When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages
High-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-02-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/2/420 |
| _version_ | 1827755223349723136 |
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| author | Taylor Miller-Ensminger Genevieve Johnson Swarnali Banerjee Catherine Putonti |
| author_facet | Taylor Miller-Ensminger Genevieve Johnson Swarnali Banerjee Catherine Putonti |
| author_sort | Taylor Miller-Ensminger |
| collection | DOAJ |
| description | High-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how phages shape bacterial communities. Here we present the Prophage Induction Estimator (PIE) to identify induced phages in genomic and metagenomic sequences. PIE takes raw sequencing reads and phage sequence predictions, performs read quality control, read assembly, and calculation of phage and non-phage sequence abundance and completeness. The distribution of abundances for non-phage sequences is used to predict induced phages with statistical confidence. In silico tests were conducted to benchmark this tool finding that PIE can detect induction events as well as phages with a relatively small burst size (10×). We then examined isolate genome sequencing data as well as a mock community and urinary metagenome data sets and found instances of induced phages in all three data sets. The flexibility of this software enables users to easily include phage predictions from their preferred tool of choice or phage sequences of interest. Thus, genomic and metagenomic sequencing now not only provides a means for discovering and identifying phage sequences but also the detection of induced prophages. |
| first_indexed | 2024-03-11T08:01:08Z |
| format | Article |
| id | doaj.art-d47c69831c8f45cdb8ab2c40c951a4d0 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-11T08:01:08Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-d47c69831c8f45cdb8ab2c40c951a4d02023-11-16T23:48:46ZengMDPI AGViruses1999-49152023-02-0115242010.3390/v15020420When Plaquing Is Not Possible: Computational Methods for Detecting Induced PhagesTaylor Miller-Ensminger0Genevieve Johnson1Swarnali Banerjee2Catherine Putonti3Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USABioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USADepartment of Mathematics and Statistics, Loyola University Chicago, Chicago, IL 60660, USABioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USAHigh-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how phages shape bacterial communities. Here we present the Prophage Induction Estimator (PIE) to identify induced phages in genomic and metagenomic sequences. PIE takes raw sequencing reads and phage sequence predictions, performs read quality control, read assembly, and calculation of phage and non-phage sequence abundance and completeness. The distribution of abundances for non-phage sequences is used to predict induced phages with statistical confidence. In silico tests were conducted to benchmark this tool finding that PIE can detect induction events as well as phages with a relatively small burst size (10×). We then examined isolate genome sequencing data as well as a mock community and urinary metagenome data sets and found instances of induced phages in all three data sets. The flexibility of this software enables users to easily include phage predictions from their preferred tool of choice or phage sequences of interest. Thus, genomic and metagenomic sequencing now not only provides a means for discovering and identifying phage sequences but also the detection of induced prophages.https://www.mdpi.com/1999-4915/15/2/420prophageinductiontemperate phagesmetagenomicsgenomics |
| spellingShingle | Taylor Miller-Ensminger Genevieve Johnson Swarnali Banerjee Catherine Putonti When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages Viruses prophage induction temperate phages metagenomics genomics |
| title | When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages |
| title_full | When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages |
| title_fullStr | When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages |
| title_full_unstemmed | When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages |
| title_short | When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages |
| title_sort | when plaquing is not possible computational methods for detecting induced phages |
| topic | prophage induction temperate phages metagenomics genomics |
| url | https://www.mdpi.com/1999-4915/15/2/420 |
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