Table 1.
Cecal bacterial profile of piglets (n = 11/group) fed either with human milk (HM) or milk formula (MF) at PND 21.
| Bacterial Organism 1 | HM 2 | SD | MF 2 | SD | log2 FC 3 | p-Value 4 |
|---|---|---|---|---|---|---|
| Bacteroides clarus | 6.9 | 27.1 | 95.8 | 68.4 | −3.8 | <0.0001 |
| Bacteroides stercoris CAG:120 | 3.4 | 13.3 | 44.5 | 33.9 | −3.7 | 0.0028 |
| Bacteroides sp. AF35-22 | 39.2 | 49.2 | 266.5 | 194.2 | −2.8 | 0.0076 |
| Clostridium clostridioforme CAG:132 | 3.0 | 6.2 | 21.7 | 21.7 | −2.9 | 0.0076 |
| Bacteroides stercoris ATCC 43183 | 4.0 | 15.7 | 35.9 | 30.4 | −3.2 | 0.0112 |
| Bacteroides sp. AM44-19 | 57.6 | 62.1 | 312.0 | 229.9 | −2.4 | 0.0131 |
| Firmicutes bacterium CAG:129 | 1.8 | 6.9 | 18.0 | 12.8 | −3.3 | 0.0159 |
| Firmicutes bacterium CAG:137 | 2.5 | 11.2 | 78.9 | 82.5 | −5.0 | 0.0164 |
| Firmicutes bacterium CAG:176 | 2.2 | 3.8 | 17.0 | 16.0 | −3.0 | 0.0197 |
| Bacteroides clarus YIT 12056 | 3.4 | 13.3 | 32.0 | 30.7 | −3.2 | 0.0375 |
| (Clostridium) clostridioforme 90A7 | 6.7 | 7.9 | 26.9 | 27.2 | −2.0 | 0.0375 |
| Clostridium bolteae (strain ATCC BAA-613/WAL 16351) | 2.5 | 6.4 | 16.2 | 15.0 | −2.7 | 0.0375 |
| (Ruminococcus) lactaris | 135.1 | 113.0 | 3.6 | 10.9 | 5.2 | <0.0001 |
| Firmicutes bacterium OM07-11 | 82.1 | 51.3 | 2.5 | 5.4 | 5.1 | 0.0001 |
| Ruminococcus gnavus | 303.5 | 202.5 | 7.1 | 15.4 | 5.4 | 0.0001 |
| Firmicutes bacterium AM41-5BH | 199.0 | 119.8 | 15.6 | 15.9 | 3.7 | 0.0001 |
| Mediterraneibacter sp. gm002 | 47.7 | 39.0 | 4.5 | 7.7 | 3.4 | 0.0009 |
| Firmicutes bacterium AM43-11BH | 275.4 | 158.2 | 19.5 | 18.6 | 3.8 | 0.0012 |
| (Ruminococcus) torques ATCC 27756 | 73.2 | 67.4 | 3.2 | 11.2 | 4.5 | 0.0028 |
| Firmicutes bacterium AM31-12AC | 209.2 | 169.6 | 6.4 | 10.8 | 5.0 | 0.0067 |
| Firmicutes bacterium CAG:212 | 116.8 | 57.1 | 3.5 | 8.3 | 5.0 | 0.0087 |
| Faecalicatena orotica | 50.3 | 38.1 | 6.2 | 12.6 | 3.0 | 0.0131 |
| Selenomonas ruminantium | 233.3 | 140.5 | 41.9 | 106.8 | 2.5 | 0.0152 |
| Dorea sp. CAG:317 | 13.1 | 11.0 | 2.0 | 5.1 | 2.7 | 0.0485 |
| Hespellia stercorisuis DSM 15480 | 12.8 | 11.7 | 0.0 | 0.0 | NA | 0.0152 |
| Lachnospiraceae bacterium AM40-2BH | 139.2 | 116.6 | 33.0 | 51.5 | 2.1 | 0.0152 |
| Faecalicatena contorta | 164.5 | 122.5 | 33.1 | 41.5 | 2.3 | 0.0174 |
| Lachnospiraceae bacterium 2_1_58FAA | 88.4 | 73.1 | 0.3 | 0.9 | 8.3 | 0.0197 |
| Lachnospiraceae bacterium TM07-2AC | 117.5 | 112.5 | 0.0 | 0.0 | NA | 0.0197 |
| Dorea sp. OM07-5 | 44.0 | 36.5 | 0.0 | 0.0 | NA | 0.0389 |
| Lachnospiraceae bacterium OF09-33XD | 18.8 | 20.5 | 0.0 | 0.0 | NA | 0.0482 |
1 The raw spectral counts matching to the identified bacterial species were analyzed using tweeDEseq package in Bioconductor. 2 HM and MF columns indicate mean value of the total spectral counts followed by the standard deviation of the mean (SD). 3 Log2 FC is the log2 of the HM to MF ratio. 4 Benjamini–Hochberg correction for multiple testing was applied to adjust p-values.