# Request to determine the threshold for strain transfer

**URL:** <https://forum.biobakery.org/t/request-to-determine-the-threshold-for-strain-transfer/6437>\
**Category:** StrainPhlAn\
**Created:** [January 10, 2024, 8:09am UTC](https://forum.biobakery.org/t/request-to-determine-the-threshold-for-strain-transfer/6437 "2024-01-10T08:09:23Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![LuXX](https://avatars.discourse-cdn.com/v4/letter/l/e19b73/32.png) [@LuXX](https://forum.biobakery.org/u/LuXX)\
**Post date:** [January 10, 2024, 8:09am UTC](https://forum.biobakery.org/t/request-to-determine-the-threshold-for-strain-transfer/6437/1 "2024-01-10T08:09:23Z")

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Hi, bioBakery team

I recently came across your high-quality study, “The person-to-person transmission in the landscape of the gut and oral microbiomes,” and I was particularly interested in the transmission of strains between mother and child in the study. I wanted to inquire about the threshold for judging the transmission of Bifidobacterium longum and Bifidobacterium pseudomidobacterium, as I did not find relevant data in the article.

I considered repeating the 5 data sets you set as the training data set to find the relevant threshold, but I encountered difficulties due to the large amount of original data in the 5 data sets. The server I used could not bear this calculation. Therefore, I was wondering if it would be convenient for you to provide the relevant thresholds?

Additionally, I have another question regarding the use of my data, which is the whole genome sequencing and assembly result of pure culture isolates. I am interested in using the assembly result to build an SNP tree to judge strain transmission using the threshold in your study. Is this possible?

I would greatly appreciate any guidance or assistance you could provide on these matters. Thank you for your time and consideration.

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**Author:** ![Michal\_Puncochar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/michal_puncochar/32/2321_2.png) [@Michal\_Puncochar](https://forum.biobakery.org/u/Michal_Puncochar)\
**Post date:** [March 18, 2024, 1:18pm UTC](https://forum.biobakery.org/t/request-to-determine-the-threshold-for-strain-transfer/6437/2 "2024-03-18T13:18:30Z")

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Hi LuXX,

the thresholds from that paper for the Jan21 database we provide in the github repository [MetaPhlAn/metaphlan/utils/VallesColomerM\_2022\_Jan21\_thresholds.tsv at master · biobakery/MetaPhlAn · GitHub](https://github.com/biobakery/MetaPhlAn/blob/master/metaphlan/utils/VallesColomerM_2022_Jan21_thresholds.tsv)

For the pure isolates, if you have the assembled genome as a fasta file, you can pass it to the strainphlan run with --references argument and calculate the mutation rates and transmission events between that reference and the other metagenomic samples from the tree.

Best  
Michal