Table 4 Differences in closed-reference OTUs of 16S rRNA gene sequence reads classified to family level taxa due to sample source (stool vs. swab) and participant source.

From: Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples

Family Level Taxa^a	Stool vs. Swab			Participant p value^c	R-square Marginal^d	R-squared Conditional^e
	Log-Normalized Mean Abundance ± Standard Deviation
	Stool	Swab	p value^b
Acidaminococcaceae	2.943 ± 1.1	2.728 ± 2.73	0.147	6.74 × 10^-40	0.012	0.759
Actinomycetaceae	1.342 ± 0.69	1.327 ± 1.33	0.998	0.066	0	0.108
Aerococcaceae	0.169 ± 0.38	0.326 ± 0.33	0.004	0.341	0.027	0.078
Bacillaceae_1	1.866 ± 0.6	3.338 ± 3.34	3.18 × 10^-53	0.148	0.482	0.526
BacillalesIncertae_Sedis_XI	0.702 ± 0.71	0.51 ± 0.51	0.055	0.278	0.016	0.076
Bacteroidaceae	4.564 ± 0.29	4.512 ± 4.51	0.275	2.88 × 10^-12	0.011	0.436
Beijerinckiaceae	0.331 ± 0.51	0.304 ± 0.3	0.934	5.05 × 10^-04	0.003	0.212
Bifidobacteriaceae	0.451 ± 0.6	0.317 ± 0.32	0.062	2.44 × 10^-08	0.014	0.35
Burkholderiaceae	0.425 ± 0.62	0.499 ± 0.5	0.632	2.13 × 10^-04	0.006	0.23
Burkholderialesincertae_sedis	0.697 ± 1.03	0.703 ± 0.7	0.998	8.92 × 10^-43	0	0.779
Campylobacteraceae	0.331 ± 0.49	1.485 ± 1.49	1.10 × 10^-31	2.47 × 10^-05	0.304	0.482
Carnobacteriaceae	0.792 ± 0.68	0.32 ± 0.32	2.83 × 10^-15	0.004	0.148	0.293
Chloroplast	0.751 ± 0.75	0.25 ± 0.25	2.30 × 10^-14	0.197	0.138	0.201
Clostridiaceae_1	1.415 ± 1.15	1.033 ± 1.03	0.003	9.08 × 10^-17	0.028	0.525
ClostridialesIncertae_SedisXI	0.884 ± 0.72	2.887 ± 2.89	1.13 × 10^-71	0.019	0.611	0.665
ClostridialesIncertae_Sedis XII	1.403 ± 0.96	0.938 ± 0.94	5.60 × 10^-07	3.71 × 10^-26	0.076	0.664
ClostridialesIncertae_Sedis XIII	2.176 ± 0.7	2.076 ± 2.08	0.435	8.62 × 10^-10	0.009	0.384
Comamonadaceae	0.195 ± 0.41	0.242 ± 0.24	0.648	0.011	0.003	0.154
Coriobacteriaceae	2.958 ± 0.56	2.652 ± 2.65	9.63 × 10^-08	0.004	0.074	0.235
Corynebacteriaceae	0.105 ± 0.26	0.836 ± 0.84	1.52 × 10^-23	0.320	0.226	0.269
Desulfovibrionaceae	1.91 ± 1.03	1.935 ± 1.94	0.998	1.43 × 10^-29	0.001	0.672
Enterobacteriaceae	1.423 ± 1.16	2.129 ± 2.13	5.59 × 10^-09	2.17 × 10^-17	0.09	0.565
Enterococcaceae	0.296 ± 0.68	0.386 ± 0.39	0.562	2.87 × 10^-27	0.006	0.649
Erysipelotrichaceae	3.189 ± 0.58	3.225 ± 3.23	0.863	4.53 × 10^-07	0.009	0.315
Eubacteriaceae	0.859 ± 0.7	0.547 ± 0.55	7.28 × 10^-06	0.000305	0.055	0.263
Flavobacteriaceae	0.362 ± 0.52	0.394 ± 0.39	0.921	4.53 × 10^-11	0.001	0.406
Fusobacteriaceae	0.594 ± 0.97	1.199 ± 1.2	4.98 × 10^-08	1.47 × 10^-12	0.084	0.503
Hyphomicrobiaceae	0.96 ± 0.88	0.885 ± 0.89	0.800	2.24 × 10^-37	0.004	0.74
Incertae_Sedis_XI	0.176 ± 0.37	1.618 ± 1.62	3.71 × 10^-47	0.024	0.433	0.508
Lachnospiraceae	4.556 ± 0.19	4.512 ± 4.51	0.158	0.141	0.03	0.113
Lactobacillaceae	0.896 ± 0.84	0.947 ± 0.95	0.921	1.60 × 10^-05	0.002	0.263
Microbacteriaceae	0.296 ± 0.58	0.353 ± 0.35	0.740	1.65 × 10^-14	0.006	0.475
Micrococcaceae	0.436 ± 0.63	0.326 ± 0.33	0.177	2.95 × 10^-08	0.009	0.346
Moraxellaceae	0.067 ± 0.26	0.986 ± 0.99	8.74 × 10^-37	0.162	0.347	0.4
Pasteurellaceae	0.568 ± 0.81	0.55 ± 0.55	0.998	1.81 × 10^-09	0.002	0.369
Peptococcaceae_1	0.416 ± 0.67	0.778 ± 0.78	3.33 × 10^-06	3.15 × 10^-22	0.06	0.614
Peptostreptococcaceae	1.924 ± 0.99	2.017 ± 2.02	0.717	1.62 × 10^-14	0.003	0.479
Porphyromonadaceae	3.615 ± 0.67	3.683 ± 3.68	0.648	3.75 × 10^-19	0.005	0.548
Prevotellaceae	2.633 ± 1	3.126 ± 3.13	1.27 × 10^-06	4.60 × 10²⁸	0.066	0.68
Propionibacteriaceae	0.172 ± 0.39	0.269 ± 0.27	0.077	0.000326	0.017	0.23
Rikenellaceae	3.356 ± 0.69	2.995 ± 3	1.77 × 10^-06	1.60 × 10^-19	0.052	0.576
Ruminococcaceae	4.368 ± 0.33	4.321 ± 4.32	0.435	6.04 × 10^-12	0.009	0.434
Streptococcaceae	2.79 ± 0.77	2.825 ± 2.83	0.968	1.62 × 10^-11	0.001	0.416
Sutterellaceae	2.569 ± 1.11	2.722 ± 2.72	0.435	7.57 × 10^-41	0.01	0.767
Synergistaceae	0.544 ± 0.79	0.664 ± 0.66	0.435	2.57 × 10^-14	0.007	0.473
Thermaceae	0.206 ± 0.4	1.581 ± 1.58	2.53 × 10^-52	0.138	0.476	0.522
Veillonellaceae	2.225 ± 1.2	2.492 ± 2.49	0.061	2.15 × 10^-22	0.017	0.599
Verrucomicrobiaceae	1.55 ± 1.22	1.202 ± 1.2	0.011	1.59 × 10^-14	0.021	0.49

^aLimited to families present in at least 25% of samples. ^bBenjamini-Hochberg corrected p-value derived from ANOVA of mixed linear model. ^cBenjamini-Hochberg corrected p-value derived from ANOVA of linear models with and without participant as a random effect. ^dR-squared marginal represents the variation that is explained by the model without the mixed effect (participant) while ^ethe conditional R-squared represents the variation that is explained by the model including both fixed effects and mixed effects.

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Table 4 Differences in closed-reference OTUs of 16S rRNA gene sequence reads classified to family level taxa due to sample source (stool vs. swab) and participant source.

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