Table 1.
Analysis of microbial communities through shotgun metagenomic sequencing (only environmental samples are shown).
Sample | Library size | Host or vector system used | Average insert size (kbp) | Biodiversity | References |
---|---|---|---|---|---|
Sargasso Sea | 1 985 561a | Bst XI linearized pBR322 derivative | 2–6 | Samples were dominated by genes from Proteobacteria (primarily subgroups Alpha, Beta and Gamma) with moderate contributions from Firmicutes, Cyanobacteria and species in the CFB phyla (Cytophaga, Flavobacterium and Bacteroides). Poor sequencing coverage enabled the assembly of only two near‐complete genomes. Here, 1.6 G base pair of unique metagenomic DNA sequences were obtained. | Venter et al. (2004) |
Soil | 1129 (Bacteria)a 527 (Archaea)a 919 (Fungi)a 4577 (Viruses)a | pCR®2.1‐TOPO (Bacterial, Archaeal and Fungal) pSMART (viral) | 0.49 (Viruses) | This is the first study to use sequencing to characterize soil viral communities. Within each of the four microbial groups, data showed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi and viruses are globally as well as locally diverse. | Fierer et al. (2007) |
Acid mine drainage biofilm | 103 462a | pUC18 | 3.2 | Authors report the reconstruction of near‐complete genomes of Leptospirillum group II and Ferroplasma type II and partial recovery of three other genomes. | Tyson et al. (2004) |
Global Ocean | 7 697 926a | Bst XI linearized pBR322 derivative | 2 | Authors report a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analysed as part of the Sorcerer II Global Ocean Sampling expedition. The resulting 7.7 million sequencing reads form 41 samples provide an unprecedented look at the great diversity and heterogeneity in naturally occurring microbial populations. | Rusch et al. (2007) |
Soil | 1 186 200b | pJN105/pCF430 (small inserts) pBeloBAC11 (big inserts) | 2.7–45 | Authors designed a metagenomic analysis to isolate antibiotic resistance genes from 6 libraries of soil. They identified nine clones expressing resistance to aminoglycoside antibiotics and one expressing tetracycline resistance. | Riesenfeld et al. (2004) |
Number of reads produced or
b. independent clones.