Genome-wide transcriptional profiling of Clostridium species during sporulation

Dormancy strategies utilized by bacteria contribute to their survival under adverse conditions, as well as persistence and transmission between hosts. The formation of endospores produces some of the most resilient forms of life by members of the Firmicutes phylum. Genome studies of the human gut bacteria have shown that sporulation genes are widespread among commensal Clostridia, which play an essential role in maintaining gut homeostasis, but sporulation of non-pathogenic bacteria has been poorly studied. Defining the sporulation conditions and the genetic makeup behind cell differentiation into endospores may allow for practical applications in the treatment of gut disease and to promote well-being. Select commensal Clostridia strains were cultivated under conditions that promote sporulation in Bacillus and Clostridium species. Spore-like cells were observed by phase-contrast and electron microscopy, but could not be cultured. Gene expression studies and 16s rRNA sequencing revealed that the strains belonged to non-sporulating species of Actinotignum schaalii and Staphylococcus epidermidis, which have close family members capable of exospore formation and entry into a viable but non culturable state. Differentially regulated genes during S. epidermidis entry into a VBNC state were analyzed using RNA sequencing. The upregulated expression of membrane proteins, cell transport, stress response, and a shift in metabolism towards protein and carbohydrate catabolism were similar to gene expression patterns in other bacteria previously reported to enter the VBNC state. The subject of bacterial dormancy has been gaining momentum through techniques such as RNA sequencing, which allows the discovery of genetic factors previously unassociated with cell differentiation