Streptomyces phytophilus sp. nov., an endophytic actinobacterium with biosynthesis potential as an antibiotic producer.

An endophytic actinobacterium, strain PIP175T, was isolated from the root sample of a native apricot tree (Pittosporum angustifolium) growing on the Bedford Park campus of Flinders University, Adelaide, South Australia. This strain is a Gram stain-positive, aerobic actinobacterium with well-developed substrate mycelia. Aerial mycelia rarely produce spores and the spore chain is spiral. Strain PIP175T showed the highest 16S rRNA gene sequence similarity to Streptomyces aculeolatus DSM 41644T (99.4 %). Other closely related phylogenetic representatives include Streptomyces synnematoformans DSM 41902T (98.3 %), Streptomyces albospinus NBRC 13846T (97.6 %), Streptomyces cacaoi subsp. cacaoi NRRL B-1220T (97.5 %) and Streptomyces ruber NBRC 14600T (97.4 %). The major cellular fatty acid of this strain was iso-C16 : 0 and the major menaquinone was MK-9(H6). The whole-cell sugar contained galactose, glucose and mannose. Chemotaxonomic data confirmed that strain PIP175T belonged to the genus Streptomyces. Digital DNA-DNA hybridization, average nucleotide identity based on blast and OrthoANIu results between strain PIP175T and S. aculeolatus DSM 41644T were 60.0, 94.1 and 94.9 %, respectively. Genotypic and phenotypic data and genome analysis results allowed the differentiation of strain PIP175T from its closest species with validly published names. Strain PIP175T showed good activity against methicillin-resistant Staphylococcus aureus 03120385. Genome mining of strain PIP175T revealed biosynthetic genes encoding proteins relating to antibiotic production, plant growth promotion and biodegradation enzymes. The name proposed for the new species is Streptomyces phytophilus sp. nov. The type strain is PIP175T (=DSM 103379T=TBRC 6026T).

[1]  Khushboo,et al.  Biotechnological and industrial applications of Streptomyces metabolites , 2021, Biofuels, Bioproducts and Biorefining.

[2]  S. Tanasupawat,et al.  Potential antibiotic production of Streptomyces justiciae sp. nov., isolated from the root of Justicia subcoriacea. , 2021, International journal of systematic and evolutionary microbiology.

[3]  Alexander M. Kloosterman,et al.  antiSMASH 6.0: improving cluster detection and comparison capabilities , 2021, Nucleic Acids Res..

[4]  Chongxi Liu,et al.  Streptomyces typhae sp. nov., a novel endophytic actinomycete with antifungal activity isolated the root of cattail (Typha angustifolia L.) , 2021, Antonie van Leeuwenhoek.

[5]  Onuma Kaewkla,et al.  Genome mining and description of Streptomyces albidus sp. nov., an endophytic actinobacterium with antibacterial potential , 2021, Antonie van Leeuwenhoek.

[6]  Jan P. Meier-Kolthoff,et al.  List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ , 2020, International journal of systematic and evolutionary microbiology.

[7]  Jian Gao,et al.  Streptomyces aquilus sp. nov., a novel actinomycete isolated from a Chinese medicinal plant. , 2020, International journal of systematic and evolutionary microbiology.

[8]  Xiao-Ming Yang,et al.  Effect of Alkylresorcinols on Autophagy, Migration, and Invasion of HepG2 Cells. , 2019, Journal of food science.

[9]  Jan P. Meier-Kolthoff,et al.  TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy , 2019, Nature Communications.

[10]  K. Sudesh,et al.  Identification and characterization of ectoine-producing bacteria isolated from Can Gio mangrove soil in Vietnam , 2019, Annals of Microbiology.

[11]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[12]  Onuma Kaewkla,et al.  Actinomycetospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilised root of an Australian native pine tree , 2018, Antonie van Leeuwenhoek.

[13]  A. Dubey,et al.  Diversity and Applications of Endophytic Actinobacteria of Plants in Special and Other Ecological Niches , 2018, Front. Microbiol..

[14]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[15]  Henrik Christensen,et al.  Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. , 2018, International journal of systematic and evolutionary microbiology.

[16]  Onuma Kaewkla,et al.  Streptomyces roietensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of jasmine rice, Oryza sativa KDML 105. , 2017, International journal of systematic and evolutionary microbiology.

[17]  J. Chun,et al.  Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies , 2017, International journal of systematic and evolutionary microbiology.

[18]  Rida Assaf,et al.  Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center , 2016, Nucleic Acids Res..

[19]  W. Metcalf,et al.  Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis , 2017, Antonie van Leeuwenhoek.

[20]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[21]  J. Chun,et al.  OrthoANI: An improved algorithm and software for calculating average nucleotide identity. , 2016, International journal of systematic and evolutionary microbiology.

[22]  Jörg Peplies,et al.  JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison , 2015, Bioinform..

[23]  Olivier Gascuel,et al.  FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program , 2015, Molecular biology and evolution.

[24]  K. Oishi,et al.  Wheat alkylresorcinols suppress high-fat, high-sucrose diet-induced obesity and glucose intolerance by increasing insulin sensitivity and cholesterol excretion in male mice. , 2015, The Journal of nutrition.

[25]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[26]  J. Chun,et al.  Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. , 2014, International Journal of Systematic and Evolutionary Microbiology.

[27]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[28]  P. Jensen,et al.  Cytotoxic and Antimicrobial Napyradiomycins from Two Marine-Derived, MAR 4 Streptomyces Strains. , 2013, European journal of organic chemistry.

[29]  Alexander F. Auch,et al.  Genome sequence-based species delimitation with confidence intervals and improved distance functions , 2013, BMC Bioinformatics.

[30]  Onuma Kaewkla,et al.  Rational Approaches to Improving the Isolation of Endophytic Actinobacteria from Australian Native Trees , 2013, Microbial Ecology.

[31]  Ying Huang,et al.  Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. , 2012, Systematic and applied microbiology.

[32]  R. Rosselló-Móra,et al.  Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.

[33]  C. Thawai,et al.  Planotetraspora thailandica sp. nov., isolated from soil in Thailand. , 2009, International journal of systematic and evolutionary microbiology.

[34]  Ying Huang,et al.  Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis D. Don. , 2009, International journal of systematic and evolutionary microbiology.

[35]  Peter Dawyndt,et al.  Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). , 2008, International journal of systematic and evolutionary microbiology.

[36]  M. Goodfellow,et al.  Streptomyces synnematoformans sp. nov., a novel actinomycete isolated from a sand dune soil in Egypt. , 2007, International journal of systematic and evolutionary microbiology.

[37]  S. Ōmura,et al.  Isolation and Identification of Three New 5-Alkenyl-3,3(2H)-furanones from Two Streptomyces species using a Genomic Screening Approach , 2006, The Journal of Antibiotics.

[38]  M. Nei,et al.  Prospects for inferring very large phylogenies by using the neighbor-joining method. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Marguerita Sasser,et al.  Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Technical Note # 101 , 2001 .

[40]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[41]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[42]  P. Baker,et al.  A80915, a new antibiotic complex produced by Streptomyces aculeolatus. Discovery, taxonomy, fermentation, isolation, characterization, and antibacterial evaluation. , 1990, The Journal of antibiotics.

[43]  K. Komagata,et al.  4 Lipid and Cell-Wall Analysis in Bacterial Systematics , 1988 .

[44]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[45]  S. Shaw,et al.  Simple rapid methods of cell wall analysis as an aid in the identification of aerobic coryneform bacteria , 1985 .

[46]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[47]  D. Minnikin,et al.  AN INTEGRATED PROCEDURE FOR THE EXTRACTION OF BACTERIAL ISOPRENOID QUINONES AND POLAR LIPIDS , 1984 .

[48]  M. Nei,et al.  Estimation of evolutionary distance between nucleotide sequences. , 1984, Molecular biology and evolution.

[49]  T. Hasegawa,et al.  A rapid analysis for chemical grouping of aerobic actinomycetes. , 1983 .

[50]  H. Lechevalier,et al.  Chemotaxonomy of aerobic Actinomycetes: Phospholipid composition , 1977 .

[51]  R. Gordon,et al.  Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain , 1974 .

[52]  J. A. Schmitt,et al.  Numerical taxonomy of Nocardia. , 1973, Canadian journal of microbiology.

[53]  J. Farris.  Estimating Phylogenetic Trees from Distance Matrices , 1972, The American Naturalist.

[54]  E. B. Shirling,et al.  Methods for characterization of Streptomyces species , 1966 .

[55]  K. Miura,et al.  PREPARATION OF TRANSFORMING DEOXYRIBONUCLEIC ACID BY PHENOL TREATMENT. , 1963, Biochimica et biophysica acta.