TY  - JOUR
AU  - Moravčíková, Dagmar
AU  - Žiarovská, Jana
AU  - Žiarovská, Alžbeta
PY  - 2025
DA  - 2025/07/15
TI  - Impact of Normalization Methods on Metagenomic Characterization of <i>Amaranthus Cruenthus</i> var. Pribina-Associated Microbiomes Under Cadmium Stress
JO  - OBM Genetics
SP  - 303
VL  - 09
IS  - 03
AB  - The study of endophytic and rhizosphere microbiota offers considerable potential for applications in agriculture, biotechnology, and bioremediation, given the phytoremediation capacity of Amaranthus cruentus var. Pribina performed a detailed analysis of the root and rhizosphere microbial communities under cadmium (Cd) stress. Although metagenomics provides powerful tools for microbial community profiling, the reproducibility and interpretability of the results are strongly influenced by the data processing strategies. In this study, special emphasis was placed on comparing normalization techniques and their effects on downstream analyses. Sequence data were processed in R using DADA2 to infer amplicon sequence variants (ASVs), followed by diversity, compositional, and statistical analyses using phyloseq, vegan, ggplot2, and stats. By evaluating multiple normalization approaches, it was demonstrated how the choice of method can significantly impact alpha and beta diversity metrics. These findings underscore the importance of normalization in microbiome studies and offer a tailored pipeline for analyzing Cd-induced shifts in plant-associated microbial communities.
SN  - 2577-5790
UR  - https://doi.org/10.21926/obm.genet.2503303
DO  - 10.21926/obm.genet.2503303
ID  - Moravčíková2025
ER  -