Dear all
First of all apologies for spamming the forum but this is the only place that has the right people that can answer my question.
We recently got a review from a paper we submitted and among other things we did a differential representation analysis using the indicspecies package.
Just a bit of background: the study examines two groups of samples coming from cows called shedders (or O157 group) and non-shedders (non-O157 group) (if the O157 pathogen is detected in the cow feces, then the animals are called shedders, if not they are called non-shedders)…
And here is the reviewer’s comment:
« The microbiome study is interesting, and again several cited studies support the idea that microbiota composition may play a role in persistence. An indicator species analysis was successful in identifying OTUs that was found in non-O157 shedding microbiomes and other found in O157 shedding genomes. Unfortunately, the suggested indicator variants were not tested on an independent non/shedding dataset, so there was no validation of the significance of the identified variants.”
Is that person -in all seriousness- asking us to go and get a different set of samples from non-O157 animals and check if the non-O157 OTUs (which we found to be representative of the non-O157 group) are still there?
Thank you all for your responses in advances, just wanna make sure I got his/her point!
P