MOESM1 of Phylogeny-structured carbohydrate metabolism across microbiomes collected from different units in wastewater treatment process
Creators: name: Xia, Yu
name: Chin, Francis
name: Yuanqing Chao
name: Zhang, Tong
Publisher: name: Figshare
Year: 2015
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Plant Biology

description: Additional file 1: Table S1. 16S/18S rRNA annotation efficiency of sludge samples collected from different process of WWTP. Table S2. Phylogenetic and functional correlation between technical and biological replicates (Pearsonâ  s correlation coefficient). Table S3. All CAG families detected in the sludge samples. CAGs are quantified based on the number of ORFs containing the particular CAG domain. CAG families are sorted alphabetically according to their names. Table S4. Comparison of CAGs involves in lignocellulose hydrolysis between sludge system and other four plant feeding microbiota. Glycoside hydrolase (GH) families are assigned to enzyme categories based on the classification previously published [3]. Table S5. Quantification of 46 major CAG families detected based on ORFs containing the particular CAG domain. CAG families are sorted descending according to their average relative abundance across sludge samples. Table S6. Quantification of 40 major orders within the compared sludge samples based on 16S rRNA gene sequences. Orders are sorted descending according to their average relative abundance across sludge samples. Table S7. Topological properties of the co-occurrence network (positive network) of 46 major CAG families and 40 prevalent phylogenetic orders. Table S8. Observed and random co-occurring incidence within network modules. Table S9. Information of the metagenomic libraries of sludge samples and technical/biological replicates. Table S10. Statistics of assembled scaffolds from metagenome of sludge samples and technical/biological replicates. Figure S1. Illustration of the experimental design of metagenomes used for this study. Frames of technical and biological replicates are respectively filled with blue and green color. Figure S2. Rarefaction analysis of the sludge metagenomes. Figure S3. Phylogenetic orders showed significant variation (P-value&lt; 0.05 and proportion difference &gt; 1%) between biological replicates. Figure S4. Similarity distribution of GH-encoding ORFs to their best BLASTN hit against NCBI nr database. Left and right figure respectively shows the ORFs counts and accumulative abundance of GH-encoding ORFs from different sludge microbiomes. Figure S5. Heatmap of the most prevalent phylogenetic groups (order level) determined by the CAGs-encoding genes (a) and 16S rRNA gene sequences (b). Figure S6. Major CAG families showed significant variation (p-value &lt; 0.05 by one-way ANOVA analysis) among sludge samples with different dissolved oxygen (left), temperature (middle) and salinity (right). Abbreviations in the figures: M: Mesophilic; A: Ambient temperature; T: Thermophilic. Figure S7. Whole network among 46 major CAG families and 40 prevalent phylogenetic orders. Nodes representing either CAG families or phylogenetic orders, are colored according to the network modules (that is clusters) determined by multi-level aggregation method (Louvain algorithm [18]). Each edge represents a strong (Spearmanâ  s rank correlation coefficient r2 &gt; 0.6) and significant (p-value &lt; 0.01) correlation between node-pairs. Edges are colored according to the value of r2 with red stands for positive correlation; blue represents negative correlation. The size of each node and the font size of label is proportion to the number of connections (that is degree) of that node. And the thickness of edge is proportion to the correlation coefficient between nodes. Figure S8. Co-exclusion network (that is the negative network) among 46 major CAG families and 40 prevalent phylogenetic orders. Nodes representing either CAG families or phylogenetic orders, are colored according to the network modules (that is clusters) determined by multi-level aggregation method (Louvain algorithm [18]). Each edge representing a strong (Spearmanâ  s rank correlation coefficient r2 &gt; 0.6) and significant (p-value &lt; 0.01) correlation between node-pairs, are in the same color with its source node. The size of each node and the font size of label is proportion to the number of connections (that is degree) of that node. And the thickness of edge is proportion to the correlation coefficient between nodes.