A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals

Abstract

Intestinal microbiota facilitates food breakdown for energy metabolism and influences the immune response, maintaining mucosal homeostasis. Overall, HIV infection is associated with intestinal dysbiosis and immune activation, which has been related to seroconversion in HIV-exposed individuals. However, it is unclear whether microbiota dysbiosis is the cause or the effect of immune alterations and disease progression or if it could modulate the risk of acquiring the HIV infection. We characterize the intestinal microbiota and determine its association with immune regulation in HIV-exposed seronegative individuals (HESN), HIV-infected progressors (HIV+), and healthy control (HC) subjects. For this, feces and blood were collected. The microbiota composition of HESN showed a significantly higher alpha (p = 0.040) and beta diversity (p = 0.006) compared to HC, but no differences were found compared to HIV+. A lower Treg percentage was observed in HESN (1.77%) than HC (2.98%) and HIV+ (4.02%), with enrichment of the genus Butyrivibrio (p = 0.029) being characteristic of this profile. Moreover, we found that Megasphaera (p = 0.017) and Victivallis (p = 0.0029) also are enriched in the microbiota composition in HESN compared to HC and HIV+ subjects. Interestingly, an increase in Succinivibrio and Prevotella, and a reduction in Bacteroides genus, which is typical of HIV-infected individuals, were observed in both HESN and HIV+, compared to HC. Thus, HESNs have a microbiota profile, similar to that observed in HIV+, most likely because HESN are cohabiting with their HIV+ partners.

Fig 1. Specific microbial communities in HESN fecal microbiota compared to HC.

Genera abundance and prevalence in HESN, HIV+, and HC (A) are shown. (B) presents the top 25 genera correlated between HESN and HC and HESN and HIV+. Finally, (C) shows the main genera correlated in previous analyses performed using Spearman correlation with statistical significance *(r>0.50 and p<0.05).

Fig 2. Higher diversity in HESN and similarities with HIV+.

(A) Microbial community diversity, assessed by the sample’s richness with Chao1 index (alpha diversity) by T-test statistical (p = 0.070). (B) Comparison between samples in HESN and HIV+. (C) Comparison between samples in HESN and HC, by Principal Coordinates Analysis (PCoA), and using Permutational Multivariate Analysis of Variance (PERMANOVA) in statistical analysis (p = 0.011).

Fig 3. Lower percentage of Treg cells in HESN and influence of immunological characteristics on fecal microbiota composition.

The percentage of CD38^- and HLA-DR^-expressing CD4⁺ T cells (A) and CD8⁺ T cells (B) is shown. The percentage of Treg cells (C), Th17-like (CD161⁺CD4⁺) T cells (D), and the ratio of Treg/Th17-like cells in each group (E) are presented. The statistical analysis among groups was estimated using the Mann-Whitney U test. (F) The top 25 genera correlated with a high (>3%) or low (<3%) percentage of Treg cells on fecal microbiota composition is shown. (statistical analysis were performed using Spearman test; p-value <0.05). *p-value <0.05. **p-value <0.01.

Fig 4. The Abundance of Prevotella and Succinivibrio in fecal microbiota composition of HESN.

(A) shows the correlation network of the most abundant genera in HESN (green), HIV+ (purple), and HC (orange), and interaction between microbial community’s genera; the circle’s size represents the abundance of genera in microbial composition. The correlations were estimated using Spearman correlations (p<0.05, r>±0,5), the most significant bacteria are highlighted as positive (red) or negative (blue) correlations. Venn diagram (B) shows the main genera of each group studied as well as those shared between them.