Simulating metagenomic stable isotope probing datasets with MetaSIPSim
Abstract Background DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and...
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-020-3372-6 |
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| author | Samuel E. Barnett Daniel H. Buckley |
| author_facet | Samuel E. Barnett Daniel H. Buckley |
| author_sort | Samuel E. Barnett |
| collection | DOAJ |
| description | Abstract Background DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment. Results Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance. Conclusions Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data. |
| first_indexed | 2024-12-18T00:53:04Z |
| format | Article |
| id | doaj.art-1b72621a2dc043369b2efa28f7475da2 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T00:53:04Z |
| publishDate | 2020-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-1b72621a2dc043369b2efa28f7475da22022-12-21T21:26:36ZengBMCBMC Bioinformatics1471-21052020-01-0121111710.1186/s12859-020-3372-6Simulating metagenomic stable isotope probing datasets with MetaSIPSimSamuel E. Barnett0Daniel H. Buckley1School of Integrative Plant Science, Cornell UniversitySchool of Integrative Plant Science, Cornell UniversityAbstract Background DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment. Results Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance. Conclusions Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.https://doi.org/10.1186/s12859-020-3372-6Stable isotope probingSIPMetagenomicsSimulation |
| spellingShingle | Samuel E. Barnett Daniel H. Buckley Simulating metagenomic stable isotope probing datasets with MetaSIPSim BMC Bioinformatics Stable isotope probing SIP Metagenomics Simulation |
| title | Simulating metagenomic stable isotope probing datasets with MetaSIPSim |
| title_full | Simulating metagenomic stable isotope probing datasets with MetaSIPSim |
| title_fullStr | Simulating metagenomic stable isotope probing datasets with MetaSIPSim |
| title_full_unstemmed | Simulating metagenomic stable isotope probing datasets with MetaSIPSim |
| title_short | Simulating metagenomic stable isotope probing datasets with MetaSIPSim |
| title_sort | simulating metagenomic stable isotope probing datasets with metasipsim |
| topic | Stable isotope probing SIP Metagenomics Simulation |
| url | https://doi.org/10.1186/s12859-020-3372-6 |
| work_keys_str_mv | AT samuelebarnett simulatingmetagenomicstableisotopeprobingdatasetswithmetasipsim AT danielhbuckley simulatingmetagenomicstableisotopeprobingdatasetswithmetasipsim |