Effects of Fecal Microbial Transplantation on Microbiome and Immunity in Simian Immunodeficiency Virus-Infected Macaques

Abstract

An altered intestinal microbiome during chronic human immunodeficiency virus (HIV) infection is associated with mucosal dysfunction, inflammation, and disease progression. We performed a preclinical evaluation of the safety and efficacy of fecal microbiota transplantation (FMT) as a potential therapeutic in HIV-infected individuals. Antiretroviral-treated, chronically simian immunodeficiency virus (SIV)-infected rhesus macaques received antibiotics followed by FMT. The greatest microbiota shift was observed after antibiotic treatment. The bacterial community composition at 2 weeks post-FMT resembled the pre-FMT community structure, although differences in the abundances of minor bacterial populations remained. Immunologically, we observed significant increases in the number of peripheral Th17 and Th22 cells and reduced CD4(+) T cell activation in gastrointestinal tissues post-FMT. Importantly, the transplant was well tolerated with no negative clinical side effects. Although this pilot study did not control for the differential contributions of antibiotic treatment and FMT to the observed results, the data suggest that FMT may have beneficial effects that should be further evaluated in larger studies.

Importance: Due to the immunodeficiency and chronic inflammation that occurs during HIV infection, determination of the safety of FMT is crucial to prevent deleterious consequences if it is to be used as a treatment in the future. Here we used the macaque model of HIV infection and performed FMT on six chronically SIV-infected rhesus macaques on antiretroviral treatment. In addition to providing a preclinical demonstration of the safety of FMT in primates infected with a lentivirus, this study provided a unique opportunity to examine the relationships between alterations to the microbiome and immunological parameters. In this study, we found increased numbers of Th17 and Th22 cells as well as decreased activation of CD4(+) T cells post-FMT, and these changes correlated most strongly across all sampling time points with lower-abundance taxonomic groups and other taxonomic groups in the colon. Overall, these data provide evidence that changes in the microbiome, particularly in terms of diversity and changes in minor populations, can enhance immunity and do not have adverse consequences.

FIG 1

Timeline showing the times of sampling of blood and GI tract biopsy specimens from 6 SIV-infected rhesus macaques before and after antibiotic treatment and fecal microbial transplantation. The macaques were intrarectally challenged with 100,000 50% tissue culture infective doses of SIV_MAC239x. ART consisted of subcutaneous tenofovir and emtricitabine and oral raltegravir. ABX consisted of vancomycin for 7 days, followed by a combination of vancomycin and enrofloxacin (Baytril) for 12 additional days. FMT consisted of administration of stool from SIV-negative rhesus macaques homogenized in PBS by gavage to the upper and lower GI tracts of the 6 SIV-infected rhesus macaques.

FIG 2

ABX and FMT treatment resulted in microbiome composition changes. (A) Principal-component analysis using the relative abundances of all genera from colon biopsy specimens across all time points. Green, pre-ABX (week −3); orange, post-ABX (week −1); blue, 2 weeks post-FMT (week 2); red, 6 weeks post-FMT (week 6). (B) Relative abundance of bacterial genera from colon biopsy specimens pre- and post-ABX and post-FMT. The 20 most abundant genera are shown. Less abundant genera were grouped into the “other” category (pink).

FIG 3

Increased amounts of peripheral Th17 and Th22 cells after fecal microbial transplantation. (A) Absolute amounts of peripheral CD4⁺ and CD8⁺ T cells, calculated using the percentage of total CD45⁺ cells obtained by flow cytometry and the total leukocyte count obtained by complete blood count analysis. (B) Percentages of IL-22-producing (IL-22⁺) and IL-17-producing (IL-17⁺) CD4⁺ T cells in PBMCs measured via flow cytometry after stimulation with PMA-ionomycin. CD4⁺ T cells were identified as CD45⁺ CD3⁺ CD4⁺ CD8⁻ cells. Asterisks indicate significant differences determined by a paired t test (*, P < 0.05; **, P < 0.01; ***, P < 0.001).

FIG 4

Reduced CD4⁺ T cell activation after fecal microbial transplantation. (A) HLA-DR-positive (HLA-DR⁺) CD4⁺ T cells in colon, jejunum, and rectum biopsy specimens. CD4⁺ T cells were identified as CD45⁺ CD3⁺ CD4⁺ CD8⁻ cells. Asterisks indicate significant differences determined by a paired t test (*, P < 0.05; **, P < 0.01). (B) Representative flow plots showing HLA-DR expression on CD4⁺ T cells from the jejunum of an SIV-infected rhesus macaque before ABX (left) and 6 weeks post-FMT (right). SSC, side scatter.

FIG 5

Correlation matrix of taxonomic groups that most strongly correlated with immunological or physiological parameters. Colors indicate Spearman correlation coefficient values ranging from −1 (dark blue) to 1 (dark red). The ellipse shape indicates the relative spread of data points and the slope of the correlation, with a wider ellipse indicating a greater relative spread and a narrower ellipse indicating less of a spread.