, Russia
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Asif M, Li-Qun Z, Zeng Q, Atiq M, Ahmad K, Tariq A, Al-Ansari N, Blom J, Fenske L, Alodaini HA, Hatamleh AA. Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism. Comput Struct Biotechnol J 2023; 21:4647-4662. [PMID: 37841331 PMCID: PMC10568305 DOI: 10.1016/j.csbj.2023.09.043] [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: 08/26/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.
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Affiliation(s)
- Muhammad Asif
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhang Li-Qun
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khalil Ahmad
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Aqil Tariq
- Department of Wildlife, Fisheries, and Aquaculture, College of Forest Resources, Mississippi State, University, MS 39762-9690, USA
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Linda Fenske
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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15
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Huq MA, Lee SY, Moon B, Ma J, Siddiqi MZ, Srinivasan S, Rahman MS, Akter S. Sphingobium agri sp. nov., isolated from rhizospheric soil of eggplant. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787389 DOI: 10.1099/ijsem.0.006074] [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: 10/04/2023] Open
Abstract
A Gram-stain-negative, aerobic, short rod-shaped and motile bacterial strain, designated MAH-33T, was isolated from rhizospheric soil of eggplant. The colonies were observed to be yellow-coloured, smooth, spherical and 0.1-0.3 mm in diameter when grown on TSA agar medium for 2 days. Strain MAH-33T was found to be able to grow at 10-40 °C, at pH 5.0-10.0 and at 0-3.0 % NaCl (w/v). The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of tyrosine and aesculin. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingobium and to be closely related to Sphingobium quisquiliarum P25T (98.4 % similarity), Sphingobium mellinum WI4T (97.8 %), Sphingobium fuliginis TKPT (97.3 %) and Sphingobium herbicidovorans NBRC 16415T (96.9 %). The novel strain MAH-33T has a draft genome size of 3 908 768 bp (28 contigs), annotated with 3689 protein-coding genes, 45 tRNA and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-33T and closely related type strains were in the range of 79.8-81.6 % and 23.2-24.5 %, respectively. The genomic DNA G+C content was determined to be 62.2 %. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipids identified in strain MAH-33T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine; one unknown phospholipid and one unknown lipid. On the basis of digital DNA-DNA hybridization, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAH-33T represents a novel species within the genus Sphingobium, for which the name Sphingobium agri sp. nov. is proposed, with MAH-33T (=KACC 19973T = CGMCC 1.16609T) as the type strain.
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Sun-Young Lee
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - BoKyung Moon
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Juncai Ma
- World Data Center for Microorganisms (WDCM); Institute of Microbiology, Chinese Academy of Sciences (IMCAS), Beijing, PR China
| | - Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
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Zheng ZH, Lu CY, Lian WH, Han JR, Chen F, Zhou T, Li S, Dong L, Li WJ. Danxiaibacter flavus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from forest soil on Danxia Mountain. Int J Syst Evol Microbiol 2023; 73. [PMID: 37791661 DOI: 10.1099/ijsem.0.006082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
A Gram-stain-negative, aerobic, short rod-shaped, yellow bacterium, designated SYSU DXS3180T, was isolated from forest soil of Danxia Mountain in PR China. Growth occurred at 15-37 °C (optimum, 28-30 °C), pH 6.0-10.0 (optimum, pH 7.0-8.0) and with 0-2.0 % NaCl (optimum, 0-0.5 %, w/v). Strain SYSU DXS3180T was positive for hydrolysis of Tween 20, Tween 60, Tween 80 and starch, but negative for urease, H2S production, nitrate reduction, Tween 40 and gelatin. Phylogenetic analysis based on 16S rRNA gene and genome sequences showed that SYSU DXS3180T belonged to the family Chitinophagaceae. The closely related members were Foetidibacter luteolus YG09T (94.2 %), Limnovirga soli KCS-6T (93.9 %) and Filimonas endophytica SR 2-06T (93.7 %). The genome of strain SYSU DXS3180T was 7287640 bp with 5782 protein-coding genes, and the genomic DNA G+C content was 41.4 mol%. The main respiratory quinone was MK-7 and the major fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The major polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain SYSU DXS3180T is proposed to represent a novel species of a novel genus named Danxiaibacter flavus gen. nov., sp. nov., within the family Chitinophagaceae. The type strain is SYSU DXS3180T (=KCTC 92895T=GDMCC 1.3825 T).
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Affiliation(s)
- Zhuo-Huan Zheng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Fang Chen
- Administrative Commission of Danxiashan National Park, Shaoguan, 512300, PR China
| | - Ting Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 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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Li S, Dong L, Lian WH, Lin ZL, Wei QC, Xiao M, Li WJ. Rufibacter roseolus sp. nov. and Rufibacter aurantiacus sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37861396 DOI: 10.1099/ijsem.0.006093] [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: 10/21/2023] Open
Abstract
Two novel bacterial strains, designated as SYSU D00344T and SYSU D00433T, were isolated from soil of Gurbantunggut Desert in Xinjiang, north-west PR China. Cells of both strains were Gram-stain-negative, aerobic, short-rod-shaped, catalase-positive and non-motile. Oxidase activities of SYSU D00344T and SYSU D00433T were negative and positive, respectively. Optimal growth occurred at 30 °C, with 0-0.5 % (w/v) NaCl and at pH 7.0. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that they represented members of the genus Rufibacter and were closely related to Rufibacter hautae NBS58-1T. The results of phylogenomic analysis indicated that the two strains formed two independent and robust branches distinct from all reference type strains. The analyses of average nucleotide identity (ANI), digital DNA-DNA hybridisation (dDDH) values and 16S rRNA gene similarities between the two strains and their relatives further demonstrated that SYSU D00344T and SYSU D00433T represented two different novel genospecies. The polar lipids consisted of phosphatidylethanolamine, one unidentified glycolipid, two unidentified aminophospholipids, and two or four unidentified lipids. MK-7 was the only respiratory quinone. The major fatty acids (>10 %) for both strains were identified as iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), as well as summed feature 4 (anteiso-C17 : 1B and/or iso-C17 : 1I) for SYSU D00344T and C16 : 1ω5c for SYSU D00433T. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, we propose Rufibacter roseolus sp. nov. and Rufibacter aurantiacus sp. nov. as two novel species in the genus Rufibacter. The type strains are SYSU D00344T (=CGMCC 1.8625T=MCCC 1K04971T=KCTC 82274T) and SYSU D00433T (=CGMCC 1.8617T=MCCC 1K04982T=KCTC 82277T), respectively.
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Affiliation(s)
- Shuai Li
- School of Life Science, Jiaying University, Meizhou, PR China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Qi-Chuang Wei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, PR China
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18
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Zhang Y, Zhao J, Zhang G, Lin N, Sha Y, Lu J, Zhu T, Zhang X, Li Q, Zhang H, Lin X, Li K, Bao Q, Li D. Identification and characterization of a novel β-lactamase gene, blaAMZ-1, from Achromobacter mucicolens. Front Microbiol 2023; 14:1252427. [PMID: 37808287 PMCID: PMC10552758 DOI: 10.3389/fmicb.2023.1252427] [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: 07/03/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Background Achromobacter is a genus of gram-negative bacteria that can act as opportunistic pathogens. Recent studies have revealed that some species of Achromobacter show inherent resistance to β-lactams, but the resistance mechanisms of Achromobacter mucicolens have rarely been reported. Method The bacterium was isolated using standard laboratory procedures. The agar dilution method was used to determine the minimum inhibitory concentrations (MICs). Genome sequencing was performed using the PacBio RS II and Illumina HiSeq 2500 platforms, and the Comprehensive Antibiotic Resistance Database (CARD) was used to annotate the drug resistance genes. The localization of the novel β-lactamase AMZ-1 was determined, and its characteristics were determined via molecular cloning and enzyme kinetic analysis. The phylogenetic relationship and comparative genomic analysis of the resistance gene-related sequences were also analyzed. Result Achromobacter mucicolens Y3, isolated from a goose on a farm in Wenzhou, showed resistance to multiple antibiotics, including penicillins and cephalosporins. BlaAMZ-1 showed resistance to amoxicillin, penicillin G, ampicillin, cephalothin and cefoxitin, and the resistance activity could be inhibited by β-lactamase inhibitors. Enzyme kinetic analysis results showed that AMZ-1 has hydrolytic activity against a wide range of substrates, including cephalothin, amoxicillin, penicillin G, and cefoxitin but not ampicillin. The hydrolytic activity of AMZ-1 was greatly inhibited by avibactam but much more weakly inhibited by tazobactam. Mobile genetic elements could not be found around the blaAMZ-1-like genes, which are conserved on the chromosomes of bacteria of the genus Achromobacter. Conclusion In this study, a novel AmpC gene, blaAMZ-1, from the animal-origin bacterium A. mucicolens Y3 was identified and characterized. It conferred resistance to some penicillins and first- and second-generation cephalosporins. The identification of this novel resistance gene will be beneficial for the selection of effective antimicrobials to treat associated infections.
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Affiliation(s)
- Yuan Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jingxuan Zhao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Guozhi Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Naru Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuning Sha
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Tingting Zhu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Dong Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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Liu WL, Yang ZW, Guo DY, Deng QQ, Li JL, Wang PD, Chen SH, Liu L, Nie GX, Li WJ. Cereibacter flavus sp. nov., a novel member of the family Rhodobacteraceae isolated from seawater of the South China Sea and reclassification of Rhodobacter alkalitolerans as Cereibacter alkalitolerans comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37773605 DOI: 10.1099/ijsem.0.006051] [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: 10/01/2023] Open
Abstract
A Gram-stain-negative, aerobic, motile, ovoid-shaped and yellow-coloured strain, designated SYSU M79828T, was isolated from seawater collected from the South China Sea. Growth of this strain was observed at 4-37 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-6% NaCl (optimum, 3.0 %, w/v). The respiratory quinone was found to be Q-10. Major fatty acid constituents were C18 : 1 ω7c/C18 : 1 ω6c, C18 : 1 ω7c11-methyl and C18 : 0 (>5 % of total). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, two unidentified phospholipid, one unidentified lipid and an unidentified glycolipid. The genomic DNA G+C content was 64.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M79828T belonged to the genus Cereibacter and had the highest sequences similarity to 'Rhodobacter xinxiangensis' TJ48T (98.41 %). Based on 16S rRNA gene phylogeny, physiological and chemotaxonomic characterizations, we consider that strain SYSU M79828T represents a novel species of the genus Cereibacter, for which the name Cereibacter flavus sp. nov. is proposed. The type strain is SYSU M79828T (=GDMCC 1.3803T=KCTC 92893T). In addition, according to the results of phylogenetic analysis and similar taxonomic characteristics, we propose that Rhodobacter alkalitolerans should be reclassified as Cereibacter alkalitolerans comb. nov.
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Affiliation(s)
- Wen-Li Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Dan-Yuan Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Sen-Hua Chen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519000, PR China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519000, PR China
| | - Guo-Xing Nie
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 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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20
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Xamxidin M, Dong H, Wang JY, Qu W, Xu L, Wu M. Parerythrobacter lacustris sp. nov., a novel member of the family Erythrobacteraceae isolated from an inland alpine lake. Arch Microbiol 2023; 205:279. [PMID: 37420141 DOI: 10.1007/s00203-023-03616-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
A novel bacterium, designated as strain RS5-5T, was isolated from lake water in northwestern China. Cells of the isolate were observed to be rod shaped and Gram stain negative. Its growth occurred at 4-37 ℃, pH 6.5-9.0 and in the presence of 0-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RS5-5T was most closely related to Qipengyuania sediminis GDMCC 1.2497T (97.5%), followed by Erythrobacter dokdonensis DSW-74T (97.3%) and Qipengyuania algicida GDMCC 1.2535T (97.0%). Phylogenomic analysis revealed that strain RS5-5T formed a distinct branch with the genus Parerythrobacter. The sole quinone was ubiquinone-10, and the major fatty acids (≥ 10%) were unsaturated fatty acids including C17:1 ω6c, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified sphingoglycolipid, three unidentified glycolipids, one unidentified aminoglycolipid, one unidentified aminolipid, two unidentified phospholipids and four unidentified polar lipids. Chemotaxonomic characteristics of strain RS5-5T were coincident with those of the genus Parerythrobacter members. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain RS5-5T and two Parerythrobacter reference strains were in the ranges of 73.2-77.7%, 69.0-78.0% and 18.9-20.4%, respectively. The genomic DNA G + C content of strain RS5-5T was 64.1%. The results of phenotypic, phylogenetic and genomic analyses suggested that strain RS5-5T represents a novel species in the genus Parerythrobacter, for which the name Parerythrobacter lacustris sp. nov. is proposed. The type strain is RS5-5T (= GDMCC 1.3163T = KCTC 92277T).
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Affiliation(s)
- Maripat Xamxidin
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Han Dong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Jia-Yan Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, People's Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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Han JR, Li S, Lu CY, Lian WH, Shi GY, Feng CY, Li WJ, Dong L. Rubellimicrobium arenae sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37490404 DOI: 10.1099/ijsem.0.005990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Two Gram-stain-negative strains, designated as SYSU D00286T and SYSU D00782, were isolated from a sand sample collected from the Kumtag Desert in Xinjiang, north-west China. Cells were aerobic, non-motile and positive for both oxidase and catalase. Growth occurred at 4-37 °C (optimum, 28-30 °C), pH 6.0-7.0 (optimum, pH 7.0) and NaCl concentration of 0-1.5 % (w/v; optimum, 0%). Growth was observed on Reasoner's 2A agar and nutrient agar, but not on Luria-Bertani agar and trypticase soy agar. The polar lipids were identified as diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, three unidentified aminolipids, one unidentified glycolipid and two unidentified phospholipids. The major respiratory quinone was ubiquinone-10 and the major fatty acids (>10 %) were C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The 16S rRNA gene sequence similarity between strains SYSU D00286T and SYSU D00782 was 100%, and their average nucleotide identity (ANI), average amino acid identity and (AAI) digital DNA-DNA hybridization (dDDH) values were all 100.0 %. Phylogenetic analysis indicated that these two strains belong to the same species of the genus Rubellimicrobium and show the highest sequence similarity to Rubellimicrobium rubrum KCTC 72461T (98.2 %) and Rubellimicrobium roseum CCTCC AA 208029T (97.5 %). The ANI, AAI and dDDH values between SYSU D00286T (as well as SYSU D00782) and the other five Rubellimicrobium type strains were all less than or equal to 83.2, 80.1 and 23.6 %, respectively. Based on their phylogenetic, phenotypic and chemotaxonomical features, strains SYSU D00286T and SYSU D00782 represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium arenae sp. nov. is proposed. The type strain is SYSU D00286T (=MCCC 1K04981T=CGMCC 1.8626T=KCTC 82271T).
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Affiliation(s)
- Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- School of Life Sciences, Jiaying University, Meizhou, 514015, PR China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Guo-Yuan Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Chu-Ying Feng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 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
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
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Lu J, Sha Y, Gao M, Shi W, Lin X, Li K, Bao Q, Feng C. Identification and characterization of a novel aminoglycoside O-nucleotidyltransferase ANT(6)-If from Paenibacillus thiaminolyticus PATH554. Front Microbiol 2023; 14:1184349. [PMID: 37455719 PMCID: PMC10343464 DOI: 10.3389/fmicb.2023.1184349] [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: 03/11/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Background Paenibacillus thiaminolyticus, a species of genus Paenibacillus of the family Paenibacillaceae, exists widely in environments and habitats in various plants and worms, and occasionally causes human infections. This work aimed to characterize the function of a novel aminoglycoside O-nucleotidyltransferase resistance gene, designated ant(6)-If, from a P. thiaminolyticus strain PATH554. Methods Molecular cloning, antimicrobial susceptibility testing, enzyme expression and purification, and kinetic analysis were used to validate the function of the novel gene. Whole-genome sequencing and comparative genomic analysis were performed to investigate the phylogenetic relationship of ANT(6)-If and other aminoglycoside O-nucleotidyltransferases, and the synteny of ant(6)-If related sequences. Results The recombinant with the cloned ant(6)-If gene (pMD19-ant(6)-If/DH5α) demonstrated a 128-fold increase of minimum inhibitory concentration level against streptomycin, compared with the control strains (DH5α and pMD19/DH5α). The kinetic parameter kcat/Km of ANT(6)-If for streptomycin was 9.01 × 103 M-1·s-1. Among the function-characterized resistance genes, ANT(6)-If shared the highest amino acid sequence identity of 75.35% with AadK. The ant(6)-If gene was located within a relatively conserved genomic region in the chromosome. Conclusion ant(6)-If conferred resistance to streptomycin. The study of a novel resistance gene in an unusual environmental bacterium in this work contributed to elucidating the resistance mechanisms in the microorganisms.
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Affiliation(s)
- Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Yuning Sha
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
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Huq MA, Ma J, Srinivasan S, Parvez MAK, Rahman MM, Naserkheil M, Abuhena M, Maitra P, Islam F, Nam K, Park JH, Akter S. Massilia agrisoli sp. nov., isolated from rhizospheric soil of banana. Int J Syst Evol Microbiol 2023; 73. [PMID: 37224056 DOI: 10.1099/ijsem.0.005897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10-35 °C (optimum, 28 °C), pH 6.0-9.5 (optimum, pH 7.0-7.5), and in the presence of 0-1.0 % NaCl (optimum 0 %). The strain was positive for catalase and oxidase tests, as well as hydrolysis of gelatin, casein, starch and Tween 20. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-52T clustered together within the genus Massilia. Strain MAHUQ-52T was closely related to Massilia soli R798T (98.6 %) and Massilia polaris RP-1-19T (98.3 %). The novel strain MAHUQ-52T has a draft genome size of 4 677 454 bp (25 contigs), annotated with 4193 protein-coding genes, 64 tRNA and 19 rRNA genes. The genomic DNA G+C content was 63.0 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-52T and closely related type strains were ≤88.4 and 35.8 %, respectively. The only respiratory quinone was ubiquinone-8. The major fatty acids were identified as C16 : 0 and summed feature 3 (C15 : 0 iso 2-OH and/or C16 : 1 ω7c). Strain MAHUQ-52T contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. On the basis of dDDH and ANI values, as well as genotypic, chemotaxonomic and physiological data, strain MAHUQ-52T represents a novel species within the genus Massilia, for which the name Massilia agrisoli sp. nov. is proposed, with MAHUQ-52T (=KACC 21999T=CGMCC 1.18577T) as the type strain.
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Juncai Ma
- World Data Center for Microorganisms (WDCM); Institute of Microbiology, Chinese Academy of Sciences (IMCAS), PR China
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | | | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
| | - Masoumeh Naserkheil
- Animal Breeding and Genetics Division, National Institute of Animal Science, Cheonan 31000, Republic of Korea
| | - Md Abuhena
- Department of Research & Development, Apex Biofertilizers & Biopesticides Limited, Gobindaganj-5740, Gaibandha, Bangladesh
| | - Pulak Maitra
- Institute of Dendrology, Polish Academy of Sciences, 62-035 Kórnik, Poland
| | - Fahadul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Kihong Nam
- Department of Horticultural Life Science, Hankyong National University, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
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Ancylobacter moscoviensis sp. nov., novel facultatively methylotrophic bacteria from activated sludge and the reclassification of Starkeya novella (Starkey 1934) Kelly et al. 2000 as Ancylobacter novellus comb. nov., Starkeya koreensis Im et al. 2006 as Ancylobacter koreensis comb.nov., Angulomicrobium tetraedrale Vasil'eva et al. 1986 as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme Fritz et al. 2004 as Ancylobacter amanitiformis comb. nov., and Methylorhabdus multivorans Doronina et al. 1996 as Ancylobacter multivorans comb. nov., and emended description of the genus Ancylobacter. Antonie Van Leeuwenhoek 2023; 116:153-170. [PMID: 36462112 DOI: 10.1007/s10482-022-01788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/23/2022] [Indexed: 12/04/2022]
Abstract
Three novel facultatively methylotrophic bacteria, strains 3CT, 1A, 8P, were isolated from activated sludges. The isolates were aerobic, Gram-stain-negative, non-motile, non-spore forming rods multiplying by binary fission. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethylethanolamine, phosphatidylmonomethylethanolamine, and diphosphatidylglycerol. The major fatty acids of cells were С18:1ω7c, C19:0ω8c cyclo and C16:0. Levels of 16S rRNA gene similarity indicates that the closely relatives are representatives of the genera Starkeya, Ancylobacter, Angulomicrobium and Methylorhabdus (96.4-99.4%). Genomic comparisons of 3CT and its closest relatives, S. novella DSM 506T and S. koreensis Jip08T, shared 87.3 and 86.8% nucleotide identity and 28.3 and 26.8% digital DNA-DNA hybridization values, respectively. The average amino acid identities between the strain 3CT and representatives of Starkeya, Ancylobacter and Angulomicrobium were in the range of 75.6-84.3%, which combines these strains into a single genus and gives rise to their reclassification. Based on polyphasic analyses, the strains 3CT, 1A, 8P represents a novel species of the genus Ancylobacter, for which the name Ancylobacter moscoviensis sp. nov. is proposed. The type strain is 3CT (= VKM B-3218T = KCTC 62336T). Furthermore, we also suggested the reclassification of Starkeya novella as Ancylobacter novellus comb. nov., Starkeya koreensis as Ancylobacter koreensis comb. nov., Angulomicrobium tetraedrale as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme as Ancylobacter amanitiformis comb. nov. and Methylorhabdus multivorans as Ancylobacter multivorans comb. nov. with the emended description of the genus Ancylobacter.
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Li CJ, Zhang Z, Zhan PC, Lv AP, Li PP, Liu L, Li WJ, Yang LL, Zhi XY. Comparative genomic analysis and proposal of Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov., three novel Clostridium sensu stricto endophytes with diverse capabilities of acetic acid and ethanol production. Anaerobe 2023; 79:102686. [PMID: 36535584 DOI: 10.1016/j.anaerobe.2022.102686] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Genus Clostridium sensu stricto is generally regarded as the true Clostridium genus, which includes important human and animal pathogens and industrially relevant microorganisms. Besides, it is also a prominent member of plant-associated endophytes. However, our knowledge of endophytic Clostridium is limited. METHODS In this study, the endophytes were isolated under anaerobic condition from the roots of Paris polyphylla Smith var. yunnanensis. Subsequently, a polyphasic taxonomic approach was used to clarify their taxonomic positions. The fermentation products were measured in the isolates with HPLC analysis. Comparative genomics was performed on these new strains and other relatives. RESULTS In total, nine endophytic strains belonging to the genus Clostridium sensu stricto were isolated, and three of them were identified as new species. Seven of nine strains could produce acetate, propionate, and butyrate. Only two strains could produce ethanol, although genomics analysis suggested that only two of them were without genes for solventogenesis. Different from the endophytic strains, the phylogenetically closely related non-endophytic strains showed significant enrichment effects on some metabolic pathways involving environmental information processing, carbohydrate, and amino acid metabolisms, etc. It suggests that the genomes of these endophytic strains had undergone subtle changes associated with environmental adaptations. CONCLUSION Consequently, strains YIM B02505T, YIM B02515T, and YIM B02565T are proposed to represent a new species of the genus Clostridium sensu stricto, for which the names Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov. are suggested.
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Affiliation(s)
- Cong-Jian Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China
| | - Zhen Zhang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China
| | - Peng-Chao Zhan
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Pan-Pan Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China.
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China.
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Complete Genome Sequence of Vulcanisaeta souniana Strain IC-059, a Hyperthermophilic Archaeon Isolated from Hot Spring Water in Japan. Microbiol Resour Announc 2023; 12:e0108022. [PMID: 36598242 PMCID: PMC9872577 DOI: 10.1128/mra.01080-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Vulcanisaeta souniana strain IC-059T (=JCM 11219T) is an anaerobic hyperthermophilic archaeon isolated from a Japanese hot spring field. Here, we report the complete genome sequence (2.43 Mbp) of this strain using a hybrid approach with Illumina short-read sequencing and Nanopore long-read sequencing.
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Azospirillum Endophyticum sp. nov., an Endophyte of Paris Polyphylla Smith var. Yunnanensis. Curr Microbiol 2022; 80:34. [PMID: 36508041 DOI: 10.1007/s00284-022-03142-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
A Gram-negative, facultative anaerobic bacterial strain, designated YIM B02556T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan Province, southwest China. By using a polyphasic approach, its taxonomic position was investigated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B02556T belonged to the genus Azospirillum and the 16S rRNA gene sequence similarity values of strain YIM B02556T to the type strains of members of this genus ranged from 94.9 to 98.3%. Overall genome relatedness index (OGRI) analysis estimated based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between YIM B02556T and other Azospirillum species type strains were <90.8% and <37.8%, lower than the limit of species circumscription. Cells of the strain were characterized as oxidase- and catalase-positive, with motility provided by flagella. The growth conditions of the strain were found to occur at 20-40 °C (optimum, 35 °C), and pH 6.0-9.5 (optimum, pH 7.5). Strain YIM B02556T can tolerate 2% NaCl concentration. Strain YIM B02556T contained Q-10 as the major ubiquinone. The major fatty acids were C18:1 ω7c and summed feature three (C16:1 ω7c and/or C16:1 ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Based on polyphasic analysis, strain YIM B02556T could be differentiated genotypically and phenotypically from recognized species of the genus Azospirillum. Therefore, the isolate represents a novel species, for which the name Azospirillum endophyticum is proposed. The type strain is YIM B02556T (=JCM 34631T=CGMCC 1.18654T).
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Li J, Hu A, Liang X, Yang X, Jia Y, Yu CP. Zobellella iuensis sp. nov., an aerobic denitrifying bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An aerobic denitrifying bacterium, designated as strain CPY4T, was isolated from activated sludge treating urban sewage under alternating aerobic/anaerobic conditions by an enrichment culture technique. Cells of strain CPY4T were Gram-stain-negative, aerobic, long rod-shaped, motile by means of single polar flagellum and capable of aerobic denitrification with citrate as the carbon source. Growth of strain CPY4T was observed at 10–45 °C (optimum, 30–35 °C), at pH 6.0–10.5 (optimum, pH 8.0–8.5) and in 0–5 % NaCl (optimum, 0–3 %; w/v). The 16S rRNA gene sequence of strain CPY4T showed the highest similarity to
Zobellella denitrificans
ZD1T (97.9 %), followed by
Zobellella endophytica
59N8T (97.6 %),
Zobellella aerophila
JC2671T (97.2 %),
Zobellella taiwanensis
ZT1T (97.1 %) and
Zobellella maritima
102-Py4T (96.3 %). Genome comparisons between CPY4T and other
Zobellella
species showed highest digital DNA–DNA hybridization with
Z. denitrificans
ZD1T (43.8 %) and highest average nucleotide identity (ANIb and ANIm) of genome nucleotide sequences with
Z. denitrificans
ZD1T(90.7 and 92 %, respectively). Phylogenetic analysis revealed that strain CPY4T fell within the clade comprising the type strains of
Zobellella
species and formed a phyletic line with them, which was distinct from other members of the family
Aeromonadaceae
. The sole respiratory ubiquinone was quinone 8. The predominant fatty acids (>10 % of the total fatty acids) of strain CPY4T were summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c), summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) and C16 : 0. The genomic DNA G+C content was 62.7 mol %. In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl ethanolamine, phospholipids and aminolipids were the major compounds. Based on the genotypic and phenotypic data, strain CPY4T represents a novel species of the genus
Zobellella
, for which the name Zobellella iuensis sp. nov. is proposed. The type strain is CPY4T (=JCM 34456T=CGMCC 1.18722T).
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Affiliation(s)
- Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Xiaoxuan Liang
- Graduate Institute of Environmental Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, PR China
| | - Xiaoyong Yang
- Department of Environmental Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Yanwen Jia
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
- Graduate Institute of Environmental Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, PR China
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Sun YP, Wang BB, Zheng XW, Wu ZP, Hou J, Cui HL. Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Three extremely halophilic archaeal strains (LT55T, SQT-29-1T and WLHS5T) were isolated from Gobi saline soil and a salt lake, China. These strains were most related to the genera
Natribaculum
and
Halovarius
(92.6–95.1 % similarities), and showed low similarities with other genera within the family
Natrialbaceae
based on 16S rRNA genes. Phylogenomic analysis confirmed that the three strains formed a distinct clade separated from the related genera
Halostagnicola
and
Natronococcus
, which indicated that they may represent a novel genus of the family
Natrialbaceae
. The average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH) and average amino acid identity (AAI) values among the three strains were no more than 87, 34 and 85 %, respectively, much lower than the threshold values for species demarcation. The major phospholipids of the three strains were phosphatidic acid (PA), phosphatidylglycerol (PG) and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid profiles of the three strains were diverse; sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD) were found in strains LT55T and WLHS5T, while mannosyl glucosyl diether (DGD-1) and S-DGD-1 in strain SQT-29-1T. The combination of phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strains WLHS5T (=CGMCC 1.13781T = JCM 33558T), SQT-29-1T (=CGMCC 1.16065T = JCM 33554T) and LT55T (=CGMCC 1.15188T = JCM 30838T) represent three novel species of a new genus within the family
Natrialbaceae
, for which the names, Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus gelatinilyticus sp. nov. and Halosolutus halophilus sp. nov., are proposed. Genome-based classification of genera
Natribaculum
and
Halovarius
revealed that
Halovarius luteus
should be transferred to the genus
Natribaculum
as Natribaculum luteum comb. nov. and
Natribaculum longum
as a heterotypic synonym of
Natribaculum breve
Liu et al. 2015.
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Affiliation(s)
- Ya-Ping Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Bei-Bei Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xi-Wen Zheng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Zhang-Ping Wu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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30
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Pseudomonas oryzagri sp. nov., isolated from a rice field soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAHUQ-58T, was isolated from soil sample of a rice field. The colonies were observed to be light pink-coloured, smooth, spherical and 0.6–1.0 mm in diameter when grown on nutrient agar (NA) medium for 2 days. Strain MAHUQ-58T was found to be able to grow at 15–40 °C, at pH 5.5–10.0 and with 0–1.0 % NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, NA, MacConkey agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of Tween 20 and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus
Pseudomonas
and to be closely related to
Pseudomonas oryzae
WM-3T (98.9 % similarity),
Pseudomonas linyingensis
LYBRD3-7T (97.7 %),
Pseudomonas sagittaria
JCM 18195 T (97.6 %) and
Pseudomonas guangdongensis
SgZ-6T (97.2 %). The novel strain MAHUQ-58T has a draft genome size of 4 536 129 bp (46 contigs), annotated with 4064 protein-coding genes, 60 tRNA genes and four rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-58T and four closely related type strains were in the range of 85.5–89.5 % and 29.5–38.0 %, respectively. The genomic DNA G+C content was determined to be 67.0 mol%. The predominant isoprenoid quinone was ubiquinone 9. The major fatty acids were identified as C16:0, summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) and summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c). On the basis of dDDH and ANI values, genotypic results, and chemotaxonomic and physiological data, strain MAHUQ-58T represents a novel species within the genus
Pseudomonas
, for which the name Pseudomonas oryzagri sp. nov. is proposed, with MAHUQ-58T (=KACC 22005T=CGMCC 1.18518T) as the type strain.
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31
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Guerra M, Carrasco-Fernández J, Valdés JH, Panichini M, Franco Castro J. Draft genome of Pseudomonas sp. RGM 2987 isolated from Stevia philippiana roots reveals its potential as a plant biostimulant and potentially constitutes a novel species. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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32
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Li S, Dong L, Han JR, Shi GY, Lu CY, Xu L, Lian WH, Alkhalifah DHM, Hozzein WN, Li WJ. Longitalea arenae gen. nov., sp. nov. and Longitalea luteola sp. nov., two new members of the family Chitinophagaceae isolated from desert soil. Arch Microbiol 2022; 204:499. [PMID: 35849221 DOI: 10.1007/s00203-022-03119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Two strains designated as SYSU D01084T and SYSU D00799T, were isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells of both strains were Gram-stain-negative, strictly aerobic, long-rod-shaped, oxidase- and catalase-negative, motile or non-motile. Colonies were circular, translucent, convex, smooth and light-yellow in color on R2A agar. The two isolates were found to grow at 4-50 ºC, at pH 6.0-8.0 and with 0-1.0% (w/v) NaCl. Analysis of their 16S rRNA gene sequences indicated that they belonged to the family Chitinophagaceae, and closely related to the genera Paraflavitalea, Niastella, Pseudoflavitalea and Flavitalea. The two novel strains shared 98.1% 16S rRNA sequence similarity and represent different species on the basis of low average nucleotide identity (ANI, 83.8%) and digital DNA-DNA hybridization (dDDH, 51.4%) values. The genomic DNA G + C contents of strains SYSU D01084T and SYSU D00799T were 46.0 and 45.6%, respectively. Phylogenetic trees showed that the two isolates were clustered in an individual lineage and not grouped consistently into any specific genus. The polar lipids contained of phosphatidylethanolamine, four unidentified aminolipids, two unidentified aminoglycolipids, and three or four unidentified lipids. The predominant respiratory quinone was MK-7 and the major fatty acids (> 10%) were identified as iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. Based on the combined phenotypic, genomic and phylogenetic analyses, the two strains represent two novel species of a new genus in the family Chitinophagaceae, for which the name Longitalea gen. nov. is proposed, comprising the type species Longitalea arenae sp. nov. (type strain SYSU D01084T = CGMCC 1.18641T = MCCC 1K05006T = KCTC 82283T) and Longitalea luteola sp. nov. (type strain SYSU D00799T = MCCC 1K04987T = KCTC 82282T = NBRC 114888T).
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.,School of Life Sciences, Jiaying University, Meizhou, 514015, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Guo-Yuan Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dalal Hussien M Alkhalifah
- Biology Department, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 11564, Kingdom of Saudi Arabia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, 999088, Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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33
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Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov. BMC Genomics 2022; 23:380. [PMID: 35590262 PMCID: PMC9118873 DOI: 10.1186/s12864-022-08623-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/10/2022] [Indexed: 12/02/2022] Open
Abstract
Background Drug-resistant bacteria have posed a great threat to animal breeding and human health. It is obviously urgent to develop new antibiotics that can effectively combat drug-resistant bacteria. The commensal flora inhabited in the intestines become potential candidates owing to the production of a wide range of antimicrobial substances. In addition, host genomes do not encode most of the enzymes needed to degrade dietary structural polysaccharides. The decomposition of these polysaccharides mainly depends on gut commensal-derived CAZymes. Results We report a novel species isolated from the chicken intestine, designated as Paenibacillus jilinensis sp. nov. and with YPG26T (= CCTCC M2020899T) as the type strain. The complete genome of P. jilinensis YPG26T is made up of a single circular chromosome measuring 3.97 Mb in length and containing 49.34% (mol%) G + C. It carries 33 rRNA genes, 89 tRNA genes, and 3871 protein-coding genes, among which abundant carbohydrate-degrading enzymes (CAZymes) are encoded. Moreover, this strain has the capability to antagonize multiple pathogens in vitro. We identified putative 6 BGCs encoding bacteriocin, NRPs, PKs, terpenes, and protcusin by genome mining. In addition, antibiotic susceptibility testing showed sensitivity to all antibiotics tested. Conclusions This study highlights the varieties of CAZymes genes and BGCs in the genome of Paenibacillus jilinensis. These findings confirm the beneficial function of the gut microbiota and also provide a promising candidate for the development of new carbohydrate degrading enzymes and antibacterial agents. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08623-4.
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34
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Li Y, Li W, Luo R, Sakandar HA, Zhang H, Liu W. Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005359] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two lactic acid bacterial strains (IMAU80584T and IMAU92037) were isolated from naturally fermented dairy products (kurut and yoghurt) in China and Russia. Based on sequence analysis of the 16S rRNA gene it was revealed that these strains belonged to
Lentilactobacillus rapi
. However, phylogenetic tree analyses of two housekeeping genes, rpoA (encoding RNA polymerase alpha subunit) and pheS (encoding phenylalanyl-tRNA synthase alpha subunit), and 88 core genes, indicated the two strains were separated into an independent monophyletic branch from
L. rapi
DSM 19907T, forming an infra-specific subgroup. The average nucleotide identity and digital DNA–DNA hybridization values between IMAU80584T and
L. rapi
DSM 19907T were 93.1 and 52.8 %, respectively. Strains IMAU80584T and IMAU92037 are distinguished from
L. rapi
DSM 19907T because they have different polar lipids and fatty acids. The novel subgroup strains could not ferment gluconate potassium. The DNA G+C content of strain IMAU80584T was 42.3 mol%. The major cellular fatty acids were C16 : 0, C18 : 1
ω9t and summed feature 5 (C18 : 0 ante and/or C18 : 2
ω6c and/or C18 : 2
ω9c). Therefore, based on the results of polyphasic taxonomic analysis, IMAU80584T and IMAU92037 could be considered as a novel subspecies in the species
L. rapi
with the proposed name
Lentilactobacillus rapi
subsp. dabitei subsp. nov. The type strain is IMAU80584T (=GDMCC 1.2566T=JCM 34647T).
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Affiliation(s)
- Yu Li
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Weicheng Li
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Rui Luo
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Hafiz Arbab Sakandar
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Heping Zhang
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Wenjun Liu
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
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Geng N, Yang D, Hua J, Huang LJ, Dong H, Sun C, Xu L. Complete genome sequence of Kordiimonas pumila N18T sheds light on biogeochemical roles of the genus Kordiimonas. Mar Genomics 2022; 62:100930. [DOI: 10.1016/j.margen.2022.100930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 10/19/2022]
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Sedláček I, Holochová P, Busse HJ, Koublová V, Králová S, Švec P, Sobotka R, Staňková E, Pilný J, Šedo O, Smolíková J, Sedlář K. Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov. Microorganisms 2022; 10:microorganisms10040704. [PMID: 35456753 PMCID: PMC9028926 DOI: 10.3390/microorganisms10040704] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were psychrophilic, oligotrophic, resistant to chloramphenicol, and exhibited strong hydrolytic activities. To clarify the taxonomic position of these isolates, a polyphasic taxonomic approach was applied based on sequencing of the 16S rRNA, gyrB and lepA genes, whole-genome sequencing, rep-PCR, MALDI-TOF MS, chemotaxonomy analyses and biotyping. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the entire group are representatives of the genus Massilia. The closest relatives of the reference strain P8398T were Massilia atriviolacea, Massilia violaceinigra, Massilia rubra, Massilia mucilaginosa, Massilia aquatica, Massilia frigida, Massilia glaciei and Massilia eurypsychrophila with a pairwise similarity of 98.6–100% in the 16S rRNA. The subsequent gyrB and lepA sequencing results showed the novelty of the analysed group, and the average nucleotide identity and digital DNA–DNA hybridisation values clearly proved that P8398T represents a distinct Massilia species. After all these results, we nominate a new species with the proposed name Massilia antarctica sp. nov. The type strain is P8398T (= CCM 8941T = LMG 32108T).
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Affiliation(s)
- Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
- Correspondence: ; Tel.: +420-549-496-922
| | - Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria;
| | - Vendula Koublová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Roman Sobotka
- Centrum Algatech, Institute of Microbiology, Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic; (R.S.); (J.P.)
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Jan Pilný
- Centrum Algatech, Institute of Microbiology, Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic; (R.S.); (J.P.)
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic;
| | - Jana Smolíková
- Department of Physical Geography and Geoecology, Faculty of Science, Charles University, Albertov 6, 128 00 Praha, Czech Republic;
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 12, 616 00 Brno, Czech Republic;
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, 803 33 Munich, Germany
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Zhang YN, Zhang TS, Chen XY, Gong Y, Du ZJ. Pseudohalioglobus sediminis sp. nov., isolated from coastal sediment. Arch Microbiol 2022; 204:207. [PMID: 35274186 DOI: 10.1007/s00203-022-02816-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022]
Abstract
A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, designated NY5T, was isolated from marine sediment collected from coastal area in Weihai, China (122°07' 38.80'' E, 37°33' 57.60'' N). Cells of strain NY5T were 0.6-0.7 μm width and 1.9-2.0 μm length, catalase-positive and oxidase-positive. Growth of NY5T was observed at 25-37 °C (optimum, 28 °C) and pH 6.5-9.5 (optimum, pH 7.5-8.0) and in the presence of 0.5-7.0% (w/v) NaCl (optimum, 2.0%). The isoprenoid quinone was Q-8 and the predominant fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and C17:1 ω8c. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. The DNA G+C content of strain NY5T was 60.1%. Strain NY5T showed the highest 16S rRNA gene sequence similarity (98.2%) with Pseudohalioglobus lutimaris followed by Parahaliea aestuarii (96.9%), Parahaliea maris (96.7%), Parahaliea mediterranea (95.9%), and Halioglobus japonicus (94.9%). Given these phenotypic and chemotaxonomic properties and phylogenetic analyses, strain NY5T was considered to represent a novel species of the genus Pseudohalioglobus, for which the name Pseudohalioglobus sediminis sp. nov. is proposed. The type strain is NY5T (=KCTC 72416T=MCCC 1H00401T).
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Affiliation(s)
- Ya-Ning Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Tian-Shu Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Xu-Yang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Ya Gong
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China. .,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, People's Republic of China.
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China. .,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, People's Republic of China.
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Goussarov G, Claesen J, Mysara M, Cleenwerck I, Leys N, Vandamme P, Van Houdt R. Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics. ENVIRONMENTAL MICROBIOME 2022; 17:9. [PMID: 35248155 PMCID: PMC8898458 DOI: 10.1186/s40793-022-00403-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/17/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Although the total number of microbial taxa on Earth is under debate, it is clear that only a small fraction of these has been cultivated and validly named. Evidently, the inability to culture most bacteria outside of very specific conditions severely limits their characterization and further studies. In the last decade, a major part of the solution to this problem has been the use of metagenome sequencing, whereby the DNA of an entire microbial community is sequenced, followed by the in silico reconstruction of genomes of its novel component species. The large discrepancy between the number of sequenced type strain genomes (around 12,000) and total microbial diversity (106-1012 species) directs these efforts to de novo assembly and binning. Unfortunately, these steps are error-prone and as such, the results have to be intensely scrutinized to avoid publishing incomplete and low-quality genomes. RESULTS We developed MAGISTA (metagenome-assembled genome intra-bin statistics assessment), a novel approach to assess metagenome-assembled genome quality that tackles some of the often-neglected drawbacks of current reference gene-based methods. MAGISTA is based on alignment-free distance distributions between contig fragments within metagenomic bins, rather than a set of reference genes. For proper training, a highly complex genomic DNA mock community was needed and constructed by pooling genomic DNA of 227 bacterial strains, specifically selected to obtain a wide variety representing the major phylogenetic lineages of cultivable bacteria. CONCLUSIONS MAGISTA achieved a 20% reduction in root-mean-square error in comparison to the marker gene approach when tested on publicly available mock metagenomes. Furthermore, our highly complex genomic DNA mock community is a very valuable tool for benchmarking (new) metagenome analysis methods.
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Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Jürgen Claesen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Department of Epidemiology & Biostatistics, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ilse Cleenwerck
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.
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Zhan PC, Li CJ, Zhang Z, Mao RF, Liu JR, Jiang XW, Zhi XY, Yang LL. Neobacillus paridis sp. nov., an endophyte of Paris polyphylla Smith var. yunnanensis. Arch Microbiol 2022; 204:129. [PMID: 34999970 DOI: 10.1007/s00203-021-02753-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 11/02/2022]
Abstract
A novel endophytic strain, designated YIM B02564T, was isolated from the root of Paris polyphylla Smith var. yunnanensis obtained from Yunnan Province, southwest China. By using a polyphasic approach, cells of the strain were characterized as facultative anaerobic, Gram-positive and rod-shaped. The growth conditions of the strain were found to occur at 20-55 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.0). Strain YIM B02564T can tolerate 2% NaCl concentration. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B02564T belonged to the genus Neobacillus and the 16S rRNA gene sequence similarity values of strain YIM B02564T to the type strains of members of this genus ranged from 95.6 to 97.8%. The DNA G+C content of strain YIM B02564T calculated from the whole genome sequence was 41.6 mol%. Values of the ANI and the dDDH between strain YIM B02564T and its closely related Neobacillus species were below 77.9% and 21.5%. Strain YIM B02564T contained MK-7 as the major menaquinone, iso-C15:0 and anteiso-C15:0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and four unidentified lipids. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. On the basis of polyphasic analysis, strain YIM B02564T could be differentiated genotypically and phenotypically from recognized species of the genus Neobacillus. The isolate therefore represents a novel species, for which the name Neobacillus paridis is proposed. The type strain is YIM B02564T (= JCM 34668T = CGMCC 1.18655T).
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Affiliation(s)
- Peng-Chao Zhan
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Cong-Jian Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Zhen Zhang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Rui-Feng Mao
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jing-Ran Liu
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Xing-Wang Jiang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China.
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Janibacter endophyticus sp. nov., an Endophytic Actinobacterium Isolated from the Root of Paris polyphylla Smith var. Yunnanensis. Curr Microbiol 2022; 79:52. [PMID: 34982259 DOI: 10.1007/s00284-021-02745-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/10/2021] [Indexed: 11/03/2022]
Abstract
A novel endophytic actinobacterium, designated as strain YIM B02568T, was isolated from the root of Paris polyphylla Smith var. Yunnanensis obtained from Yunnan Province, southwest China. Strain YIM B02568T was characterized using a polyphasic approach. Phylogenetic analysis indicated that this isolate belonged to the genus Janibacter. The 16S rRNA gene sequence similarity values of strain YIM B02568T to the type strains of members of this genus ranged from 95.8 to 98.6%. However, overall genome relatedness indices were significantly lower than the widely accepted species-defined threshold. The cell wall of strain YIM B02568T contained meso-diaminopimelic acid. The major menaquinone was MK-8(H4). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. The major cellular fatty acids were comprised of iso-C16:0 and C18:1 ω9c. The DNA G + C content was 71.6 mol%. Based on the data from the polyphasic studies, we propose that strain YIM B02568T represents a novel species within the genus Janibacter, Janibacter endophyticus sp. nov. The type strain is YIM B02568T (= JCM 34639T = CGMCC 1.18658T).
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Geng N, Sun G, Liu WJ, Gao BC, Sun C, Xu C, Hua E, Xu L. Distribution, Phylogeny and Evolution of Clinical and Environmental Vibrio vulnificus Antibiotic-Resistant Genes. Evol Bioinform Online 2022; 18:11769343221134400. [PMID: 36404992 PMCID: PMC9669696 DOI: 10.1177/11769343221134400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Vibrio vulnificus is an emergent marine pathogen and is the
cause of a deadly septicemia. However, the evolution mechanism of
antibiotic-resistant genes (ARGs) is still unclear. Twenty-two high-quality
complete genomes of V. vulnificus were obtained and grouped
into 16 clinical isolates and 6 environmental isolates. Genomic annotations
found 23 ARG orthologous genes, among which 14 ARGs were shared by V.
vulnificus and other Vibrio members. Furthermore,
those ARGs were located in their chromosomes, rather than in the plasmids.
Phylogenomic reconstruction based on single-copy orthologous protein sequences
and ARG protein sequences revealed that clinical and environmental V.
vulnificus isolates were in a scattered distribution. The
calculation of non-synonymous and synonymous substitutions indicated that most
of ARGs evolved under purifying selection with the
Ka/Ks ratios lower than one, while
h-ns, rsmA, and soxR in several clinical
isolates evolved under the positive selection with
Ka/Ks ratios >1. Our result indicated
that V. vulnificus antibiotic-resistant armory was not only
confined to clinical isolates, but to environmental ones as well and clinical
isolates inclined to accumulate beneficial non-synonymous substitutions that
could be retained to improve competitiveness.
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Affiliation(s)
- Nan Geng
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Guojin Sun
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Wen-Jia Liu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
| | - Bin-Cheng Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd, Shaoxing, People’s Republic of China
| | - Cundong Xu
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Ertian Hua
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd, Shaoxing, People’s Republic of China
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Sugita K, Aoki K, Komori K, Nagasawa T, Ishii Y, Iwata S, Tateda K. Molecular Analysis of blaKPC-2-Harboring Plasmids: Tn 4401a Interplasmid Transposition and Tn 4401a-Carrying ColRNAI Plasmid Mobilization from Klebsiella pneumoniae to Citrobacter europaeus and Morganella morganii in a Single Patient. mSphere 2021; 6:e0085021. [PMID: 34730375 PMCID: PMC8565517 DOI: 10.1128/msphere.00850-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
The spread of Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacterales is a public health concern. KPC-encoding blaKPC is predominantly spread by strains of a particular phylogenetic lineage, clonal group 258, but can also be spread by horizontal transfer of blaKPC-carrying plasmids. Here, we report the transfer of a blaKPC-2-harboring plasmid via mobilization from K. pneumoniae to Citrobacter freundii complex and Morganella morganii strains in a single patient. We performed draft whole-genome sequencing to analyze 20 carbapenemase-producing Enterobacterales strains (15 of K. pneumoniae, two of C. freundii complex, and three of M. morganii) and all K. pneumoniae strains using MiSeq and/or MinION isolated from a patient who was hospitalized in New York and Montreal before returning to Japan. All strains harbored blaKPC-2-containing Tn4401a. The 15 K. pneumoniae strains each belonged to sequence type 258 and harbored a Tn4401a-carrying multireplicon-type plasmid, IncN and IncR (IncN+R). Three of these K. pneumoniae strains also possessed a Tn4401a-carrying ColRNAI plasmid, suggesting that Tn4401a underwent interplasmid transposition. Of these three ColRNAI plasmids, two and one were identical to plasmids harbored by two Citrobacter europaeus and three M. morganii strains, respectively. The Tn4401a-carrying ColRNAI plasmids were each 23,753 bp long and incapable of conjugal transfer via their own genes alone, but they mobilized during the conjugal transfer of Tn4401a-carrying IncN+R plasmids in K. pneumoniae. Interplasmid transposition of Tn4401a from an IncN+R plasmid to a ColRNAI plasmid in K. pneumoniae and mobilization of Tn4401a-carrying ColRNAI plasmids contributed to the acquisition of blaKPC-2 in C. europaeus and M. morganii. IMPORTANCE Plasmid transfer plays an important role in the interspecies spread of carbapenemase genes, including the Klebsiella pneumoniae carbapenemase (KPC)-coding gene, blaKPC. We conducted whole-genome sequencing (WGS) analysis and transmission experiments to analyze blaKPC-2-carrying mobile genetic elements (MGEs) between the blaKPC-2-harboring K. pneumoniae, Citrobacter europaeus, and Morganella morganii strains isolated from a single patient. blaKPC-2 was contained within an MGE, Tn4401a. WGS of blaKPC-2-carrying K. pneumoniae, C. europaeus, and M. morganii strains isolated from one patient revealed that Tn4401a-carrying ColRNAI plasmids were generated by plasmid-to-plasmid transfer of Tn4401a from a multireplicon-type IncN and IncR (IncN+R) plasmid in K. pneumoniae strains. Tn4401a-carrying ColRNAI plasmids were incapable of conjugal transfer in C. europaeus and M. morganii but mobilized from K. pneumoniae to a recipient Escherichia coli strain during the conjugal transfer of Tn4401a-carrying IncN+R plasmid. Therefore, Tn4401a-carrying ColRNAI plasmids contributed to the acquisition of blaKPC-2 in C. europaeus and M. morganii.
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Affiliation(s)
- Kayoko Sugita
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kohji Komori
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Tatsuya Nagasawa
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Satoshi Iwata
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
- Department of Infectious Diseases, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
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Abstract
A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8-3.0 mm in diameter when grown on nutrient agar medium for 2 days. Strain MAH-13T was found to be able to grow at 20-40 °C, at pH 5.0-10.0 and with 0-1.0% NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria-Bertani agar, nutrient agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of casein, starch, DNA and l-tyrosine. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Frateuria and to be closely related to Frateuria terrea DSM 26515T (98.2% similarity), Dyella thiooxydans ATSB10T (98.2 %), Frateuria defendens HyOGT (97.9 %), Rhodanobacter glycinis MO64T (97.8 %) and Frateuria aurantia DSM 6220T (97.8 %). The novel strain MAH-13T has a draft genome size of 3 682 848 bp (40 contigs), annotated with 3172 protein-coding genes, 49 tRNA genes and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-13T and five closely related type strains were in the range of 73.7-85.5 % and 20.7-30.1%, respectively. The genomic DNA G+C content was determined to be 68.0 mol%. The predominant isoprenoid quinone was ubiquinone 8. The major fatty acids were identified as iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17 : 1 ω9c and/or C16:0 10-methyl). On the basis of dDDH and ANI values, genotypic analysis, and chemotaxonomic and physiological data, strain MAH-13T represents a novel species within the genus Frateuria, for which the name Frateuria flava sp. nov. is proposed, with MAH-13T (=KACC 19743T=CGMCC 1.13655T) as the type strain.
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Affiliation(s)
- Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam 461-701, Republic of Korea
| | - Sun-Young Lee
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
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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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Huq MA, Siddiqi MZ, Balusamy SR, Rahman MM, Ashrafudoulla M, Apu MAI, Maitra P, Naserkheil M, Park JH, Akter S. Pinibacter aurantiacus gen. nov., sp. nov., isolated from rhizospheric soil of a pine tree. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870572 DOI: 10.1099/ijsem.0.005132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7-1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26T was able to grow at 10-40 °C, at pH 6.0-9.0 and with 0-1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria-Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26T was closely related to Flavihumibacter sediminis CJ663T and Parasegetibacter terrae SGM2-10T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae. Strain MAH-26T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. The genomic DNA G+C content was 41.5 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain MAH-26T represents a novel species of a novel genus of the family Chitinophagaceae, for which the name Pinibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of Pinibacter aurantiacus is MAH-26T (=KACC 19749T=CGMCC 1.13701T).
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do 17546, Republic of Korea
| | - Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, Anseong, Gyeonggi-do 17579, Republic of Korea
| | - Sri Renukadevi Balusamy
- Department of Food Science and Technology, Sejong University Gwangjin-gu, Seoul, 143-747, Republic of Korea
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
| | - Md Ashrafudoulla
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Md Aminul Islam Apu
- Graduate School of International Agricultural Technology, Seoul National University, Seoul, Republic of Korea
| | - Pulak Maitra
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644000, PR China
| | - Masoumeh Naserkheil
- Animal Breeding and Genetics Division, National Institute of Animal Science, Cheonan 31000, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam 461-701, Republic of Korea
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam 461-701, Republic of Korea
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Okido T, Kodama Y, Mashima J, Kosuge T, Fujisawa T, Ogasawara O. DNA Data Bank of Japan (DDBJ) update report 2021. Nucleic Acids Res 2021; 50:D102-D105. [PMID: 34751405 PMCID: PMC8689959 DOI: 10.1093/nar/gkab995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
The Bioinformation and DDBJ (DNA Data Bank of Japan) Center (DDBJ Center; https://www.ddbj.nig.ac.jp) operates archival databases that collect nucleotide sequences, study and sample information, and distribute them without access restriction to progress life science research as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute. Besides the INSDC databases, the DDBJ Center also provides the Genomic Expression Archive for functional genomics data and the Japanese Genotype-phenotype Archive for human data requiring controlled access. Additionally, the DDBJ Center started a new public repository, MetaboBank, for experimental raw data and metadata from metabolomics research in October 2020. In response to the COVID-19 pandemic, the DDBJ Center openly shares SARS-CoV-2 genome sequences in collaboration with Shizuoka Prefecture and Keio University. The operation of DDBJ is based on the National Institute of Genetics (NIG) supercomputer, which is open for large-scale sequence data analysis for life science researchers. This paper reports recent updates on the archival databases and the services of DDBJ.
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Affiliation(s)
- Toshihisa Okido
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuichi Kodama
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Mashima
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehide Kosuge
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takatomo Fujisawa
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Osamu Ogasawara
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Chitinophaga chungangae sp. nov., isolated from a Korean grape garden and its potential to biosynthesize ginsenoside Rg2. Arch Microbiol 2021; 203:5483-5489. [PMID: 34417651 DOI: 10.1007/s00203-021-02533-x] [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: 05/27/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 12/29/2022]
Abstract
A ginsenoside Rg2-producing, Gram stain-negative, aerobic, catalase and oxidase-positive, rod-shaped, non-motile and orange pigmented novel bacterium designated strain MAH-28 T was isolated from soil sample of a grape garden. Strain MAH-28 T hydrolyzed aesculin, casein and DNA. Flexirubin-type pigments are present. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MAH-28 T formed a cluster within the genus Chitinophaga and the most close relatives were Chitinophaga alhagiae T22T (98.9% 16S rRNA gene sequence similarity), Chitinophaga humicola Ktm-2 T (98.8%), Chitinophaga barathri YLT18T (98.3%) and Chitinophaga lutea ZY74T (97.4%). The novel strain MAH-28 T has a draft genome size of 6,043,180 bp (14 contigs), annotated with 4,863 protein-coding genes, 53 tRNA and 6 rRNA genes. The ANI and dDDH values between strain MAH-28 T and the closely related type strains were in the range of 76.0-83.4% and 20.3-26.7%, respectively. The novel strain MAH-28 T was able to synthesize ginsenoside Rg2 from major ginsenoside Re. The genome annotation revealed 152 carbohydrate genes which may involve with the synthesis of ginsenoside Rg2. The respiratory quinone of strain MAH-28 T was MK-7 and the dominant cellular fatty acids were C15:0 iso, C16:1 ω5c and C17:0 iso 3-OH. The DNA G + C content of strain MAH-28 T was 53.3 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic studies, strain MAH-28 T represents a new member of genus Chitinophaga for which the name Chitinophaga chungangae sp. nov. is proposed with type strain MAH-28 T (= KACC 19968 T = CGMCC 1.16605 T).
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Huq MA, Akter S. Characterization and Genome Analysis of Arthrobacter bangladeshi sp. nov., Applied for the Green Synthesis of Silver Nanoparticles and Their Antibacterial Efficacy against Drug-Resistant Human Pathogens. Pharmaceutics 2021; 13:1691. [PMID: 34683984 PMCID: PMC8538746 DOI: 10.3390/pharmaceutics13101691] [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: 08/30/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
The present study describes the isolation and characterization of novel bacterial species Arthrobacter bangladeshi sp. nov., applied for the green synthesis of AgNPs, and investigates its antibacterial efficacy against drug-resistant pathogenic Salmonella Typhimurium and Yersinia enterocolitica. Novel strain MAHUQ-56T is Gram-positive, aerobic, non-motile, and rod-shaped. Colonies were spherical and milky white. The strain showed positive activity for catalase and nitrate reductase, and the hydrolysis of starch, L-tyrosine, casein, and Tween 20. On the basis of the 16S rRNA gene sequence, strain MAHUQ-56T belongs to the Arthrobacter genus and is most closely related to Arthrobacter pokkalii P3B162T (98.6%). Arthrobacter bangladeshi MAHUQ-56T has a genome 4,566,112 bp long (26 contigs) with 4125 protein-coding genes, 51 tRNA and 6 rRNA genes. The culture supernatant of Arthrobacter bangladeshi MAHUQ-56T was used for the easy and green synthesis of AgNPs. Synthesized AgNPs were characterized by UV-vis spectroscopy, FE-TEM, XRD, DLS, and FT-IR. Synthesized AgNPs were spherical and 12-50 nm in size. FT-IR analysis revealed various biomolecules that may be involved in the synthesis process. Synthesized AgNPs showed strong antibacterial activity against multidrug-resistant pathogenic S. typhimurium and Y. enterocolitica. MIC values of the synthesized AgNPs against S. typhimurium and Y. enterocolitica were 6.2 and 3.1 ug/mL, respectively. The MBC of synthesized AgNPs for both pathogens was 12.5 ug/mL. FE-SEM analysis revealed the morphological and structural alterations, and damage of pathogens treated by AgNPs. These changes might disturb normal cellular functions, which ultimately leads to the death of cells.
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Affiliation(s)
- Md. Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong 17546, Korea
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam 461-701, Korea
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Binati RL, Salvetti E, Bzducha-Wróbel A, Bašinskienė L, Čižeikienė D, Bolzonella D, Felis GE. Non-conventional yeasts for food and additives production in a circular economy perspective. FEMS Yeast Res 2021; 21:6380488. [PMID: 34601574 DOI: 10.1093/femsyr/foab052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/27/2021] [Indexed: 12/18/2022] Open
Abstract
Yeast species have been spontaneously participating in food production for millennia, but the scope of applications was greatly expanded since their key role in beer and wine fermentations was clearly acknowledged. The workhorse for industry and scientific research has always been Saccharomyces cerevisiae. It occupies the largest share of the dynamic yeast market, that could further increase thanks to the better exploitation of other yeast species. Food-related 'non-conventional' yeasts (NCY) represent a treasure trove for bioprospecting, with their huge untapped potential related to a great diversity of metabolic capabilities linked to niche adaptations. They are at the crossroad of bioprocesses and biorefineries, characterized by low biosafety risk and produce food and additives, being also able to contribute to production of building blocks and energy recovered from the generated waste and by-products. Considering that the usual pattern for bioprocess development focuses on single strains or species, in this review we suggest that bioprospecting at the genus level could be very promising. Candida, Starmerella, Kluyveromyces and Lachancea were briefly reviewed as case studies, showing that a taxonomy- and genome-based rationale could open multiple possibilities to unlock the biotechnological potential of NCY bioresources.
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Affiliation(s)
- Renato L Binati
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Elisa Salvetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Anna Bzducha-Wróbel
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159c St., 02-776 Warsaw, Poland
| | - Loreta Bašinskienė
- Department of Food Science and Technology, Kaunas University of Technology, Radvilėnų St. 19A, 44249 Kaunas, Lithuania
| | - Dalia Čižeikienė
- Department of Food Science and Technology, Kaunas University of Technology, Radvilėnų St. 19A, 44249 Kaunas, Lithuania
| | - David Bolzonella
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
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Sedláček I, Holochová P, Sobotka R, Busse HJ, Švec P, Králová S, Šedo O, Pilný J, Staňková E, Koublová V, Sedlář K. Classification of a Violacein-Producing Psychrophilic Group of Isolates Associated with Freshwater in Antarctica and Description of Rugamonas violacea sp. nov. Microbiol Spectr 2021; 9:e0045221. [PMID: 34378950 PMCID: PMC8552646 DOI: 10.1128/spectrum.00452-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 11/20/2022] Open
Abstract
A group of 11 bacterial strains was isolated from streams and lakes located in a deglaciated northern part of James Ross Island, Antarctica. They were rod-shaped, Gram-stain-negative, motile, and catalase-positive and produced blue-violet-pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, automated ribotyping, repetitive element sequence-based PCR (rep-PCR), MALDI-TOF MS, fatty acid profile, chemotaxonomy analyses, and extensive biotyping was applied in order to clarify the taxonomic position of these isolates. Phylogenetic analysis based on the 16S rRNA gene indicated that all the isolates constituted a coherent group belonging to the genus Rugamonas. The closest relatives to the representative isolate P5900T were Rugamonas rubra CCM 3730T, Rugamonas rivuli FT103WT, and Rugamonas aquatica FT29WT, exhibiting 99.2%, 99.1%, and 98.6% 16S rRNA pairwise similarity, respectively. The average nucleotide identity and digital DNA-DNA hybridization values calculated from the whole-genome sequencing data clearly proved that P5900T represents a distinct Rugamonas species. The G+C content of genomic DNAs was 66.1 mol%. The major components in fatty acid profiles were summed feature 3 (C16:1ω7c/C16:1ω6c), C 16:0, and C12:0. The cellular quinone content contained exclusively ubiquinone Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The polyamine pattern was composed of putrescine, 2-hydroxputrescine, and spermidine. IMPORTANCE Our polyphasic approach provides a new understanding of the taxonomy of novel pigmented Rugamonas species isolated from freshwater samples in Antarctica. The isolates showed considerable extracellular bactericidal secretions. The antagonistic activity of studied isolates against selected pathogens was proved by this study and implied the importance of such compounds' production among aquatic bacteria. The psychrophilic and violacein-producing species Roseomonas violacea may play a role in the diverse consortium among pigmented bacteria in the Antarctic water environment. Based on all the obtained results, we propose a novel species for which the name Rugamonas violacea sp. nov. is suggested, with the type strain P5900T (CCM 8940T; LMG 32105T). Isolates of R. violacea were obtained from different aquatic localities, and they represent the autochthonous part of the water microbiome in Antarctica.
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Affiliation(s)
- Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Vienna, Austria
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Pilný
- Centrum Algatech, MBÚ AV ČR, Třeboň, Czech Republic
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Vendula Koublová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
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