Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid

Novosphingobium rhizovicinum sp. nov. and Novosphingobium kalidii sp. nov., two novel species isolated from rhizosphere soil and a root of halophyte Kalidium cuspidatum

Two bacteria, designated strain M1R2S20T and RD2P27T, were isolated from rhizosphere soil and a root of Kalidium cuspidatum in Baotou, Inner Mongolia, China. Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strains M1R2S20T and RD2P27T were tightly clustered and both shared the highest 16S rRNA gene similarities (98.6 and 98.5 %) to Novosphingobium fluoreni ACCC 19180T and less than 97.8% similarities with all other current type strains. Values of the digital DNA-DNA hybridization (dDDH), the average nucleotide identity based on the blast method (ANIb) and the average amino acid identity (AAI) of the two strains and their closely related species were 32.2, 79.0, and 84.5%, which were lower than the threshold values (70% for dDDH, 95% for ANIb and 95% for AAI). The major fatty acids of strains M1R2S20T and RD2P27T were C18 : 1  ω7c and summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c). The only quinone was ubiquinone-10. Spermidine was the predominant polyamine. The genomic DNA G+C contents for strain M1R2S20T and RD2P27T were 62.4 and 62.7%. The phenotypic, chemotaxonomic and phylogenetic results supported that strains M1R2S20T and RD2P27T could be identified as two novel species within the genus Novosphingobium, for which the name Novosphingobium rhizovicinum sp. nov. and Novosphingobium kalidii sp. nov. are proposed. The type strains are N. rhizovicinum M1R2S20T (=CGMCC 1.62060T=KCTC 8106T) and N. kalidii RD2P27T (=CGMCC 1.62131T=KCTC 8107T).

Unique gel-like colony forming bacterium Novosphingobium pituita sp. nov., isolated from a membrane bioreactor (MBR) treating sewage

A novel, gelatinous, colony-forming, rod-shaped bacterial strain, designated IK01T was isolated from biofilms formed on the membrane surface of a sewage-treating membrane bioreactor (MBR). Strain IK01T produced gelatinous and almost transparent colonies at lower medium concentrations. Fourier transform infrared analysis of the gelatinous colony matrix showed that the matrix could be a biofilm substance. This suggests that strain IK01T is a fouling-causing bacteria in the MBR. Furthermore, 16S rRNA gene sequence analysis showed that strain IK01T was phylogenetically placed in the genus Novosphingobium. The average nucleotide identity values for IK01T and the other 50 species of the genus Novosphingobium ranged from 78.5 to 83.9 %. Correspondingly, the estimated digital DNA-DNA hybridization values ranged from 20.8 to 24.4 %. The genomic DNA G + C content was 66.0 %. 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 C14:0 2-OH. A polar lipid profile revealed phosphatidylethanolamine, two unidentified phospholipids, and three aminoglycophospholipids as major compounds. The major respiratory quinone was ubiquinone Q-10. Genotypic, chemotaxonomic, and phenotypic analyses characterized the newly identified strain IK01T, as a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium pituita sp. nov. The type strain is IK01T (NBRC 116408T = DSM 116658T).

Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil

An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).

Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation

Background: Advancements in DNA sequencing technology have transformed the field of bacterial genomics, allowing for faster and more cost effective chromosome level assemblies compared to a decade ago. However, transforming raw reads into a complete genome model is a significant computational challenge due to the varying quality and quantity of data obtained from different sequencing instruments, as well as intrinsic characteristics of the genome and desired analyses. To address this issue, we have developed a set of container-based pipelines using Nextflow, offering both common workflows for inexperienced users and high levels of customization for experienced ones. Their processing strategies are adaptable based on the sequencing data type, and their modularity enables the incorporation of new components to address the community's evolving needs. Methods: These pipelines consist of three parts: quality control, de novo genome assembly, and bacterial genome annotation. In particular, the genome annotation pipeline provides a comprehensive overview of the genome, including standard gene prediction and functional inference, as well as predictions relevant to clinical applications such as virulence and resistance gene annotation, secondary metabolite detection, prophage and plasmid prediction, and more. Results: The annotation results are presented in reports, genome browsers, and a web-based application that enables users to explore and interact with the genome annotation results. Conclusions: Overall, our user-friendly pipelines offer a seamless integration of computational tools to facilitate routine bacterial genomics research. The effectiveness of these is illustrated by examining the sequencing data of a clinical sample of Klebsiella pneumoniae.