Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts
IntroductionIt has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of com...
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Frontiers Media S.A.
2024-02-01
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| Series: | Frontiers in Veterinary Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2024.1321202/full |
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| author | Fedor S. Sharko Ali Mazloum Alena O. Krotova Olga P. Byadovskaya Larisa B. Prokhvatilova Ilya A. Chvala Ustin E. Zolotikov Alexandra D. Kozlova Anastasia S. Krylova Erika V. Grosfeld Erika V. Grosfeld Anastasia V. Prokopenko Aleksei A. Korzhenkov Maxim V. Patrushev Zorigto B. Namsaraev Alexander V. Sprygin Stepan V. Toshchakov |
| author_facet | Fedor S. Sharko Ali Mazloum Alena O. Krotova Olga P. Byadovskaya Larisa B. Prokhvatilova Ilya A. Chvala Ustin E. Zolotikov Alexandra D. Kozlova Anastasia S. Krylova Erika V. Grosfeld Erika V. Grosfeld Anastasia V. Prokopenko Aleksei A. Korzhenkov Maxim V. Patrushev Zorigto B. Namsaraev Alexander V. Sprygin Stepan V. Toshchakov |
| author_sort | Fedor S. Sharko |
| collection | DOAJ |
| description | IntroductionIt has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis.MethodsIn this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus.ResultsThe analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified.DiscussionThis study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained. |
| first_indexed | 2024-03-08T02:02:28Z |
| format | Article |
| id | doaj.art-1f891829bde0427e862f59abd567af92 |
| institution | Directory Open Access Journal |
| issn | 2297-1769 |
| language | English |
| last_indexed | 2024-03-08T02:02:28Z |
| publishDate | 2024-02-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Veterinary Science |
| spelling | doaj.art-1f891829bde0427e862f59abd567af922024-02-14T05:01:38ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692024-02-011110.3389/fvets.2024.13212021321202Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hostsFedor S. Sharko0Ali Mazloum1Alena O. Krotova2Olga P. Byadovskaya3Larisa B. Prokhvatilova4Ilya A. Chvala5Ustin E. Zolotikov6Alexandra D. Kozlova7Anastasia S. Krylova8Erika V. Grosfeld9Erika V. Grosfeld10Anastasia V. Prokopenko11Aleksei A. Korzhenkov12Maxim V. Patrushev13Zorigto B. Namsaraev14Alexander V. Sprygin15Stepan V. Toshchakov16National Research Center “Kurchatov Institute”, Moscow, RussiaFederal Center for Animal Health FGBI ARRIAH, Vladimir, RussiaFederal Center for Animal Health FGBI ARRIAH, Vladimir, RussiaFederal Center for Animal Health FGBI ARRIAH, Vladimir, RussiaFederal Center for Animal Health FGBI ARRIAH, Vladimir, RussiaFederal Center for Animal Health FGBI ARRIAH, Vladimir, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaMoscow Institute of Physics and Technology, National Research University, Dolgoprudny, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaFederal Center for Animal Health FGBI ARRIAH, Vladimir, RussiaNational Research Center “Kurchatov Institute”, Moscow, RussiaIntroductionIt has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis.MethodsIn this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus.ResultsThe analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified.DiscussionThis study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained.https://www.frontiersin.org/articles/10.3389/fvets.2024.1321202/fulllumpy skin disease virussheep pox virusmetagenomebacterial communityshotgun sequencingskin microbiome |
| spellingShingle | Fedor S. Sharko Ali Mazloum Alena O. Krotova Olga P. Byadovskaya Larisa B. Prokhvatilova Ilya A. Chvala Ustin E. Zolotikov Alexandra D. Kozlova Anastasia S. Krylova Erika V. Grosfeld Erika V. Grosfeld Anastasia V. Prokopenko Aleksei A. Korzhenkov Maxim V. Patrushev Zorigto B. Namsaraev Alexander V. Sprygin Stepan V. Toshchakov Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts Frontiers in Veterinary Science lumpy skin disease virus sheep pox virus metagenome bacterial community shotgun sequencing skin microbiome |
| title | Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts |
| title_full | Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts |
| title_fullStr | Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts |
| title_full_unstemmed | Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts |
| title_short | Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts |
| title_sort | metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus infected hosts |
| topic | lumpy skin disease virus sheep pox virus metagenome bacterial community shotgun sequencing skin microbiome |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2024.1321202/full |
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