Not all ingested bacteria will be able to colonize the intestines upon arrival.  Some bacteria may not be adapted to living in the GI tract, and are merely passersby waiting to be ejected into the environment to find their favored niche.  Other bacteria are happy to be in the GI tract where nutrients are abundant, but must contend with the other hungry microbes and the vigilant immune system.  When competition is fierce, a particular bacterial species may “win” by producing toxins that kill competing species, or by specializing on macromolecules that not anyone can metabolize.  The immune system will not be a problem if microbes stay on their side of the GI tract (i.e., don’t invade the epithelial lining), and if they don’t: disguises to evade the immune system abound.

But these strategies I’ve listed neglect what is likely to be one of the most important determinants of bacterial colonization and persistence in the intestines: bacteriophages, or phages.  Phages are tiny viruses that infect bacterial cells by climbing onto bacterial extracellular appendages, trekking to the cell surface, and injecting their DNA through the cell wall and membrane(s).  Once inside the cell, phage DNA can either integrate into the bacterial chromosome for later production of phages (lysogeny), or be immediately used as a blueprint for the production of thousands of phages that will ultimately lyse the cell (lytic). 

A recent paper by Duerkop et al. proposes that a particular phage mediates the colonization dynamics of the bacterium Enterococcus faecalis.  The authors showed that phage DNA embedded in the chromosome of E. faecalis is made into functional phages when the bacteria are growing with an abundance of amino acids (in a test tube or the mouse intestine).  Only some strains of E. faecalis had the phage DNA in their genome, and when phages were produced, these strains were able to grow to a (modestly) higher density than E. faecalis strains that did not carry the phage DNA in their genomes.  This growth advantage was shown in test tube co-cultures as well as co-inoculations of mouse intestines.

What is going on?  When phages are induced in the strains that have them embedded in their chromosomes, these phages will kill the cell that produced them, and any other cells that are not resistant to them (often times carrying the phage DNA in the chromosome will make the cell resistant to re-infection by the same phage).  The authors indicate that in doing this, these phage-producing E. faecalis strains are able to “use” the phage to kill off competitors, which is evidenced by their higher growth in co-culture.  

This paper was a nice example of the dynamics that are likely occurring within a bacterial species. Unfortunately because most microbiota are only studied using nucleic acid sequencing that identifies them at the genus level (or even at broader levels), such dynamics would be completely missed.  But have no fear: technologies are already enabling the characterization of these within species dynamics on a microbial ecosystem scale.  It will simply take time before they are affordable for all.