Some studies point out that 16S and WGS-derived bacterial community compositions are significantly different.
But I have not seen any works actually comparing the accuracy of these 2 methods. What if we apply both of them to a gnotobiotic community? Which one will be more accurate?
While 16S produce more OTUs (possibly due to PCR chimeras), WGS might omit rare bacteria.
Both these methods produce protocol-dependent result, so even in a gnotobiotic experiment the true accuracy might be compromised by implementing a bad protocol for a possibly better method.
But what type of data should I use given the choice (e.g as in HMP that provides both 16S and WGS data)?
Thank you for the reply, I'll be waiting for you.
BTW, right now I'm trying to find compatible human gut metagenome data sets to study Crohn's disease (CD). So far, the HMP data looks big and good. It has 16S-metagenomes made with v1-v3, v3-v5 and v6-v9 primers and WGS-metagenomes. But CD-associated data have no WGS-metagenomes and their 16S-metagenomes are made with v1-v2 primers. Is it legit to compare communities derived from v13569 and v12 16S-sequencing?
If you could consult me on such details of metagenome sequencing, I'd like to contact you.
Sorry about the (very) delayed reply. After further study, 16S seems to be better for certain use-cases but I'd almost always suggest WGS at this point. There is also the major advantage of WGS being able to identify non-bacterial microbes, while 16S is limited to bacteria. Shoot me an email if you still need advice on this: email@example.com (alternatively, if you are looking to buy services, I work for a genomics service provider doing bioinformatics work)