High-quality de novo genome assembly and functional genomic insights into Thermobifida alba DSM43795T, a mesophilic actinobacterium isolated from garden soil

Luzics, Szabina and Baka, Erzsébet and Margot, Otto and Kosztik, Judit and Szalontai, Helga and Batáné Vidács, Ildikó and Nagy, István and Tóth, Ákos and Táncsics, András and Pápai, Márton and Nagy, István and Orsini, Massimiliano and Kukolya, József (2025) High-quality de novo genome assembly and functional genomic insights into Thermobifida alba DSM43795T, a mesophilic actinobacterium isolated from garden soil. BIOLOGIA FUTURA, 76. pp. 541-558. ISSN 2676-8615

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Abstract

Thermobifida alba DSM43795 T , a mesophilic actinobacterium isolated from garden soil, plays a vital role in lignocellulose degradation and holds biotechnological and pharmaceutical potential. We present a high-quality, complete de novo genome assembly of T. alba DSM43795 T using combined PacBio long-read and Illumina short-read sequencing, resulting in a single circular chromosome of 4.9 Mbp with 72.1% GC content. Comparative genomics with the thermophilic relative T. fusca YX revealed 83.39% average nucleotide identity and extensive genome synteny alongside niche-specific differences. Functional annotation identified 4345 genes, including a rich complement of carbohydrate-active enzymes (CAZymes) such as glycoside hydrolases (GHs), esterases, and polysaccharide lyases, supporting versatile plant biomass degradation. GH gene sets were largely conserved between the species in both gene number and distribution, but T. alba uniquely encodes a novel GH10 endo-xylanase near a characterised palindrome regulatory sequence, indicating species-specific regulation. We hypothesise that thermophilic adaptation in T. fusca requires more proteins for ribosome integrity and amino acid metabolism, with reduced emphasis on carbohydrate metabolism and defence compared to T. alba . Moreover, T. alba harbours a broader array of defence-related genes and mobile genetic elements, including integrases and transposases. Although lacking a complete CRISPR-Cas system, two CRISPR arrays were detected, suggesting alternative immune strategies. Virulence factor homologs shared by both species likely reflect environmental survival rather than pathogenicity. This genomic characterisation elucidates T. alba ’s metabolic versatility and ecological adaptations, laying the groundwork for its potential applications in biomass conversion, environmental biotechnology, and drug discovery.

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