A hallmark of HIV disease is a profound depletion of CD4+ T cells in the gut-associated lymphoid tissue and increased translocation of microbial products across this compromised epithelial barrier. In addition, significant dysbiosis is clearly evident in fecal biota of untreated HIV-1¿infected subjects as compared to uninfected individuals. Recently it has been proposed that prophage induction may contribute to intestinal dysbiosis through the concept of ¿community shuffling,¿ resulting in an alteration in the ratio of symbionts to pathobionts.
Currently there are no data concerning gut phages role within the gut microbiota system in HIV positive individuals, therefore, the main purpose of this project is to study the phages component and bacterial microbioma in HIV+ patients and donors.
Specifically the study aims to establish whether: a) differences in terms of type and percentage of species resident in gut exist between HIV positive and healthy donors; b) gut damage may affect microbioma and phages diversity; c) antiretroviral therapy may affect gut microbial and phages population equilibrium.
All patients and donors will be recruited from Policlinico Umberto I University Hospital. Both total DNA from viral particles and eukaryotic and bacterial-cell-sized particles, will be separately extracted, using the QIAmp Investigator kit . - Illumina MiSeq library preparation will be carring out by standard Illumina methods. The final library containing all the pooled sample will be amplified and sequenced by an Illumina MiSeq instrument. Sequence reads will be searched for putative viral matches by alignment algorithms BLAST against the NCBI RefSeq reference genomes.
We believe that this study may contribute to a better understanding of the nature of HIV-induced dysbiosis and consequently to identify future therapeutic strategies aimed to improve the health of HIV-1¿infected subjects
The alterations to the microbiome in HIV infection have been demonstrated to result in direct effects on immunity and increased inflammation. Recently bacteriophages have re-emerged as powerful regulators of bacterial population in natural ecosystem and several authors proposed that phages play an often invisible role in shaping the composition of the human intestinal microbiota.
To date no data exist on the phage component in HIV infected individuals. We believe that studies addressing this issue are needed to develop a complete understanding of the nature of HIV-induced dysbiosis. The presence of free virulent phages in the gut has been reported to be more common among sufferers of intestinal diseases and this phenomenon seems to be associated with an increased use of antibiotics usage. Many of these phages evolve from prophages of intestinal bacteria and emerge under conditions where their bacterial hosts encounter stress suggesting that prophages can significantly alter the microbial community composition. Therefore prophage induction may contributes to intestinal dysbiosis by altering the ratio of symbionts to pathobionts, and this phenomenon may also occur in HIV positive patients.
In the early stage of infection HIV patients show a depletion and functional alteration of GI-resident CD4+ T cells and possible alterations to the composition of the gut microbiota due to viral replication. So the initial dysbiosis could induce virulent phages that continues to lead damage to the GI, altering the microbial population and increasing systemic translocation of microbial products. Translocated microbial products directly stimulate the immune system causing a state of chronic immune activation in HIV-1 patients. Furthermore, the persistence of elevated levels of immune activation is observed in patients despite otherwise effective antiretroviral therapy (ART).
In the light of above, the knowledge on the physiological importance of phages in gut microbiome could provide new solid basis for several future therapeutic strategies aimed at targeting the microbiome to improve the health of HIV-1¿infected subjects.