Viruses play paramount roles in the biosphere and are very abundant in all environments including human microenvironments. Our research focused on the uncultured human viral community present in saliva. Although several surveys have studied the natural viral assemblages in human saliva (Willner et al., 2011; Abeles et al., 2014; Pride et al., 2012), very little in known about differences in viral composition between healthy and selective immunoglobulin A (IgA) immunodeficiency people. IgA plays a critical role in the mucous membranes acting as an important first line of defense against microbes. In the present study we combine metaviromics and Single Virus Genomics to unveil the genetic information of ecologically predominant viruses present in these contrasting biological conditions of the human mucus. Single Virus Genomics allows to obtain the genetic information directly from one virus at a time without the need of culturing the host. First, single viral particles are directly separated by flow cytometry from the saliva by fluorescence activated viral sorting. Then, the genetic material of single sorted viruses was whole genome amplified by multiple displacement amplification and finally sequenced. Initially, several methodological steps were optimized within the single virus genomic pipeline to process with success saliva samples. In parallel, metaviromes from same sample were sequenced and used for a cross genomic comparison with single virus genome datasets. Albeit we are at the beginning of our research, so far, preliminary sequencing results from three available single virus genomes, two of them related to virus isolates infecting Streptococcus pneumoniae and Moraxella, indicated that this promising methodology will open new ways to contrast hypothesis in the human microbiome.