Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells

Abstract

BackgroundSurface-associated communities of bacteria, known as biofilms, play a critical role in the persistence and dissemination of bacteria in various environments. Biofilm development is a sequential dynamic process from an initial bacterial adhesion to a three-dimensional structure formation, and a subsequent bacterial dispersion. Transitions between these different modes of growth are governed by complex and partially known molecular pathways.ResultsUsing RNA-seq technology, our work provided an exhaustive overview of the transcriptomic behavior of the opportunistic pathogen Klebsiella pneumoniae derived from free-living, biofilm and biofilm-dispersed states. For each of these conditions, the combined use of Z-scores and principal component analysis provided a clear illustration of distinct expression profiles. In particular, biofilm-dispersed cells appeared as a unique stage in the bacteria lifecycle, different from both planktonic and sessile states. The K-means cluster analysis showed clusters of Coding DNA Sequences (CDS) and non-coding RNA (ncRNA) genes differentially transcribed between conditions. Most of them included dominant functional classes, emphasizing the transcriptional changes occurring in the course of K. pneumoniae lifestyle transitions. Furthermore, analysis of the whole transcriptome allowed the selection of an overall of 40 transcriptional signature genes for the five bacterial physiological states.ConclusionsThis transcriptional study provides additional clues to understand the key molecular mechanisms involved in the transition between biofilm and the free-living lifestyles, which represents an important challenge to control both beneficial and harmful biofilm. Moreover, this exhaustive study identified physiological state specific transcriptomic reference dataset useful for the research community.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2557-x) contains supplementary material, which is available to authorized users.

Insights on Klebsiella pneumoniae Biofilms Assembled on Different Surfaces Using Phenotypic and Genotypic Approaches

“…This result kept our attention since prophages activation was reported in other microorganism as an inducer of cell death inside microcolonies leading to biofilm dispersion [34]. Nevertheless, a direct link could not be drawn as several unique prophages and prophage-like elements were also found for the best biofilm assemblers Kp703 and Kp45.…”

Biofilm dispersal: multiple elaborate strategies for dissemination of bacteria with unique properties

“…A). In this study, dispersed bacteria overexpressed a large proportion of genes involved in translation compared with the planktonic and sessile states (Guilhen et al ., ), suggesting that biofilm‐dispersed bacteria are metabolically more active. This was also demonstrated by enzymatic measurements of ATP and lactate production in S. pneumoniae , which showed that the metabolism of dispersed cells is increased compared with that in biofilm and planktonic lifestyles (Pettigrew et al ., ) (Fig.…”

“…A. Biofilm development is a sequential process involving adhesion of cells to a surface, formation of microcolonies and biofilm maturation with the emergence of three‐dimensional structures, from which bacteria can disperse and colonize new environments. The planktonic (gray bacteria), sessile (green bacteria) and dispersed (red bacteria) states have unique transcriptional patterns (Guilhen et al ., ). B.…”

“…This was first shown by transcriptional investigations performed with P. aeruginosa and Streptococcus pneumoniae that defined dispersed cells as a unique state, different from both planktonic and sessile lifestyles (Chua et al ., ; Pettigrew et al ., ). Results of similar transcriptional experiments performed with Klebsiella pneumoniae spontaneously biofilm‐dispersed bacteria are consistent with these observations (Guilhen et al ., ) (Fig. A).…”

“…Most research investigating the functions of c-di-GMP in biofilm dispersal has focused on Gram-negative species (Fazli et al, 2014;Ha and O'Toole, 2015;Kim and Lee, 2016), especially in P. aeruginosa, but this signaling molecule is also involved in the biofilm development A. Biofilm development is a sequential process involving adhesion of cells to a surface, formation of microcolonies and biofilm maturation with the emergence of three-dimensional structures, from which bacteria can disperse and colonize new environments. The planktonic (gray bacteria), sessile (green bacteria) and dispersed (red bacteria) states have unique transcriptional patterns (Guilhen et al, 2016). B.…”