I've always been curious whether interpreting taxonomic data resulting from 16S rRNA profiling of microbiomes treating a genus or species assignment as a uniform genus or species might be problematic. Seems like there should be strain differences that could arise within or between microbiomes. I get that it is a question of resolution, that we can measure what we can measure, and we are looking at population and community effects. But, it strikes me that no one seems to describe the potential for oversimplification (of such really complex systems). Appreciate any thoughts or citations addressing this question.
Yes, I agree with you. When you colapse all ASVs or OTUs in taxonomic ranks you are trowing away all the genomic background of strains. This remindes me of the Sucrose-negative Vibrio cholerae strain, it is known that V. cholerae is succrose positive, but this one was not, and it was indeed a V. cholerae. But as you said, even if we work at strain level, or individual ASVs level, we will never grasp the functional and metabolic potential of these strains with metabarcoding alone.
Robert D Barber - I also agree with your comments. From some papers it appears that they do provide some indication of strain differences, primarily those with antibiotic resistance genes. The problem of oversimplification in identifying any taxonomic unit will always occur. especially comparing a population. This then gets extremely complex when we study all the organisms in a microbiome, and even more so when we try to compare many different microbiomes (even those of the same species or environment). I have some fairly simple data on microbiomes, in large part to keep costs down, and so I know it only gives a siimplified picture of a more complex system. I also have some data that indicates we may be missing some of the important members of the microbiome, but I have not seen a paper that discusses this testing bias.
BTW: I taught adjunct at UW Parkside for two years while working on my PhD.
Thank you for the nice question. Actually in prokaryote taxonomic profiling 16S rRNA sequencing is vastly used, however the technique has some inherent drawbacks and can detect only up to genus (and/or species) level taxonomic resolution, and and limiting information on gene abundance and functional profiling . The accuracy is questionable, only 3-5% compared to whole metagenome shotgun sequencing. I can suggest you to perform whole metagenome sequencing (WMS) targeting at least 40 million reads/sample to get the maximum insight into the phylogenetic composition, species and/or strain, and functional diversity for a variety of biomes. You can go through two our recent publication with WMS metagenome study (doi.org/10.1038/s41598-019-49468-4; doi.org/10.3389/fmicb.2020.00860).
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