Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii
Abstract 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 pa...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-10062-2 |
| _version_ | 1827328532167000064 |
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| author | Neža Orel Eduard Fadeev Gerhard J. Herndl Valentina Turk Tinkara Tinta |
| author_facet | Neža Orel Eduard Fadeev Gerhard J. Herndl Valentina Turk Tinkara Tinta |
| author_sort | Neža Orel |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-07T15:19:04Z |
| format | Article |
| id | doaj.art-7c27ec3f45d34ca5b4830bcf06243d03 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-07T15:19:04Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7c27ec3f45d34ca5b4830bcf06243d032024-03-05T17:47:07ZengBMCBMC Genomics1471-21642024-02-0125111510.1186/s12864-024-10062-2Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbelliiNeža Orel0Eduard Fadeev1Gerhard J. Herndl2Valentina Turk3Tinkara Tinta4Marine Biology Station Piran, National Institute of BiologyDepartment of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of ViennaDepartment of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of ViennaMarine Biology Station Piran, National Institute of BiologyMarine Biology Station Piran, National Institute of BiologyAbstract 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.https://doi.org/10.1186/s12864-024-10062-2Whole-genome assemblyNon-axenic cultureVibrio campbelliiPlasmidMarine bacteria |
| spellingShingle | Neža Orel Eduard Fadeev Gerhard J. Herndl Valentina Turk Tinkara Tinta Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii BMC Genomics Whole-genome assembly Non-axenic culture Vibrio campbellii Plasmid Marine bacteria |
| title | Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii |
| title_full | Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii |
| title_fullStr | Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii |
| title_full_unstemmed | Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii |
| title_short | Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii |
| title_sort | recovering high quality bacterial genomes from cross contaminated cultures a case study of marine vibrio campbellii |
| topic | Whole-genome assembly Non-axenic culture Vibrio campbellii Plasmid Marine bacteria |
| url | https://doi.org/10.1186/s12864-024-10062-2 |
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