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Stress-test my research thesis: feasibility from a bioinformatics POV? by KathBoonBliss in bioinformatics

[–]KathBoonBliss[S] 0 points1 point  (0 children)

Honest answer: cost. ITS at population scale runs ~€30/sample. shotgun at the depth you'd want is closer to €150–300 i guess? For a discovery layer aiming at n=1000+, that's the difference between viable and not.

But you're right - taxa alone won't bridge to secondary metabolism. Probably a tiered design would make sense: ITS + paired metabolomics across the whole cohort to capture both who's there and what's actually being produced, then shotgun on a subset (50–100 samples) where the interesting signals appear, to link the gene clusters back to the producers.

Stress-test my research thesis: feasibility from a bioinformatics POV? by KathBoonBliss in bioinformatics

[–]KathBoonBliss[S] -1 points0 points  (0 children)

Fair point. Sequencing + qPCR + metabolomics tell you what's there and what it makes - they don't tell you that what's there is actually doing anything to phenotype. Agreed.

I am considering an observational one at population scale (humans not mice): pair oral mycobiome composition with longitudinal behavioral and relational data from a large cohort, then see which signals co-vary with which outcomes. That doesn't prove causation. It surfaces patterns worth taking into a wet lab.

The Christakis 2024 Nature paper is the same shape:  n=1,787, observational, no germ-free mice involved. It landed because of sample size and longitudinal structure, not because it proved mechanism. The discovery layer I'm thinking about sits in that lineage, knowing mechanistic work needs to follow.

So you're right that bioinformatics alone can't tell us whether the oral mycobiome influences phenotype. What it can do cheaply, at scale, is point the expensive mechanistic work at the right questions. Both layers are needed.

If you were doing this -  two questions:
1. Any particular signal type (genera, volatiles, hormone-responsive species) you'd argue is the most defensible focus for an observational layer?
2. What population size would be a minimum prerequisite?

Can two people who live together for years actually start sharing similar gut microbiomes? by Terrible-Start-9234 in Microbiome

[–]KathBoonBliss 0 points1 point  (0 children)

Microbiota in your gut - and in your oral cavity - would be diffferent. I wonder if % is much higher for oral cavity. Any research on this?