Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we prese...
| Main Authors: | , , , , , |
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| Format: | Article |
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eLife Sciences Publications, Ltd
2018
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| Online Access: | http://hdl.handle.net/1721.1/113647 https://orcid.org/0000-0001-7014-3830 |
| _version_ | 1826202026247192576 |
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| author | Yu, Feiqiao Brian Schulz, Frederik Woyke, Tanja Horowitz, Mark A Quake, Stephen R Blainey, Paul C |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Yu, Feiqiao Brian Schulz, Frederik Woyke, Tanja Horowitz, Mark A Quake, Stephen R Blainey, Paul C |
| author_sort | Yu, Feiqiao Brian |
| collection | MIT |
| description | Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell. |
| first_indexed | 2024-09-23T12:01:01Z |
| format | Article |
| id | mit-1721.1/113647 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T12:01:01Z |
| publishDate | 2018 |
| publisher | eLife Sciences Publications, Ltd |
| record_format | dspace |
| spelling | mit-1721.1/1136472022-09-27T23:32:06Z Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples Yu, Feiqiao Brian Schulz, Frederik Woyke, Tanja Horowitz, Mark A Quake, Stephen R Blainey, Paul C Massachusetts Institute of Technology. Department of Biological Engineering Blainey, Paul C Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell. 2018-02-14T14:08:58Z 2018-02-14T14:08:58Z 2017-07 2017-03 2018-02-14T13:59:03Z Article http://purl.org/eprint/type/JournalArticle 2050-084X http://hdl.handle.net/1721.1/113647 Yu, Feiqiao Brian et al. “Microfluidic-Based Mini-Metagenomics Enables Discovery of Novel Microbial Lineages from Complex Environmental Samples.” eLife 6 (July 2017): e26580 © 2017 Yu et al https://orcid.org/0000-0001-7014-3830 http://dx.doi.org/10.7554/ELIFE.26580 eLife Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/ application/pdf eLife Sciences Publications, Ltd eLife |
| spellingShingle | Yu, Feiqiao Brian Schulz, Frederik Woyke, Tanja Horowitz, Mark A Quake, Stephen R Blainey, Paul C Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples |
| title | Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples |
| title_full | Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples |
| title_fullStr | Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples |
| title_full_unstemmed | Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples |
| title_short | Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples |
| title_sort | microfluidic based mini metagenomics enables discovery of novel microbial lineages from complex environmental samples |
| url | http://hdl.handle.net/1721.1/113647 https://orcid.org/0000-0001-7014-3830 |
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