Two B. licheniformis strains isolated from extreme environments are isolated from the Five Sisters hot spring in Yellowstone National Park and whole-genome sequencing reveals an open pangenome of 10,374 genes, providing a genomic foundation for future exploration of novel bioactive compounds with potential applications in drug discovery, agriculture, and biotechnology.
Abstract
Bacillus licheniformis is a Gram-positive, endospore-forming bacterium with broad biotechnological applications. Thermophilic environments such as hot springs may harbor strains with unique biosynthetic capabilities relevant to drug discovery. In this study, we isolated two B. licheniformis strains (S3 and S4) from the Five Sisters hot spring in Yellowstone National Park (68 °C and 65 °C, pH 8) and performed whole-genome sequencing using both the Oxford Nanopore long read and Illumina platforms. Hybrid de novo assembly using Unicycler yielded genome sizes of 4.80 Mbp (S3, 14 contigs) and 4.79 Mbp (S4, 22 contigs); GC contents were 45.12% and 45.10%, and N50 values were 4,546,802 bp and 2,415,736 bp, for S3 and S4, respectively. Both strains were assigned to Multi-Locus Sequence Typing sequence type ST-42. Pangenome comparison with 61 complete B. licheniformis genomes revealed an open pangenome of 10,374 genes, with 3,272 core genes, 430 soft core, 1,250 shell, and 5,422 cloud genes. AMRFinderPlus identified the blaP, encoding a class A beta-lactamase and its regulatory elements (blaI and blaR1); erm(D), encoding a 23S rRNA methyltransferase conferring macrolide–lincosamide–streptogramin B resistance; and catA, encoding a chloramphenicol O-acetyltransferase that inactivates chloramphenicol through acetylation in both strains. A chromosomal arsBC locus was identified in both B. licheniformis S3 and S4, consistent with the arsenic-rich geothermal environment of Five Sisters hot spring. These findings highlight the biosynthetic potential of B. licheniformis strains isolated from extreme environments and provide a genomic foundation for future exploration of novel bioactive compounds with potential applications in drug discovery, agriculture, and biotechnology.
Findings establish B. velezensis strains BP5 and BP103 as highly promising biocontrol agents, combining high genetic stability with diverse secondary metabolite profiles, suitable for development into sustainable microbial bio-bactericides.
Lê Uyển Thanh, Vu Nhat Tan, T. Huyen et al.· Frontiers in Microbiology· 0 citations
Four novel bacterial strains representing two novel species were isolated from in situ coal samples. Comparative analysis of 16S rRNA gene sequences showed that strains W1153T and W1478 share the highest sequence similarity with Leucobacter tardus K 70/01T (98.3%), whereas strains Z1108T and W1038 share the highest sequence similarity with L. tardus K 70/01T and Leucobacter exalbidus K-540BT (98.0%). Phylogenetic analysis based on 16S rRNA gene sequences and a core-genome phylogeny constructed from 665 core genes demonstrated that the four strains form two distinct clades, clearly separated from other species within the genus Leucobacter. Whole-genome sequencing revealed genome sizes ranging from 2.6 to 2.8 Mb, with G+C contents of 62.5-63.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between the four strains and all recognized species within the genus Leucobacter ranged from 71.1 to 75.6% and 19.3 to 25.6%, respectively. The major cellular fatty acids of the four strains were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The respiratory quinone types were MK-11 for strain W1153T and MK-9(H8) for strain Z1108T. The main cell-wall sugars were rhamnose and ribose, with 2,4-diaminobutyric acid present as the diagnostic diamino acid. Based on phenotypic characteristics, phylogenetic analyses and chemotaxonomic evidence, strains W1153T and W1478, and Z1108T and W1038, are proposed as representing two novel species within the genus Leucobacter, named Leucobacter shiyiweii sp. nov. and Leucobacter fengyongliangi sp. nov., respectively. The type strains are W1153T (=GDMCC 1.5845T=KCTC 59606T) and Z1108T (=GDMCC 1.5846T=KCTC 59607T).
Junyao Xie, Yi-Hang Yang, Fangyu Gao et al.· International Journal of Sys...· 0 citations
This article presents the draft genome sequence of strain MF0224, an anaerobic bacterium representing an unclassified Fusobacterium-related lineage isolated from a coastal sediment sample collected in Puducherry, India. Whole-genome sequencing was performed using the Illumina paired-end sequencing platform and assembled into a draft genome of 2.02 Mb comprising 26 contigs with a genomic DNA G+C content of 28.19%. Genome annotation predicted 1889 coding sequences, 47 tRNA genes, and multiple genes associated with anaerobic carbon metabolism, acetate production, sulfur metabolism, volatile fatty acid metabolism, and carbohydrate-active enzymes. Genome quality assessment indicated high completeness with low contamination. Comparative genomic analysis using TYGS identified the strain as a potential novel species within the genus Fusobacterium, supported by low digital DNA–DNA hybridization (dDDH) values (∼20%) relative to currently described species. Average amino acid identity (AAI; 68.9%) supported its placement within the genus Fusobacterium while indicating substantial genomic divergence. Comparative genomic analysis also determined a percentage of conserved proteins (POCP) value of 65.9%, providing additional genomic characterization of strain MF0224. Phylogenetic analyses based on 16S rRNA gene sequences and whole-genome phylogeny consistently positioned strain MF0224 within the Fusobacterium-associated clade. The genome provides a valuable resource for investigating anaerobic carbon metabolism, acetate biosynthesis, sulfur-associated pathways, and the ecological adaptation of Fusobacterium-related bacteria in coastal sediment ecosystems.
M. Prathaban, R. Prathiviraj, M. Sobanaa et al.· Data in Brief· 0 citations
Estuarine mangrove environments are unique, highly dynamic habitats harboring a rich and unexplored diversity of bioactive actinobacteria. In this study, we highlight the extensive molecular identification, genetic sequencing, and evolutionary positioning of the bacterial isolate ANU-27, which exhibited superior broad-spectrum antimicrobial efficacy during initial phenotypic screenings. Genomic DNA was successfully extracted using the CTAB-lysozyme methodology, yielding634±32 µg/gof high-integrity DNA with a distinct genomic G+C content of 55.1% calculated via thermal denaturation midpoint (Tm= 92.3C).The 16S rRNA gene locus was targeted and amplified via PCR utilizing 27F and 1492R universal primers, generating a sharp ~1500 bp amplicon. Bidirectional Sanger sequencing resolved a definitive sequence spanning 1177 nucleotides with a high ribosomal G+C ratio 59.13%. Comprehensive homology mapping via NCBI BLASTn paired with a1000-replicate Maximum Parsimony cladogram clustered the strain with 100% sequence identity( E-Value = 0.0) within the genus Streptomyces, revealing an immediate phylogenetic node shared with Streptomyces maritimus strain SBK2-IR9 and Streptomyces rochei strain ABU8. These findings firmly clarify the taxonomic assignment of strain ANU-27, spotlighting its high secondary metabolic and biotechnological promise.
Anusha Rani Yavvari, N. D. Mundla· Journal of Integral Sciences· 0 citations
ABSTRACT Polyethylene terephthalate (PET) waste represents a major environmental challenge due to limited recycling solutions. Thermophilic bacteria from geothermal environments harbor diverse enzymatic machinery adapted to extreme conditions, offering promising biocatalysts for plastic degradation; however, biological resources from Peru and other South American countries remain scarce. We characterized four bacterial strains isolated from two geothermal sites in Cajamarca, Peru, screened for PET hydrolysis at 50°C. Whole‐genome sequencing using hybrid assembly achieved near‐complete circular genomes. GTDB‐Tk classification identified three species: Neobacillus thermocopriae (strain 19A), Bacillus licheniformis (strains 16P and BI2), and Brevibacillus agri (strain BI8). Quantitative assays revealed that strain 16P achieved the highest mass loss (0.598%), followed by strain BI8 (0.449%). ATR‐FTIR analysis of the incubated sheets showed a significant reduction of the ester carbonyl index in strains 16P, 19A, and BI8 relative to both non‐incubated PET and an abiotic control, whereas strain BI2 did not differ from the controls, indicating preferential modification of ester bonds at the sheet surface. Genome mining and structure‐based homology searches identified multiple candidate enzymes similar to validated PETases and carboxylesterases, including PETase46‐like homologs in strains BI8 and 16P and a terephthalate‐active carboxylesterase homolog in strain 16P. Molecular docking supported the conservation of catalytic geometry and substrate‐binding sites in these candidates. This work represents one of the first systematic genomic and structural characterizations of putative PET‐hydrolases in Peruvian geothermal bacteria, expanding knowledge of extremophile diversity and advancing thermostable enzymes for sustainable plastic waste management.
Marco A Rivera-Jacinto, Claudia Rodríguez-Ulloa, Sara R Briones-Ramírez et al.· MicrobiologyOpen· 0 citations
Strains MA13-6T and MA13-13, two Gram-stain-positive, aerobic, short rod-shaped actinobacteria, were isolated from a saline lake in Ngari Prefecture, Xizang Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these two strains belonged to the genus Aquipuribacter, with the closest relationship to Aquipuribacter hungaricus IV-75T (98.47% sequence similarity) and Aquipuribacter nitratireducens AMV4T (97.36% sequence similarity). Phylogenetic analysis based on genomes further confirmed their classification as a distinct cluster within the genus Aquipuribacter. The average nucleotide identity and digtal DNA-DNA hybridization values between these two strains and their closest relative Aquipuribacter hungaricus IV-75T, were 82.44-82.49% and 23.00%, respectively, clearly indicating that strains MA13-6T and MA13-13 represent a novel species. The 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA-DNA hybridization values between these two strains were 99.79%, 99.97% and 99.40%, respectively, unequivocally confirming their classification within the same species. However, DNA fingerprinting analysis distinguished them as non-clonal variants. The polar lipids comprised phosphatidylglycerol, two unidentified phospholipids, two unidentified glycolipids, and two unidentified lipids. The predominant respiratory quinone was MK-10 (H4). The major fatty acids were anteiso-C15:0, C18:1ω9c, isoC16:0 and anteiso-C17:0. The cell wall diagnostic diamino acid was meso-diaminopimelic acid. 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. nov. is proposed. The type strain is MA13-6T (=MCCC 1K10045T = KCTC 59572T).
Xia Luo, Mingzhu Zhang, Yumo Li et al.· Systematic and Applied Micro...· 0 citations