The human gastrointestinal (GI) tract microbiota acts like a virtual organ and is suggested to be of great importance in human energy balance and weight control. This study included 40 monozygotic (MZ) twin pairs to investigate the influence of the human genotype on GI microbiota structure as well as microbial signatures for differences in body mass index (BMI). Phylogenetic microarraying based on 16S rRNA genes demonstrated that MZ twins have more similar microbiotas compared with unrelated subjects (P<0.001), which allowed the identification of 35 genus-like microbial groups that are more conserved between MZ twins. Half of the twin pairs were selected on discordance in terms of BMI, which revealed an inverse correlation between Clostridium cluster IV diversity and BMI. Furthermore, relatives of Eubacterium ventriosum and Roseburia intestinalis were positively correlated to BMI differences, and relatives of Oscillospira guillermondii were negatively correlated to BMI differences. Lower BMI was associated with a more abundant network of primary fiber degraders, while a network of butyrate producers was more prominent in subjects with higher BMI. Combined with higher butyrate and valerate contents in the fecal matter of higher BMI subjects, the difference in microbial networks suggests a shift in fermentation patterns at the end of the colon, which could affect human energy homeostasis.