Table 2.

Statistically significant results from differential abundance analysis.

Phylum	Class	Order	Family	Genus	OTU	Mean abundance	Log2 fold change	SE of log2 fold change	P-value	Adjusted P-value
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia/Shigella	–	3194.8	5.5	1.6	2.19E-06	1.22E-04
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus	–	91.0	3.5	1.0	5.39E-04	1.51E-02
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia/Shigella	Otu0006	3160.8	5.5	1.2	4.84E-06	8.90E-04
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacteriaceae_unclassified	Otu0038	560.9	−7.9	1.9	2.56E-05	2.35E-03

All statistically significant results from differential abundance analysis between the control and APECED groups at genus and OTU levels. Mean abundance in the data set is based on the internally normalized count data from DESeq2. P values were adjusted using the Benjamini–Hochberg method to control the false discovery rate (FDR) in multiple testing.