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
