Table 1.

Overview of the most significant changes in taxa seen post antibiotic exposure in males compared to females at the phylum, family, and genus levels in both the stool and small bowel microbiomes.

	Male controls vs. female controls	Male ABX exposed vs. female ABX exposed
Stool microbiome	Baseline	AbxD8	PAbxD13
Alpha diversities
Simpson’s index	NS	↓	NS
Shannon’s index	NS	↓	NS
Phylum level
Firmicutes#	NS	↓	↓
Bacteroidetes#	NS	NS	↑
Proteobacteria#	NS	↑	↓
Verrucomicrobia	↓	↑	↓
Actinobacteria	NS	↓	↓
Family level
Verrucomicrobiaceae	↓	↑	↓
Unknown family, order RF32	↓	NS	NS
Corynebacteriaceae	↑*	NS	NS
Enterobacteriaceae	NS	↑*	↓
Staphylococcaceae	NS	NS	↑
Genus level
Lactobacillus#	NS	↑	NS
Oscillospira#	NS	NS	NS
Ruminococcus#	NS	NS	↓
Bacteroides#	NS	NS	NS
Sutterella#	NS	↑	↑
Turicibacter#	NS	↓	↑
Parabacteroides#	NS	NS	↑
Akkermansia	↓	↑	↓
Unknown genus, order RF32	↓	NS	NS
Lactococcus	↓	NS	↓
Coprococcus	↓	NS	NS
Unknown genus, Enterobacteriaceae	NS	↑	↓
Serratia	NS	↑	NS
Enterococcus	NS	↓	↓
Small bowel microbiome	PAbxD13		PAbxD13
Alpha diversities
Simpson’s index	NS		NS
Shannon’s index	NS		NS
Phylum level
Firmicutes#	NS		↑
Bacteroidetes#	NS		↓
Proteobacteria	NS		↓
Verrucomicrobia	↓		↓
Actinobacteria	NS		↓
Genus level
Lactobacillus	↑		NS
Oscillospira	NS		↓
Ruminococcus	NS		NS
Bacteroides	NS		NS
Sutterella	NS		↓
Turicibacter	NS		↑
Parabacteroides	NS		↑
Akkermansia	↓		↓
Unknown genus, order RF32	NS		NS
Lactococcus	NS		NS
Coprococcus	NS		↓

NS, not significant; ↑, higher relative abundance in male rats compared to female rats; and ↓, lower relative abundance in male rats compared to female rats.

^*Indicates trend toward significance (p < 0.05, FDR p > 0.05).

^#Taxa that were part of the core microbiome in control female and male rats.