I admittedly just skimmed the article, but I thought that it was well established that bacteria can acquire genetic material from other cells that they consume. Why is it surprising that human genetic material can be acquired this way too?
Cool! I also was amazed when I first learned that the human genome contains an archeology of ancient viruses whose DNA we incorporated over the millennia.
I'd guess the obvious first question is, is this a sequencing artifact? I wouldn't like to judge, but it looks like they are alive to the possibility (different isolates etc.)
Interesting. It's known that viruses and transducing phages can incorporate host DNA into their genomes.
And of course, going the opposite direction at a metalevel, one theory of the origin of eukaryotic mitochondria is that it is of bacterial origin (an idea proposed by, among others, Lynn Margulis, who was married to Carl Sagan)...
...and leads to the following provocative idea: "According to Margulis and Dorion Sagan, 'Life did not take over the globe by combat, but by networking' (i.e., by cooperation).
It's not really a hypothesis anymore. Mitochondria have their own DNA so we can put them on a phylogeny. The closest living relatives to mitochondria are http://en.wikipedia.org/wiki/Alphaproteobacteria
Similarly, plastids are most closely related to cyanobacteria.
