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Whole genome sequencing and functional analysis of a novel biofilm-eradicating strain Nocardiopsis lucentensis EMB25

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Abstract

The process of biofilm formation is intricate and multifaceted, requiring the individual cells to secrete extracellular polymeric substances (EPS) that subsequently aggregate and adhere to various surfaces. The issue of biofilms is a significant concern for public health due to the increased resistance of microorganisms associated with biofilms to antimicrobial agents. The current study describes the whole genome and corresponding functions of a biofilm inhibiting and eradicating actinobacteria isolate identified as Nocardiopsis lucentensis EMB25. The N. lucentensis EMB25 has 6.5 Mbp genome with 71.62% GC content. The genome analysis by BLAST Ring Image Generator (BRIG) revealed it to be closely related to Nocardiopsis dassonvillei NOCA502F. Interestingly, based on orthologous functional groups reflected by average nucleotide identity (ANI) analysis, it was 81.48% similar to N. arvandica DSM4527. Also, it produces lanthipeptides and linear azole(in)e-containing peptides (LAPs) akin to N. arvandica. The secondary metabolite search revealed the presence of major gene clusters involved in terpene, ectoine, siderophores, Lanthipeptides, RiPP-like, and T1PKS biosynthesis. After 24 h of treatment, the cell-free extract effectively eradicates the pre-existing biofilm of P. aeruginosa PseA. Also, the isolated bacteria exhibited antibacterial activity against MRSA, Staphylococcus aureus and Bacillus subtilis bacteria. Overall, this finding offers valuable insights into the identification of BGCs, which contain enzymes that play a role in the biosynthesis of natural products. Specifically, it sheds light on the functional aspects of these BGCs in relation to N. lucentensis.

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Data Availability

The bacterial genome of N. lucentensis EMB25 has been submitted to NCBI database with accession number: JAMTDN000000000, Bioproject: PRJNA729595 and Biosample: SAMN19135856.

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Acknowledgements

The first author (NG) would like to acknowledge the financial assistance provided by the Ministry of Human Resource Development (MHRD), Govt. of India, and IIT Delhi. SZ is grateful to CSIR for providing the Senior research fellowship.

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Authors and Affiliations

  1. Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India

    Nikky Goel, Saniya Zaidi & Sunil Kumar Khare

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  1. Nikky Goel
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  2. Saniya Zaidi
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  3. Sunil Kumar Khare
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Contributions

Nikky Goel: Conceptualization, Methodology, Formal analysis, writing original draft; Saniya Zaidi: Methodology, Formal analysis, writing; Sunil K. Khare: Conceptualization, Formal analysis, Supervision, Review MS.

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Correspondence to Sunil Kumar Khare.

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Goel, N., Zaidi, S. & Khare, S.K. Whole genome sequencing and functional analysis of a novel biofilm-eradicating strain Nocardiopsis lucentensis EMB25. World J Microbiol Biotechnol 39, 292 (2023). https://doi.org/10.1007/s11274-023-03738-6

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