An RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection

Despite being genetically diverse, bacterial pathogens can adapt to similar stressful environments in human host, but how this diversity allows them to achive this is yet not fully understood. Knowledge gained through comparative genomics is insufficient as it lacks the level of gene expression reflecting gene usage.

To fill this gap, Umeå University researchers investigated the transcriptome of 32 diverse bacterial pathogens under 11 host related stress conditions. They revealed that diverse bacterial pathogens have common responses to similar stresses to a certain extent but mostly employ their unique repertoire with intersections between different stress responses. The researchers also identified universal stress responders which shed light on the nature of antimicrobial targets. In addition, they found that known and unknown putative novel ncRNAs comprised a significant proportion of the responses. All the data is collected in PATHOgenex atlas, providing ample opportunities to discover novel players critical for virulence and maintenance of infection.

Experimental setup for PATHOgenex RNA atlas


(A) Phylogenetic clustering of bacterial species included in the study. Phylogenetic orders as well as Gram staining groups and oxygen dependency are indicated by color. (B) Schematic overview of the 11 infection-related stress conditions and control (Ctrl) sample not exposed to any stress: acidic stress (As), pH 3-5 for 10 minutes; bile stress (Bs), 0.5% bile salts for 10 minutes; low iron (Li), 250 μM 2,2-dipyridryl for 10 minutes; hypoxia (Hyp), low oxygen for 4 hours; nutritional downshift (Nd), incubation in 1X M9 salts for 30 minutes; nitrosative stress (Ns), 250 μM Spermine NONOate for 10 minutes; osmotic stress (Oss), 0.5% NaCl for 10 minutes; oxidative stress (Oxs), 0.5- 10 mM H2O2 for 10 minutes; stationary phase (Sp); temperature (Tm), 41°C for 20 minutes; varied virulence inducing condition (Vic). Some adjustments were made for certain bacteria (see Table S1). (C) Schematic illustration of the RNAtag-Seq approach allowing multiple samples (36 in this study) per library used for obtaining 1 122 transcriptomes deposited in the PATHOgenex RNA atlas.

Availability – The PATHOgenex RNA atlas is available at:

Avican K, Aldahdooh J, Togninalli M, Tang J, Borgwardt KM, Rhen M, Fallman M. (2020) RNA Atlas of Human Bacterial Pathogens Uncovers Stress Dynamics Linked to Infection. bioRXiv [online preprint]. [abstract]

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