Journal Article

Genome mining and metabolite profiling illuminate the taxonomy status and the cytotoxic activity of a mangrove-derived Microbacterium alkaliflavum sp. nov

Qing, Jin-Ling, Pan, Xinli, Huang, Yi-Ying, Hu, Wen-Jin, Deng, Li-Xian, Zhou, Xiao-Ying, Chu, Jie-Mei, Wang, Xiao-Chun, Zhou, Xing, Zhu, Hao-Jun

2025

Overview

The genus Microbacterium in the phylum Actinomycetota contains over 100 species to date that little is known about their bioactive metabolites production. In this study, a mangrove sediment-derived strain B2969 T was identified as a novel type strain within the genus Microbacterium due to the low 16S rRNA gene sequence similarity (< 99%), and low overall genome relatedness indices (ANI, 75.4%-79.5%; dDDH, 18.5%-22.7%, AAI, 68.7%-76.3%; POCP, 48.3%-65.0%) with the validly named species of the genus. The type strain B2969 T (= MCCC 1K099113 T  = JCM 36707  T ) is proposed to represent Microbacterium alkaliflavum sp. nov.. The crude extracts of strain B2969 T showed weak cytotoxicity against NPC cell lines TW03 and 5-8F, with IC 50 values of ranging from 3.5 µg/µL to 2.4 µg/µL respectively. Genome analysis of strain B2969 T found 8 clusters of genes responsible for secondary metabolite biosynthesis, including cytotoxic compounds desferrioxamines. In addition, the application of liquid chromatography tandem mass spectrometry (LC–MS/MS)-based molecular networking strategy led to the identification of 10 compounds with potent cytotoxic activity in ethyl acetate extracts of strain B2969 T . Results from the cytotoxicity assay, genome mining, and metabolite profiling based on LC–MS/MS analysis revealed its ability to produce bioactive compounds. Background Mangrove ecosystems are largely unexplored sources of Actinomycetota , which represent potential important reservoirs of bioactive compounds. The genus Microbacterium in the phylum Actinomycetota contains over 100 species to date that little is known about their bioactive metabolites production. In this study, a novel species, namely B2969 T , within the genus Microbacterium that showed cytotoxicity against nasopharyngeal carcinoma (NPC) cell lines was isolated from mangrove sediments. Genome mining and metabolic profiling analyses were explored here to assess its biosynthetic potential of metabolites with cytotoxic properties. Results Here, a mangrove sediment-derived strain B2969 T was identified as a novel species within the genus Microbacterium due to the low 16S rRNA gene sequence similarity (< 99.0%), and low overall genome relatedness indices (ANI, 75.4%-79.5%; dDDH, 18.5%-22.7%, AAI, 68.7%-76.3%; POCP, 48.3%-65.0%) with the type strains of this genus. We proposed that strain B2969 T represents a new species, in which the name Microbacterium alkaliflavum sp. nov. is proposed. The strain showed weak cytotoxicity against NPC cell lines TW03 and 5-8F, with IC 50 values of ranging from 3.512 µg/µL to 2.428 µg/µL respectively. Genome analysis of strain B2969 T found 8 clusters of genes responsible for secondary metabolite biosynthesis, including desferrioxamines. In addition, the application of liquid chromatography tandem mass spectrometry (LC–MS/MS)-based molecular networking strategy led to the identification of 10 potent cytotoxic compounds in ethyl acetate extracts of strain B2969 T . Conclusions This study confirmed the taxonomy status of type strain B2969 T (= MCCC 1K099113 T  = JCM 36707  T ) within the genus Microbacterium , in which the name Microbacterium alkaliflavum sp. nov.. Results from the cytotoxicity assay, genome mining, and metabolite profiling based on LC–MS/MS analysis revealed its ability to produce bioactive substances, providing sufficient evidence for the potential of Microbacterium species in the discovery of novel pharmaceuticals.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Acetic acid / Actinobacteria / Amino acids / Analysis / Anopheles / Antibiotics / Bioactive compounds / Biocompatibility / Bioinformatics / Biological activity / Biological Microscopy / Biomedical and Life Sciences / Biosynthesis / Cancer / Carbohydrates / Cell death / Cell Line, Tumor / Chemical properties / Clusters / Cytotoxicity / Data mining / DNA sequencing / DNA, Bacterial - genetics / Environmental aspects / Esters / Ethyl acetate / Genes / Genetic aspects / Genome mining / Genome, Bacterial / Genomes / Genomic analysis / Genomics / Geologic Sediments - microbiology / Gram-positive bacteria / Health aspects / Heavy metals / Humans / Identification and classification / Life Sciences / Liquid chromatography / Mangrove plants / Mangroves / Mass spectrometry / Mass spectroscopy / Metabolism / Metabolite profiling / Metabolites / Metabolome / Metabolomics / Methods / Microbacterium / Microbacterium - classification / Microbacterium - genetics / Microbacterium - isolation & purification / Microbacterium - metabolism / Microbiology / Mines and mineral resources / Morphology / Mycology / Nasopharyngeal carcinoma / Networking / New species / Nucleotide sequence / Organic compounds / Parasitology / Phosphatase / Phylogenetics / Phylogeny / Plant growth / Rifamycins / RNA / RNA sequencing / RNA, Ribosomal, 16S - genetics / rRNA 16S / Sediments / Sediments (Geology) / Similarity / Strain analysis / Sulfur / Taxonomy / Throat cancer / Toxicity / Tumor cell lines / Virology