In silico analysis toward functional genomic profiling and bioprospecting Serratia rubidaea VITVS26 for its anti-inflammatory and antioxidant potential

Background Proteases from bacteria and their secondary metabolites have bioactivity which can be utilized in therapeutical industries to overcome the negative effects of existing conventional medicines. Methods This study focused on isolating bacteria from different kinds of soil and contaminated coconut samples. The protease-positive isolates were screened for anti-inflammatory potential using the human red blood cell (HRBC) membrane stabilization assay and the inhibition of protein denaturation by an egg albumin method. Whole-genome sequencing was carried out for most promising isolate followed by in silico genomic analysis using antiSMASH, deepBGC, Kyoto Encyclopedia of Genes and Genomes (KEGG), KofamScan, and eggNOG-mapper automatic annotation servers. Result The current work targets the anti-inflammatory and antioxidant potential of an isolated bacterial strain VITVS26, which was taxonomically identified as Serratia rubidaea through whole-genome sequencing with a genome size of 5.29 Mb and a GC content of 58.56%. Protease-producing S. rubidaea VITVS26 has exhibited a maximum of 90.5% ± 0.4% of human red blood cell stabilization and 83.33% ± 0.152% of protein denaturation inhibiting capacity during the egg albumin method. High-performance liquid chromatography (HPLC) confirmed the presence of a putative anti-inflammatory protease in VITVS26. In addition, the isolate has shown 52.62% ± 1.158% free radical scavenging capacity at 1,000 μg/mL concentration with an IC 50 value of 632 μg/mL. Upon the purification of the anti-inflammatory protease, specific activity was increased from 15,461.18 to 25,182.86 with a purification fold of 1.63 and a recovery of 12.26%. The draft genome profiling of S. rubidaea VITVS26 revealed a total of 4,883 genes with 68.8% functional assignment, and in silico analysis predicted 41 host-immunomodulatory genes, 49 antioxidant genes, and 15 biosynthetic gene cluster (BGC) regions. The pigmentation of VITVS26 is supported by the secondary metabolite prodigiosin and its associated genes with a possible role in the bioactivity of the isolate. Bioinformatic screening confirmed the complete absence of horizontally acquired antimicrobial resistance genes in strain VITVS26. Conclusion An overall strong positive anti-inflammatory and antioxidant activity was exhibited by S. rubidaea VITVS26 supported by bioactive, functional, and genomic evidence. The presence of prodigiosin and aryl polyene provides better scope in the future for utilization of S. rubidaea VITVS26 in biotechnology industries after safety evaluation.