It is speculated that the microbiome plays an important role in the oncogenic process. Helicobacter pylori is a proven class I carcinogen in gastric cancer (GC). The intratumoral microbiome, however, is home to several microbes that play critical roles in GC development and progression. Here, researchers described the whole range of GC microorganisms and separated them into several molecular classes. They built a bioinformatics pipeline for analyzing the microbiome that can be used with any next-generation sequencing system. Alpha diversity and enrichment microbiome profiles were constructed for two large, demographically different cohorts: the internal Memorial Sloan Kettering Cancer Center (MSKCC) cohort and The Cancer Genome Atlas (TCGA) cohort. A total of 520 GC samples were compared to some nonmalignant tissue samples taken from the area around tumors. There are distinct microbiome differences amongst GC molecular subtypes. Overall, microbial diversity was lower in GC samples in the MSKCC and TCGA cohorts compared to nonmalignant samples (P<0.05). There was a statistically significant (P<0.05) increase in the relative abundance of Helicobacter, Lactobacillus, Streptococcus, Prevotella, and Bacteroides in GC samples compared to nonmalignant tissue. When compared to other GC molecular subtypes, GC with a high level of microsatellite instability displayed a very specific kind of microbial enrichment. The microbiome of GC patients exhibited unique patterns of microbial diversity and species enrichment. Given the wide range of GC disease development and therapeutic response, deciphering distinct microbial fingerprints will pave the way for investigating important microbial targets for treatment.