Huge thanks to co-authors Trina Knotts, Sean Adams, Mohammed Ali, @mattolm.bsky.social, and to my PI, Joanne Emerson, who handled all of the wet-lab sample processing.
🧵 5/5

Viromes and metagenomes captured partially overlapping but differently biased components of the total gut viral community. This has significant implications for inter-study comparisons.

🧵 4/5

DNase treating your viromes? Unlike soil viromes, this looks like it might not have as big an effect in stool (at least in our study).

🧵 3/5

Firing up the MDA kit? We got STRONG compositional distortions and reduced richness. Whilst this effect is generally known, MDA continues to be used. Filtering out ssDNA viruses partially compensated for this, but at a cost in downstream data analyses.

🧵 2/5

Huge thanks to co-authors Trina Knotts, Sean Adams, Mohammed Ali, @mattolm.bsky.social, and to my PI, Joanne Emerson, who handled all of the wet-lab sample processing.

🧵 5/5

Viromes and metagenomes capture partially overlapping but differently biased components of the total gut viral community. This has significant implications for inter-study comparisons.

🧵 4/5

DNase treating your viromes? Unlike soil viromes, this looks like it might not have as big an effect in stool (at least in our study).

🧵 3/5

Firing up the MDA kit? Get STRONG compositional distortions and reduced richness. Whilst this effect is generally known, MDA continues to be used. Filtering out ssDNA viruses can compensate, but it’ll cost you in downstream data analyses.

🧵 2/5

No problem. A temperate phage can switch between being lysogenic or lytic, so can be either. A virulent phage can only be in a lytic lifecycle. There are also a bunch of alternatives doi.org/10.1098/rsob...

Same. It’s not helped when lots of biotech companies, including Illumina, misuse the term.

Also, as always, 16S rRNA gene amplicon sequencing != metagenomics