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To expand on what others have said beyond mutation rates; many organisms are endoploids so cell genomes are different by sizes within organisms.


In addition to the points raised in the other answers, organisms like bacteria frequently engage in horizontal transfer of genetic material. This means that the relationships between organisms are more complex than the relationships between the stable core elements like ribosomal RNA (see, for example the mosaic genome of Rickettsia felis). Focusing on only ...


In my experience, the primary impetus is number 3 on your list, but it's also related to number 1. There's a lot you can learn from 16s sequencing, but reviewers want functional data that can help elucidate causal mechanisms. 16s is mostly limited to providing information about the taxonomy of a community. While there are ways of "predicting" the ...


There is simply no variation in the 16S rRNA gene between different species/strains that it would be useful to tell apart for a more accurate analysis. The amount of sequence variation depends on the region of the 16S rRNA gene amplified, and the choice of region depends on the desired universality of your primers as well as the read length constraints of ...

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