Functional and Comparative Genomics of Niche-Specific Adapted Actinomycetes Kocuria rhizophila Strain D2 Isolated from Healthy Human Gut

Abstract

Incidences of infection and occurrence of Kocuria rhizophila in human gut are prominent but certainly no reports on the species ability to withstand human gastrointestinal dynamics. Kocuria rhizophila strain D2 isolated from healthy human gut was comprehensively characterized. The functional analysis revealed the ability to produce various gastric enzymes and sensitive to major clinical antibiotics. It also exhibited tolerance to acidic pH and bile salts. Strain D2 displayed bile-salt hydrolytic (BSH) activity, strong cell surface traits such as hydrophobicity, auto-aggregation capacity and adherence to human HT-29 cell line. Prominently, it showed no hemolytic activity and was susceptible to the human serum. Exploration of the genome led to the discovery of the genes for the above said properties and has ability to produce various essential amino acids and vitamins. Further, comparative genomics have identified core, accessory and unique genetic features. The core genome has given insights into the phylogeny while the accessory and unique genes has led to the identification of niche specific genes. Bacteriophage, virulence factors and biofilm formation genes were absent with this species. Housing CRISPR and antibiotic resistance gene was strain specific. The integrated approach of functional, genomic and comparative analysis denotes the niche specific adaption to gut dynamics of strain D2. Moreover the study has comprehensively characterized genome sequence of each strain to know the genetic difference and intern recognize the effects of on phenotype and functionality complexity. The evolutionary relationship among strains along and adaptation strategies has been included in this study.\n\nSignificanceReports of Kocuria rhizophila isolation from various sources have been reported but the few disease outbreaks in humans and fishes have been prominent, but no supportive evidence about the survival ability of Kocuria spp. within human GIT. Here, we report the gut adaption potential of K. rhizophila strain D2 by functional and genomic analysis. Further; comparative genomics reveals this adaption to be strain specific (Gluten degradation). Genetic difference, evolutionary relationship and adaptation strategies have been including in this study.