I performed a set of inhibition experiments where Lactobacilli supernatants where tested against a pathogen cell culture. These experiments were carried out in a 96-well plate where pathogen was cultured alone (control), 11 technical replicates, and with a % of lactobacilli supernatant, 3 technical replicates. Absorbance was measured each 2h and growth curves were fitted using grofit R package to calculate growth tax (mu), lag phase (lambda) and max absorbance.
I did an initial screening of +100 lactobacilli strain supernatants using the method described above. In order to perform an initial selection of the best candidate strains I compared statistically using Mann-Whitney U test to compare control technical replicates to each of the strain supernatants cultures contained in a plate ( I had like 21 different supernatants in each plate) since number of replicate were low and normality cannot be tested properly.
Once I got a selection of best inhibiting strains I did 3 biological experiment replicates to get concluding results. Since pathogen does not grow equally among the plates I normalized growth parameters of each 3 biological replicates in a %. I compared all technical replicates from one strain supernatant from the 3 experiments against control technical replicates. I used again Mann-Whitney U test to compare each strain supernatant against a control.
I wonder if Mann-Whitney U is an appropriate statistical analysis in this case because, in fact, I think I am performing a multicomparision since different samples are compared against a control. So, I wonder if using Kruskall-Wallis test and Dunn test as a post-hoc analysis would be the best option.
Thank you for your advice,