Table 1.

Sex and hpg genotype affect alpha diversity in the cecum only

Fixed effect	Shannon index			Faith’s PD
	Duodenum p	Ileum p	Cecum p	Duodenum p	Ileum p	Cecum p
Sample type	6.63E−08	0.0173	2.20E−39	1.43E−09	7.90E−08	6.71E−07
Sex	0.9971	0.1686	0.1891	0.8487	0.0507	0.5933
Genotype	0.1288	0.4723	0.5406	0.1600	0.8488	0.9787
Sex*Genotype	0.6619	0.5185	0.7816	0.6576	0.6193	0.0488
Sex*Sample type	0.5894	0.5485	0.8357	0.3540	0.9291	0.0387
Genotype*Sample type	0.8476	0.3929	0.0537	0.4951	0.1120	0.3934
Sex*Genotype*Sample type	0.2929	0.3647	0.5487	0.4467	0.1322	0.0170

p value shown for linear mixed-effect model to determine effects of sex, hpg genotype, and sample type (lumen vs. mucosa). P values < 0.05 shown in bold