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Holy shift! Changes in poop mark disease progression

August 23, 2016

Animal models of disease are crucial to understanding disease progression in humans. In a recent article published in the American Journal of Primatology, Hannah Barbian (pictured below), a fifth-year MVP student in Beatrice Hahn’s lab, exemplified this concept. The Hahn lab researches the disease progression and evolution of simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV). A long-standing collaboration with the Jane Goodall Institute and Gombe National Park in Tanzania has supplied the lab with a breadth of chimpanzee samples. The Hahn lab previously used chimpanzee samples to demonstrate that HIV-1, the etiologic agent of the human AIDS epidemic, originated from a cross-species transmission from chimpanzees into humans. Samples from Gombe National Park are especially useful because despite being wild, the chimpanzees are closely monitored, so information about their health, age, and behavior is readily available.


Hannah used fecal samples from Gombe National Park to investigate the relationship between SIVcpz infection and the chimpanzee gut microbiome. Understanding the effect of SIVcpz infection on wild chimpanzees is challenging because routine blood collection of wild chimpanzees is invasive and therefore unethical. This prevents monitoring of viral load or CD4 T cell numbers in infected individuals. “This project was exciting because we hoped to use the microbiome to get more clues into what is going on in SIVcpz infected animals,” said Hannah. “Most markers of AIDS progression in humans are found in blood.  So when studies were published showing that the human gut microbiome becomes dysbiotic with HIV-1 infection, and may even be linked to disease progression, we were really excited to apply this technique to our chimpanzee fecal samples.”


Hannah and colleagues isolated nucleic acids from chimpanzee fecal samples and used multiple approaches to identify the constituents of the gut microbiome. Metagenomic sequencing identifies all organisms within a sample, including bacteria and viruses, but it requires large quantities of fecal material. Since fecal samples are valuable and limited, only a few samples were analyzed by metagenomic sequencing. There were no statistically significant differences between the bacteria identified in samples from SIVcpz-infected and uninfected chimpanzees. However, samples from all infected chimpanzees had greater amounts of bacteria from the Prevotellaceae family.


The authors also identified bacteria from fecal samples with 16S ribosomal RNA sequencing. Unlike metagenomic sequencing, this approach requires little starting material, which allowed the use of a much larger pool of samples from the past fifteen years. Results from 16S rRNA sequencing were similar to those obtained from metagenomics sequencing: the gut composition of infected chimpanzees was not significantly different than that of uninfected chimpanzees, but Prevotellaceae was again enriched in infected samples. Analysis of the virus composition showed an abundance of Chimpanzee Stool Associated Circular Virus and Chimpanzee Adenovirus in both uninfected and infected chimpanzees.


Interestingly, there was a dramatic difference observed in samples from infected chimpanzees that were collected shortly before their AIDS-related deaths. The bacterial composition of these samples was significantly different from uninfected chimpanzees and from infected chimpanzees that died of other causes. The samples collected close to death were also significantly different from samples collected from the same individuals at earlier time points. These results demonstrate that there is a drastic shift in the composition of the chimpanzee gut microbiome shortly before an AIDS-related death. The authors comment that this is likely due to the decline of effective immune responses.

Changes to the gut microbiome of SIVcpz-infected chimpanzees are observed shortly before AIDS-related death. SIVcpz infection does not dramatically affect the composition of the gut microbiome during earlier stages of disease. (Illustration by Hannah Barbian)


The microbiome changes observed at the end stages of SIVcpz infection have implications for future SIVcpz studies and for chimpanzee health. Monitoring infected chimpanzees for a shift in the gut microbiome could serve as an indicator of upcoming rapid disease progression that could prompt close observation of the chimpanzees to learn more about the final stages of AIDS. Identifying chimpanzees that are close to death could even prompt medical intervention if necessary. Beyond informing SIVcpz pathology, Hannah’s studies also have implications for HIV-1. Previous studies have shown that HIV-1 infection, like several other infections, is correlated with changes to the gut microbiome. Since antibiotic and antiretroviral use is common in HIV-1-infected patients, it is unclear whether the observed alterations are directly due to HIV-1 infection. Wild-living chimpanzees, therefore, provide a suitable model system to study the impact of retroviral infection on the primate gut microbiome in the absence of antibiotic and antiretroviral use. Since Hannah and colleagues found that infection of wild chimpanzees did not significantly affect the gut microbiome until close to death, the previously reported effects of HIV-1 infection on the human gut microbiome are likely indirect effects of antiretroviral and antibiotic use.


Hannah continues to use fecal samples from Gombe National Park in her thesis work to study SIVcpz progression. She is currently analyzing recently collected fecal samples for new and existing SIVcpz infection and is developing more sensitive assays to sequence and quantify RNA from fecal samples.


A commentary on:

"Destabilization of the Gut Microbiome Marks the End-Stage of Simian Immunodeficiency Virus Infection in Wild Chimpanzees", Barbian et al., 2016 


Link to the PubMed page.


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