I am very interested in the finding of Truong et al (Microbial strain-level population structure and genetic diversity from metagenomes) that in the gut microbiome, although that most species are dominated by single strains, even where there is evidence of multiple strains.
Do you know if this has been demonstrated for other human-associated biomes? I’d be very interested to know whether this is generally the case too in oral microbiomes.
If not, are there any scripts available which would assist in quantifying strain dominance on my pharyngeal metagenomic data?
You could quantify the strain dominance in your samples in the same way as Truong et al did in the first StrainPhlAn paper by looking at the polymorphic rates.
You can assess that in the
s__*species_name*.polymorphic file that is create after StrainPhlAn execution in a similar way as Truong et al did in the Figure 2 analysis. I hope this helps.
This is really helpful, thanks. I’ll take a look at the polymorphic files. I’ve also started looking at pStrain (GitHub - wshuai294/PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data.) which proposes to extract multiple strains per sample, with phasing - though I think this will be pretty tough!