Discuss Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits
Peptoniphilaceae[edit source]
This taxon was originally recorded on the LEfSe graph as Family XI (experiments 1 & 2). Supplementary information 3 listed it under Order Clostridia, Class Peptostreptococcales-Tissierellales and had the genus Parvimonas and species Peptoniphilus grossensis under it. NCBI taxonomy places these under the Peptoniphilaceae family. YokoC (talk) 00:09, 28 October 2024 (UTC). Nevertheless I believe this could also be Clostridium cluster XI = Peprosterptococcales.
Vagococcaceae[edit source]
This family was changed to Enterococcaceae, based on https://lpsn.dsmz.de/family/enterococcaceae
candidate division VadinBE97[edit source]
This taxa was originally recorded on the LEfSe graph as vadinBE97. Supplementary information 3 listed it under the following taxonomic classification: Verrucomicrobiota, Lentisphaeria, Victivallales, vadinBE97. NCBI classifies Lentisphaeria (Taxonomy ID: 1313211) as a class which contains candidate division VadinBE97.
Genus sp. C sp1/sp2 format[edit source]
This format was used on several species in the Boxplot graphs for experiment 6, i.e. Streptococcus sp.C equinus/infantarius/lutetiensis. In Supplementary information 3, they are recorded with brackets (i.e. Streptococcus sp. [C equinus/infantarius/lutetiensis]) and have a NCBI ID (i.e. 1301), which is for the genus only. The [C. sp/sp/sp] format suggests the species needs to be confirmed from a set of possibilities. Originally I was going to record these as Genus sp. to get a matching NCBI ID, but decided keeping the original format was more informative.
Streptococcus sp. [C equinus/infantarius/lutetiensis],
Actinomyces sp. [C ICM58/oral taxon 172],
Streptococcus sp. [C equinus/gallolyticus/macedonicus/pasteurianus],
Actinomyces sp. [C oral taxon 181/ph3],
Bifidobacterium sp. [C catenulatum/kashiwanohense],
Streptococcus sp. [C I-G2/I-P16],
Bacteroides sp. [C dorei/vulgatus],
Bacteroides sp. [C rodentium/uniformis],
Eggerthella lenta [C Clostridioides difficile], wasn't changed.
Experiments 11 and 12[edit source]
The description on the graph specifies this is a heatmap for genera, however it seems to be for species, so I used this for the descripyion.
Prevotella 9 copri[edit source]
Prevotella copri is the homotypic synonym for Segatella copri, however I didn't change it due to the 9 after the genera.
Figure 3D[edit source]
This graph is curatable, its focus is on specific bacteria families (VANISH/BloSSUM), however, I did not curate it because signatures would repeat experiments 1-5 (without the other families).
Alpha Experiment 5[edit source]
Because the alpha significance difference is not grouped by lifestyle and rather by country with the lifestyle I did not record it.
