Hi all, just a quick question I hope someone can clarify.
Why is it sometimes you can have a high abundance of the 16s rRNA gene when measuring with qPCR but a fairly low species richness when looking at alpha diversity?
Hi @Mantella86 ,
Good question. I think the short answer is that 16S rRNA gene abundance simply does not equate to or correlate with species richness. In other words, just because there are many 16S rRNA gene copies does not mean that we can necessarily expect a greater number of species to be present. In fact, these can be inversely correlated in some systems.
Good luck!
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Hi @Mantella86,
this is a common issue in microbiome analysis that also extends to relative abundances of taxa. We recently published a paper on this issue which may helps to understand why absolute abundances are not necessarily related to community composition and diversity. Although the paper is tailored to absolute vs. relative abundances, the concept can easily be applied to diversity metrics:
Microbiome count data obtained by amplicon sequencing reflect ratios among abundances of members of the community (relative abundances or frequencies) but they do not reveal the size of populations (absolute abundances) and their changes [48]. This is an often-ignored limitation of microbiome analysis by amplicon sequencing. The lack of information about population size is of particular concern in studies of the effect of environmental parameters such as soil characteristics on microbial communities. For instance, species stimulated by an environmental factor may appear unaffected or even suppressed in amplicon counts. This may happen when other species were stimulated to the same or a higher degree, but also when other species were stimulated to a lower degree yet their population size was larger. Therefore, even qualitative trends such as stimulation versus suppression of microbial groups cannot be inferred from amplicon sequencing alone. Recently, the problem has been recognized and sequencing of bacterial 16S rRNA amplicons was combined with qPCR [48,49], digital PCR [50] or flow cytometry [51,52], which provided estimates of absolute abundances of bacterial taxa. [...]
You may check also want out the references we cited.
Hope this helps,
Lukas
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