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Zhang MJ, Li XH, Peng LY, Yun ST, Liu ZC, Zhou YX. Williamsia soli sp. nov., an actinobacterium isolated from soil at a thermal power plant in Yantai, China. Arch Microbiol 2021; 204:102. [DOI: 10.1007/s00203-021-02714-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022]
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2
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Fatahi-Bafghi M. Role of Williamsia and Segniliparus in human infections with the approach taxonomy, cultivation, and identification methods. Ann Clin Microbiol Antimicrob 2021; 20:10. [PMID: 33485346 PMCID: PMC7825236 DOI: 10.1186/s12941-021-00416-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/12/2021] [Indexed: 02/01/2023] Open
Abstract
The genera Williamsia and Segniliparus are of aerobic actinomycetes and at the time of writing, they have 12 and 2 species, respectively. These genera cause various infections in humans. In this review, we surveyed their taxonomy, isolation, identification, as well as their role to cause human infections.
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Affiliation(s)
- Mehdi Fatahi-Bafghi
- Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran.
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3
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de Menezes CBA, Afonso RS, de Souza WR, Parma MM, de Melo IS, Fugita FLS, Moraes LAB, Zucchi TD, Fantinatti-Garboggini F. Williamsia aurantiacus sp. nov. a novel actinobacterium producer of antimicrobial compounds isolated from the marine sponge. Arch Microbiol 2019; 201:691-698. [PMID: 30799528 DOI: 10.1007/s00203-019-01633-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 01/04/2019] [Accepted: 02/14/2019] [Indexed: 01/15/2023]
Abstract
An antibiotic-producing actinobacterium, designated isolate B375T, was isolated from marine sponge Glodia corticostylifera collected from Praia Guaecá, São Paulo, Brazil (23°49S; 45°25W), and its taxonomic position established using data from a polyphasic study. The organism showed a combination of morphological, physiological, biochemical and chemotaxonomic characteristics consistent with its classification in the genus Williamsia. Comparative 16S rRNA gene sequence analysis indicated that the strain B375T was most closely related to Williamsia serinedens DSM 45037T and Williamsia spongiae DSM 46676T and having 99.43% and 98.65% similarities, respectively, but was distinguished from these strains by a low level of DNA-DNA relatedness (53.2-63.2%) and discriminatory phenotypic properties. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and N-glycolated muramic acid residues present in the wall cells. The cells contained C16:0 (23.3%), C18:0 10-methyl (23.2%) and C18:1 ω9c (21.6%) as the major cellular fatty acids. The strain B375T inhibited growing of Staphylococcus aureus and Colletotrichum gloeosporioides strains and was considered a producer of antimicrobial compounds. Based on the data obtained, the isolate B375T (= CBMAI 1090T = DSM 46677T) should, therefore, be classified as the type strain of a novel species of the genus Williamsia, for which the name Williamsia aurantiacus sp. nov. is proposed.
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Affiliation(s)
- Cláudia Beatriz Afonso de Menezes
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, Paulínia, SP, CEP 13148-218, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, Campinas, SP, 13083-970, Brazil
| | - Rafael Sanches Afonso
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, Paulínia, SP, CEP 13148-218, Brazil
| | - Wallace Rafael de Souza
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil
| | - Márcia Maria Parma
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil
| | - Itamar Soares de Melo
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil
| | - Fernando Lucas Satoru Fugita
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Av. Bandeirantes,3900, Monte Alegre, Ribeirão Preto, São Paulo, 12040-901, Brazil
| | - Luiz Alberto Beraldo Moraes
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Av. Bandeirantes,3900, Monte Alegre, Ribeirão Preto, São Paulo, 12040-901, Brazil
| | | | - Fabiana Fantinatti-Garboggini
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, Paulínia, SP, CEP 13148-218, Brazil. .,Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, Campinas, SP, 13083-970, Brazil.
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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: 421] [Impact Index Per Article: 70.2] [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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Afonso de Menezes CB, Afonso RS, Souza WRD, Parma M, Melo ISD, Zucchi TD, Fantinatti-Garboggini F. Williamsia spongiae sp. nov., an actinomycete isolated from the marine sponge Amphimedon viridis. Int J Syst Evol Microbiol 2017; 67:1260-1265. [PMID: 28100308 DOI: 10.1099/ijsem.0.001796] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated isolate B138T, was isolated from the marine sponge, Amphimedon viridis, which was collected from Praia Guaecá (São Paulo, Brazil), and its taxonomic position was established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Williamsia and it formed a distinct phyletic line in the Williamsia 16S rRNA gene tree. It was most closely related to Williamsia serinedens DSM 45037T and Williamsia deligens DSM 44902T (99.0 % 16S rRNA gene sequence similarity) and Williamsia maris DSM 44693T (97.5 % 16S rRNA gene sequence similarity), but was distinguished readily from these strains by the low DNA-DNA relatedness values (62.3-64.4 %) and by the discriminatory phenotypic properties. Based on the data obtained, the isolate B138T (=CBMAI 1094T=DSM 46676T) should be classified as the type strain of a novel species of the genus Williamsia, for which the name Williamsia spongiae sp. nov. is proposed.
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Affiliation(s)
- Cláudia Beatriz Afonso de Menezes
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, CEP 13148-218, Paulínia, SP, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, 13083-970, Campinas, SP, Brazil
| | - Rafael Sanches Afonso
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, CEP 13148-218, Paulínia, SP, Brazil
| | - Wallace Rafael de Souza
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, CEP 13820-000, Jaguariúna, SP, Brazil
| | - Márcia Parma
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, CEP 13820-000, Jaguariúna, SP, Brazil
| | - Itamar Soares de Melo
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, CEP 13820-000, Jaguariúna, SP, Brazil
| | - Tiago Domingues Zucchi
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, CEP 13820-000, Jaguariúna, SP, Brazil.,Agrivalle - Biotecnologia Agrícola, Rua Moisés Lopes Silva 50, CEP 37550-000, Pouso Alegre, MG, Brazil
| | - Fabiana Fantinatti-Garboggini
- Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, 13083-970, Campinas, SP, Brazil.,Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, CEP 13148-218, Paulínia, SP, Brazil
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Dinesh R, Srinivasan V, T E S, Anandaraj M, Srambikkal H. Endophytic actinobacteria: Diversity, secondary metabolism and mechanisms to unsilence biosynthetic gene clusters. Crit Rev Microbiol 2017; 43:546-566. [PMID: 28358596 DOI: 10.1080/1040841x.2016.1270895] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Endophytic actinobacteria, which reside in the inner tissues of host plants, are gaining serious attention due to their capacity to produce a plethora of secondary metabolites (e.g. antibiotics) possessing a wide variety of biological activity with diverse functions. This review encompasses the recent reports on endophytic actinobacterial species diversity, in planta habitats and mechanisms underlying their mode of entry into plants. Besides, their metabolic potential, novel bioactive compounds they produce and mechanisms to unravel their hidden metabolic repertoire by activation of cryptic or silent biosynthetic gene clusters (BGCs) for eliciting novel secondary metabolite production are discussed. The study also reviews the classical conservative techniques (chemical/biological/physical elicitation, co-culturing) as well as modern microbiology tools (e.g. next generation sequencing) that are being gainfully employed to uncover the vast hidden scaffolds for novel secondary metabolites produced by these endophytes, which would subsequently herald a revolution in drug engineering. The potential role of these endophytes in the agro-environment as promising biological candidates for inhibition of phytopathogens and the way forward to thoroughly exploit this unique microbial community by inducing expression of cryptic BGCs for encoding unseen products with novel therapeutic properties are also discussed.
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Affiliation(s)
- Raghavan Dinesh
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| | | | - Sheeja T E
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| | | | - Hamza Srambikkal
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
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Xie CL, Niu SW, Zhou TT, Zhang GY, Yang Q, Yang XW. Chemical constituents and chemotaxonomic study on the marine actinomycete Williamsia sp. MCCC 1A11233. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Horn H, Keller A, Hildebrandt U, Kämpfer P, Riederer M, Hentschel U. Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1. Stand Genomic Sci 2016; 11:8. [PMID: 26779305 PMCID: PMC4715301 DOI: 10.1186/s40793-015-0122-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022] Open
Abstract
The Gram-positive actinomycete Williamsia sp. ARP1 was originally isolated from the Arabidopsis thaliana phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus Williamsia and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.
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Affiliation(s)
- Hannes Horn
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany ; GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105 Kiel, Germany
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, D-97074 Germany
| | - Ulrich Hildebrandt
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26, D-35392 Giessen, Germany
| | - Markus Riederer
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany ; GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105 Kiel, Germany
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Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01230-13. [PMID: 24459282 PMCID: PMC3900914 DOI: 10.1128/genomea.01230-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first draft genome of a member of the genus Williamsia (strain D3) isolated from Antarctic soil. The genome of this psychrotolerant bacterium may help to elucidate crucial survival mechanisms for organisms inhabiting cold desert soil systems.
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Bouizgarne B, Ait Ben Aouamar A. Diversity of Plant Associated Actinobacteria. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2014. [DOI: 10.1007/978-3-319-05936-5_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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