More new features on Microbiome Prescript site

Blog entry posted by Lassesen, Mar 30, 2018.

Another portion of the revision has been completed. This consists of two parts:

  • Displaying the percentage of gut samples that have a specific bacteria level
  • Refactor of information on each bacteria level
I have expanded the reference to every level of the hierarchy

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Bacteria Level
An example is shown below

Bacteria Species_group
Click the appropriate link if you have an overgrowth or undergrowth

Bacteria (% of samples with it) Modifiers Data Punk NCBI Taxonomy
Acinetobacter calcoaceticus/baumannii complex (0.6% of Samples) Modifiers Bacteria Information Literature
Bacillus subtilis group (3.59% of Samples) Modifiers Bacteria Information Literature
Enterobacter cloacae complex (1.8% of Samples) Modifiers Bacteria Information Literature
Lactobacillus casei group (7.78% of Samples) Modifiers Bacteria Information Literature
Pseudomonas aeruginosa group (3.59% of Samples) Modifiers Bacteria Information Literature
Pseudomonas fluorescens (0% of Samples) Modifiers Bacteria Information Literature
Streptococcus anginosus group (1.8% of Samples) Modifiers Bacteria Information Literature
Streptococcus dysgalactiae group (1.2% of Samples) Modifiers Bacteria Information Literature
The literature link takes you to the National Institute of Health site, where you have many additional links of a technical nature.

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And DataPunk for the other

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Hierarchy Tree
If you go to Bacteria Hierarchy or Bacteria Hierarchy Down To Species you will see the percentage of gut samples that have a specific bacteria.

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This is important because my long standing question is which low or no count bacteria should we be concerned about to increase. A low Olsenella level is likely not a concern, because most people have none of it. A low Coriobacteriaceae level may be a concern.

If you have a very high level of Olsenella, then this may be a concern. The pending refactor of recommendations will allow have a default (my own assumptions) filtering and the ability for readers to modify it to suit their own assumptions.

Bottom Line
These enhancements allow easy access to additional technical information and also allow us to see which bacteria we expect to see normally. This means we can include bacteria that should be there but which are at an abnormally low level in the revised recommendations.
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Lassesen

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