Temperate bacteriophage populations in the human gut: culturomics and experimental insights
While often overlooked, the most abundant entity within the gut are the viruses that infect bacteria, called bacteriophages (phages). Large-scale metagenomic and data mining efforts have uncovered an expansive diversity of phages within the human gut. However, the functional understanding of phage-host interactions and their impacts within this complex ecosystem have been limited due to a lack of cultured isolates for experimental validation. In recent work, we characterise 182 active prophages originating from 252 diverse human gut bacterial isolates using diverse induction conditions, including chemical cues, metabolites, starvation, and human cell derivatives. We found that active Bacteroidota prophages were among the most prevalent members of the gut virome, with extensive use of diversity generating retroelements and exhibiting broad host ranges. Moreover, active polylysogeny was present in 58% of studied gut lysogens and led to coordinated prophage induction. Transcriptomic analysis of selected isolates revealed fundamental information on life cycles of gut phages, including the constitutive expression of defence and counter-defence genes across both polylysogenic phages and their hosts. In this presentation, I will summarise our recent and unpublished work into the study and use of experimentally validated gut prophages, providing key insights into their diversity, biology, genetics, and function within these complex microbial communities. More broadly, this presentation will highlight the importance of experimental validation alongside genomic based computational prediction to enable further functional understanding of these commensal viruses within the human gut.
Short bio
Jeremy completed his PhD in microbiology at The University of Queensland in 2011. He then moved to San Diego, USA to complete a postdoctoral position under the tutelage of Prof. Forest Rohwer at San Diego State University. While there he studied the interactions of bacteriophage with mucosal surfaces and was involved in a world-first phage therapy case treating a patient with disseminated, multidrug-resistant infection. In 2016, he joined Monash University’s School of Biological Sciences where he is currently an Associate Professor and Group Leader. His research group studies bacteriophages and their interactions with their bacterial hosts and the human body. In 2020, he joined the Centre to Impact AMR where he leads the Monash Phage Foundry as an in-house manufacturing facility. In 2024, he was awarded a prestigious NHMRC Investigator Fellow L1 in recognition of their translational work using phage therapy to combat antimicrobial resistance. In 2025, he was promoted to full Professor at Monash University in the School of Biological Sciences.
Laboratory of the speaker
Barr Lab, Monash University
Invited by
Jeffrey Cornuault
