Functional and Comparative Genomics of Niche-Specific Adapted ActinomycetesKocuria rhizophilaStrain D2 Isolated from Healthy Human Gut

Abstract

19Incidences of infection and occurrence of Kocuria rhizophila in human gut are prominent but 20 certainly no reports on the species ability to withstand human gastrointestinal dynamics. Kocuria 21 rhizophila strain D2 isolated from healthy human gut was comprehensively characterized. The 22 functional analysis revealed the ability to produce various gastric enzymes and sensitive to major 23 clinical antibiotics. It also exhibited tolerance to acidic pH and bile salts. Strain D2 displayed 24 bile-salt hydrolytic (BSH) activity, strong cell surface traits such as hydrophobicity, auto-25 aggregation capacity and adherence to human HT-29 cell line. Prominently, it showed no 26 hemolytic activity and was susceptible to the human serum. Exploration of the genome led to the 27 discovery of the genes for the above said properties and has ability to produce various essential 28 amino acids and vitamins. Further, comparative genomics have identified core, accessory and 29 unique genetic features. The core genome has given insights into the phylogeny while the 30 accessory and unique genes has led to the identification of niche specific genes. Bacteriophage, 31 virulence factors and biofilm formation genes were absent with this species. Housing CRISPR 32 and antibiotic resistance gene was strain specific. The integrated approach of functional, genomic 33 and comparative analysis denotes the niche specific adaption to gut dynamics of strain D2. 34Moreover the study has comprehensively characterized genome sequence of each strain to know 35 the genetic difference and intern recognize the effects of on phenotype and functionality 36 complexity. The evolutionary relationship among strains along and adaptation strategies has been 37 included in this study. 38Significance: Reports of Kocuria rhizophila isolation from various sources have been reported 40 but the few disease outbreaks in humans and fishes have been prominent, but no supportive 41 3 evidence about the survival ability of Kocuria spp. within human GIT. Here, we report the gut 42 adaption potential of K. rhizophila strain D2 by functional and genomic analysis. Further; 43 comparative genomics reveals this adaption to be strain specific (Gluten degradation). Genetic 44 difference, evolutionary relationship and adaptation strategies have been including in this study. 45 48 positive, non-hemolytic, non-endospore-forming, non-motile and can grow at different oxygen 49 levels (aerobic, facultative and anaerobic) (1, 2). Presence of galactosamine and glucosamine 50 (amino sugars) as the main component of the cell wall, differ them from other members of the 51class Actinobacteria (2). This genus is normally inhabitants of dust, soil, water and food and in 52 humans colonizes skin, mucosa, oropharynx and gastrointestinal tract (GIT) (3-5). 53K. rhizophila was isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia). 54 in 1999 (6). The strain ATCC 9341 was reclassified as K. rhizophila from Micrococcus luteus 55 (7). It has been isolated from viz. c...

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