For the first time, Zhu et al.  utilized metagenomics data to quantify the degree of difference in gene content between strains of the same species of gut bacteria from different people. They examined 11 different bacterial species and, based on the degree of gene deletions, quantified the lower limit of gene variation at 13%. Interestingly, the most marked differences in gene functions among gut bacterial species related to polysaccharide utilization and polysaccharide capsid synthesis.
These findings suggest that to understand fully the role of the human microbiome in health and disease, we have to characterize it at the level of the taxonomic strain. A strain, in microbial ecology, refers to the taxonomic differentiation of organisms within a species. In bacteria, the level of genetic difference between strains of the same species can sometimes be dramatic, and can lead to significant changes in the phenotype of the microbe. Such changes could have profound influences on the phenotype of the host, possibly leading to changes in digestive ability, or in disease states, including those relating to autism, obesity and diabetes, among other conditions.
Recent work from Jill Banfield’s group at University of California, Berkeley has shown that inter-individual differences in the gut microbiome are apparent very soon after birth . In this study, Raveh-Sadka and colleagues re-assembled hundreds of high-quality gut microbial genomes from infants in the same neonatal intensive care unit. Surprisingly, they found that there was very little sharing of bacteria between these infants. In fact, the strains of bacteria that colonized each child were unique. There are a number of reasons that might explain why this can occur.
First, it is possible that the children were colonized by bacteria specific to their mother: from her vaginal tract, from skin and oral contact, or through breast milk. A newborn infant is immediately colonized by microbes that are associated with the mode of delivery: either through the vagina or through the skin during cesarean section delivery . Additionally, during the first year of life and sometimes beyond, a human child often receives milk from its mother, which we know maintains a complex microbiome originating from the mother’s gut and other mucosal surfaces . Additionally, the mother’s own genome can shape the types of bacteria that can colonize breast milk , which comprises both a prebiotic of sugars, proteins and fats and a probiotic of bacterial organisms that transform foodstuffs into vital nutrients for the child. This would suggest that vertical transmission is an essential process for shaping our unique microbiome.
Second, the dispersal and interaction potential of microbes in the neonatal intensive care unit environment could be almost limitless, making the likelihood that any two infants would gain the same microbiome infinitesimally small. Additionally, host genetics can shape individual microbiomes . Finally, the gut microbiome is a dynamic ecosystem, and as such is undergoing successional ecology. This means that when a new bacterium arrives, whether it colonizes or just passes through the ecosystem will depend on its phenotype and its interaction with any organisms already present there.