TABLE 2.

Relative abundance of genera affected by human milk or milk formula in piglets at postnatal day 21¹

Regions	Genus	HM	MF	Log2 FC	P adj
Duodenum	Campylobacter	2.11 ± 3.5	0.128 ± 0.1	3.2	0.037
Duodenum	f__Flavobacteriaceae	0.12 ± 0.2	0.762 ± 0.9	−3.6	0.037
Jejunum	Campylobacter	1.72 ± 3.8	0.067 ± 0.1	4.7	0.023
Jejunum	f__Peptostreptococcaceae	0.36 ± 1.0	0.817 ± 1.7	−1.9	0.048
Ileum	Campylobacter	0.202 ± 0.3	0.018 ± 0.04	4.0	0.015
Ileum	Veillonella	1.161 ± 2.2	1.624 ± 2.4	−2.4	0.015
Ileum	Clostridium	0.73 ± 1.9	2.43 ± 5.2	−3.9	0.003
Ileum	f__Clostridiaceae	0.52 ± 0.6	4.727 ± 8.4	−3.3	0.005
Ileum	Sarcina	0.005 ± 0.02	0.091 ± 0.2	−4.5	0.015
Ileum	Turicibacter	0.079 ± 0.2	2.412 ± 4.5	−5.4	0.002
Cecum	c__Bacteroidia	5.194 ± 9.1	2.328 ± 7.7	7.8	0.001
Cecum	c__Mollicutes	3.137 ± 6.1	0.153 ± 0.4	6.4	0.001
Cecum	Dorea	2.637 ± 2.1	0.25 ± 0.3	3.5	0.001
Cecum	Actinobacillus	1.99 ± 1.7	0.495 ± 0.7	2.2	0.005
Cecum	Prevotella	1.553 ± 2.8	0.015 ± 0.1	5.9	0.009
Cecum	f__S24-7	1.505 ± 3.9	0.523 ± 1.7	5.7	0.005
Cecum	Campylobacter	0.575 ± 0.9	0.039 ± 0.1	5.5	0.005
Cecum	Haemophilus	0.428 ± 0.7	0.058 ± 0.1	2.7	0.013
Cecum	Anaerovibrio	0.176 ± 0.4	0.001 ± 0.002	7.6	0.015
Cecum	f__Prevotellaceae	0.069 ± 0.1	0.001 ± 0.002	6.0	0.045
Cecum	Fusobacterium	0.546 ± 1.4	3.935 ± 7.3	−3.4	0.016
Cecum	Turicibacter	0.022 ± 0.1	0.558 ± 0.8	−5.2	0.001
Cecum	rc4-4	0.016 ± 0.02	0.159 ± 0.3	−3.7	0.006
Proximal colon	c__Bacteroidia	3.634 ± 7.5	1.455 ± 4.6	5.9	0.008
Proximal colon	Dorea	3.305 ± 3.1	0.34 ± 0.3	3.8	0.001
Proximal colon	Actinobacillus	1.249 ± 1.9	0.178 ± 0.3	3.1	0.001
Proximal colon	f__S24-7	0.635 ± 1.3	0.608 ± 1.9	5.0	0.044
Proximal colon	Campylobacter	0.394 ± 0.8	0.01 ± 0.03	6.1	0.012
Proximal colon	f__Prevotellaceae	0.124 ± 0.3	0.00 ± 0.00	22	0.001
Proximal colon	Anaerovibrio	0.062 ± 0.1	0.00 ± 0.00	22	0.001
Proximal colon	Turicibacter	0.013 ± 0.03	0.67 ± 1.3	−5.4	0.001
Proximal colon	rc4-4	0.01 ± 0.02	0.148 ± 0.2	−4.0	0.019
Distal colon	Dorea	1.907 ± 1.3	0.577 ± 0.7	1.8	0.011
Distal colon	Actinobacillus	0.89 ± 1.6	0.02 ± 0.02	5.2	0.001
Distal colon	Campylobacter	0.743 ± 1.5	0.023 ± 0.1	5.1	0.004
Distal colon	Prevotella	0.341 ± 0.6	0.083 ± 0.3	8.7	0.001
Distal colon	Haemophilus	0.141 ± 0.3	0.004 ± 0.009	5.2	0.003
Distal colon	Oscillospira	1.151 ± 0.4	4.317 ± 5.8	−1.3	0.018
Distal colon	Ruminococcus	0.322 ± 0.7	0.86 ± 1.3	−2.6	0.002
Distal colon	Turicibacter	0.003 ± 0.005	0.381 ± 1.0	−4.6	0.003
Rectum	Dorea	3.103 ± 3.4	0.64 ± 0.6	2.5	0.005
Rectum	Akkermansia	2.623 ± 6.2	1.099 ± 3.4	5.7	0.001
Rectum	c__Bacteroidia	1.884 ± 3.8	0.102 ± 0.3	4.6	0.019
Rectum	f__S24-7	1.538 ± 2.5	0.067 ± 0.1	5.2	0.003
Rectum	f__Erysipelotrichaceae	0.762 ± 1.3	0.347 ± 0.8	2.7	0.017
Rectum	Streptococcus	0.622 ± 1.1	1.018 ± 1.1	−1.9	0.019
Rectum	Fusobacterium	0.241 ± 0.6	3.739 ± 9.8	−3.1	0.007
Rectum	Eubacterium	0.118 ± 0.1	1.222 ± 1.8	−2.7	0.028
Rectum	Turicibacter	0.006 ± 0.01	0.172 ± 0.5	−2.6	0.046
Rectum	f__Mogibacteriaceae	0.001 ± 0.003	0.056 ± 0.1	−5.3	0.001

¹Values are mean relative abundance ± SEMs, n = 8–11 per diet group. Adjusted P values from Wald test indicate differences between log2 FC values, calculated by DeSeq2 where reference group is HM. Genera that were significant with an adjusted P value < 0.05 are shown. c__, Class; f__, Family; FC, fold change; HM, human milk; MF, milk formula.