The human body typically harbors about 100 trillion cells of microbial origin – commonly referred to as the human microbiome – the vast majority of which resides in the gastrointestinal tract (Savage 1977). While studying the extent of human genetic variation, for example in the 1,000 genomes project (The 1000 Genomes Project Consortium, 2010), and the understanding of its practical impact have advanced rapidly, the genetic variation of the human microbiome has remained largely unexplored. One of the reasons is attributed to the difficulty in cultivating the multitude of microbial species that inhabit our intestines. The possibility to high-throughput sequence DNA directly isolated from the environment has revolutionized the study of microbial communities, but analyzing single nucleotide polymorphisms (SNPs) in mixed microbial populations has remained a challenge. We therefore developed a methodological and statistical framework for metagenomic variation analysis and applied it to published sequencing data derived from 252 faecal samples of 207 European and North American individuals (The Human Microbiome Project Consortium 2012 and Qin et al. 2010). Exploiting the information generated by aligning 7.4 billion Illumina reads to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), almost as many as have been identified in humans so far. Population variation of gut microbial communities with accompanying changes in species abundances over long time periods have not been studied yet in large cohorts. It has been unclear if host-specific strains are retained over time or constantly replenished via the environment. To address this question, we used 88 gut metagenomes collected from 43 healthy subjects that were sampled at least twice over time intervals of up to 1 year and measured population similarities of dominant gut species using fixation indices (FST). The most striking result was that subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and furthermore, that an individual may have a unique metagenomic genotype, which may also imply gut physiological individuality and consequences for personalized diet or drug intake.