MOESM3 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

Additional file 3. Taxonomy assignment and characteristics of the GBs. The taxonomy of the GBs identified was determined using different methods and a taxonomic assignment was suggested considering the results obtained. In columns (A–V) are reported: (A) the acronym of the GBs as reported in the main text (Sp = Spirochetes; Sy = Synergistetes; Th = Thermotogae; Pr = Proteobacteria; Fi = Firmicutes; Te = Tenericutes; Ac = Actinobacteria; Ba = Bacteroidetes; Tm = TM7 phylum; Eu = Euryarchaeota) the Phylum was determined using Phylophlan and, secondly, the results obtained from BLASTP search versus nr databases filtered using MEGAN; (B) the tentative taxonomic assignment; (C) domain of the genome bin; (D) phylum; (E) taxonomic level considered for the name assignment (the result obtained using Phylopythia was used when more than 50 % of the genome bin sequence was assigned to the same taxonomic group); (F) confidence for taxonomic assignment obtained using Phylophlan; (G–I) domain, phylum, class determined using Phylophlan; (J) taxonomic assignment determined using Phylopythia; (K) percentage of the genome assigned as reported in “J”; (L) taxonomic level reported in “J”; (M) number of genes having BLASTP e-value lower than 1*E-5; (N) average similarity for BLASTP results; (O) number of genes having BLASTN e-value lower than 1*E-5; (P) average similarity for BLASTN results; (Q) the species having the highest number of best match in BLASTP column “M”; (R) taxonomy assignment obtained using RDP classifier on the 16S rRNA gene, similarity, contig where the 16S gene was identified; (S) total length of the scaffolds assigned to the genome bin; (T) number of scaffolds, (U) scaffolds N50, (V) scaffolds N90, (W) average scaffolds length, (X) number of contigs determined after splitting scaffolds on stretched of 10 or more unknown bases “N”, (Y) contigs N50, (Z) contigs N90, (AA) average contigs length, (AB) number of protein encoding genes identified using SEED subsystem; (AC) number of protein encoding genes identified using Prodigal; (AD) total number of essential genes identified, (AE) univocal number of essential genes (removed those in multiple copies); (AF) estimated completeness of the GB; (AG) average number of essential genes in phylum 1. Bold text in columns (A, U, Y, Z, AA, AF) refers to GBs that satisfy the Human Microbiome Project quality criteria; (AH) estimated contamination level determined considering the univocal number of essential genes and the total number of essential genes in multiple copies; (AI) estimated completeness of the GB determined using CheckM software; (AJ) estimated level of contamination determined using CheckM software.