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

ABSTRACT

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

Disclosure statement

No potential conflict of interest was reported by the author(s).

Author contributions

A.C.M. conducted wet lab work, data analysis and wrote the manuscript; E.G. conducted wet lab work; R.D. and S.R.S. performed bioinformatics and data analysis; L.A.D. managed the project; R.P.R., A.N.S. and C.H. secured funding and supervised the project. All authors reviewed and edited the manuscript.

Data availability statement

All data generated or analyzed during this study are included in this report and in the supplementary material. The genome of φPDS1 is deposited into GenBank under accession MN929097 (assembled and annotated genome). The genome of the bacterial host of φPDS1, Parabacteroides distasonis APCS2/PD, is deposited under the following accession codes: BioProject PRJNA556872, GenBank CP042285 (assembled and annotated genome) and associated plasmid pPDS2–1, GenBank CP042284.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2298254

Additional information

Funding

This research was performed with the financial support of the Science Foundation Ireland (SFI) under Grant Numbers [SFI/12/RC/2273]; Science Foundation Ireland Spokes Programme which is co-funded under the European Regional Development Fund under Grant Number [SFI/14/SP APC/B3032] and a research grant from Janssen Biotech, Inc, and the European Union’s Horizon 2020 Research and Innovation Programme under the INSPIRE COFUND Marie Skłodowska Curie grant agreement No. [101034270].