Table 4.

Top 10 statistically significant decreases in operational taxonomic unit (OTU) abundance from 3 months to 1 year of infant age at the genus and species level.

Vaginal, breastfed, and no antibiotic use		Vaginal, breastfed, and antibiotic use		Vaginal, not breastfed, and no antibiotic use		Vaginal, not breastfed, and antibiotic use		Elective CS, breastfed, and antibiotic use		Elective CS, not breastfed, and antibiotic use		Emergency CS, breastfed, and antibiotic use
↓ OTU	Significance analysis of microarrays (SAM) score	↓ OTU	SAM Score	↓OTU	SAM Score	↓ OTU	SAM Score	↓OTU	SAM Score	↓OTU	SAM Score	↓OTU	SAM Score
Bacteroides sp.	−5.9	Unclassified Lachnospiraceae sp.	−5.9	Bacteroides caccae	−4.0	Escherichia sp.	−3.1	Parabacteroides distasonis	−5.7	Bacteroides sp.	−10.1	Unclassified Ruminococcaceae sp.	−5.2
Faecalibacterium prausnitzii	−5.7	Bacteroides sp.	−5.4	Unclassified Enterobacteriaceae sp.	−4.0	Faecalibacterium sp.	−3.1	B. caccae	−4.9	Veillonella dispar	−4.8	Bacteroides sp.	−5.1
Unclassified Ruminococcaceae sp.	−5.5	P. distasonis	−5.2	F. prausnitzii	−3.9	P. distasonis	−3.0	Lactobacillus reuteri	−4.6	Akkermansia muciniphila	−4.8	Bacteroides ovatus	−4.6
Streptococcus sp.	−5.3	Streptococcus sp.	−5.2	Escherichia sp.	−3.5	Unclassified Alphaproteobacteria	−3.0	Roseburia sp.	−4.4	Unclassified Enterobacteriaceae sp.	−4.6	Butyricimonas sp.	−4.5
Unclassified Enterobacteriaceae sp.	−5.3	F. prausnitzii	−5.0	Roseburia sp.	−3.5	Oscillospira sp.	−3.0	Unclassified Lachnospiraceae sp.	−4.4	Anaerococcus hydrogenalis	−4.1	Prevotella copri	−4.5
f__Ruminococcaceae Unclassified genus and species	−5.2	f__Enterobacteriaceae Unclassified genus and species	−4.8	g__Oscillospira f__Ruminococcaceae	−3.5	g__Enterococcus f__Enterococcaceae	−3.0	g__Faecalibacterium f__Ruminococcaceae	−4.2			f__Lachnospiraceae Unclassified genus and species	−4.1
f__Peptostreptococcac Unclassified genus and species	−5.2	s__ovatus g__Bacteroides	−4.7	s__fragilis g__Bacteroides	−3.3	f__Ruminococcaceae Unclassified genus and species	−3.0	g__Escherichia f__Enterobacteriaceae	−4.1			g__Bifidobacterium f__Bifidobacteriaceae	−4.4
g__Lactobacillus f__Lactobacillaceae	−5.1	g__Butyricimonas f__Odoribacteraceae	−4.6	s__fragilis g__Bacteroides	−3.2	s__copri g__Prevotella	−2.9	f__Ruminococcaceae Unclassified genus and species	−3.9			f__Ruminococcaceae Unclassified genus and species	−4.4
f__Rikenellaceae Unclassified genus and species	−5.1	f__Ruminococcaceae Unclassified genus and species	−4.6	f__Ruminococcaceae Unclassified genus and species	−3.2	s__fragilisg__Bacteroides	−2.9	f__Lachnospiraceae Unclassified genus and species	−3.7			s__fragilisg__Bacteroides	−4.4
g__Blautia f__Lachnospiraceae	−4.9	s__gnavus g__Ruminococcus	−4.5	g__Bacteroides f__Bacteroidaceae	−3.2	g__Eubacterium f__Erysipelotrichaceae	−2.9	f__Lachnospiraceae Unclassified genus and species	−3.6			f__Lactobacillaceae Unclassified genus and species	−4.6