How Does Human Saliva Compare to a Chimp's?
Humans (genus Homo) and chimpanzees and bonobos (genus Pan) share roughly 99% of their DNA. But that doesn't necessarily mean we share the same bacteria. An organism's microbiome -- that is, all the microorganisms that live in or on the body -- is shaped not just by genetics, but also by diet and the environment. Indeed, the exact composition of the human microbiome differs from person to person, and it can even change within an individual over time. Currently, it's unclear if there even exists a "core microbiome" that all humans share.
Combined with the fact that our three species have tremendous differences in diet and lifestyle (e.g., humans typically don't live in trees or throw feces at each other), we might predict very few similarities in our microbiomes. And that would be exactly right.
Researchers collected saliva samples from 22 chimps and 13 human workers from a sanctuary in Sierra Leone (SL) and from 23 bonobos and 15 human workers from a sanctuary in Democratic Republic of Congo (DRC). Then, they amplified and sequenced the bacterial gene encoding 16S rRNA which allowed them to identify the composition of the various microbiomes. Finally, they determined how similar the microbiomes were between the four groups (two human, one chimp, and one bonobo), and they detailed their findings in the following Venn diagram.
As shown above, the two human groups shared 5.5% of their microbiomes, chimps and bonobos shared 6.9% of theirs and all four groups shared 2.6% of their microbiomes. This is fairly weak evidence for the existence of a core microbiome across species. However, it should be noted that different bacteria can perform the same metabolic function, therefore it is still possible that a "core functional microbiome" exists. More research can resolve this question.
Source: Jing Li, Ivan Nasidze, Dominique Quinque, Mingkun Li, Hans-Peter Horz, Claudine André, Rosa M Garriga, Michel Halbwax, Anne Fischer and Mark Stoneking. "The saliva microbiome of Pan and Homo." BMC Microbiology 13:204 (2013). doi:10.1186/1471-2180-13-204