prevalence and detection threshold of core microbiome
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11 months ago
ieie ▴ 10

Hi,

I am working on bacterial and fungal core microbiome analyses using the packagemicrobiome.

I am following this tutorial: https://microbiome.github.io/tutorials/Core.html However, it is not clear to me how to define prevalence and detection threshold.

Can somebody give me a simple exapanation of these two parameters? it is not clearly stated in the microbiome documentation I think Thanks a lot!

microbiome taxa • 673 views
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11 months ago
acvill ▴ 340

A detection threshold (also called a limit of detection) is the minimum relative abundance value at which taxa are called as "present" in compositional data. A detection threshold can be user-defined or determined empirically based on sequencing depth. Statistical techniques like YACHT allow for presence / absence calling with confidence scores without the need to determine or define a limit of detection.

Prevalence is the proportion of samples in which a particular taxa is detected given a detection threshold. As an example, consider this mock data for relative abundance of Bifidobacterium bifidum in 10 human fecal microbiome samples:

Sample | Relative abundance (%)
-------|-----------------------
  01   |        0.02
  02   |        0.04
  03   |        0.06
  04   |        0.55
  05   |        1.14
  06   |        1.58
  07   |        2.33
  08   |        5.04
  09   |        5.87
  10   |        6.69

If we lower the detection threshold, the calculated prevalence of B. bifidum increases.

Detection threshold (%) | Prevalence
------------------------|-----------
          1             |    0.6
          0.1           |    0.7
          0.01          |    1.0
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thanks a lot!!! it ia a very clear answer!

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