16S_abundance_95-15

Summary of 16S rRNA based abundance calculation resul

Blastn results

Applying blastn to obtain the taxonomic information of each direct shotgun sequencing read that contain 16S rRNA gene sequenc

Readme

Readm

16S_GraPhlAn_20RA

Code for constructing phylogenetic tree in GraPhlA

Additional file 1: of Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

Supplimentary material on metagemic analysis. (DOCX 312 kb

An Invertebrate Warburg Effect: A Shrimp Virus Achieves Successful Replication by Altering the Host Metabolome via the PI3K-Akt-mTOR Pathway

<div><p>In this study, we used a systems biology approach to investigate changes in the proteome and metabolome of shrimp hemocytes infected by the invertebrate virus WSSV (white spot syndrome virus) at the viral genome replication stage (12 hpi) and the late stage (24 hpi). At 12 hpi, but not at 24 hpi, there was significant up-regulation of the markers of several metabolic pathways associated with the vertebrate Warburg effect (or aerobic glycolysis), including glycolysis, the pentose phosphate pathway, nucleotide biosynthesis, glutaminolysis and amino acid biosynthesis. We show that the PI3K-Akt-mTOR pathway was of central importance in triggering this WSSV-induced Warburg effect. Although dsRNA silencing of the mTORC1 activator Rheb had only a relatively minor impact on WSSV replication, <i>in vivo</i> chemical inhibition of Akt, mTORC1 and mTORC2 suppressed the WSSV-induced Warburg effect and reduced both WSSV gene expression and viral genome replication. When the Warburg effect was suppressed by pretreatment with the mTOR inhibitor Torin 1, even the subsequent up-regulation of the TCA cycle was insufficient to satisfy the virus's requirements for energy and macromolecular precursors. The WSSV-induced Warburg effect therefore appears to be essential for successful viral replication.</p></div

WSSV induces the Warburg effect in the cellular proteome and metabolome of shrimp hemocytes at the replication stage (12 hpi) but not at the late stage (24 hpi).

<p>Changes in the levels of enzymes and proteins (ellipses) and metabolites (rectangles) relative to PBS-injected controls are color-coded to represent up- (red) or down- (green) regulation. Yellow represents no change. Colorless boxes and ellipses indicate that no data was detected. Protein data were collected from 3–5 pooled samples of 5 shrimp using quantitative label-free proteomics and expressed on a logarithmic scale. Metabolomic data were collected from 5–6 pooled samples of 10 shrimp using LC-ESI/MS. Numeric values for the proteomic and metabolomic data are given in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat.1004196.s004" target="_blank">Tables S1</a> and <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat.1004196.s005" target="_blank">S2</a>, respectively.</p

Schematic representation of the WSSV-induced Warburg effect and the involvement of the PI3K-Akt-mTOR pathway at the viral genome replication stage (12 hpi) of the first WSSV replication cycle.

<p>For the proteins investigated in this study, red indicates a positive involvement and gray indicates a partial involvement. Blue indicates important upregulated proteins and intermediates from previous studies: Glucose transporter (GLU1) is from Huang <i>et al.. </i><a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat.1004196-Huang1" target="_blank">[25]</a>, and G6PDH is from Chen <i>et al.. </i><a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat.1004196-Chen1" target="_blank">[9]</a>. Elevated metabolic pathways are shown in pink. Pathway inhibitors are indicated in black boxes. Dashed lines indicate inferred regulatory mechanisms that were not investigated in the present study.</p

Pretreatment with Torin 1 inhibited the WSSV-induced Warburg effect at the genome replication stage of WSSV infection (12 hpi) in shrimp hemocytes.

<p>Two hours after treatment with Torin 1, shrimp were injected with PBS or a WSSV inoculum. At 12(10 shrimp per pool) were collected from each group. Changes in the metabolomic levels of the WSSV-infected samples relative to the PBS controls are color-coded as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat-1004196-g001" target="_blank">Figure 1</a>. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat.1004196.s003" target="_blank">Figure S3</a> shows changes in the metabolome at 24 hpi. Numerical data for 12 hpi and 24 hpi is given in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat.1004196.s005" target="_blank">Table S2</a>. Changes in the metabolome for Torin-PBS versus PEG-PBS are shown in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat.1004196.s003" target="_blank">Fig. S3</a>, with numerical data given in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat.1004196.s005" target="_blank">Table S2</a>.</p

At 12-induced Warburg effect was suppressed by inhibiting mTOR, PI3K and Akt.

<p>(A) At 12 h post WSSV injection, the accumulation of plasma lactate that was seen in the PEG-injected control group was suppressed by both Rapamycin (RAP) and Torin 1 (TR1). Each bar represents the mean ± SD from four pooled samples of hemolymph (3 shrimp in each sample). An asterisk indicates a significant statistical difference between groups (p<0.05). The effect of Rapamycin and Torin1 on (B) the expression of the WSSV genes IE1, DNA pol, VP28 and ICP11, and (C) WSSV genome copy number. Data were based on pooled samples of hemocytes (gene expression) or pleopods (genome copy number), with all samples being taken from the same sets of shrimp as those used in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004196#ppat-1004196-g002" target="_blank">Figure 2B</a>. Specifically, the PEG results were from sets E–H, the RAP results from I–L, and the TR1 results from N–P. (Please note that data from the set M was excluded because phosphorylation of 4E-BP1 was not successfully inhibited in this set.). (D) Each bar represents the mean ± SD of the relative glucose or lactate concentration of five pooled samples of hemolymph (3 shrimp in each pooled sample) under the indicated conditions. Statistically significant differences are shown by 1–3 asterisks, which respectively indicate p<0.05, p<0.005 and p<0.0005.</p