Microbiome and metabolites play an important role in the progression of Human Immunodeficiency virus type 1 infection. Understanding the microbial composition of elite controllers has provided insights into the viral control mechanisms involved, which may be beneficial for developing therapeuticsforHIVinfection.The intestineis considered as theprimarysiteforHIV-1 infection. During the process of infection, pathogens disrupt the gut-associated lymphoid tissues which lead to bacterial translocation. This results in disease progression, imbalances of microbial communityanddisturbancesof gutmicrobiota composition andfunction.Thecurrentstudywas performed in elite controllers (EC); theyaregroupofindividualswhichhastheabilitytocontrolthe viral infection in the absence of therapy; viremic progressors (VP) are HIV infected and treatment-naive individuals; healthy controls (HC) are the HIV uninfected individuals; to functionally interpret the difference in the microbial composition and significantly enriched pathways between the groups. The bacterial diversity and richness were high in EC when compared to other two groups. Proteobacteria was significantly abundant in EC at the phylum level. Increased abundance of Lachnospiraceae, Prevotellaceae and Lactobacillaceae in EC and decreased abundance of Ruminococcaceae in VP were observed compared to HC atthe family level. Significantly enriched metabolites were also studied and integrated along with the significantly abundant microbiome to elucidate the pathways involved in each group. Pyrimidine and Purine metabolism pathways and Sphingolipid metabolism pathways were the common pathways found in the three groups. In conclusion, EC have higher microbial richness and diversity than treatment-naive VP patients, with unique bacterial composition and distinct pathways which may contribute to the control ofthe viral infection.