Comparing Extreme 3% to Kaltoft-Moltrup Selection

A reader contacted me about a disagreement and the cause was a bug in the code for Kaltoft-Moltrup — subsequently fixed. This post looks at the bacteria selected by each for similarities and differences — so people can better understand the difference (which is a little abstract).

I am going to use one the demo samples from BiomeSight (BiomeSight:2019-06-10 Self).

  • Extreme 3% picked 29 bacteria
  • KM picked 24 bacteria

I sorted their selections below in alphabetical order, 13 are in common (just over 50% of the KM choices).

Kaltoft-MoltrupExtreme 3%
Actinomyces : Too HighActinomyces : Too High
Actinomyces naturae : Too High
Anaerofilum : Too High
Actinomycetaceae : Too High
Bacillales Family X. Incertae Sedis : Too HighBacillales Family X. Incertae Sedis : Too High
Bacteroides cellulosilyticus : Too High
Bacteroides denticanum : Too High
Bacteroides dorei : Too Low
Bacteroides intestinalis : Too LowBacteroides intestinalis : Too Low
Bacteroides rodentium : Too HighBacteroides rodentium : Too High
Bacteroides sartorii : Too HighBacteroides sartorii : Too High
Bacteroides thetaiotaomicron : Too High
Bacteroides vulgatus : Too LowBacteroides vulgatus : Too Low
Blautia : Too High
Blautia obeum : Too LowBlautia obeum : Too Low
Brochothrix : Too High
Brochothrix thermosphacta : Too High
Chitinophagaceae : Too High
Clostridium paradoxum : Too HighClostridium paradoxum : Too High
Coprobacillus : Too High
Coprococcus : Too HighCoprococcus : Too High
cunicula : Too Low
Dehalogenimonas : Too High
Desulfovibrio vietnamensis : Too Low
Johnsonella : Too HighJohnsonella : Too High
Johnsonella ignava : Too HighJohnsonella ignava : Too High
Lachnospira : Too High
Lactococcus : Too HighLactococcus : Too High
Leuconostoc : Too High
Listeriaceae : Too High
Micrococcaceae : Too High
Oscillospira : Too High
Prevotellaceae : Too Low
Streptococcaceae : Too High
Streptococcus vestibularis : Too HighStreptococcus vestibularis : Too High
Sutterella : Too Low
Syntrophobacteraceae : Too High
Tetragenococcus : Too High
Thiothrix : Too High
Turicibacter sanguinis : Too Low

Looking at a chart of Prevotellaceae, we see that KM low is 2.25%, thus be this sample being between 2.25 and 3 resulted it being excluded on one and included on another. For Listeriaceae : Too High, KM used 95.6% instead of 97%.

For Sutterella, KM uses 22% for low, hence it included. This is reasonable because there is a distinctive drop off around that!

For Coprobacillus, it looks like I need to do some adjustments of the KM, a chunk of unusual data caused a “step” that incorrectly triggered the high computation.

Bottom Line

We have good overlap with the differences being due to the curves being different. With the extreme 3% approach, we are insensitive to the difference of shapes. With KM we are sensitive (and some parameters to the algorithm needs a little adjustment).

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