Relative abundance of Top 100 genera assigned by RDP Classifier at 50% bootstrap cutoffs and percentage of ten divided subsets for all ranked genera.

<p>The genera were ranked based on the average relative abundance for each pyrotag. All rankings in each subfigure were sorted from high to low level and displayed in the right column from bottom to top accordingly. For instance, Ranking 1, 2, 3, …, and 100 represented genera of <i>Zoogloea</i>, <i>Dechloromonas</i>, <i>Flavobacteria</i>, …, and <i>Pseudorhodobacter</i>, respectively. Greek letters of <i>α</i>, <i>β</i>, <i>γ</i>, <i>δ</i>, or <i>ε</i> modified in the terminus of genus name represented classes of <i>α-</i>, <i>β-</i>, <i>γ-</i>, <i>δ-</i>, or <i>ε- Proteobacteria</i>, respectively. Similarly, <i>A</i>, <i>Acido</i>, <i>B</i>, <i>Chla</i>, <i>Chlo</i>, <i>F</i>, <i>N</i>, <i>O</i>, <i>P</i>, <i>S</i>, <i>T</i>, and <i>V</i>, indicated phyla of <i>Actinobacteria</i>, <i>Acidobacteria</i>, <i>Bacteroidetes</i>, <i>Chlamydiae</i>, <i>Chloroflexi</i>, <i>Firmicutes</i>, <i>Nitrospira</i>, <i>OD1</i>, <i>Planctomycetes</i>, <i>Spirochaetes</i>, <i>TM7</i>, and <i>Verrucomicrobia</i>, respectively. The total number of these Top 100 genera assigned into the phyla/class was summarized as: <i>α</i> (13), <i>β</i> (27), <i>γ</i> (9), <i>δ</i> (5), <i>ε</i> (1), <i>A</i> (9), <i>Acido</i> (3), <i>B</i> (13), <i>Chla</i> (1), <i>Chlo</i> (1), <i>F</i> (9), <i>N</i> (1), <i>O</i> (1), <i>P</i> (2), <i>S</i> (1), <i>T</i> (1), and <i>V</i> (3).</p

Schematic representation of experimental design employed in this study.

<p>The full length of <i>E. coli</i> 16S rRNA gene was used as the reference scale. Fourteen blue arrow lines indicated all pyrotags analyzed in this study. S (L)-V1V2 represented the pyrotag contained 16S V1V2 region derived from a Short (Long) amplicon. Four small PCR fragments covered 16S V1V2, V3V4, V5V6, and V7V8V9 regions were defined as Short amplicons. The remainder three large PCR fragments targeted 16S regions of V1–V4, V3–V6, and V5–V9 were defined as Long amplicons.</p

Overview of processed pyrotags.

<p>The raw pyrotags were the original reads generated by the 454 run. After removal of low quality reads, short reads, chimera, noise, and archaea reads, the clean pyrotags were finally obtained and used for downstream bioinformatic analysis.</p

Primers used in this study.

<p>The positions of all primers are referred to the 16S rRNA gene of <i>E. coli</i> str. K12 substr. DH10B. The bold italic nucleotide ‘<i>G</i>’ fused into the 5′ terminus of each barcode is to offer an unbiased ligation between amplicons and 454 adaptors.</p

Cluster analysis of all pyrotags based on relative abundance of Top 100 genera.

<p>‘Average’ represented the average relative abundance. The Past statistical software was used to calculate the distance using Bray-Curtis similarity measure.</p

S-type and L-type pyrotags classified into six different taxonomic units assigned by RDP Classifier at 50% bootstrap cutoffs.

<p>The equal sequencing depths of 23609 reads and 3276 reads were subsampled to make fair comparison for S-type and L-type pyrotags, respectively.</p

Relative abundance at phylum or class (only for <i>Proteobacteria</i>) level assigned by RDP Classifier at 50% confidence thresholds.

<p>The extremely low percentage phyla of ‘<i>Aquificae</i>, <i>BRC1</i>, <i>Caldiserica</i>, <i>Chlorobi</i>, <i>Cyanobacteria</i>, <i>Deferribacteres</i>, <i>Deinococcus-Thermus</i>, <i>Fibrobacteres</i>, <i>Fusobacteria</i>, <i>Gemmatimonadetes</i>, <i>Lentisphaerae</i>, <i>OD1</i>, <i>OP10</i>, <i>OP11</i>, <i>Spirochaetes</i>, <i>SR1</i>, <i>Synergistetes</i>, <i>Tenericutes</i>, <i>Thermotogae</i>, and <i>WS3</i>’ were not displayed in detail and summarized as rare phyla.</p

Statistical data of Top 500 (a) and Top 100 (b) genera not detected for each S-type pyrotag.

<p>Every subset of 100 genera was divided and calculated independently (a). Genera detected by all S-type pyrotags simultaneously were not listed and the not detected genera were all marked with crosses (b).</p

Additional file 1: of Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection

Table S1. Sequencing statistics of mRNA transcriptomes. Table S2. Significantly enriched Gene Ontology terms in response to H5N1 virus infection. Table S3. Sequencing statistics of miRNA transcriptomes. Table S4. MiRNAs and their target mRNAs in RIG-I like receptor signaling pathway. (DOCX 41 kb

Additional file 5: of Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection

Pathway enrichment of the mRNA genes inversely regulated with the targeting miRNAs for H1N1 and H5N1 virus-infected macrophage cells at 1-, 3-, and 6-h post-infection. (XLS 154 kb