Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial "spaceflight response"

Abstract

Several studies have been undertaken with the goal of understanding how bacterial transcriptomes respond to the human spaceflight environment. However, these experiments have been conducted using a variety of organisms, media, culture conditions, and spaceflight hardware, and to date no cross-experiment analyses have been performed to uncover possible commonalities in their responses. In this study, eight bacterial transcriptome datasets deposited in NASA's GeneLab Data System were standardized through a common bioinformatics pipeline then subjected to meta-analysis to identify among the datasets (i) individual genes which might be significantly differentially expressed, or (ii) gene sets which might be significantly enriched. Neither analysis resulted in identification of responses shared among all datasets. Principal Component Analysis of the data revealed that most of the variation in the datasets derived from differences in the experiments themselves.

Figure 1

PCA plots of datasets for which 2 independent spaceflight experiments have been conducted. Datasets included are: (A) BRIC-21 and BRIC-23 (B. subtilis), (B) MESSAGE 2 and BASE A (R. rubrum) and (C). STS-115 and STS-123 (S. enterica).

Figure 2

Venn diagrams depicting genes found to be up-regulated (A) or down-regulated (B) in common among the MESSAGE 2, BASE A, (both R. rubrum) and STS-115 (S. enterica) spaceflight datasets.

Figure 3

Functional characterization of the differentially expressed genes identified in the datasets for Gram-negative organisms. Depicted are numbers of genes belonging to the indicated biological pathways (KEGG Orthologies) found to up-regulated (A) or down-regulated (B) in FL samples from the R. rubrum BASE A and MESSAGE 2 experiments (gray and purple bars, respectively), and the S. enterica STS-115 experiment (yellow bars) experiment. Asterisks denote pathways deemed to be significantly enriched (adjusted P < 0.05, Fisher’s exact test).

Figure 4

Venn diagrams depicting genes found to be up-regulated (A) or down-regulated (B) in common among the BRIC-21 and BRIC-23 (both B. subtilis) and BRIC-23 (S. aureus) spaceflight datasets.

Figure 5

Functional characterization of the differentially expressed genes identified in the datasets for Gram-positive organisms. Depicted are numbers of genes belonging to the indicated biological pathways (KEGG Orthologies) found to up-regulated (A) or down-regulated (B) in FL samples from the B. subtilis BRIC-21 (red bars) and BRIC-23 (blue bars) experiments, and the S. aureus BRIC-23 (green bars) experiment. Asterisks denote pathways deemed to be significantly enriched within the up- or down-regulated genes (adjusted P < 0.05, Fisher’s exact test).

Figure 6

Venn diagrams depicting KEGG gene sets found to be enriched in FL (A) or GC (B) samples in common among the MESSAGE 2 (R. rubrum), STS-115 (S. enterica), and STS-115 (P. aeruginosa) spaceflight datasets.

Figure 7

Venn diagrams depicting KEGG gene sets found to be enriched in FL (A) or GC (B) samples in common among the BRIC-21 and BRIC-23 (both B. subtilis) and BRIC-23 (S. aureus) spaceflight datasets.