ReprDB and panDB: minimalist databases with maximal microbial representation
Abstract Background Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapp...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-01-01
|
| Series: | Microbiome |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s40168-018-0399-2 |
| _version_ | 1819055588028448768 |
|---|---|
| author | Wei Zhou Nicole Gay Julia Oh |
| author_facet | Wei Zhou Nicole Gay Julia Oh |
| author_sort | Wei Zhou |
| collection | DOAJ |
| description | Abstract Background Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes. Results We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets. Conclusions reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses. |
| first_indexed | 2024-12-21T13:09:54Z |
| format | Article |
| id | doaj.art-73c6b98d2eba4bc9a3d5fd51fc4f7c6a |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-21T13:09:54Z |
| publishDate | 2018-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-73c6b98d2eba4bc9a3d5fd51fc4f7c6a2022-12-21T19:02:55ZengBMCMicrobiome2049-26182018-01-016111510.1186/s40168-018-0399-2ReprDB and panDB: minimalist databases with maximal microbial representationWei Zhou0Nicole Gay1Julia Oh2The Jackson Laboratory for Genomic MedicineThe Jackson Laboratory for Genomic MedicineThe Jackson Laboratory for Genomic MedicineAbstract Background Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes. Results We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets. Conclusions reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.http://link.springer.com/article/10.1186/s40168-018-0399-2Reference databaseShotgun metagenomicsPan-genomeWhole-genome alignment |
| spellingShingle | Wei Zhou Nicole Gay Julia Oh ReprDB and panDB: minimalist databases with maximal microbial representation Microbiome Reference database Shotgun metagenomics Pan-genome Whole-genome alignment |
| title | ReprDB and panDB: minimalist databases with maximal microbial representation |
| title_full | ReprDB and panDB: minimalist databases with maximal microbial representation |
| title_fullStr | ReprDB and panDB: minimalist databases with maximal microbial representation |
| title_full_unstemmed | ReprDB and panDB: minimalist databases with maximal microbial representation |
| title_short | ReprDB and panDB: minimalist databases with maximal microbial representation |
| title_sort | reprdb and pandb minimalist databases with maximal microbial representation |
| topic | Reference database Shotgun metagenomics Pan-genome Whole-genome alignment |
| url | http://link.springer.com/article/10.1186/s40168-018-0399-2 |
| work_keys_str_mv | AT weizhou reprdbandpandbminimalistdatabaseswithmaximalmicrobialrepresentation AT nicolegay reprdbandpandbminimalistdatabaseswithmaximalmicrobialrepresentation AT juliaoh reprdbandpandbminimalistdatabaseswithmaximalmicrobialrepresentation |