Clostridium perfringens-Induced Host-Pathogen Transcriptional Changes in the Small Intestine of Broiler Chickens
Abstract
:1. Introduction
2. Materials and methods
2.1. Animals Used for This Study
2.2. Challenge Infection by C. perfringens and RNA Extraction
2.3. Library Construction and Sequencing Analysis
2.4. Statistical Analysis
3. Results
3.1. Growth Underperformance Post C. perfringens Infection
3.2. Identification of DEGs in the Small Intestines between C. perfringens-Infected and Control Groups
3.3. Identification of Highly Abundant Up-/Down-Regulated Genes in Response to C. perfringens Infection
3.4. GO Annotation for DEGs
3.5. The Mapping of C. perfringens and Other Foodborne Pathogens
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
NE | necrotic enteritis |
RNA-seq | RNA sequencing |
NV | uninfected sham control |
RBWG% | relative body weight gain percentage |
GO | Gene Ontology |
DGE | Differential gene expression |
DEG | Differentially expressed genes |
FDR | False discovery rate |
References
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Gene ID# | FDR | Chromosome | Gene Symbol | Description | Absolute Fold Change |
---|---|---|---|---|---|
ENSGALT00000099249 | 0.001 | 9 | PCYT1A | phosphate cytidylyltransferase 1, choline, alpha | 26.26 |
ENSGALT00000065275 | 0 | 2 | CBX3 | chromobox 3 (CBX3) | 25.65 |
ENSGALT00000102383 | 0.026 | 12 | FLNB | filamin B (FLNB) | 25.32 |
ENSGALT00000080045 | 0 | 10 | VPS33B, | late endosome and lysosome associated | 24.22 |
ENSGALT00000047160 | 0.012 | 7 | SPEG | complex locus [SourceNCBIgene; Acc429033] 0 | 20.46 |
ENSGALT00000017218 | 0.013 | 3 | STRN | striatin [SourceHGNC Symbol;AccHGNC11424] 00 | 18.08 |
ENSGALT00000103665 | 0.044 | 31 | NA | 16.51 | |
ENSGALT00000065256 | 0.025 | 3 | DAAM2 | dishevelled associated activator of morphogenesis | 16.38 |
ENSGALT00000101515 | 0.008 | 28 | TCF3 | transcription factor 3 | 12.86 |
ENSGALT00000108349 | 0 | 17 | NACC2 | NACC family member | 12.76 |
ENSGALT00000095627 | 0.005 | 33 | CCS | copper chaperone for superoxide dismutase | 12.64 |
ENSGALT00000082640 | 0.013 | 33 | NACA | nascent polypeptide associated complex subunit | 12.29 |
ENSGALT00000047943 | 0.001 | 15 | DEP | domain containing 5 [SourceNCBI gene; Acc416956] | 11.39 |
ENSGALT00000087703 | 0 | 1 | NA | 11.32 | |
ENSGALT00000094693 | 0.001 | 26 | NA | 10.12 | |
ENSGALT00000026339 | 0.039 | 3 | GSTA2 | Glutathione S-Transferase 2 | 9.41 |
ENSGALT00000012083 | 0.009 | 9 | PCYT1A | phosphate cytidylyltransferase 1, choline, alpha | 8.66 |
ENSGALT00000090554 | 0.018 | NA | 7.86 | ||
ENSGALT00000074687 | 0 | 20 | MYL9 | myosin, light chain 9, regulatory | 7.79 |
ENSGALT00000014587 | 0.003 | 3 | EPCAM | epithelial cell adhesion | 6.86 |
ENSGALT00000091530 | 0.012 | 6 | NA | 6.45 | |
ENSGALT00000095666 | 0 | 2 | SLC4A7 | solute carrier family 4 member | 6.36 |
ENSGALT00000018245 | 0.024 | 4 | NA | 6.08 | |
ENSGALT00000050930 | 0.013 | 23 | PUM1 | pumilio RNA binding | 6.01 |
ENSGALT00000081307 | 0.001 | 2 | STT3B | STT3B, catalytic subunit | 5.98 |
ENSGALT00000067100 | 0.011 | 1 | ATP2B1 | ATese plasma membrane | 5.52 |
ENSGALT00000063811 | 0.008 | Z | ribosomal | ribosomal protein S23 | 5.36 |
ENSGALT00000107263 | 0.039 | 1 | FNDC3A | fibronectin type III | 5.30 |
ENSGALT00000099291 | 0.029 | 28 | GATAD2A | GATA zinc finger domain containing | 5.13 |
ENSGALT00000092961 | 0.019 | 25 | MTMR11 | myotubularin related protein 11 [SourceHGNC | 4.46 |
ENSGALT00000092785 | 0.016 | NA | 4.29 | ||
ENSGALT00000060227 | 0.005 | 14 | HBM | hemoglobin subunit mu | 4.26 |
ENSGALT00000056811 | 0.012 | 30 | DNM2 | dynamin 2 [SourceHGNC Symbol;AccHGNC2974] 0 | 4.17 |
ENSGALT00000057600 | 0.013 | 1 | IL17D | interleukin 17D [SourceHGNC Symbol;AccHGNC5984] 0 | 4.07 |
ENSGALT00000070149 | 0.045 | 31 | DHDH | dihydrodiol dehydrogena | 4.04 |
ENSGALT00000094063 | 0.045 | 16 | NA | 3.82 | |
ENSGALT00000026767 | 0.026 | 3 | PBK | PDZ binding kinase | 3.82 |
ENSGALT00000033333 | 0.012 | 8 | LMO4 | LIM domain only | 3.81 |
ENSGALT00000098491 | 0.004 | 6 | NA | 3.50 | |
ENSGALT00000053882 | 0.031 | 17 | NA | 3.36 | |
ENSGALT00000089781 | 0.001 | 1 | DCN | decorin (DCN), mRNA | 3.31 |
ENSGALT00000036373 | 0.04 | 1 | HBBA | hemoglobin beta, subunit A [SourceNCBI | 3.20 |
ENSGALT00000038226 | 0.035 | 15 | SMTN | smoothelin [SourceNCBI gene; Acc100858894] 00 | 3.20 |
ENSGALT00000104581 | 0.016 | 2 | 2.66 | ||
ENSGALT00000043405 | 0.047 | 28 | TIMM13 | translocase of inner mitochondrial membrane | 2.59 |
ENSGALT00000107499 | 0.047 | 18 | SRSF2 | serine/arginine-rich splicing factor | 2.55 |
ENSGALT00000068151 | 0.023 | MT | ND6 | NADH dehydrogenase subunit 6 [SourceNCBI | 2.28 |
ENSGALT00000045265 | 0.045 | 3 | Cystatin | SourceUniProtKB/Swiss-Prot; AccP01038]0000 | 2.11 |
Gene ID# | FDR | Chromosome | Gene Symbol | Description | Absolute Fold Change |
---|---|---|---|---|---|
ENSGALT00000096799 | 0.045 | #N/A | #N/A | −45.54 | |
ENSGALT00000087336 | 0.021 | 15 | CORO1C | coronin 1C (CORO1C) | −32.92 |
ENSGALT00000077706 | 0.002 | 8 | PTPRF | protein tyrosine phosphatase, receptor type | −29.51 |
ENSGALT00000081103 | 0 | 6 | PSAP | prosaposin | −27.67 |
ENSGALT00000049779 | 0 | 9 | EIF4G1 | eukaryotic translation initiation factor 4 | −24.18 |
ENSGALT00000087331 | 0.016 | 6 | microsemino protein beta | −22.96 | |
ENSGALT00000078878 | 0.043 | #N/A | #N/A | −22.35 | |
ENSGALT00000066511 | 0.023 | 2 | RPL7 | ribosomal protein L7 | −15.15 |
ENSGALT00000064276 | 0.028 | 18 | TBCD | tubulin folding cofactor | −12.68 |
ENSGALT00000018692 | 0 | 5 | EIF5 | eukaryotic translation initiation | −12.48 |
ENSGALT00000096298 | 0.036 | 3 | SMAP1 | small ArfGAP 1 | −12.08 |
ENSGALT00000021113 | 0 | 1 | DENND5B | DENN domain containing 5B | −10.93 |
ENSGALT00000036292 | 0.005 | 12 | PRKCD | protein kinase C | −10.82 |
ENSGALT00000098137 | 0 | 3 | SPTBN1 | spectrinbeta non-erythrocytic | −9.17 |
ENSGALT00000101130 | 0 | 9 | PCYT1A | phosphate cytidylyltransferase 1, choline, alpha | −8.61 |
ENSGALT00000047339 | 0.05 | 4 | SMAD1 | SMAD family member 1 | −8.45 |
ENSGALT00000095523 | 0.007 | 4 | FAT1 | FAT atypical cadherin 1 | −8.33 |
ENSGALT00000096470 | 0 | 2 | SLC4A7 | Solute carrier family4 member | −6.63 |
ENSGALT00000107225 | 0 | 24 | APOA4 | apolipoprotein A4(APOA4) | −6.43 |
ENSGALT00000055069 | 0.003 | 2 | SEMA5A | semaphorin 5A | −6.34 |
ENSGALT00000007275 | 0.027 | 20 | NCOA3 | nuclear receptor coactivator 3 | −6.32 |
ENSGALT00000090409 | 0.05 | 1 | TMCC3 | transmembrane and coiled-coil domain family | −5.76 |
ENSGALT00000107684 | 0.001 | 6 | PDCD4 | programmed cell death 4 | −5.31 |
ENSGALT00000015332 | 0.026 | 3 | BROX | BRO1 domain and CAAX motif | −4.73 |
ENSGALT00000086950 | 0.023 | 2 | YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase | −4.63 |
ENSGALT00000017711 | 0.045 | 7 | ABCB11 | ATP binding cassette subfamily B | −4.50 |
ENSGALT00000022319 | 0.003 | 3 | GTF2H5 | general transcription factor | −4.37 |
ENSGALT00000104993 | 0.009 | 8 | LMO4 | LIM domain only | −4.26 |
ENSGALT00000004104 | 0.027 | 21 | CLSTN1 | Cal syntenin 1 (CLSTN1) | −3.90 |
ENSGALT00000007773 | 0.002 | 15 | ISCU | iron-sulfur cluster assembly enzyme | −3.78 |
ENSGALT00000061711 | 0.004 | 23 | PTP4A2 | protein tyrosine phosphatase type IVA, | −3.53 |
ENSGALT00000006691 | 0.012 | 8 | SOAT1 | sterol O-acyltransferase 1 | −3.32 |
ENSGALT00000032201 | 0.025 | 4 | HPGD | 15-hydroxyprostaglandin dehydrogenase (HPGD) | −3.23 |
ENSGALT00000039749 | 0.001 | 1 | CD36 | CD36 molecule (CD36) | −3.15 |
ENSGALT00000025653 | 0 | 3 | EEF1A1 | eukaryotic translation elongation factor 1 | −3.12 |
ENSGALT00000105502 | 0.017 | #N/A | #N/A | −2.90 | |
ENSGALT00000008547 | 0.001 | 9 | RBP2 | retinol binding protein | −2.90 |
ENSGALT00000066968 | 0 | #N/A | #N/A | −2.83 | |
ENSGALT00000063525 | 0.045 | 6 | CYP2C18 | cytochrome | −2.79 |
ENSGALT00000018393 | 0.025 | 2 | RAB5A | RAB5A, member RAS | −2.74 |
ENSGALT00000024116 | 0.026 | 3 | SOT3A1L | sulfotransferase family 3A | −2.56 |
ENSGALT00000052923 | 0.023 | 11 | CA7 | carbonic anhydrase 7 | −2.54 |
ENSGALT00000089467 | 0.049 | 16 | BF1 | MHC BF1 | −2.47 |
ENSGALT00000019554 | 0.043 | 4 | FABP2 | fatty acid binding protein 2 | −2.45 |
ENSGALT00000083719 | 0.012 | 2 | MEP1B | meprin A subunit beta | −2.39 |
ENSGALT00000086032 | 0.028 | 1 | GAPDH | glyceraldehyde-3-phosphate dehydrogenase | −2.33 |
ENSGALT00000062517 | 0.035 | #N/A | #N/A | −2.21 | |
ENSGALT00000004055 | 0.028 | 15 | RAN | RAN, member RAS | −2.15 |
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Lu, M.; Yuan, B.; Yan, X.; Sun, Z.; Lillehoj, H.S.; Lee, Y.; Baldwin-Bott, C.; Li, C. Clostridium perfringens-Induced Host-Pathogen Transcriptional Changes in the Small Intestine of Broiler Chickens. Pathogens 2021, 10, 1607. https://doi.org/10.3390/pathogens10121607
Lu M, Yuan B, Yan X, Sun Z, Lillehoj HS, Lee Y, Baldwin-Bott C, Li C. Clostridium perfringens-Induced Host-Pathogen Transcriptional Changes in the Small Intestine of Broiler Chickens. Pathogens. 2021; 10(12):1607. https://doi.org/10.3390/pathogens10121607
Chicago/Turabian StyleLu, Mingmin, Baohong Yuan, Xianghe Yan, Zhifeng Sun, Hyun S. Lillehoj, Youngsub Lee, Calder Baldwin-Bott, and Charles Li. 2021. "Clostridium perfringens-Induced Host-Pathogen Transcriptional Changes in the Small Intestine of Broiler Chickens" Pathogens 10, no. 12: 1607. https://doi.org/10.3390/pathogens10121607
APA StyleLu, M., Yuan, B., Yan, X., Sun, Z., Lillehoj, H. S., Lee, Y., Baldwin-Bott, C., & Li, C. (2021). Clostridium perfringens-Induced Host-Pathogen Transcriptional Changes in the Small Intestine of Broiler Chickens. Pathogens, 10(12), 1607. https://doi.org/10.3390/pathogens10121607