Derozier, S. | Search bioRxiv

bioRxiv2022

Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach

The dramatic increase in the amount of microbe descriptions in databases, reports and papers presents a two-fold challenge for accessing the information: integration of heterogeneous data in a standard ontology-based representation and normalization of the textual descriptions by semantic analysis. Recent text mining methods offer powerful ways to extract textual information and generate ontology-based representation. This paper describes the design of the Omnicrobe application that gathers comprehensive information on habitats, phenotypes and usages of microbes from scientific sources of high interest to the microbiology community. The Omnicrobe database contains around 1 million descriptions of microbe properties that are created by analyzing and combining six information sources of various kinds, i.e. biological resource catalogues, sequence database and scientific literature. The microbe properties are indexed by the Ontobiotope ontology and their taxa are indexed by an extended version of the taxonomy maintained by the National Center for Biotechnology Information. The Omnicrobe application covers all domains of microbiology. It provides an easy-to-use support in the resolution of scientific questions related to the habitats, phenotypes and uses of microbes through simple and complex ontology-based queries. We illustrate the potential of Omnicrobe with a use case from the food innovation domain.

bioinformatics↗

bioRxiv2022

Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase.

Reprogramming of gene expression during transition from exponential growth to stationary phase is crucial for bacterial survival. In the model Gram-positive bacterium Bacillus subtilis, this process is mainly governed by the activity of the global transcription regulators AbrB, CodY and Spo0A. We recently showed that the transcription termination factor Rho, known for its ubiquitous role in the inhibition of antisense transcription, is involved in Spo0A-mediated regulation of differentiation programs specific to the stationary phase in B. subtilis. To identify other aspects of the regulatory role of Rho during adaptation to starvation, we have constructed a B. subtilis strain that expresses rho at a relatively stable high level in order to circumvent its decrease occurring in the wild-type cells entering the stationary phase. We show that B. subtilis cells stably expressing Rho fail to sporulate and to develop genetic competence, which is largely, but not exclusively, due to abnormally low expression of the master regulator Spo0A. Moreover, in addition to a global decrease of antisense transcription, these cells exhibit genome-wide alterations of sense transcription. A significant part of these alterations affects genes from global regulatory networks of cellular adaptation to the stationary phase and reflects the attenuated de-repression of the AbrB and CodY regulons and the weakened stringent response. Accordingly, stabilization of Rho level reprograms stationary phase-specific physiology of B. subtilis cells, negatively affects cellular adaptation to nutrient limitations and alters cell-fate decision-making to such an extent that it blocks development of genetic competence and sporulation. Taken together, these results indicate that the activity of termination factor Rho constitutes a previously unknown layer of control over the stationary phase and post-exponential adaptive strategies in B. subtilis, from the adjustment of cellular metabolism to the activation of survival programs.

microbiology↗