Gandhi, S. G. | Search bioRxiv

bioRxiv2024

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

The pursuit of new probiotic targets has seen a surge, aided by next-generation sequencing, facilitating a thorough exploration of bacterial traits. The genus Geobacillus stands out as a promising target for uncovering its potential as a probiotic. The study explored the genetic attributes of the genus Geobacillus for 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 genus Geobacillus. A comparative genomic analysis was also carried out using 18 validly published genomes of the genus Geobacillus and a few other genomes of Lactobacillus and Bifidobacterium were 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 the Geobacillus genus. 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 for Geobacillus. Pan-genome exhibited variability, particularly in genes linked to environmental interaction and secondary metabolite synthesis. In conclusion, Geobacillus appears potentially safe and well-suited for the gut habitat. However, further in vitro studies are essential to add to the knowledge of the probiotic potential of Geobacillus species. ImportanceThis comprehensive study highlights the significant probiotic potential and genetic makeup of the Geobacillus genus, shedding light on its unique attributes in adapting to extreme environmental conditions. Understanding the probiotic properties of Geobacillus is crucial amidst growing concerns over antibiotic resistance, offering promising alternatives for combating pathogenic microbes. Additionally, exploring the genetic diversity and adaptive mechanisms of Geobacillus through 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 of Geobacillus, paving the way for further research in harnessing its beneficial traits for various applications in health, biotechnology, and environmental remediation.

microbiology↗

bioRxiv2023

Luteibacter sahnii sp. nov., a novel yellow-pigmented probiotic bacterium from rice seed microbiome.

The genus Luteibacter, a member of the family Rhodanobacteraceae, encompasses Gram-negative bacteria found in diverse environments. In the present study, four yellow-pigmented bacterial isolates designated as PPL193T, PPL201, PPL552, and PPL554 were obtained and identified as Gram-negative, rod-shaped, and motile bacteria. Biochemical characterization and examination of the 16S rRNA gene sequence, derived from the genomic sequence, identified it as belonging to the genus Luteibacter. The isolates are closely related to Luteibacter yeojuensis R2A16-10T, forming a distinct monophyletic lineage with L. aegosomatis KCTC 92392T and L. anthropi CCUG25036T. The calculated values for pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization in comparison to previously reported Luteibacter species fell below the established thresholds for species delineation. As this novel species was isolated from rice seeds as a potential Xanthomonas due to its distinctive yellow-colored colonies, we sought to identify the presence of xanthomonadin pigment in this species. Intriguingly, our findings revealed the presence of the typical peak corresponding to xanthomonadin in the UV spectra, confirming its presence in this novel species and adaptation to plant habitat. Furthermore, the detailed genomic investigation also uncovered the genomic locus corresponding to xanthomonadin biosynthetic gene cluster, further suggesting that members of this novel species are co-habitants of plant pathogenic and plant probiotic Xanthomonas group of phytobacteria within rice seeds. Apart from protease production, the species was found to produce Indole-3-Acetic Acid (IAA) in higher quantities and was also able to protect plants from Xanthomonas oryzae pv. oryzae, a major pathogen of rice indicating its probiotic nature. Genome scanning revealed the presence of genomic region(s) encoding loci for biosynthesis of anti-microbial peptides and other metabolites with probiotic properties, further confirming its probiotic properties. This study highlights the importance of using a combination of phenotypic and genotypic methods for bacterial identification and expands our knowledge of the diversity and distribution of diverse bacteria associated with rice seeds and their microbiome. Luteibacter sahnii sp. nov. is proposed as a novel species of the genus Luteibacter with PPL193T=MTCC 13290T=ICMP 24807T=CFBP 9144T as its type strain and PPL201, PPL552, and PPL554 as other constituent members.

microbiology↗