Table 1.

Humanized gut microbiota contribute to significant changes in quantitative neural microstructure in salient regions implicated in neurologic and psychiatric illness.

Age	DWI Measure	Hemi.	ROI	Mean ±SEM		p-value
				Germ-free	Gnotobiotic
P55	FA	Left	HC	0.18315 ± 0.00530	0.18546 ± 0.00235	0.363
			FAC	0.15794 ± 0.00305	0.15979 ± 0.00271	0.345
			Amg	0.18017 ± 0.00344	0.17920 ± 0.00725	0.458
		Right	HC	0.18743 ± 0.00328	0.18871 ± 0.00258	0.393
			FAC	0.16682 ± 0.00501	0.15997 ± 0.00215	0.142
			Amg	0.19596 ± 0.00331	0.19550 ± 0.00253	0.461
	MD	Left	HC	0.38320 ± 0.00389	0.34560 ± 0.00545	<0.01*
			FAC	0.36760 ± 0.00570	0.32140 ± 0.00906	<0.01*
			Amg	0.36620 ± 0.00532	0.32980 ± 0.01027	<0.05*
		Right	HC	0.39140 ± 0.00430	0.34760 ± 0.00569	<0.01*
			FAC	0.36600 ± 0.00789	0.33640 ± 0.00658	<0.05*
			Amg	0.37100 ± 0.01221	0.32700 ± 0.00509	<0.01*
	NDI	Left	HC	0.27929 ± 0.00401	0.33678 ± 0.00871	<0.01*
			FAC	0.33005 ± 0.01774	0.40784 ± 0.02171	<0.05*
			Amg	0.31323 ± 0.00812	0.36850 ± 0.01866	<0.05*
		Right	HC	0.26832 ± 0.00641	0.33041 ± 0.00768	<0.01*
			FAC	0.33399 ± 0.03864	0.39707 ± 0.02270	0.117
			Amg	0.31268 ± 0.00634	0.36305 ± 0.00693	<0.01*
	ODI	Left	HC	0.28833 ± 0.01104	0.33706 ± 0.00446	<0.01*
			FAC	0.35944 ± 0.00625	0.43192 ± 0.01841	<0.01*
			Amg	0.34415 ± 0.01085	0.38631 ± 0.02160	0.075
		Right	HC	0.26686 ± 0.00623	0.32940 ± 0.00633	<0.01*
			FAC	0.32640 ± 0.01327	0.41286 ± 0.01424	<0.01*
			Amg	0.30175 ± 0.01577	0.36514 ± 0.00894	<0.01*
P90	FA	Left	HC	0.17947 ± 0.00321	0.17692 ± 0.00664	0.277
			FAC	0.14894 ± 0.00259	0.15253 ± 0.00441	0.172
			Amg	0.16868 ± 0.00484	0.16050 ± 0.00688	0.357
		Right	HC	0.18248 ± 0.00461	0.17599 ± 0.00305	0.178
			FAC	0.15173 ± 0.00193	0.14860 ± 0.00127	0.373
			Amg	0.18298 ± 0.00834	0.17442 ± 0.00324	0.218
	MD	Left	HC	0.45550 ± 0.00669	0.42325 ± 0.00239	<0.01*
			FAC	0.40650 ± 0.00462	0.37500 ± 0.00628	<0.01*
			Amg	0.48417 ± 0.01220	0.47075 ± 0.02176	0.175
		Right	HC	0.46800 ± 0.00870	0.43800 ± 0.01968	0.117
			FAC	0.39873 ± 0.01026	0.36650 ± 0.01538	<0.05
			Amg	0.49067 ± 0.01766	0.46625 ± 0.00872	0.085
	NDI	Left	HC	0.37533 ± 0.00123	0.38404 ± 0.00123	<0.01*
			FAC	0.39376 ± 0.00464	0.40728 ± 0.00653	0.067
			Amg	0.37361 ± 0.00338	0.38199 ± 0.00777	0.144
		Right	HC	0.37332 ± 0.00051	0.38896 ± 0.00543	<0.05*
			FAC	0.39929 ± 0.01250	0.44848 ± 0.02088	<0.05*
			Amg	0.37223 ± 0.00378	0.38086 ± 0.00313	<0.05
	ODI	Left	HC	0.24198 ± 0.00439	0.26345 ± 0.00832	<0.05
			FAC	0.30100 ± 0.00383	0.35007 ± 0.00969	<0.01*
			Amg	0.25615 ± 0.00555	0.27611 ± 0.01576	0.196
		Right	HC	0.23252 ± 0.00841	0.25692 ± 0.00831	0.089
			FAC	0.30288 ± 0.01264	0.36021 ± 0.01150	<0.05*
			Amg	0.22202 ± 0.00796	0.25563 ± 0.00597	<0.05

All values are mean ± standard error of the mean (SEM). Units of measure for FA, MD, NDI, and ODI are [10⁻³ mm²/s]. Bolded and italicized p-values are statistically significant. Starred p-values are statistically significant after controlling the false discovery rate with the Benjamini-Hochberg procedure (false discovery rate = 0.05). Regions of interest (ROIs) correspond to ROIs defined from the Center for in vivo Microscopy (CIVM) mouse brain atlas. Ages of P55 and P90 animals are 45 and 90 days post-natal, respectively. P55 germ-free (n = 5) and gnotobiotic (n = 5) and P90 germ-free (n = 4) and gnotobiotic (n = 4) animals are all male. Hemi, hemisphere; FA, fractional anisotropy; NDI, neurite density index; ODI, orientation dispersion index; HC, hippocampus; FAC, frontal associations cortex; Amg, amygdala.