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Supplementary Figure 1. Proportions of annotated sequences in percentage (for all sequences, protein metabolism, regulation and cell signaling, and virulence) are compared by varying the percentage of identity threshold. Box plots are based on the distribution fluctuations among six selected metagenomes corresponding to the Rothamsted Park Grass soil.

Supplementary Figure 2. Proportion of annotated sequences in percentage (for motility and chemotaxis, nucleosides and nucleotides, phosphorous metabolism and virulence) are compared by varying the E-value threshold. Six selected metagenomic datasets corresponding to the human feces environment. Accession numbers are provided.

Supplementary Figure 3. Proportion of annotated sequences in percentage (for all sequences as well as five categories) are compared by varying the E-value threshold. Standard deviation is based on the distribution fluctuations among three metagenomic datasets (read length of 100 nt) corresponding to saliva microbial communities.

Supplementary Table 1. Number of reads, reads length average and percentage of annotated reads (SEED annotation through MG-RAST, E-value cut-off: 10–5) for the 18 metagenomic datasets selected for representing human feces, oceans, and the Rothamsted soil metagenome

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