879 ISSN 1746-0913 Future Microbiol. (2014) 9(7), 879–886 part of 10.2217/FMB.14.47 © 2014 Future Medicine Ltd SPECIAL REPORT Identifying and analyzing bacteriophages in human fecal samples: what could we discover? Maite Muniesa 1 & Juan Jofre* ,1 1 Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain *Author for correspondence: Tel.: +34 934 021 487; Fax: +34 934 039 047; jjofre@ub.edu ABSTRACT: The human gut is a complex ecosystem, densely populated with microbes including enormous amounts of phages. Metagenomic studies indicate a great diversity of bacteriophages, and because of the variety of gut bacterial species, the human or animal gut is probably a perfect ecological niche for phages that can infect and propagate in their bacterial communities. In addition, some phages have the capacity to mobilize genes, as demonstrated by the enormous fraction of phage particles in feces that contain bacterial DNA. All these facts indicate that, through predation and horizontal gene transfer, bacteriophages play a key role in shaping the size, structure and function of intestinal microbiomes, although our understanding of their efects on gut bacterial populations is only just beginning. KEYWORDS • bacteriophages • feces • human • microbiota After the discovery of bacteriophages in the early 20th century by Twort and d’Herelle [1,2] , bacterio- phages were extensively studied as potential antibacterial remedies up until the beginning of the 1930s. Starting in the late 1930s, phages were used as model systems and were pivotal in the early develop- ment of molecular biology [3] . However, interest in bacteriophages waned at the end of the 1960s and for many years there was little research into bacteriophages. Nowadays, the interest in bacteriophages has revived and, because of the current advances in microscopic and genomic techniques, researchers mainly focus on the study of noncultured phages present in different ecosystems, including human microbial populations. Therefore, as research into bacteriophages is about to celebrate its centenary, this field is experiencing a true renaissance. Analytical procedures Traditional methods for the detection of bacteriophages were based on the observation of cell lysis after phage infection, which was detected by the appearance of clear areas on monolayers of host bacteria [4] . The low numbers of host bacteria in which a given bacteriophage replicates and the small fraction of cultivable bacterial hosts available frustrated the study of bacteriophage abundance, their characteristics and the role they play in different microbiomes. Nowadays, different procedures allow us to study the phages present in microbiomes without needing to replicate them in a bacterial host. Such studies require preparatory steps to obtain sus- pensions of viral particles that are as concentrated and refined as possible. These processes include concentration and purification of viral particles from the samples, the elimination of contaminat- ing cells and other debris and, in the case of genomic methods, the removal of free nucleic acids [5] or nucleic acids in membrane vesicles [6] . These methods are based on separation by size through filtration or centrifugation and, consequently, many authors prefer to call the particles recovered by these procedures ‘virus-like particles’ (VLPs). For reprint orders, please contact: reprints@futuremedicine.com