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Metagenomic investigation of gut microbiome is a comprehensive and rapid technique for analysis and diagnosis of several diseases. Gut microbiome is a intricate ecosystem, structured by the interaction of various microbes and the metabolites produced by them, which helps in emerging and sustaining immunity and homeostasis. A healthy gut microbiome is driven by different factors such as nutrition, lifestyle etc. The current study examines the association of diet on gut microbiome dysbiosis and their role in disease conditions. Gut microbiome data collected from 73 patients, tested at BioAro Inc. lab, using shotgun metagenomics through next generation sequencing, analyzed and compared with data from 20 healthy subjects from HMP database. An in-house bioinformatics pipeline (PanOmiQ) was utilized for secondary and tertiary analysis was accomplished using R software. Results showed a higher number of opportunistic pathogen microorganisms in gut microbiome of subjects on a meat-based diet, as compared to a plant-based diet. These opportunistic pathogens included Ruminococcus torques (>3.34%), Ruminococcus gnavus (>2.22%) and Clostridium symbiosum (>1.87%). The study also found a higher relative abundance of these pathogens in cancer patients, as compared to healthy subjects. We also observed a highly significant (p< 0.0001) correlation of high meat-based diet with obesity in comparison to the subjects on a predominantly plant-based diet and the classified healthy subjects. Our findings suggest that patients following a plant-based diet have a lower relative abundance of pathogens, associated with cancer and or obesity. These findings provide critical insight into how we can use shotgun metagenomics to study composition and diversity of gut microbiome, how the diet affects gut microbiome and play an important role in metabolic and terminal diseases. This is the first report on investigating gut microbiota using shotgun metagenomics, correlating with different diseases and diet followed, which might impact the presence of opportunistic pathogens or keystones species. Additionally, it can provide valuable visions to physicians and dietetic practitioners for providing personalized treatment or to customize the diet plan.