Table 2.

Bold taxonomies were identified via literature search, and indicate taxonomies altered in the same direction in published studies in RTT patients. Table 2 depicts OTUs significantly altered in RTT rats compared to WT across developmental timepoints (Lefse analysis, LDA cutoff of 4.0). Bold taxonomies depict bacteria that were also found to be altered in the same direction in LEfSe analyses in published work on the microbiome in human RTT patients.

Age	OTU	RTT enriched or WT enriched	LDA score	Human RTT Studies
p35	n.s.	n.s	n.s
p49	Streptococcus agalactiae	RTT	4.26
	Bifidobacterium bifidum	RTT	4.17	genus in Strati et al., 2016
	Lactobacillus acidipiscis	RTT	4.17	genus in Strati et al., 2016
p77	Campylobacter rectus	WT	4.81
	Bifidobacterium pseudolongum	WT	4.79
	Streptococcus agalactiae	RTT	4.77
	g_Pediococcus	RTT	5.17
p105	g_Anaerofustis	WT	4.77
	Enterococcus casseliflavus	WT	4.32
	g_Lachnobacterium	WT	4.32
	WAL 1855D	WT	4.30
	Lactobacillus ruminis	RTT	4.42	genus in Strati et al., 2016
	g_Bilophila	RTT	4.43
	Lactobacillus acidipiscis	RTT	4.42	genus in Strati et al., 2016
	g_Holdemania	RTT	4.56
	g_Pediococcus	RTT	5.31
p133	Bifidobacterium longum	WT	4.92
	g_Anaerofustis	WT	4.76
	Bifidobacterium pseudolongum	WT	4.68
	g_Turicibacter	WT	4.62
	g_AF12	RTT	4.54
	o_SHA_98	RTT	4.58
	g_Mannheimia	RTT	4.62
	g_Pediococcus	RTT	5.37
p196	Bifidobacterium longum	WT	4.97
	Anaerofustis	WT	4.88
	Bifidobacterium pseudolongum	WT	4.73
	Facklamia	WT	4.71
	Pediococcus	RTT	5.12