Request to determine the threshold for strain transfer

Microbial community profiling StrainPhlAn
1

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.

2

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.

Best
Michal