Exploring Probiotic Potential: A Comparative Genomics and In Silico Assessment of Genes within the GenusGeobacillus

Abstract

AbstractThe pursuit of new probiotic targets has seen a surge, aided by next-generation sequencing, facilitating a thorough exploration of bacterial traits. The genusGeobacillusstands out as a promising target for uncovering its potential as a probiotic. The study explored the genetic attributes of the genusGeobacillusfor their resilience to gastrointestinal conditions, nutrient production, and immunomodulatory compound creation, revealing potential probiotic traits. Additionally, the research undertook predictive analyses of genomic elements such as prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes, and CAZymes. These evaluations aimed to assess the safety aspects associated with the genusGeobacillus. A comparative genomic analysis was also carried out using 18 validly published genomes of the genusGeobacillusand a few other genomes ofLactobacillusandBifidobacteriumwere taken as control. Genes associated with probiotic traits like adhesion, stress tolerance (acid/bile, osmotic, oxidative), immune modulation, and molecular chaperones were uniformly detected in theGeobacillusgenus. Notably, mobile genetic elements such as plasmids, prophages, and insertion sequences were absent, as were virulence factors, toxins, and Antibiotic resistance genes. Additionally, CRISPR-Cas systems and CAZymes were present. The pan-genome encompassed 25,284 protein-coding genes with translation. Comparative genomic analysis revealed an open pan-genome forGeobacillus. Pan-genome exhibited variability, particularly in genes linked to environmental interaction and secondary metabolite synthesis. In conclusion,Geobacillusappears potentially safe and well-suited for the gut habitat. However, furtherin vitrostudies are essential to add to the knowledge of the probiotic potential ofGeobacillusspecies.ImportanceThis comprehensive study highlights the significant probiotic potential and genetic makeup of theGeobacillusgenus, shedding light on its unique attributes in adapting to extreme environmental conditions. Understanding the probiotic properties ofGeobacillusis crucial amidst growing concerns over antibiotic resistance, offering promising alternatives for combating pathogenic microbes. Additionally, exploring the genetic diversity and adaptive mechanisms ofGeobacillusthrough genomic and metagenomic approaches provides valuable insights into its biotechnological applications and evolutionary history. By employing in-silico methods and comparative analyses with established probiotic genera, this study contributes to elucidating the probiotic characteristics ofGeobacillus, paving the way for further research in harnessing its beneficial traits for various applications in health, biotechnology, and environmental remediation.