What are the best peer-reviewed studies showing accuracy of 16S rRNA gene sequencing at the genus level? If anyone has citations that they think address this issue well I would appreciate seeing those. I did a quick PubMed search and was not thrilled by most of what came back.
2 Likes
Hi @pone,
Can I ask for clarification. What's meant here by the term "accuracy"? Like, biological truth? Ability to discriminate between closely related but known taxa in a complex community? Something else? Is this a technical question: are you looking for tools which will improve resolution?
Which model are you considering as the "ground truth", understanding that taxonomy is a model, and we're comparing everything against it? Is the goal to re-capitulate metagenomics? Specific type strains in culture? Taxonomic assignments previously produced in the literature?
Best,
Justine
3 Likes
I like these two studies on taxonomy and why it's so hard to do:
This one is good, but not peer reviewed:
Why Genus level and not species level?
I guess accuracy would be the specificity and sensitivity for a genus identification in something like a food ferment / yogurt.
I'm not focused on any particular model.
16s sequencing can often be extremely inaccurate at the species level. So I am not trying to rely on it for species. But at the genus level, I want to know how well I can rely on it. If the test of a yogurt tells me that 10% of the yogurt is Lactobacillus genus, I want to be 95% sure that the truth is not an enormous range around that. If there is a 50% chance that there is actually 80% Lactobacillus, that is not a reliable test.
I think I understand what you are saying. Like, you want to get a sense of the 'typical variation' of the number you are getting.
I like how you differentiate error in taxonomy ('actually Lactobacillus') and error in composition ('10% and not 80% of reads in sample'). Good thinking!