Hi all,

I am working with a mixed microbial community consisting of both bacteria and archaea. To estimate the composition of my community, I performed two separate PCR amplifications using 16S-specific primers, one set targeting bacteria and the other targeting archaea. After sequencing, I obtained a total of X bacterial reads and Y archaeal reads, with Z reads assigned to a specific bacterial species (Species A).

Initially, I considered using qPCR to quantify the total bacterial and archaeal 16S rRNA gene copies in my samples to get a better estimate of their relative proportions. However, I was advised that I could estimate the relative abundance of Species A within the entire community (bacteria + archaea) using the following approach:

Compute the relative abundance of Species A among the bacterial reads: Z/X

Adjust this value based on the proportion of bacterial reads in the total community: X/(X+Y)

Multiply these values to estimate the relative abundance of Species A in the full microbial community:(Z/X)*(X/(X+Y))

I'm a bit unsure if this is the best way to proceed. Does this approach seem valid? Are there any known references or studies that describe a similar methodology for combining data from separate 16S PCRs to estimate species abundance at the community level? Would using qPCR instead be a better alternative? Any insights or suggestions would be greatly appreciated!