Can I rely on temporal dynamics with predicted minimal doubling time about 5 hours?

[bhagavadgitadu22]

I am working on metagenomes from river biofilms (average temperature of the river about 10 degrees). I have 6 samples (5 to 10) that were sampled every few days from the river when biofilms were growing and I wanna check if the average minimal doubling time changed overtime.

1. I used gRodon with all ribosomal proteins predicted by Bakta including the subunits as highly expressed genes: should I maybe remove the subunits?

I tried gRodon metagenome_v2 with a temperature of 10 (panel A) and the default temperature (panel B) which give me these results:

2. It looks like I have a decreasing doubling time on average but the panel I trust the most (panel A with temperature=10) is the one where nearly all values are above 5hours, which is outside the zone where the algorithm can be trusted according to the documentation. But what I do not know is: is the decreasing tendency probably accurate or even that cannot be trusted considering we are above 5 hours?

3. For the calculations with metagenome_v2 and the default temperature setting, I cannot plot error bars because all UpperCI values are NA. Also all the LowerCI values are bigger than which sounds wrong. Do you know what could be the problem here?

4. Also I am concerned by how different the results are just because of the temperature. Considering I am working on biofilms and not river organisms taking the river temperature as a parameter can be too much of an approximation considering the apparent impact of this parameter?

5. If you have insight to understand this analysis that would be great. Also if I can use extra statistics from gRodon to interpret it that would be valuable: I wanted to plot the GC values but I am not sure what GCdiv is?

Martin