ArticlePloS one2023
Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 11 citations in OpenAlex.
- Genomic and metabolomic insights into carotenoid biosynthesis in a novel deep-sea bacterium, Paracoccus niotae sp. nov., isolated from an Arabian Sea seamount.World journal of microbiology & biotechnology · 2026Article
- Functional diversity and ecological consequences of endophytic Bacillus-plant interactions.Folia microbiologica · 2026Review
- Biological and Genomic Characterization of Two Astaxanthin-ProducingJournal of microbiology and biotechnology · 2026Article
- Isolation, Screening, and Characterization of Gordonia paraffinivorans DGM-81 Exhibiting Antimicrobial Activity Against Methicillin-Resistant Staphylococcus aureus (MRSA).Current microbiology · 2026Article
- Magnetite Nanoparticles Enhancing HGlobal challenges (Hoboken, NJ) · 2025Article
- Multicenter exploration of microbial communities in hospital toilets reveals: antibiotic exposure in a nosocomial settings selects for coEnterococcus over commensal taxa.Antimicrobial resistance and infection control · 2025Article
- Genome sequence ofmicroPublication biology · 2025Article
- Microbial community shifts during salt mitigation treatments of historic buildings using mineral poultices: a long-term monitoring of salt and associated biofilms.Frontiers in microbiology · 2025Article
- Genome and pan-genome analysis of a new exopolysaccharide-producing bacteriumFrontiers in microbiology · 2024Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.
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