1. You report resistance to ciprofloxacin (a fluoroquinolone) but claim the strain has no antibiotic resistance genes based on WGS. How do you reconcile this phenotypic resistance with the genomic prediction, and how do you definitively rule out acquired resistance mechanisms (e.g., efflux pumps, gyrase mutations) given the zone diameter of 13.5 mm clearly falls in the resistant category?
2. Table 5 header indicates it represents “Total aerobic mesophilic microorganism…lactobacilli count…pH change of cheese groups”. However, the results section states this was a pilot-scale production of a single batch without replicates (n=1). Statistical comparisons using ANOVA between groups and days are inappropriate for a single production run (no true biological replicates), making your statistical significance claims invalid. How do you justify using ANOVA on data from a single experiment without replication?
3. The data in Table 5 shows the “control” cheese already contains approximately 2.31 to 2.61 log cfu/g of lactobacilli throughout ripening. Given that your L. paracasei AD22 was the only added culture, what species constitute this native population, and why is there no significant difference in the lactobacilli count between the control and AD22-inoculated cheese until day 60? This makes it impossible to attribute any observed effects solely to the added strain.
4. The fold changes (Table 6) for all stress genes show extremely high standard deviations. More critically, the p-values for the time-dependent changes are all > 0.05, indicating no statistically significant differential expression. Despite this, you discuss up/downregulation profiles as if they are meaningful. Given the lack of statistical significance, what is the biological basis for claiming a transcriptional stress response occurs during ripening?
