The rats and the infected subjects have a similar composition in their microbiomes. Both have similar amounts of Bacteroidetes and Fusobacteria. However the rats do not have a significant amount of Proteobacteria, whereas in the infected human microbiome Proteobacteria is one of the most significant groups of bacteria. This means that there will be several variables that will not match when using the rats microbiome as a model. While there is very little Proteobacteria in the rats microbiome, there is a similar amount of Actinobacteria in both the infected humans and rats. Therefore, the composition the fisher rats would most likely be the best model for HIV testing.
A close second would be the deer mice. The deer mice have a more significant relative abundance of Proteobacteria compared to the rats. This is noteworthy because the infected humans had a large abundance of Proteobacteria. However the deer mice do have a significant abundance of Spirochaetes, which is only found in small quantities within infected humans. Also the deer mice have almost no Actinobacteria which is found in the infected humans. This is a significant enough change that, while close, the deer mice microbiome might not be a compatible model for studying HIV drug metabolism.
While it is true that the rats and the HIV infected humans had the closest composition they were not completely similar. They have very different shannon diversity. The Shannon diversity index is an index that is commonly used to characterize species diversity in a community. On the Shannon diversity index, the lower numbers show the most diversity, with the larger numbers showing less diversity. In infected humans the Shannon diversity was an average of 3.4 (1.3-4.5). This shows that even being infected the microbiome of a human is extremely diverse. The rats had an average of 7.791 (7.729- 7.892), the mice had an average of 6.98825 (6.706-7.179), and the deer mice have an average of 7.6825 (7.448-7.902) Shannon diversity. This clearly shows that all the lab animals have a much lower diversity in their microbiome compared to the humans. The Shannon diversity in the mice was the most like the human’s. This shows that based on Shannon diversity the mice would be the best model for HIV testing.