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Naslov:Recovering high-quality bacterial genomes from cross-contaminated cultures : a case study of marine Vibrio campbellii
Avtorji:ID Orel, Neža (Avtor)
ID Fadeev, Eduard (Avtor)
ID Herndl, Gerhard J. (Avtor)
ID Turk, Valentina (Avtor)
ID Tinta, Tinkara (Avtor)
Datoteke:URL URL - Izvorni URL, za dostop obiščite https://doi.org/10.1186/s12864-024-10062-2
 
.pdf PDF - Izvorna datoteka, prenos (5,87 MB)
MD5: D8ECD8B8CA4DE0FD0DEF9D1054401FD1
 
Jezik:Angleški jezik
Tipologija:1.01 - Izvirni znanstveni članek
Organizacija:Logo NIB - Nacionalni inštitut za biologijo
Povzetek: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.
Ključne besede:whole-genome assembly, non-axenic culture, plasmid, marine bacteria, marine biology
Status publikacije:Objavljeno
Verzija publikacije:Objavljena publikacija
Datum objave:06.02.2024
Leto izida:2024
Št. strani:str. 1-15
Številčenje:Vol. 25, art. no ǂ146
PID:20.500.12556/DiRROS-18578 Novo okno
UDK:577
ISSN pri članku:1471-2164
DOI:10.1186/s12864-024-10062-2 Novo okno
COBISS.SI-ID:184984323 Novo okno
Opomba:Soavtorji: Eduard Fadeev, Gerhard J. Herndl, Valentina Turk & Tinkara Tinta; Nasl. z nasl. zaslona; Opis vira z dne 13. 2. 2024;
Datum objave v DiRROS:28.03.2024
Število ogledov:96
Število prenosov:35
Metapodatki:XML RDF-CHPDL DC-XML DC-RDF
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Gradivo je del revije

Naslov:BMC genomics
Skrajšan naslov:BMC Genomics
Založnik:BioMed Central
ISSN:1471-2164
COBISS.SI-ID:2438420 Novo okno

Gradivo je financirano iz projekta

Financer:ARIS - Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije
Program financ.:Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije
Številka projekta:P1-0237
Naslov:Coastal Sea Research

Financer:ARIS - Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije
Program financ.:Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije
Številka projekta:J1-9157
Naslov:Drivers that structure coastal marine microbiome with emphasis on pathogens – an integrated approach

Financer:ARIS - Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije
Program financ.:Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije
Številka projekta:J7-2599
Naslov:Vpliv razpada masovne populacije invazivne rebrače na mikrobno združbo obalnega morja - od molekul do ekosistema - celosten interdisciplinarni pristop

Financer:FWF - Austrian Science Fund
Številka projekta:M2797-B

Licence

Licenca:CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
Povezava:http://creativecommons.org/licenses/by/4.0/deed.sl
Opis:To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

Sekundarni jezik

Jezik:Latinski jezik
Ključne besede:sekvenciranje celotnega genoma, neaksenična kultura, plazmidi, morske bakterije, morska biologija, Vibrio campbellii


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