Still a good deal in deed :)

That is an insane depth for 70 dollars, if DNA extraction and library prep are calculated in the cost. Would be curious to know how many samples one needs to multiplex to get costs this liw. Like, really - definitely sth I'd like to look into implementing.

The annual increase in number of dereplicated species representative genomes in GTDB or GlobDB shows how undersampled. And reference based MG profiling works best at species level, but not so great at higher phylogenetic distance.
Anyways, what I want to say is amplicon sequencing ain't dead (yet)

Agreed, our amp system pays of most if done high throughput and standardized, as we do.
How many MG reads do you get for 70 CAD?
Shallow MGs are wonderful, if you work in well sampled environments (i.e. human gut). However, the majority of habitats is still very undersampled.

Jup :)
jmf.univie.ac.at

But if you sequence loads, anyone can set the system up in house and adjust turnaround time. 10.3389/fmicb.2021.669776
Or depth per samples (which affect price only a bit, majorityof cost is PCR, not seq), but more depth does you no good (less is OK for most samples, but that's a different topic).

5-15k reads of any amplicon per sample. Turnaround time depends on other workload, since we are researcher lab and not a company ;) 5 weeks for 1000 samples inc DNA extraction and data analysis.

You got the point. The V4EXT can become the platinum standard ;)

Also allows you to assess better how deep your MGs need to be. If you are working in an underexplored or highly variable habitat, it's hard to tell otherwise. Better 12€ and a few weeks for amplicons, than hundreds of € for depth you didn't need.

With the amount of contaminated and mixed up samples, or experiment gone wrong I've seen over 7 years and literally over 1000 amplicon sequencing projects I personally inspected for data quality, trust me, it's money well spent and responsible grant money handling to amplicon screen first.

While I see where the idea comes from, running a microbiome sequencing facility clearly shows it isn't. The overwhelming majority of projects is amplicon sequencing.
Also, genuinely, with our approach running amplicons before metagenomes costs 12€.

Organizer Thilo Hofmann @cemess.bsky.social, contributions from 30+ @univie.ac.at scientists, incl @michiwagner4.bsky.social, @christinakaiser.bsky.social, Stephan Krämer, @jillianmpetersen.bsky.social, @ppjevac.bsky.social, @andreasrichter.bsky.social, and @loutsi.bsky.social from our cluster.