Open Access Highly Accessed Research article

The saliva microbiome of Pan and Homo

Jing Li12, Ivan Nasidze1, Dominique Quinque134, Mingkun Li1, Hans-Peter Horz4, Claudine André5, Rosa M Garriga6, Michel Halbwax17, Anne Fischer18 and Mark Stoneking1*

Author Affiliations

1 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D-04103, Germany

2 Current address: Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China

3 Current address: Department of Genetics, Harvard Medical School, 77 Louis Pasteur Avenue, Boston 02115, MA, USA

4 Division of Oral Microbiology and Immunology and Department of Medical Microbiology, RWTH Aachen University Hospital, Pauwelsstrasse 30, Aachen D-52057, Germany

5 Lola Ya Bonobo Sanctuary, Petites Chutes de la Lukaya, Kimwenza – Mont Ngafula, Kinshasa, Democratic Republic of Congo

6 Tacugama Chimpanzee Sanctuary, P.O. Box 469, Freetown, Sierra Leone

7 Current address: EcoHealth Alliance, 460 West 34th Street – 17th floor, New York 10001, NY, USA

8 Current address: Molecular Biology and Biotechnology Department, International Center for Insect Physiology and Ecology, P.O. Box 30772–00100, Nairobi, Kenya

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BMC Microbiology 2013, 13:204  doi:10.1186/1471-2180-13-204

Published: 11 September 2013



It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced by both internal factors (such as phylogeny and host physiology) and external factors (such as diet and local environment), and interspecific comparisons can aid in understanding the importance of these factors.


To gain insights into the relative importance of these factors on saliva microbiome diversity, we here analyze the saliva microbiomes of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) from two sanctuaries in Africa, and from human workers at each sanctuary. The saliva microbiomes of the two Pan species are more similar to one another, and the saliva microbiomes of the two human groups are more similar to one another, than are the saliva microbiomes of human workers and apes from the same sanctuary. We also looked for the existence of a core microbiome and find no evidence for a taxon-based core saliva microbiome for Homo or Pan. In addition, we studied the saliva microbiome from apes from the Leipzig Zoo, and found an extraordinary diversity in the zoo ape saliva microbiomes that is not found in the saliva microbiomes of the sanctuary animals.


The greater similarity of the saliva microbiomes of the two Pan species to one another, and of the two human groups to one another, are in accordance with both the phylogenetic relationships of the hosts as well as with host physiology. Moreover, the results from the zoo animals suggest that novel environments can have a large impact on the microbiome, and that microbiome analyses based on captive animals should be viewed with caution as they may not reflect the microbiome of animals in the wild.