Title |
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
|
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Published in |
Frontiers in Microbiology, April 2016
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DOI | 10.3389/fmicb.2016.00469 |
Pubmed ID | |
Authors |
Ankit Gupta, Sanjiv Kumar, Vishnu P. K. Prasoodanan, K. Harish, Ashok K. Sharma, Vineet K. Sharma |
Abstract |
Several metagenomic projects have been accomplished or are in progress. However, in most cases, it is not feasible to generate complete genomic assemblies of species from the metagenomic sequencing of a complex environment. Only a few studies have reported the reconstruction of bacterial genomes from complex metagenomes. In this work, Binning-Assembly approach has been proposed and demonstrated for the reconstruction of bacterial and viral genomes from 72 human gut metagenomic datasets. A total 1156 bacterial genomes belonging to 219 bacterial families and, 279 viral genomes belonging to 84 viral families could be identified. More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes. Selected draft assembled genomes could be validated with 99.8% accuracy using their ORFs. The study provides useful information on the assembly expected for a species given its number of reads and abundance. This approach along with spiking was also demonstrated to be useful in improving the draft assembly of a bacterial genome. The Binning-Assembly approach can be successfully used to reconstruct bacterial and viral genomes from multiple metagenomic datasets obtained from similar environments. |
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United States | 6 | 26% |
France | 2 | 9% |
Italy | 1 | 4% |
Switzerland | 1 | 4% |
Sweden | 1 | 4% |
Spain | 1 | 4% |
China | 1 | 4% |
United Kingdom | 1 | 4% |
Netherlands | 1 | 4% |
Other | 1 | 4% |
Unknown | 7 | 30% |
Demographic breakdown
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Scientists | 13 | 57% |
Members of the public | 10 | 43% |
Mendeley readers
Geographical breakdown
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Brazil | 2 | 2% |
United Kingdom | 1 | 1% |
Canada | 1 | 1% |
Sweden | 1 | 1% |
Mexico | 1 | 1% |
Egypt | 1 | 1% |
Japan | 1 | 1% |
Korea, Republic of | 1 | 1% |
Other | 0 | 0% |
Unknown | 81 | 87% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 26 | 28% |
Student > Ph. D. Student | 23 | 25% |
Student > Master | 11 | 12% |
Professor > Associate Professor | 8 | 9% |
Student > Bachelor | 5 | 5% |
Other | 13 | 14% |
Unknown | 7 | 8% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 23 | 25% |
Engineering | 3 | 3% |
Immunology and Microbiology | 3 | 3% |
Computer Science | 3 | 3% |
Other | 9 | 10% |
Unknown | 9 | 10% |