Roadmap for Phage technologies

What are we trying to achieve and why? What is the problem we are trying to solve?

Better understanding the biology of the bacterium/phage interrelationship within the host and in the wider environment which will enhance our knowledge of where to find new and improved phages.
Determining the phageome (basic studies are needed to determine the diversity of phages).
Phage ecology: better understanding phage stability/fragility in the environment.

What are the scientific and technological challenges (knowledge gaps needing to be addressed)?

Better understanding of the “life within bacteria” the genomes that parasitise them including phages. Plasmids and some bacteriocins.
Impact of phages on the microbiome of animals.
What are the most effective intervention points?
Use of MDA prior to sequencing preferentially amplifies small and circular ssDNA–, sequencing depth etc… complicates comparison of phageome
Gut phageomes in particular are dominated by uncharacterised sequences – Viral dark matter.
Requires a better understanding of phage survival in environment (also in building and on surfaces) and genetic exchange in the environment.
Requires better understanding of relationship, if any, between phages in the environment and those in the human and animal phageome.

What approaches could/should be taken to address the research question?

More research on the dynamics of phage.
Plasmids, bacteriocins and their suicide systems.
Funding to establish comprehensive collections. Done with time to explore phage evolution.
Studies in vitro on phage evolution.
Standardised protocols help to promote comparison across studies – challenge is to ensure that novel phages are not missed by these standardised methodologies.
Increased efforts in increasing representation of phage within databases – both animal and human focused.
Further development of alignment-free bioinformatic methods for identifying phage sequences.
Difficult in situ studies without access to sensitive PCR and RT-PCR systems. Controlled in vitro studies will help.

What else needs to be done before we can solve this need?

Methods already there for in vitro work.

Existing knowledge including successes and failures