Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut

The human gut microbiome plays a significant role in health and disease. The viral component (virome) is predominantly composed of bacteriophages (phages) and has received significantly less attention in comparison to the bacteriome. This knowledge gap is largely due to challenges associated with the isolation and characterization of novel gut phages, and bioinformatic hurdles such as the lack of a universal phage marker gene and the absence of sufficient numbers of homologs in viral databases. Here, we describe the isolation from human feces of a novel lytic phage with siphovirus morphology, φPDS1, infecting Parabacteroides distasonis APCS2/PD, and classified within a newly proposed Sagittacolavirus genus. In silico and biological characterization of this phage is presented in this study. Key to the isolation of φPDS1 was the antibiotic-driven selective enrichment of the bacterial host in a fecal fermenter. Despite producing plaques and lacking genes associated with lysogeny, φPDS1 demonstrates the ability to coexist in liquid culture for multiple days without affecting the abundance of its host. Multiple studies have shown that changes in Parabacteroides distasonis abundance can be linked to various disease states, rendering this novel phage-host pair and their interactions of particular interest.

Keywords

Bacteriophage , Parabacteroides , Phage- bacteria interaction , Phage isolation , Fecal fermentation , Gut microbiome , Phage characterization

Citation

Cortés-Martín, A., Denise, R., Guerin, E., Stockdale, S.R., Draper, L.A., Ross, R.P., Shkoporov, A.N. and Hill, C. (2024) ‘Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut’, Gut Microbes, 16(1), 2298254 (24pp). doi: 10.1080/19490976.2023.2298254