|Background: Microbiomes can be categorized based on common features, allowing the performance of deeper analyses. For example subdivisions—virome, fungal biome, resistome—are based on the totality of all genes of a specific microbial population. Spore-forming bacteria, the diversity of which is considered to be underestimated, possess unique features that differentiate them from other microorganisms (1). Bacterial endospores are arguably the most successful form of survival, because they render the resistance to unfavorable environmental conditions (2). This provides challenges in treating such infections, namely, higher rates of environmental transmission, including spread between humans; persistence within the host; high rates of relapses and recurrent infection; presence of sporulation-related virulence factors; and protection from the host immune response and antibacterial therapy (3-5). Here, we suggest that studying the totality of genes of spore-forming bacteria, which we propose to name sporobiome, will facilitate our understanding of their role in health and diseases.
Methods: Previously unculturable, aerobic, spore-forming bacteria were isolated from the microbiota of patients with lung infections and cancer. We identified bacteria by using a novel workflow that is combination of microbiological, biochemical (Vitek 2, MALDI-TOF), and genetic (Illumina HiSeq 2500) analyses. De novo assembly was performed using SPAdes genome assembler software. Antibiotic susceptibility was determined via the disc diffusion method and Vitek2.
Results: Pure cultures of 30 different species of spore-forming bacteria including 12 previously unknown species, were isolated (6,7). The complete genome sequences of the previously unknown species were deposited in GenBank. Analyzing the sporobiome of these bacteria revealed multiple genes encoding virulence factors and antibiotic resistance, including virulence factors associated solely with spore-forming bacteria. Expression of antibiotic-resistance genes was studied.
Conclusions: To our knowledge, this study for the first time indicates the link between bacteriophages and mammalian pathologies associated with increased intestinal permeability such as systemic inflammatory and psychological or autoimmune disorders. This study demonstrates that increased intestinal permeability may be induced by bacteriophages that affect microbiota. We propose that infection of microbiota by bacteriophages can be considered a new group of viral diseases of mammals including humans (4).