For a study, Intestinal immunoglobulins (Ig) were antibodies secreted in huge amounts which bind the bacteria and its components in the guts. The binding was supposed to quicken the bacterial transit time and also avoid the intercourse of the potentially immunogenic compounds along with the intestinal immune cells. Ig secretion was operated by alterations in the gut microbiome composition, it was an event that was rarely mapped in the human setting intervention. Here the intestinal and systemic Ig response was determined to be a significant intervention in the gut microbiome composition. Humans suffering from metabolic syndrome and healthy humans both got oral vancomycin 509 mg four times a day for a week. Concurring with the vancomycin-induced boost in the gram-negative bacteria, fecal levels of the immunogenic bacterial components lipopolysaccharide (LPS) and flagellin boosted up. Intestinal antibodies (IgA and IgM) were highly boosted, while peripheral antibodies (IgG, IgA, and IgM) were almost not affected by vancomycin treatment. The sorting of bacterial cells followed as 16S rRNA sequencing disclosed that most of the gram-negative bacteria, including opportunistic pathogens, were IgA-coated once the intervention was done. It was suggested that the response of intestinal Ig after vancomycin treatment prohibits the intrusion of pathogens and bacterial components into the systemic sites.