Understanding the normal development of the human gut microbiome is of great interest. This is mainly due to possibilities for predicting and preventing disease and developing probiotic treatments. Escherichia coli (E. coli) is one of the first organisms to colonize the infant gut, and is used as an indicator organism for changes in the population structure microbiome as a whole. In order to more accurately map the development of the infant gut microbiome, and to prepare for large scale studies in the future, a novel methodology was tested where fragments of the E. coli house-keeping genes malate dehydrogenase (mdh) and tryptophan synthase alpha subunit (trpa) were amplified from fecal samples taken over the course of the first year of life of a healthy human infant, and sequenced using Pacific Biosciences Single molecule real time (SMRT) sequencing with sample multiplexing. Strains were phylogenetically categorized using database sequences for known reference strains. In this study, eleven distinct mdh alleles and eight distinct trpA alleles were observed in the infant during the sampling period. In theory, this indicates that at least eleven unique E. coli strains were observed to be colonizing the infant over the study period. This is many more than previous studies have observed and is possibly due to the large number of samples from a single infant that were analyzed. All alleles have been previously recorded in the MLST databases for both the mdh and trpA alleles. However, it was only possible to match four of the mdh and trpA alleles with each other, using common occurrence in the sequencing data, and thus postulate that they occur on the same genome and represent a unique strain. Of the strains that were identified, we observed populations dynamics with some strains having a dominant position in the E. coli population during distinct time periods, separated by transitional periods with higher strain diversity. Some of these shifts in strain composition correlated with environmental factors, such as travel or changes in diet. The procedure successfully allowed for the mapping of the development of the infant gut microbiome with a much higher resolution than previous studies, and allowed for the temporal pinpointing of when changes in E. coli strain composition occurs and how strain composition fluctuates in transitional periods. The procedure can easily be adapted to map and compare the development of the early gut microbiome of multiple infants, although further optimization of the procedure would be desirable to improve the signal to noise ratio.