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Our results demonstrate the power of single cell genomics to reconstruct representative microbial genomes from complex communities, independent of their cultivability.
Tamminen, M.V. & Virta, M.P.J. Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells.
Coil, D., Jospin, G. & Darling, A. E. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.
Stewart, R. D. et al. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.
Jungbluth, S. P., Amend, J. P. & Rappe, M. S. Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids.
Comparisons with a control group representing microbial genomes from diverse natural environments indicated that HGT activity increased significantly in the genomes of human microbiota, which is confirmatory of previous findings.
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It is difficult to get the complete microbial genome from environmental samples with a high diversity of microbes.
Next-generation sequencing technologies have rapidly expanded the genomic information of numerous organisms and revealed a rich reservoir of natural product gene clusters from microbial genomes, especially from Streptomyces, the largest genus of known actinobacteria at present.
UViGs can be assembled from metagenomes, from proviruses identified in microbial genomes, or from single-virus genomes, and estimated total UViG numbers were obtained by compiling data from the literature and from the total number of sequences in the IMG/VR database in January 2017, January 2018 and July 2018 (https://img.jgi.doe.gov/vr/ 11.gov/vr/ 11
From these datasets, we constructed a mock-even community of 167 microbial genomes (72 from HC1 + 95 from HC2) that are also present in our 2,031 set of reference genomes.
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
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