Bacterial viruses (bacteriophages, phages) of the gut have increasingly become a 
focus in microbiome studies, with an understanding that they are likely key 
players in health and disease. However, characterization of the virome remains 
largely based on bioinformatic approaches, with the impact of these viromes 
inferred based on a century of knowledge from aerobic phage work. Studying the 
phages infecting anaerobes is difficult, as they are often technically demanding 
to isolate and propagate. In this review, we primarily discuss the phages 
infecting three well-studied anaerobes in the gut: Bifidobacterium, Clostridia 
and Bacteroides, with a particular focus on the challenges in isolating and 
characterizing these phages. We contrast the lessons learned from these to other 
anaerobic work on phages infecting facultative anaerobes of the gut: 
Enterococcus and Lactobacillus. Phages from the gut do appear to adhere to the 
lessons learned from aerobic work, but the additional challenges of working on 
them has required ingenious new approaches to enable their study. This, in turn, 
has uncovered remarkable biology likely underpinning phage-host relationships in 
many stable environments.