Herbiotic FS modulated metagenomic profiling in Salmonella infected chicken gut

The relentless march of antimicrobial resistance (AMR) has emerged as a public health concern, especially in the light of the fact that newer antibiotic classes have been slow to develop and investments in novel antimicrobial drug classes have been receding. AMR problem transcends international borders with antibiotic stewardship. Increasing thrust for restriction on AGP’s has instigated hunt for newer alternatives.  Present study is undertaken to establish mechanism of action of phytogenic growth promoter Herbiotic FS (M/S Indian herbs Specialities, India) in 120 Vencobb broiler based on metagenome profiling of chicken gut. There were 4 experimental groups (30 birds per group; 5 replicates of 6 birds); Healthy control, infected control (Salmonella gallinarum (1×108 CFU/ml) infection was induced on day 4th), infected & treated with Herbiotic@500g/ton and infected & treated with Linomycin@250g/ton of feed. Chicken gut metagenomics allows assessment of taxonomic & metabolic diversity of microbial communities. Metagenome of jejunum is carried to assess gut bacterial diversity. The present study illustrates analysis of the 16S rDNA based metagenome of the V3-V4 region, for DNA extracted from sixteen chicken jejunum. The Microbial composition within a sample was estimated using alpha diversity indexes, krona charts & piecharts. Rarefaction plot was generated to ensure that sampling depth was sufficient for the analysis. The microbiome diversity and species abundances was analysed using Metagenomic Rapid Annotation using sub-system technology (MG RAST) & QIIME analysis. Sample wise reports were generated that gives the abundance values from Phylum to Species referring Seed System Technology (Seed Database) & Ribosomal RNA Database (Greengenes, RDP II). Pie charts were generated using matplotlib for all unique taxa’s at a cutoff of 0.5% & above, taxa’s<0.5% represented as miscellaneous. Metagenomic bacterial diversity dominance of Lactobacillus (39.92%) in healthy control, dominance of pathogenic bacteria (40.58%) & clostridia (34.18%) in infected control, restoration of good bacteria lactobacillus (31.56%) & abnormally higher emergence of candidates bacteria (23.53%) in Lincomycin treatment and restoration & dominance of lactobacilli (61.11%, even higher than healthy control) in Herbiotic FS treatment. Herbiotic FS is efficacious for prevention of colonization of gut pathogens & augmenting peace keeping bacteria ensuring gut function modulation and attainment of eubiosis.