Biology subjects

Tuli, S. R.

Publications and source records attributed to Tuli, S. R..

3 recordsLinked to original sources

bioRxiv2024

Exploration of the Metabolic Potential of the Corallococcus Genus: A Rich Source of Secondary Metabolites, and CAZymes

Different secondary metabolites take on important roles. They can also transport metals, function as sexual hormones, facilitate harmonious coexistence of microbes and living beings, and induce differentiation, besides being used as competitive weapons against other bacteria, fungi, amoebae, plants, insects, and large animals. Progress in next-generation sequencing methods, together with microbial genome sequencing, has unveiled a wealth of natural products (NPs) with yet-untapped potential. Genome mining of Corallococcus species and C. exiguus subspecies that can make secondary metabolites that are clinically important has not been studied very much. The goal of this study is to look into Corallococcus genomes biosynthetic gene clusters (BGCs) and carbohydrate-active enzyme gene clusters. We fully characterize BGCs from Corallococcus reference genome sequences that are publicly available using bioinformatic tools in addition to phylogenetic and genomic comparisons. Our results show that there is a huge range of BGCs in different Corallococcus genomes, but the species or subspecies level affects the ability to make NPs. Additionally, we investigated unknown and less comparable BGCs at the species level and found that C. llansteffanensis has more potential as a reservoir of new secondary metabolites. These insights will pave the way for the algorithmic identification of species- and subspecies-specific pathways for NP development.

bioinformatics↗

bioRxiv2024

A Comprehensive Pangenome Approach to Exploring the Probiotic Potential of Weissella Confusa

BackgroundFermented foods harbour the bacterium Weissella confusa, which has probiotic properties but can potentially act as an opportunistic pathogen in humans and animals. Using pangenome analysis, our study aimed to improve the classification and identify functional traits of publicly available W. confusa genomes, focusing on evaluating their potential as probiotics. MethodThe genomic sequence of 120 strains of W. confusa was acquired from the NCBI RefSeq database. The downloaded sequences underwent a quality verification and filtering process. Ultimately, the chosen genomes were examined for comparative genomic analysis. We employed Roary to investigate the pangenome of W. confusa. Fishers exact test was utilised to analyse contingency tables, with a significance threshold of p < 0.05 (two-tailed). ResultsOur investigation revealed that the pangenome of W. confusa comprises 1100 core genes, 184 soft-core genes, 1407 shell genes, and 7006 cloud genes. This finding emphasises the "open" aspect of the W. confusa pangenome. The comparison of genomes showed that there were no acquired antibiotic resistance genes. However, the strains had different amounts of prophage regions, CRISPR arrays, and plasmids. Our research identified probiotic marker genes (PMGs), with the majority (78%) found in the core and soft-core genomes of various strains of W. confusa. ConclusionsAn extensive investigation of the W. confusa pangenome has concluded that it could be useful as a probiotic. Additional research is necessary to thoroughly evaluate the potential risks.

bioinformatics↗

bioRxiv2024

Characterization and molecular insights of a chromium-reducing bacterium Bacillus tropicus

Environmental pollution from metal toxicity is a widespread concern. Certain bacteria hold promise for bioremediation that converts toxic chromium into a less harmful form, promoting environmental cleanup. In this study, we report the isolation and detailed characterization of a highly chromium-tolerant bacterium, Bacillus tropicus CRB14. The isolate is capable of growing on 5000 mg/l Cr (VI) in LB agar plate while on 900 mg/l Cr (VI) in LB broth with an 86.57% reduction ability within 96 hours of culture. It can also tolerate high levels of As, Cd, Co, Fe, Zn, and Pb. The plant growth-promoting potential of the isolate was demonstrated by a significant activity of nitrogen fixation, phosphate solubilization, IAA, and siderophore production. Whole-genome sequencing revealed that the isolate lacks plasmids for Cr resistance, suggesting genes reside on its chromosome. The presence of the chrA gene points towards Cr (VI) transport, while the absence of ycnD suggests alternative reduction pathways. The genome harbors features like genomic islands and CRISPR-Cas systems, potentially aiding adaptation and defense. Analysis suggests a robust metabolism, potentially involved in Cr detoxification. Notably, genes for siderophore and NRP-metallophore production were identified. Whole Genome Sequencing (WGS) data also provides the basis for molecular validation of various genes. Findings from this study highlight the potential application of Bacillus tropicus CRB14 for bioremediation while plant growth promotion can be utilized as an added benefit.

microbiology↗