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The human gastrointestinal tract (GIT) is inhabited by a vast amount of microorganisms from different domains of life collectively denominated the gut microbiome (GM). Among its numerous functions, GM plays a crucial role in developing the immune system in early-life and contributes to maintain a balanced metabolism later in life. During the last decade, studies have revealed that imbalances in GM composition, typically known as dysbiosis, are able to trigger metabolic (and immunological) abnormalities in the host. This has been demonstrated to have implications on the development of metabolic disorders, such as obesity, elevated blood pressure, high serum triglycerides, low high-density lipoprotein (HDL) levels and insulin resistance, which constitute a cluster of risk factors for development of the so-called metabolic syndrome (MetS). In turn, these disorders may also influence muscle composition, physiological decline and frailty in older individuals (e.g. +65 years). Identifying lifestyle factors and their interactions with GM and host would be of great societal value in relation to preventing frailty and improving the life quality of the individuals, as well as for economical reasons. Our work gathers an overview on current methodologies for GM screening, with particular emphasis on viral communities, it presents an integrative approach to elucidate the interplay of dietary aspects and GM composition in relation to physiological decline, and finally, it provides insights of the putative role of viral communities in modulating GM and metabolic biomarkers in older subjects. In the first manuscript, we assessed and optimized two methods for phageextraction based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG). Through our improved procedures, we reported significantly higher yields of extracellular viral-like particles (eVLPs) and their DNA