Request to determine the threshold for strain transfer

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.

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

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.