Based on the combined genomic, phenotypic, and chemotaxonomic evidence, strain ZE1316R2Aᵀ represents a novel species of the genus Streptomyces, for which the name Streptomyces zimensis sp.
Abstract
Members of the phylum
Actinomycetota
are widely distributed across diverse environments and are well known for their metabolic versatility and capacity to produce bioactive compounds. In this study, strain ZE1316R2Aᵀ was isolated from the saline water collected from Lake Zima (Morocco) and subjected to comprehensive polyphasic taxonomic characterisation. Phylogenetic analysis based on the 16 S rRNA gene placed strain ZE1316R2Aᵀ within the genus
Streptomyces
, showing highest sequence similarity with
S. albidoflavus
DSM 40,455
T
(99.71%). However, genome-based indices, including average nucleotide identity (ANIb = 94.84%, ANIm = 96.09%) and digital DNA-DNA hybridization (dDDH = 64.9%), supported its distinction as a separate species. The draft genome (7.41 Mb; G + C = 73.26 mol%) comprises 6,464 coding sequences and reveals the presence of strain-specific genomic regions and biosynthetic gene clusters. Comparative analyses highlighted both a conserved core genome and a substantial accessory genome component, reflecting genomic differentiation relative to closely related taxa. Phenotypic and chemotaxonomic characteristics were consistent with assignment to the genus
Streptomyces
, while supporting its differentiation at the species level. Based on the combined genomic, phenotypic, and chemotaxonomic evidence, strain ZE1316R2Aᵀ represents a novel species of the genus
Streptomyces
, for which the name
Streptomyces zimensis
sp. nov., is proposed. This study expands current knowledge of
Streptomyces
diversity associated with saline environments and highlights the genomic diversity present within closely related taxa. The type strain is ZE1316R2Aᵀ (= CCMM B1331
T
= DSM 120541
T
).
Non-tuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens, yet accurate species identification remains challenging. In this study, two clinical isolates, 19-857T and 20-525, obtained from patients with suspected pulmonary tuberculosis in Beijing, were characterized using a polyphasic approach integrating phenotypic, biochemical, chemotaxonomic, and genomic analyses. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains within the genus Mycobacterium, with highest similarity to M. peregrinum DSM 43271T and M. arcueilense DSM 46715T. However, whole-genome comparisons via average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) yielded values of 85.8–94.1% and 29.1–54.3%, respectively, against their closest relatives—well below the species delineation thresholds (95–96% for ANI; 70% for dDDH)—while the two isolates shared 98.8% ANI and 90.1% dDDH, confirming their co-assignment to a single novel species. Genomic analysis further revealed a repertoire of genes potentially associated with virulence, including glycopeptidolipid biosynthesis, mce operons, ESX secretion systems, and mycobactin synthesis, alongside antimicrobial resistance determinants against rifampicin, tetracyclines, and β-lactams. Mobile genetic element analysis also uncovered extensive insertion sequences and transposon-related elements with differential distribution between the two strains. Based on the combined evidence, we propose Mycobacterium shunyiense sp. nov., with strain 19-857T (=CGMCC 38906T) as the type strain. This discovery expands the understanding of NTM diversity and provides genomic reference data for accurate clinical identification.
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Comparative genomic analysis andylogenetic analysis revealed that the strain H202T belonged to the genus Actinopolyspora and showed the highest sequence similarity to Actinopolyspora mzabensis DSM 45460T, suggesting that this strain represents a novel species.
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Based on phylogenetic analyses combined with phenotypic and chemotaxonomic characterization, strains MA13-6T and MA13-13 represent a novel species of the genus Aquipuribacter, for which the name Aquipuribacter aurantiacus sp.
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Three Gram-stain-negative bacterial strains, KR7-65T, KR7-225T and CN5-332T isolated from oil-contaminated soil in Korea and China were identified. Phylogenetic analysis based on 16S rRNA gene sequences placed the strains within the family Xanthobacteraceae, with KR7-65T and KR7-225T affiliated with the genus Xanthobacter and CN5-332T with the genus Aquabacter. Sequence similarities to type strains of validly published species were below 98.5%. Core genome phylogeny showed that the four strains formed distinct clusters occupying different positions in the phylogenetic tree and exhibited different closest relatives. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization (dDDH) values between KR7-65T and KR7-225T and members of Xanthobacter were 78.7-87.0%, 74.8-87.8% and 22.7-32.3%, respectively, whereas those between CN5-332T and members of Aquabacter were 80.2-80.7%, 79.6-80.5% and 23.4-23.9%, supporting their assignment as novel species. The DNA G+C contents were 68.0, 69.9 and 66.5 mol% for KR7-65T, KR7-225T and CN5-332T, respectively. Strains KR7-65T and KR7-225T contained phosphatidylcholine, phosphatidylglycerol, phosphatidyl monomethyl ethanolamine, diphosphatidylglycerol (DPG) and an unidentified glycolipid as major polar lipids, whereas DPG was absent in strain CN5-332T. The primary fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), cyclo C19 : 0ω8c and C16 : 0. On the basis of phylogenetic, genomic and phenotypic evidence, strains KR7-65T and KR7-225T represent two novel species of the genus Xanthobacter, for which the names Xanthobacter pollutisoli sp. nov. (type strain KR7-65T=KACC 23453T=NBRC 116939T) and Xanthobacter luteus sp. nov. (type strain KR7-225T=KACC 23282T=NBRC 116940T) are proposed. Strain CN5-332T represents a novel species of the genus Aquabacter, for which the name Aquabacter albus sp. nov. (type strain CN5-332T=KACC 23276T=CCTCC AB 2024343T) is proposed.
Thi Tuyet Nhan Le, Jaisoo Kim· International Journal of Sys...· 0 citations
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