The horizontally transferred antibiotic resistance genes from transgenic feed to the microbiome in animals may have deleterious health impacts on consumers. The present work is a complementary step analysis conducted by coupling both experimental PCR detection assay with the available bioinformatics tools to evaluate the possible functionality of the horizontally transferred aminoglycoside 3" adenyltransferase (aadA) gene from the transgenic diet to the microbiome of rats after 90 days of feeding duration.
Transferred aadA partial segments into the bacterial genomes (284 bp-target) were investigated and confirmed by analysis of the internal nucleotide sequences of the amplified DNA segments based on nucleotide sequence determination, translation to protein, and alignment with GenBank. The results indicated that the investigated partial sequence of the aadA gene, and its predicted protein are completely similar to the corresponding sequences from the aadA gene in several cloning vectors. Results also indicated that the predicted 3D structure for the investigated aadA protein segment was modeled with 100% confidence and 48% identity by the highest-scoring template of aminoglycoside adenyltransferase in the protein database. The processed PDB X-Ray structure validation report for the model quality of the template aadA protein verified that there are no bond lengths outliers, bond angle outliers, or chirality outliers. These results suggest the possible functionality of the aadA protein only when the full-length gene is fully transferred horizontally to the bacterial genome. Results also highlight the importance of studying the whole length of the protein sequence to evaluate its general physical properties and possible functionality.