Table 2.
Bacterial protein profile of cecal content of piglets (n = 11/group) fed either with human milk (HM) or milk formula (MF) at PND 21.
| Uniprot_ID | Organism | Protein Name | HM 1 (sum) |
MF 1 (sum) |
HM 2 | MF 2 | Log2 FC 3 | p-Value 4 |
|---|---|---|---|---|---|---|---|---|
| A0A412VME7 | Phocaeicola vulgatus (Bacteroides vulgatus) | RagB/SusD family nutrient uptake outer membrane protein | 51 | 573 | 3.4 | 47.5 | −3.8 | 0.002 |
| A0A412VME7 | Phocaeicola dorei | RagB/SusD family nutrient uptake outer membrane protein | 51 | 573 | 3.4 | 45.9 | −3.8 | 0.008 |
| R9H865 | Bacteroides vulgatus CL09T03C04 | Uncharacterized protein | 1783 | 111 | 3.4 | 32.9 | −3.3 | 0.03 |
| C6Z771 | Bacteroides sp. 4_3_47FAA | SusD family protein | 51 | 353 | 3.4 | 32.9 | −3.3 | 0.03 |
| A0A1Y3Z4G2 | Bacteroides clarus | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) (polynucleotide phosphorylase) (PNPase) | 44 | 386 | 3.7 | 35.4 | −3.2 | 0.05 |
| A0A397WJ15 | Phocaeicola vulgatus (Bacteroides vulgatus) | Beta-galactosidase (EC 3.2.1.23) | 107 | 614 | 8.4 | 52.2 | −2.6 | 0.02 |
| A0A415SZ11 | Phocaeicola vulgatus (Bacteroides vulgatus) | Malate dehydrogenase (EC 1.1.1.37) | 1008 | 1997 | 92.3 | 180.3 | −1 | 0.03 |
| C3RBX6 | Bacteroides vulgatus CL09T03C04 | 60 kDa chaperonin (GroEL protein) (protein Cpn60) | 3254 | 1195 | 245.9 | 118.3 | 1.1 | 0.03 |
| C3RBX6 | Bacteroides sp. AM18-9 | 60 kDa chaperonin (GroEL protein) (protein Cpn60) | 3254 | 1195 | 245.9 | 118.3 | 1.1 | 0.03 |
| A0A069SFK4 | Bacteroides vulgatus str. 3975 RP4 | TonB-linked outer membrane, SusC/RagA family protein | 1370 | 468 | 103.2 | 37.4 | 1.5 | 0.02 |
| A0A069SKV9 | Bacteroides vulgatus str. 3975 RP4 | Tetracycline resistance protein TetQ | 3792 | 1001 | 302.9 | 96.4 | 1.7 | 0.03 |
| A0A069SKV9 | Bacteroides sp. AF32-15BH | Tetracycline resistance protein TetQ | 3792 | 1001 | 302.9 | 96.4 | 1.7 | 0.03 |
| A0A1H6GDE8 | Selenomonas ruminantium | Phosphoenolpyruvate carboxykinase (ATP) (PCK) (PEP carboxykinase) (PEPCK) (EC 4.1.1.49) | 2383 | 519 | 238.1 | 43.5 | 2.5 | 0.04 |
| A0A174QRN1 | Phocaeicola vulgatus (Bacteroides vulgatus) | DUF1735 domain-containing protein (galactose oxidase) (EC 3.2.1.18) | 171 | 29 | 13.1 | 2 | 2.7 | 0.03 |
| I9UCD9 | Phocaeicola vulgatus (Bacteroides vulgatus) | SusC/RagA family TonB-linked outer membrane protein | 1370 | 469 | 32.3 | 4.7 | 2.8 | 0.03 |
| A0A417FRM0 | Firmicutes bacterium AM31-12AC | LacI family transcriptional regulator | 251 | 35 | 24.5 | 2.8 | 3.1 | 0.02 |
| A0A397WGI7 | Phocaeicola vulgatus (Bacteroides vulgatus) | RagB/SusD family nutrient uptake outer membrane protein (starch-binding associating with outer membrane) | 1087 | 111 | 96.8 | 10.5 | 3.2 | 0.02 |
| A0A316A2W0 | Faecalicatena contorta | Phosphoglycerate kinase (EC 2.7.2.3) | 1142 | 96 | 107.1 | 8.7 | 3.6 | 0.002 |
| R9H865 | Bacteroides vulgatus dnLKV7 | Uncharacterized protein | 1783 | 111 | 128.5 | 10.5 | 3.6 | 0.01 |
| A0A417FRM0 | Firmicutes bacterium AM43-11BH | LacI family transcriptional regulator | 251 | 35 | 21.6 | 1.5 | 3.8 | 0.05 |
| R5ICG7 | Firmicutes bacterium CAG:124 | L-fucose isomerase (FucIase) (EC 5.3.1.25) (6-deoxy-L-galactose isomerase) | 937 | 0 | 84.9 | 0 | NA | <0.0001 |
| A0A3C1BZY4 | Clostridiales bacterium | Carbon monoxide dehydrogenase (EC 1.2.7.4) | 0 | 535 | 0 | 53.7 | NA | 0.007 |
| F0Z4P0 | Clostridium sp. D5 | Acetate kinase (EC 2.7.2.1) (acetokinase) | 296 | 0 | 25.9 | 0 | NA | 0.008 |
| A0A374BZR2 | Firmicutes bacterium AM31-12AC | D-ribose pyranase (EC 5.4.99.62) | 155 | 0 | 13.1 | 0 | NA | 0.02 |
| A0A417BM01 | Firmicutes bacterium AM43-11BH | UPF0210 protein DW928_02850 | 148 | 0 | 12.9 | 0 | NA | 0.02 |
| A0A2N5NQW2 | Ruminococcus gnavus | Class II fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) (fructose-1,6-bisphosphate aldolase, class II) | 777 | 0 | 78.2 | 0 | NA | 0.02 |
| A0A494ZWH6 | Ruminococcus sp. B05 | UPF0210 protein D8Q48_03220 | 148 | 0 | 12.9 | 0 | NA | 0.02 |
| A0A374BZR2 | Mediterraneibacter sp. gm002 | D-ribose pyranase (EC 5.4.99.62) | 155 | 0 | 13.1 | 0 | NA | 0.02 |
| A0A316A2W0 | Dorea sp. CAG:105 | Phosphoglycerate kinase (EC 2.7.2.3) | 1142 | 96 | 47.3 | 0 | NA | 0.02 |
| F0Z4P0 | Lachnospiraceae bacterium 1_4_56FAA | Acetate kinase (EC 2.7.2.1) (acetokinase) | 296 | 0 | 18.6 | 0 | NA | 0.03 |
| A0A3A6G758 | Lachnospiraceae bacterium TM07-2AC | Class II fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) | 776 | 0 | 78.1 | 0 | NA | 0.03 |
| A0A374BZR2 | Ruminococcus sp. AM42-11 | D-ribose pyranase (EC 5.4.99.62) | 155 | 0 | 12 | 0 | NA | 0.04 |
| C3RBX6 | Firmicutes bacterium AM43-11BH | 60 kDa chaperonin (GroEL protein) (protein Cpn60) | 3254 | 1195 | 107.2 | 0 | NA | 0.05 |
1 The raw spectral counts matching to the identified proteins were analyzed using tweeDEseq package in Bioconductor. 2 HM and MF columns indicate mean value of the total spectral counts. 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.