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<p>A marine bacterium, <i>Exiguobacterium profundum</i> SW22, was isolated from sediment in the Bay of Bengal and characterised for its adaptive and biotechnological potential. The strain formed light orange, circular colonies with Gram-positive rod morphology and exhibited catalase, oxidase, and amylase activities, utilised diverse carbohydrates, and was sensitive to all tested antibiotics. <i>De novo</i> whole-genome assembly using Unicycler resulted in a 3 Mbp circular chromosome (48.2% G + C). Genome annotation with Bakta identified 3,060 protein-coding genes, 68 tRNAs, 27 rRNAs, tmRNA, and non-coding RNAs. Phylogenomic analysis, including 16&#xa0;S rRNA gene similarity, average nucleotide identity (97.1%) and digital DNA - DNA hybridization (91%), confirmed SW22 as <i>E. profundum</i>. The maximum-likelihood phylogeny placed SW22 within the <i>E. profundum</i> clade, with 100% bootstrap support. Fatty acid analysis revealed the presence of branched-chain iso- and anteiso-C<sub>17:0</sub> and C<sub>18:0</sub> species, indicating membrane adaptation to stress. Genome annotation classified 1,643 proteins into 24 KEGG categories, with notable representation in genetic information processing and carbohydrate metabolism. CAZyme profiling identified 69 carbohydrate-active enzymes across 41 clusters, including amylase-related islands. The antiSMASH predicted 17 biosynthetic gene clusters (saccharide, terpene, RiPPs), consistent with antimicrobial potential. SignalP 6.0 identified Sec-, Tat-, and pilin-type peptides with cleavage sites at residues 15–30, strongly correlated with transporter families (MFS <i>r</i> = 0.92; ABC <i>r</i> = 0.91). The results confirmed the presence of 910 <i>Exiguobacterium</i> core genes, 552 <i>E. profundum</i>-specific, and 116 SW22 strain-specific genes. The combined environmental resilience, metabolic versatility, and biosynthetic repertoire underscore the potential of SW22 as a promising source of novel biotechnological and pharmaceutical applications.</p>

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Comprehensive Genomic Characterization of the Marine Isolate Exiguobacterium profundum SW22: Insights into Adaptive Mechanisms and Biosynthetic Potential

  • 期刊论文

  • 发表日期：

    2026年3月4日

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  • Sriram Shankar,
  • Meyappan Vadivel,
  • Raman Gurusamy,
  • Natarajan Sakthivel

摘要

A marine bacterium, Exiguobacterium profundum SW22, was isolated from sediment in the Bay of Bengal and characterised for its adaptive and biotechnological potential. The strain formed light orange, circular colonies with Gram-positive rod morphology and exhibited catalase, oxidase, and amylase activities, utilised diverse carbohydrates, and was sensitive to all tested antibiotics. De novo whole-genome assembly using Unicycler resulted in a 3 Mbp circular chromosome (48.2% G + C). Genome annotation with Bakta identified 3,060 protein-coding genes, 68 tRNAs, 27 rRNAs, tmRNA, and non-coding RNAs. Phylogenomic analysis, including 16 S rRNA gene similarity, average nucleotide identity (97.1%) and digital DNA - DNA hybridization (91%), confirmed SW22 as E. profundum. The maximum-likelihood phylogeny placed SW22 within the E. profundum clade, with 100% bootstrap support. Fatty acid analysis revealed the presence of branched-chain iso- and anteiso-C17:0 and C18:0 species, indicating membrane adaptation to stress. Genome annotation classified 1,643 proteins into 24 KEGG categories, with notable representation in genetic information processing and carbohydrate metabolism. CAZyme profiling identified 69 carbohydrate-active enzymes across 41 clusters, including amylase-related islands. The antiSMASH predicted 17 biosynthetic gene clusters (saccharide, terpene, RiPPs), consistent with antimicrobial potential. SignalP 6.0 identified Sec-, Tat-, and pilin-type peptides with cleavage sites at residues 15–30, strongly correlated with transporter families (MFS r = 0.92; ABC r = 0.91). The results confirmed the presence of 910 Exiguobacterium core genes, 552 E. profundum-specific, and 116 SW22 strain-specific genes. The combined environmental resilience, metabolic versatility, and biosynthetic repertoire underscore the potential of SW22 as a promising source of novel biotechnological and pharmaceutical applications.