VSE knjižnice (vzajemna bibliografsko-kataložna baza podatkov COBIB.SI)
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Recovering high-quality bacterial genomes from cross-contaminated cultures : a case study of marine Vibrio campbellii [Elektronski vir]Orel, Neža ...Background: Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant ... economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. Results: We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. Conclusions: Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.Vir: BMC genomics [Elektronski vir]. - ISSN 1471-2164 (Vol. 25, art. no 146, 2024, str. 1-15)Vrsta gradiva - e-članek ; neleposlovje za odrasleLeto - 2024Jezik - angleškiCOBISS.SI-ID - 184984323
Avtor
Orel, Neža |
Fadeev, Eduard |
Herndl, Gerhard J. |
Turk, Valentina |
Tinta, Tinkara
Teme
sekvenciranje celotnega genoma |
neaksenična kultura |
plazmidi |
morske bakterije |
morska biologija |
whole-genome assembly |
non-axenic culture |
plasmid |
marine bacteria |
marine biology |
Vibrio campbellii
Avtor | Orel, Neža ... |
Naslov | Recovering high-quality bacterial genomes from cross-contaminated cultures : a case study of marine Vibrio campbellii [Elektronski vir] |
Datum objave | 2024-02-06 |
COBISS.SI-ID | 184984323 |
Verzija objave v repozitoriju | Založnikova različica |
Licenca objave v repozitoriju | Creative Commons Priznanje avtorstva 4.0 Mednarodna |
Embargo | Takojšnja javna objava |
Projekti, iz katerih je bila financirana objava
Naziv | Akronim | Številka projekta | Financer |
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Raziskave obalnega morja | P1-0237-2020 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
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Dejavniki, ki strukturirajo mikrobiom obalnega morja s poudarkom na patogenih; celostni pristop | J1-9157-2018 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
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Vpliv razpada masovne populacije invazivne rebrače na mikrobno združbo obalnega morja - od molekul do ekosistema - celosten interdisciplinarni pristop | J7-2599-2020 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
Datoteke, ki spadajo k objavi
Povezava |
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https://doi.org/10.1186/s12864-024-10062-2 |
https://d.cobiss.net/repository/si/files/184984323/133732/s12864-024-10062-2_Orel-et-al.pdf |
https://dirros.openscience.si/IzpisGradiva.php?id=18578 |
Stroški objave
Vrsta stroška | Skupni stroški | Plačila |
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APC – strošek objave članka | 3226.90 € |
3226.90 € : Inštitut za biologijo |
Vnos na polico
Trajna povezava
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Leto | Faktor vpliva | Izdaja | Kategorija | Razvrstitev | ||||
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
Baze podatkov, v katerih je revija indeksirana
Ime baze podatkov | Področje | Leto |
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Povezave do osebnih bibliografij avtorjev | Povezave do podatkov o raziskovalcih v sistemu SICRIS |
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Orel, Neža | 51831 |
Fadeev, Eduard | |
Herndl, Gerhard J. | |
Turk, Valentina | 03764 |
Tinta, Tinkara | 29618 |
Vir: Osebne bibliografije
in: SICRIS
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