Extended Data Table 1.

Stepwise RDA of metadata variables influencing microbial composition of all samples. Separate analyses run for samples for all body sites together and for each body site individually.

All body sites (including individual)
Factor	R2.adj	Df	AIC	F	Pr(>F)
host_subject_id	0.196	60	5979.54	4.80	0.002
sample_type	0.169	2	5759.22	118.18	0.002
age	0.038	1	5702.12	56.85	0.002
<All variables>	0.001
All body sites (excluding individual)
Factor	R2.adj	Df	AIC	F	Pr(>F)
body_site	0.170	2	5953.00	97.14	0.002
metadata_abx	0.095	1	5840.19	121.59	0.002
age	0.043	1	5784.52	59.16	0.002
birth_weight	0.016	1	5763.61	23.04	0.002
delivery_mode	0.014	1	5745.17	20.51	0.002
<All variables>	0.001
Stool (including individual)
Factor	R2.adj	Df	AIC	F	Pr(>F)
host_subject_id	0.451	58	1512.02	5.21	0.002
<All variables>	0.042
Stool (excluding individual)
Factor	R2.adj	Df	AIC	F	Pr(>F)
delivery_mode	0.141	1	1595.21	50.05	0.002
metadata_abx	0.078	1	1567.77	30.62	0.002
age	0.042	1	1552.43	17.62	0.002
randomization	0.013	2	1548.98	3.69	0.002
delivery_weight	0.006	1	1547.43	3.49	0.022
<All variables>	0.000
Oral (including individual)
Factor	R2.adj	Df	AIC	F	Pr(>F)
host_subject_id	0.441	59	1565.52	5.15	0.002
age	0.080	1	1518.29	42.90	0.002
<All variables>	0.004
Oral (excluding individual)
Factor	R2.adj	Df	AIC	F	Pr(>F)
metadata_abx	0.249	1	1605.94	104.35	0.002
age	0.100	1	1562.50	48.44	0.002
birth_weight	0.044	1	1541.63	23.42	0.002
delivery_mode	0.005	1	1540.16	3.43	0.024
<All variables>	0.003
Skin (including individual)
Factor	R2.adj	Df	AIC	F	Pr(>F)
host_subject_id	0.146	58	1485.42	1.96	0.002
age	0.119	1	1436.70	44.84	0.002
<All variables>	0.001
Skin (excluding individual)
Factor	R2.adj	Df	AIC	F	Pr(>F)
age	0.114	1	1446.51	43.11	0.002
birth_weight	0.050	1	1428.25	20.71	0.002
delivery_mode	0.008	1	1426.00	4.22	0.006
<All variables>	0.007