Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Abstract Background Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences o...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-09-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s40168-018-0550-0 |
| _version_ | 1819076494977138688 |
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| author | Johannes Alneberg Christofer M. G. Karlsson Anna-Maria Divne Claudia Bergin Felix Homa Markus V. Lindh Luisa W. Hugerth Thijs J. G. Ettema Stefan Bertilsson Anders F. Andersson Jarone Pinhassi |
| author_facet | Johannes Alneberg Christofer M. G. Karlsson Anna-Maria Divne Claudia Bergin Felix Homa Markus V. Lindh Luisa W. Hugerth Thijs J. G. Ettema Stefan Bertilsson Anders F. Andersson Jarone Pinhassi |
| author_sort | Johannes Alneberg |
| collection | DOAJ |
| description | Abstract Background Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77–99.84%) across overlapping regions (30–80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies. |
| first_indexed | 2024-12-21T18:42:12Z |
| format | Article |
| id | doaj.art-82a3ccff694545a88d9b1024eee09752 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-21T18:42:12Z |
| publishDate | 2018-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-82a3ccff694545a88d9b1024eee097522022-12-21T18:53:59ZengBMCMicrobiome2049-26182018-09-016111410.1186/s40168-018-0550-0Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomesJohannes Alneberg0Christofer M. G. Karlsson1Anna-Maria Divne2Claudia Bergin3Felix Homa4Markus V. Lindh5Luisa W. Hugerth6Thijs J. G. Ettema7Stefan Bertilsson8Anders F. Andersson9Jarone Pinhassi10School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of TechnologyCentre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityDepartment of Cell and Molecular Biology, SciLifeLab, Uppsala UniversityDepartment of Cell and Molecular Biology, SciLifeLab, Uppsala UniversityDepartment of Cell and Molecular Biology, SciLifeLab, Uppsala UniversityCentre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversitySchool of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of TechnologyDepartment of Cell and Molecular Biology, SciLifeLab, Uppsala UniversityDepartment of Ecology and Genetics, Limnology, Science for Life Laboratory, Uppsala UniversitySchool of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of TechnologyCentre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityAbstract Background Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77–99.84%) across overlapping regions (30–80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.http://link.springer.com/article/10.1186/s40168-018-0550-0Single-amplified genomesMetagenome-assembled genomesMetagenomicsBinningSingle-cell genomics |
| spellingShingle | Johannes Alneberg Christofer M. G. Karlsson Anna-Maria Divne Claudia Bergin Felix Homa Markus V. Lindh Luisa W. Hugerth Thijs J. G. Ettema Stefan Bertilsson Anders F. Andersson Jarone Pinhassi Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes Microbiome Single-amplified genomes Metagenome-assembled genomes Metagenomics Binning Single-cell genomics |
| title | Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes |
| title_full | Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes |
| title_fullStr | Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes |
| title_full_unstemmed | Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes |
| title_short | Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes |
| title_sort | genomes from uncultivated prokaryotes a comparison of metagenome assembled and single amplified genomes |
| topic | Single-amplified genomes Metagenome-assembled genomes Metagenomics Binning Single-cell genomics |
| url | http://link.springer.com/article/10.1186/s40168-018-0550-0 |
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