Species variation after longer sequencing time

Question

[firminlago]

I ran a shotgun sequencing for 48hr i analyzed the results and noticed that a species that was abundant and classified as A1 at 12 and 24hrs was reclassified as A2 at 48hrs. genus was the same. only species changed. what wil be an esplanation for that? or direct me to a reference. Thanks

[h.mon]

There is no explanation possible if we don't understand what you did. Please take some time to explain in detail your experimental setup and your analysis pipeline.

[firminlago]

Ok Thanks for your answer: I run shotgun metagenomics using nanopore MinIon I ran it for 48 hours. to reduce sequencing time and reose the flowcell, I split the data generated into 3 timepoints it is the same 48hrs data.just extracted the data after 12hrs 24hrs and 48hrs.use the fastq and load then on onecodex server for analysis. in the report there is B arachidis that is 24% in abundance at 12 and 24hr but not present in 48hrs but in the 48hrs B lablabi is 35% abunbance and not present at all in the 12 and 24hrs. I was wondering why? Thanks again