The number of fractions collected can also affect the detection limit. While a higher number of fractions will most likely increase the sensitivity, it also entails higher sample processing efforts and costs. In addition, more fractions also mean less template per fraction and thus also an increased difficulty to amplify the target and a higher chance of contamination with foreign nucleic acids from the environment. Typically 12--20 fractions are collected, of which about 10--16 end up being analysed because the lightest and heavies fractions typically contain little to no nucleic acids.
it is also advisable, if possible, to obtain an estimate of the size of the microbial guild in question in relation to the total microbial population. The smaller the size of the target commuity, the harder it will be to detect its labelling above the detection limit.