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Zhang M, Wang Z, Liang Z, Hu N. Whole Genome Sequencing of First Janibacter indicus Isolate in China Revealed Three Unique Genomic Islands Compared with Saprophytic Strains. Infect Drug Resist 2021; 14:5351-5361. [PMID: 34934330 PMCID: PMC8684397 DOI: 10.2147/idr.s341591] [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: 10/11/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022] Open
Abstract
Introduction Janibacter caused bacteriemia is one of the rare infections. Methods In the present study, we report the first isolation of Janibacter, a rare bacterial infection, from a bacteremia patient in China. Its 16S rDNA was amplified and designated as Janibacter YFY001, which belongs to J. indicus. In addition, its genome was sequenced through combined second- and third-generation genome sequencing methods. Results Based on its genome, we identified many virulence factors, such as catalase, gelatinase, FbpABC systems, and resistant genes, among others. Interestingly, three genomic islands were found in YFY001 by comparing its genome to environmental Janibacter strains. Discussion Our study not only provides the necessary genomic information for in-depth study of Janibacter, but also provides a novel methodology for studying future cases of rare bacterial infection.
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Affiliation(s)
- Min Zhang
- Department of Blood Transfusion, The Third Affiliated Hospital of Nanchang University, Nanchang City, 330006, People's Republic of China.,Department of Laboratory Medicine, The First Affiliated Hospital of Nanchang, Nanchang City, 330006, People's Republic of China
| | - Ziwen Wang
- Department of Blood Transfusion, The Third Affiliated Hospital of Nanchang University, Nanchang City, 330006, People's Republic of China.,Department of Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Zhenshan Liang
- Department of Laboratory Medicine, The Affiliated Children's Hospital of Nanchang University, Nanchang City, 330006, People's Republic of China
| | - Niya Hu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanchang, Nanchang City, 330006, People's Republic of China
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Pei S, Xie F, Zhang R, Zhang G. Complete genome sequence of Janibaecter indicus YB324 from an Atlantic marine sediment. Mar Genomics 2020; 58:100833. [PMID: 33341425 DOI: 10.1016/j.margen.2020.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/03/2020] [Accepted: 12/01/2020] [Indexed: 11/18/2022]
Abstract
Janibacter indicus YB324, a gram-positive, aerobic and non-motile actinobacterium isolated from south Atlantic sediment at a depth of 2875 m. The complete genome sequence of the strain YB324 was obtained using PacBio Sequel HGAP.4 and comprised of 3,369,845 base pairs with a 71.3 mol% G + C content, 3225 protein-coding genes, 53 RNAs. In silico analysis confirmed the genes associated with polysaccharide hydrolyzation, nitrite reduction, and phenol degradation. Multiple natural product biosynthesis gene clusters were identified as well. The complete genome sequence will provide insight into the potential use of this strain in biotechnological and natural product biosynthesis applications.
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Affiliation(s)
- Shengxiang Pei
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China; State Key Laboratory of Marine Environmental Science, College of Ocean and EarthSciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and EarthSciences, Xiamen University, Xiamen 361102, Fujian, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, PR China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China.
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Subramani R, Sipkema D. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs 2019; 17:E249. [PMID: 31035452 PMCID: PMC6562664 DOI: 10.3390/md17050249] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
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Affiliation(s)
- Ramesh Subramani
- School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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Description of Janibacter massiliensis sp. nov., cultured from the vaginal discharge of a patient with bacterial vaginosis. Antonie van Leeuwenhoek 2019; 112:1147-1159. [PMID: 30798490 DOI: 10.1007/s10482-019-01247-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/15/2019] [Indexed: 01/22/2023]
Abstract
Strain Marseille-P4121T was isolated from a vaginal sample of a 45-year-old French woman with bacterial vaginosis. It is a Gram-positive, asporogenous, non-motile and aerobic bacterium. Strain Marseille-P4121T exhibits 98.2% 16S rRNA sequence similarity with Janibacter alkaliphilus strain SCSIO 10480T, a phylogenetically closely related species with standing in nomenclature. Its major fatty acids were identified as C18:1ω9 (34.4%), C16:0 (30.1%), and C18:0 (19%). The draft genome size of strain Marseille-P4121T is 2,452,608 bp long with a 72.5% G+C content and contains 2351 protein-coding genes and 49 RNA genes including 3 rRNA genes. We propose that strain Marseille-P4121T (= CECT 9671T = CSUR P4121T) is the type strain of the new species Janibacter massiliensis sp. nov.
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 409] [Impact Index Per Article: 68.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India. Arch Microbiol 2018; 200:753-770. [PMID: 29396619 DOI: 10.1007/s00203-018-1484-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 01/04/2023]
Abstract
Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.
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Lim YK, Kweon OJ, Kim HR, Kim TH, Lee MK. First case of bacteremia caused by Janibacter hoylei. APMIS 2017; 125:665-668. [PMID: 28493430 PMCID: PMC7159562 DOI: 10.1111/apm.12693] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 02/13/2017] [Indexed: 11/28/2022]
Abstract
Janibacter hoylei has previously been isolated only from an air sample in the upper atmosphere and clinical significance of J. hoylei was not yet established. Herein, we report a case of bacteremia caused by J. hoylei. An 8-week-old previously healthy male infant presented to the emergency room with fever. Blood culture yielded growth of Gram-positive bacilli and this microorganism could not be identified with conventional phenotypic methods. The isolate was identified by 16S rRNA gene sequencing, and the patient was successfully treated with vancomycin. To our knowledge, this is the first report of the recovery of J. hoylei in humans. This case shows that J. hoylei can be a potential pathogen in young children.
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Affiliation(s)
- Yong Kwan Lim
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Oh Joo Kweon
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Hye Ryoun Kim
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Tae Hyoung Kim
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Korea
| | - Mi-Kyung Lee
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
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