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.

Clinostat Rotation Affects Metabolite Transportation and Increases Organic Acid Production by Aspergillus carbonarius , as Revealed by Differential Metabolomic Analysis

“…The results obtained for Staphylococcus mutans, Escherichia coli, Mycobacterium marinum, and Streptomyces coelicolor under these conditions have been proved to be consistent with those found on the ISS (18)(19)(20)(21)(22). However, inconsistent results were also found in several studies when different bacteria, experimental setups, and cultivation conditions were used (23). The final phenotype that a bacterium exhibits is the result of its physiological response to the spaceflight environment (23).…”

“…(22,32). Although microgravity has been studied for more than 50 years, systematic and comprehensive studies of the genetic and phenotypic responses of microorganisms to the microgravity environment in space are still lacking due to inconsistencies in the experimental designs, experimental setups, and cultivation conditions used in different studies (22,23). In particular, knowledge about the impact of microgravity on the metabolism of fungi, particularly molds with a high corrosive ability, has still been very limited, until now.…”

“…However, inconsistent results were also found in several studies when different bacteria, experimental setups, and cultivation conditions were used (23). The final phenotype that a bacterium exhibits is the result of its physiological response to the spaceflight environment (23). So, how about the response of fungal metabolites to microgravity?…”

Increased growth rate and amikacin resistance of Salmonella enteritidis after one‐month spaceflight on China’s Shenzhou‐11 spacecraft

“…It has been demonstrated that the space environment altered the transcript levels of some genes in bacteria (Morrison & Nicholson, ). In this study, transcriptomic and proteomic analyses revealed that the differentially expressed genes and proteins were primarily located in pathways including flagella assembly, two‐component system, bacterial chemotaxis, and bacterial secretion system according to KEGG pathway functions.…”

Mechanotransduction in Prokaryotes: A Possible Mechanism of Spaceflight Adaptation

“…Subsequent work mapping transcriptomic responses of S. enterica and Pseudomonas aeruginosa to spaceflight and clinorotation identified the molecular chaperone and global regulator Hfq as being implicated in the low-shear response, although its mechanism of action is currently unknown [ 33 , 34 , 36 ]. Several studies have mapped global transcriptomic responses of bacteria to the low-shear environment, comparing cells grown in spaceflight and clinostat conditions with corresponding ground controls [ 33 , 34 , 36 , 37 , 38 , 39 ], but to date, these studies have failed to yield insights into a detailed underlying molecular mechanism [ 40 , 41 ].…”