Analysis of gut microbial diversity in zebrafish

Raw sequencing reads are first quality-controlled, then taxonomically classified to profile the microbial composition of each sample at every rank. Alpha-diversity metrics quantify within-sample species richness and evenness, whereas beta-diversity measures dissimilarities in community composition and structure among samples. Inter-group differential-abundance testing is subsequently applied to detect statistically significant biomarker taxa that distinguish sample groups. Finally, 16S rRNA or ITS amplicon sequences are used for functional prediction to infer the likely gene functions or phenotypes of the microbial community and to estimate the abundances of the predicted functional genes or phenotypes.