Table 1 Intestinal epithelial gene expression modulated by microbiota in CONV versus GF piglets

Hs.444468

CTD (carboxy-terminal domain) small phosphatase 1 (CTDSP1)

0.007

1.57

Hs.433879

DNA directed RNA polymerase II polypeptide J-related gene (POLR2J2)

0.001

1.33

Hs.509226

FK506 binding protein 3, 25 kDa (FKBP3)

0.029

0.67

Hs.765

GATA binding protein 1 (globin transcription factor 1, GATA1)

0.006

0.70

Hs.247478

HLA-B associated transcript 4 (BAT4)

0.042

1.24

Hs.535030

Hypothetical protein MGC13098 (MGC13098)

0.046

1.64

Hs.200716

Methyl CpG binding protein 2 (MECP2)

0.007

0.65

Hs.509545

Pre-B-cell leukemia transcription factor 2 (PBX2)

0.007

1.51

Hs.643558

Retinoblastoma binding protein 4 (RBBP4)

0.003

1.47

Hs.388034

Retinoid × receptor, beta (RXRB)

0.003

1.41

Hs.470412

RNA binding motif, single stranded interacting protein 1 (RBMS1)

0.018

1.39

Hs.433343

Serine/arginine repetitive matrix 2 (SRRM2)

0.001

1.46

Hs.470943

Signal transducer and activator of transcription 1 (STAT1)

0.001

1.86

Hs.194756

Sine oculis homeobox homolog 6 (SIX6)

0.008

1.86

Hs.525091

Testis-specific kinase 2 (TESK2)

0.006

1.24

Hs.369762

Thymidylate synthetase (TYMS)

0.043

0.71

Hs.389734

Transcription elongation factor A (SII)-like 8 (TCEAL8)

0.007

0.62

Hs.386390

Transcriptional adaptor 3 (NGG1 homolog, yeast)-like (TADA3L)

0.007

1.58

Hs.517296

V-ets erythroblastosis virus E26 oncogene homolog 2 (ETS2)

0.002

1.40

Hs.490504

Zinc finger protein 398 (ZNF398)

0.017

1.39

Hs.438536

Zinc finger protein 705A (ZNF705A)

0.017

1.42

Hs.371794

Zinc finger, NFX1-type containing 1 (ZNFX1)

0.007

1.67

Hs.371240

A kinase (PRKA) anchor protein 12 (AKAP7)

0.003

1.77

Hs.150423

Cyclin-dependent kinase 9 (CDC2-related kinase) (CDK9)

0.039

1.59

Hs.173135

Dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2)

0.042

0.62

Hs.515415

Inositol 1,4,5-trisphosphate 3-kinase C (ITPKC)

0.033

1.37

Hs.529400

Interferon (alpha, beta and omega) receptor 1 (IFNAR1)

0.013

1.53

Hs.520414

Interferon (gamma) receptor 1 (IFNGR1)

0.030

1.52

Hs.433442

Kinesin-associated protein 3 (KIFAP3)

0.012

1.53

Hs.133421

Leukemia inhibitory factor receptor (LIFR)

0.003

2.31

Hs.485262

Mitochondrial carrier homolog 1 (MTCH1)

0.034

1.62

Hs.419640

Parkinson disease 7 (PARK7)

0.030

0.75

Hs.509067

Platelet-derived growth factor receptor, beta polypeptide (PDGFRB)

0.038

1.24

Hs.2890

Protein kinase C, gamma (PRKCG)

0.035

0.59

Hs.513683

Protein serine kinase H1 (PSKH1)

0.041

1.35

Hs.458417

Regulator of G-protein signalling 8 (RGS8)

0.036

1.45

Hs.88012

signaling threshold regulating transmembrane adaptor 1 (SIT1)

0.038

1.47

Hs.470943

Signal transducer and activator of transcription 1 (STAT1)

0.001

1.86

Hs.441498

Signal transducing adaptor molecule 1 (STAM1)

0.014

1.29

Hs.525091

Testis-specific kinase 2 (TESK2)

0.006

1.25

Hs.355899

Tumor necrosis factor receptor superfamily, member 12A (TNFRSF12A)

0.021

0.78

Hs.47061

Unc-51-like kinase 1 (ULK1)

0.040

1.52

Hs.646283

Virus-induced signaling adapter (VISA)

0.001

1.43

Hs.512079

WAS protein family, member 2 (WASF2)

0.003

2.06

Hs.515371

Calpain, small subunit 1 (CAPNS1)

0.033

0.68

Hs.443625

Collagen, type III, alpha 1 (COL3A1)

0.012

1.14

Hs.150423

Cyclin-dependent kinase 9 (CDC2-related kinase) (CDK9)

0.039

1.59

Hs.437379

Development and differentiation enhancing factor-like 1 (DDEFL1)

0.013

1.30

Hs.130316

Drebrin 1 (DBN1)

0.045

1.53

Hs.26770

Fatty acid binding protein 7 (FABP7)

0.011

0.64

Hs.87752

Moesin (MSN)

0.031

1.35

Hs.516633

NCK-associated protein 1 (NCKAP1)

0.013

0.75

Hs.191346

Septin 7 (SEPT7)

0.024

0.75

Hs.530477

Signal-induced proliferation-associated gene 1 (SIPA1)

0.001

1.56

Hs.527973

Suppressor of cytokine signaling 3 (SOCS3)

0.045

1.30

Hs.386390

Transcriptional adaptor 3 like (TADA3L)

0.015

1.58

Hs.355899

Tumor necrosis factor receptor superfamily, member 12A (TNFRSF12A)

0.021

0.78

Hs.518060

ADP-ribosylation-like factor 6 interacting protein 5 (ARL6IP5)

0.009

0.69

Hs.511311

ATPase, Class I, type 8B, member 4 (ATP8B4)

0.037

2.32

Hs.86905

ATPase, lysosomal, V1 subunit C, isoform 1 (ATP6V1C1)

0.043

2.10

Hs.503721

Dynein, cytoplasmic, heavy polypeptide 2 (DNCH2)

0.021

0.53

Hs.26770

Fatty acid binding protein 7 (FABP7)

0.011

0.64

Hs.388668

Kelch-like 2 (KLHL2)

0.026

0.50

Hs.645375

Mitochondrial carrier family protein (SLC25A)

0.015

0.70

Hs.477361

SEC22 vesicle trafficking protein homolog A (SEC22A)

0.041

0.61

Hs.458917

Secretory carrier membrane protein 2 (SCAMP2)

0.042

1.44

Hs.14846

Solute carrier family 7 (SLC7A1)

0.026

1.24

Hs.462379

Target of myb1-like 2 (TOM1L2)

0.004

1.59

Hs.352018

Transporter 1, ATP-binding cassette, sub-family B (TAP1)

0.001

3.08

Hs.591852

ADAM metallopeptidase domain 9 (ADAM9)

0.021

1.88

Hs.465720

Acyl-CoA synthetase bubblegum family member 2 (ACSBG2)

0.021

1.31

Hs.81934

Acyl-Coenzyme A dehydrogenase, short/branched chain (ACADSB)

0.012

1.98

Hs.88778

Carbonyl reductase 1 (CBR1)

0.037

1.34

Hs.437379

Development and differentiation enhancing factor-like 1 (DDEFL1)

0.013

1.30

Hs.463089

Dodecenoyl-Coenzyme A delta isomerase (DCI)

0.038

1.37

Hs.369762

Enolase superfamily member 1 (ENOSF1)

0.043

0.71

Hs.79322

Glutaminyl-tRNA synthetase (QARS)

0.035

1.37

Hs.647690

Glyceraldehyde 3-phosphate dehydrogenase (GAPDH)

0.003

1.27

Hs.524418

Glycerol-3-phosphate dehydrogenase 1 (GPD1)

0.010

0.44

Hs.180878

Lipoprotein lipase (LPL)

0.002

0.65

Hs.162757

Low density lipoprotein-related protein 1 (LRP1)

0.036

0.68

Hs.514713

Metallophosphoesterase 1 (MPPE1)

0.047

1.39

Hs.94949

Methylmalonyl CoA epimerase (MCEE)

0.039

0.54

Hs.518424

NADH dehydrogenase 1 beta subcomplex, 5 (NDUFB5)

0.008

0.49

Hs.12851

Phosphatidylserine synthase 2 (PTDSS2)

0.036

1.34

Hs.368157

Phosphorylase, glycogen (PYGB)

0.037

1.34

Hs.98381

Protease, serine, 35 (PRSS35)

0.010

0.67

Hs.471441

Proteasome subunit, beta type, 2 (PSMB2)

0.043

0.71

Hs.548558

Similar to cathepsin D (CTSD)

0.034

1.55

Hs.156668

Ubiquinone oxidoreductase complex B15 subunit (NDUFB4)

0.002

2.21

Hs.272011

UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 1 (B4GALT1)

0.037

1.26

Hs.81934

Acyl-Coenzyme A dehydrogenase, short/branched chain (ACADSB)

0.012

1.98

Hs.201667

Aldo-keto reductase family 1, member D1 (AKR1D1)

0.015

2.51

Hs.433901

Cytochrome c oxidase subunit 8A (ubiquitous) (COX8A)

0.021

1.42

Hs.511367

Cytochrome P450, family 19, subfamily A, polypeptide 1 (CYP19A1)

0.029

1.79

Hs.642706

Flavin containing monooxygenase 5 (FMO5)

0.013

1.72

Hs.211046

Hypothetical protein LOC126248 (LOC126248)

0.002

2.24

Hs.518424

NADH dehydrogenase 1 beta subcomplex, 5 (NDUFB5)

0.008

0.49

Hs.125221

Thioredoxin domain containing 1 (TXNDC1)

0.003

1.48

Hs.529019

Bactericidal/permeability-increasing protein (BPI)

0.002

2.02

Hs.534255

Beta-2-microglobulin (B2M)

0.021

1.92

Hs.504641

CD163 antigen (CD163)

0.023

1.29

Hs.278694

CD209 antigen (CD209)

0.003

1.47

Hs.372679

Fc fragment of IgG, low affinity IIIb, receptor (CD16b) (FCGR3B)

0.050

1.66

Hs.3268

Heat shock 70 kDa protein (HSP70B, HSPA6)

0.001

1.28

Hs.497723

Hypothetical protein MGC27165 (MGC27165)

0.011

1.42

Hs.449585

Immunoglobulin lambda locus (IGL@)

0.001

3.03

Hs.389724

Interferon-induced protein 44-like (IFI44L)

0.001

2.53

Hs.77961

Major histocompatibility complex, class I, B (HLA-B)

0.001

2.44

Hs.548432

Similar to CD63 antigen (CD63)

0.016

0.49

Hs.370937

TAP binding protein (tapasin, TAPBP)

0.031

1.91

Hs.352018

Transporter 1, ATP-binding cassette, sub-family B (TAP1)

0.001

3.08