mouse phage DATABASE

[minukpark1228]

Hello,
I’m currently studying bacteriophages in a mouse model. The database I’m using, masked_DBv1, seems to be built primarily based on human microbiome data. Because of this, the annotation results for mouse-derived phage sequences are quite limited or mismatched, which makes downstream analysis difficult.

I’m wondering if there are any existing phage reference databases specifically designed for mouse microbiome or mouse host bacteria, or if you could recommend suitable resources to build a mouse-specific phage database. Any guidance or suggestions on this would be greatly appreciated.

[meenachakra]

Hi Minuk! Thanks for using our tool. Indeed, our databases were built for the human gut. I wonder whether this study might be useful for you? https://link.springer.com/article/10.1186/s40168-025-02144-4#data-availability

[minukpark1228]

Hello,
I’m currently analyzing mouse gut bulk metagenome (non-VLP) samples to study bacteriophages.
When I used your database (masked_DBv1), I found that it was primarily built from human microbiome data, which caused limited annotation for mouse-derived phage sequences.

Regarding the paper you kindly shared (https://link.springer.com/article/10.1186/s40168-025-02144-4), I’d like to clarify a few points:
1. Would it be appropriate to download and use the mouse gut phage database from that study as a custom reference for read-based profiling using Phanta?
2. Or, when you recommended that paper, did you mean that I should
(a) follow the assembly-based analysis pipeline described in the study (e.g., using VirSorter2, VIBRANT, CheckV, etc.),
or (b) use the custom mouse-specific phage database established in that paper?
3. Since my samples are from bulk metagenomes (not VLP-enriched), would an assembly-based approach still be recommended in my case?

Thank you very much for your time and guidance.

[meenachakra]

Hi, I haven't read that paper in detail, but I believe you can create a custom Phanta DB from any mouse gut phage genomes they report/provide in that study.

Instructions for creating a custom Phanta DB are here: https://github.com/bhattlab/phanta/blob/main/databases.md

Hope this is helpful!

[meenachakra]

If you wish to also add a prokaryotic portion to your custom Phanta DB, you could potentially use genomes from here - https://pmc.ncbi.nlm.nih.gov/articles/PMC8763404/