This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5^T, isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5^T has 64.4% G+C content and contains 4240 genes, of which a total of 3918 genes (92.4%) were functionally assigned to the COG (clusters of orthologous groups) database. Functional genes for denitrification (narGHJI, nirK and qnor) were identified on the genomes of the strain CHu59-6-5^T, except for N₂O reductase (nos) genes for the final step of denitrification. Genes (soxBXAZY) for encoding sulfur oxidation proteins were identified, and the FSD and soxF genes encoding the monomeric flavoproteins which have sulfide dehydrogenase activities were also detected. Lastly, genes for the assembly of two different RND (resistance-nodulation division) type efflux systems and one ABC (ATP-binding cassette) type efflux system were identified in the Rhodoferax sediminis CHu59-6-5^T. Phylogenetic analysis based on 16S rRNA sequences and Average Nucleotide Identities (ANI) support the idea that the strain CHu59-6-5^T has a close relationship to the genus Rhodoferax. A polyphasic study was done to establish the taxonomic status of the strain CHu59-6-5^T. Based on these data, we proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax sediminis sp. nov. with isolate CHu59-6-5^T.

The genus Gemmobacter grows phototrophically, aerobically, or anaerobically, and utilizes methylated amine. Here, we present two high-quality complete genomes of the strains con4 and con5^T isolated from a culture of Anabaena. The strains possess sMMO (soluble methane monooxygenase)-oxidizing alkanes to carbon dioxide. Functional genes for methane-oxidation (prmAC, mimBD, adh, gfa, fdh) were identified. The genome of strain con5^T contains nirB, nirK, nirQ, norB, norC, and norG genes involved in dissimilatory nitrate reduction. The presence of nitrite reductase gene (nirK) and the nitric-oxide reductase gene (norB) indicates that it could potentially use nitrite as an electron acceptor in anoxic environments. Taxonomic investigations were also performed on two strains through polyphasic methods, proposing two isolates as a novel species of the genus Gemmobacter. The findings obtained through the whole genome analyses provide genome-based evidence of complete oxidation of methane to carbon dioxide. This study provides a genetic blueprint of Gemmobacter fulva con5^T and its biochemical characteristics, which help us to understand the evolutionary biology of the genus Gemmobacter.

The strain designated as AN120528^T was isolated from farmland soil in South Korea. This strain grows well on R2A medium at 28 °C. The cells are an off-white colour and have no hyphae. The phylogenetic analysis indicated that the strain is a member of the genus Shimazuella with a 98.11% similarity to Shimazuella alba KC615^T and a 97.05% similarity to S. kribbensis KCTC 9933^T, respectively. The strain AN120528^T shares common chemotaxonomic features with the other two type strains in the genus. It has MK-9 (H₄) and MK-10 (H₄) as its predominant menaquinones. The major fatty acids are iso-C_14:0, iso-C_15:0, anteiso-C_15:0 and iso-C_16:0. Diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), lipids (L), and aminolipids (AL) were identified as the major cellular polar lipids. Analysis of the peptidoglycan showed the presence of meso-diaminopimelic acid. Whole-genome sequencing revealed that the genome of the strain is approximately 3.3 Mbp in size. The strain showed a 77.5% average nucleotide identity (ANI) with S. alba KC615^T. The genomic DNA (gDNA) G + C content is 39.0%. Based on polyphasic taxonomy analysis, it is proposed that this strain, AN120528^T, represents a novel species in the genus Shimazuella, designated as Shimazuella soli sp. nov. The type stain is AN120528^T (=KCTC 39810^T = DSM 103571^T). Furthermore, shimazuellin I, a new 15-amino-acid peptide, was discovered in the AN120528^T through genome mining; it has the features of a lasso peptide, containing eight amino acids (-G-Q-G-G-S-N-N-D-) that form a macrolactam ring and seven amino acids (-D-G-W-Y-H-S-K-) that form a tail.

The efficient hydrolysis of lignocellulosic biomass relies on the action of enzymes, which are crucial for the development of economically feasible cellulose bioconversion processes. However, low hydrolysis efficiency and the inhibition of cellulase production by carbon catabolite repression (CCR) have been significant obstacles in this process. The aim of this study was to identify the patterns of cellulose degradation and related genes through the genome analysis of a newly isolated lignocellulose-degrading fungus Flavodon sp. x-10. The whole-genome sequencing showed that the genome size of Flavodon sp. x-10 was 37.1 Mb, with a GC content of 49.48%. A total of 11,277 genes were predicted, with a total length of 18,218,150 bp and an average length of 1615 bp. Additionally, 157 tRNA genes responsible for transporting different amino acids were predicted, and the repeats and tandem repeats accounted for only 0.76% of the overall sequences. A total of 5039 genes were annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, representing 44.68% of all genes, and 368 metabolic pathways were involved. Of the 595 genes annotated in the carbohydrate-active enzyme (CAZy) database, 183 are associated with plant cell wall-degrading enzymes (PCWDEs), surpassing those of Aspergillus niger (167), Trichoderma reesei (64), and Neurospora crassa (86). Compared to these three fungi, Flavodon sp. x-10 has a higher number of enzyme genes related to lignin degradation in its genome. Transporters were further identified by matching the whole-genome sequence to the Transporter Classification Database (TCDB), which includes 20 sugar transporters (STs) closely linked to sugar utilization. Through the comprehensive exploration of the whole-genome sequence, this study uncovered more vital lignocellulase genes and their degradation mechanisms, providing feasible strategies for improving the strains to reduce the cost of biofuel production.

Lactic acid bacteria (LAB), as significant probiotics, hold immense application potential across diverse fields. This study systematically evaluated the probiotic properties and patulin degradation capabilities of four LAB strains with potent antimicrobial effects, previously isolated from Kimchi: Weissella cibaria (KM4 and KM14), Latilactobacillus sakei KMP17, and Leuconostoc mesenteroides KM35. All exhibited favorable environmental tolerance, adhesion capacity, and safety, along with the potential to degrade patulin. Out of these, L. sakei KMP17 demonstrated outstanding probiotic characteristics, high safety, and PAT degradation potential. Further investigation revealed that viable cell metabolism is the primary mechanism for PAT degradation by L. sakei KMP17, and PAT induction was hypothesized to stimulate the production of specific degradation enzymes. Concurrent whole-genome sequencing confirmed the high safety and significant probiotic potential of L. sakei KMP17. This research provides high-quality candidate strains and a theoretical foundation for the application of LAB in the field of food mycotoxin biodegradation.

The genus Microbacterium encompasses a diverse group of Actinobacteria with broad ecological distribution and functional versatility. Here, we report the complete genome sequence of Microbacterium sp. FBCC-B4120, a novel strain isolated from a freshwater ecosystem in Korea. The genome was assembled into a single circular chromosome of 3.78 Mb with a G + C content of 70.5%, achieving 100% genome completeness. Phylogenomic analysis confirmed that FBCC-B4120 represents a distinct species within the genus, with M. thalassium identified as its closest relative. FBCC-B4120 demonstrated diverse physiological activities such as antimicrobial activity, siderophore production, glycosidase activity, and traits associated with anti-obesity and antiviral effects. Comparative genome analysis revealed a broad repertoire of carbohydrate-active enzymes and a distinct urea utilization cluster, suggesting expanded capacities for carbohydrate metabolism and nitrogen utilization. These findings establish FBCC-B4120 as a novel Microbacterium species with distinctive genomic features and multifunctional traits, highlighting its potential as a valuable resource for future biotechnological applications. However, the functional predictions presented here rely primarily on genomic annotation, and further biochemical validation will be required to confirm these activities.