title: Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes.
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.
authors.affiliation: Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India.
authors.forename: Ankit
authors.initials: A
authors.lastname: Gupta
authors.affiliation: Department of Medicine, University of Connecticut Health Center Farmington, CT, USA.
authors.forename: Sanjiv
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India.
authors.forename: Vishnu P K
authors.initials: VP
authors.lastname: Prasoodanan
authors.affiliation: Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India.
authors.forename: K
authors.initials: K
authors.lastname: Harish
authors.affiliation: Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India.
authors.forename: Ashok K
authors.initials: AK
authors.lastname: Sharma
authors.affiliation: Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India.
authors.forename: Vineet K
authors.initials: VK
authors.lastname: Sharma
keywords: bacterial draft genomes; binning; genome assembly; metagenome; spiking; viral draft genomes