{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T06:58:19Z","timestamp":1790837899631,"version":"4.1.0"},"reference-count":76,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T00:00:00Z","timestamp":1660694400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100011900","name":"Institut Carnot Sant\u00e9 Animale","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011900","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Pasteur Maladies Infectieuses"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Managing <jats:italic>Salmonella enterica<\/jats:italic> Enteritidis (SE) carriage in chicken is necessary to ensure human food safety and enhance the economic, social and environmental sustainability of chicken breeding. <jats:italic>Salmonella<\/jats:italic> can contaminate poultry products, causing human foodborne disease and economic losses for farmers. Both genetic selection for a decreased carriage and gut microbiota modulation strategies could reduce <jats:italic>Salmonella<\/jats:italic> propagation in farms. Two-hundred and twenty animals from the White Leghorn inbred lines N and 6<jats:sub>1<\/jats:sub> were raised together on floor, infected by SE at 7 days of age, transferred into isolators to prevent oro-fecal recontamination and euthanized at 12 days post-infection. Caecal content DNA was used to measure individual <jats:italic>Salmonella<\/jats:italic> counts (ISC) by droplet digital PCR. A RNA sequencing approach was used to measure gene expression levels in caecal tonsils after infection of 48 chicks with low or high ISC. The analysis between lines identified 7516 differentially expressed genes (DEGs) corresponding to 62 enriched Gene Ontology (GO) Biological Processes (BP) terms. A comparison between low and high carriers allowed us to identify 97 DEGs and 23 enriched GO BP terms within line 6<jats:sub>1<\/jats:sub>, and 1034 DEGs and 288 enriched GO BP terms within line N. Among these genes, we identified several candidate genes based on their putative functions, including <jats:italic>FUT2<\/jats:italic> or <jats:italic>MUC4<\/jats:italic>, which could be involved in the control of SE infection, maybe through interactions with commensal bacteria. Altogether, we were able to identify several genes and pathways associated with differences in SE carriage level. These results are discussed in relation to individual caecal microbiota compositions, obtained for the same animals in a previous study, which may interact with host gene expression levels for the control of the caecal SE load.<\/jats:p>","DOI":"10.1371\/journal.pone.0270012","type":"journal-article","created":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T17:34:45Z","timestamp":1660757685000},"page":"e0270012","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Comparative analysis of the caecal tonsil transcriptome in two chicken lines experimentally infected with Salmonella Enteritidis"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5834-2869","authenticated-orcid":true,"given":"Ana\u00efs","family":"Cazals","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6469-488X","authenticated-orcid":true,"given":"Andrea","family":"Rau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordi","family":"Estell\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Bruneau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Luc","family":"Coville","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierrette","family":"Menanteau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1673-5258","authenticated-orcid":true,"given":"Marie-No\u00eblle","family":"Rossignol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah","family":"Jardet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0423-4624","authenticated-orcid":true,"given":"Claudia","family":"Bevilacqua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0825-0886","authenticated-orcid":true,"given":"Bertrand","family":"Bed\u2019Hom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Velge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fanny","family":"Calenge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,8,17]]},"reference":[{"issue":"2","key":"pone.0270012.ref001","first-page":"6406","article-title":"The European Union One Health 2019 Zoonoses Report","volume":"19","author":"EFSA","year":"2021","journal-title":"EFSA J 2021"},{"issue":"9","key":"pone.0270012.ref002","doi-asserted-by":"crossref","first-page":"3246","DOI":"10.1111\/1462-2920.14294","article-title":"Role of systemic infection, cross contaminations and super-shedders in Salmonella carrier state in chicken","volume":"20","author":"P Menanteau","year":"2018","journal-title":"Environ Microbiol"},{"issue":"5","key":"pone.0270012.ref003","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/j.cimid.2012.03.004","article-title":"Early immune dynamics following infection with Salmonella enterica serovars Enteritidis, Infantis, Pullorum and Gallinarum: cytokine and chemokine gene expression profile and cellular changes of chicken cecal tonsils","volume":"35","author":"AM Setta","year":"2012","journal-title":"Comp Immunol Microbiol Infect Dis"},{"issue":"12","key":"pone.0270012.ref004","doi-asserted-by":"crossref","first-page":"5993","DOI":"10.1128\/IAI.00695-07","article-title":"Chicken cecum immune response to Salmonella enterica serovars of different levels of invasiveness","volume":"75","author":"A Berndt","year":"2007","journal-title":"Infect Immun"},{"issue":"8","key":"pone.0270012.ref005","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.3390\/ijms17081207","article-title":"Chicken-Specific Kinome Array Reveals that Salmonella enterica Serovar Enteritidis Modulates Host Immune Signaling Pathways in the Cecum to Establish a Persistence Infection","volume":"17","author":"MH Kogut","year":"2016","journal-title":"Int J Mol Sci"},{"issue":"1","key":"pone.0270012.ref006","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/1297-9716-44-37","article-title":"Chicken innate immune response to oral infection with Salmonella enterica serovar Enteritidis","volume":"44","author":"M Matulova","year":"2013","journal-title":"Vet Res"},{"issue":"2","key":"pone.0270012.ref007","doi-asserted-by":"crossref","first-page":"278","DOI":"10.5713\/ajas.2011.11174","article-title":"Analysis of Gene Expression Responses to a Salmonella Infection in Rugao Chicken Intestine Using GeneChips","volume":"25","author":"DQ Luan","year":"2012","journal-title":"Asian-Australas J Anim Sci"},{"issue":"12","key":"pone.0270012.ref008","doi-asserted-by":"crossref","DOI":"10.3390\/genes10120979","article-title":"Transcriptome Analysis of the Cecal Tonsil of Jingxing Yellow Chickens Revealed the Mechanism of Differential Resistance to Salmonella","volume":"10","author":"F Wang","year":"2019","journal-title":"Genes"},{"issue":"21","key":"pone.0270012.ref009","doi-asserted-by":"crossref","first-page":"9327","DOI":"10.1007\/s00253-020-10887-3","article-title":"Transcriptome profiling analysis of caeca in chicks challenged with Salmonella Typhimurium reveals differential expression of genes involved in host mucosal immune response","volume":"104","author":"S Khan","year":"2020","journal-title":"Appl Microbiol Biotechnol"},{"key":"pone.0270012.ref010","first-page":"154946","article-title":"Identification of key genes in the response to Salmonella enterica Enteritidis, Salmonella enterica Pullorum, and poly(I:C) in chicken spleen and caecum","volume":"2014","author":"T Ma","year":"2014","journal-title":"BioMed Res Int"},{"issue":"14","key":"pone.0270012.ref011","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1016\/j.micinf.2004.07.005","article-title":"Salmonella carrier state in chicken: comparison of expression of immune response genes between susceptible and resistant animals","volume":"6","author":"JR Sadeyen","year":"2004","journal-title":"Microbes Infect"},{"issue":"1","key":"pone.0270012.ref012","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1186\/s12864-021-07748-2","article-title":"Transcriptomic analysis of caecal tissue in inbred chicken lines that exhibit heritable differences in resistance to Campylobacter jejuni","volume":"22","author":"KM Russell","year":"2021","journal-title":"BMC Genomics"},{"issue":"1","key":"pone.0270012.ref013","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1297-9686-42-11","article-title":"Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review","volume":"42","author":"F Calenge","year":"2010","journal-title":"Genet Sel Evol"},{"issue":"5","key":"pone.0270012.ref014","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1186\/1297-9686-37-6-539","article-title":"A genome scan for quantitative trait loci affecting the Salmonella carrier-state in the chicken","volume":"37","author":"P Tilquin","year":"2005","journal-title":"Genet Sel Evol GSE"},{"issue":"5","key":"pone.0270012.ref015","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1111\/j.1365-2052.2009.01884.x","article-title":"QTL for resistance to Salmonella carrier state confirmed in both experimental and commercial chicken lines","volume":"40","author":"F Calenge","year":"2009","journal-title":"Anim Genet"},{"issue":"3","key":"pone.0270012.ref016","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/s00438-011-0600-9","article-title":"New QTL for resistance to Salmonella carrier-state identified on fowl microchromosomes","volume":"285","author":"F Calenge","year":"2011","journal-title":"Mol Genet Genomics"},{"issue":"1","key":"pone.0270012.ref017","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s12711-022-00699-6","article-title":"Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens","volume":"54","author":"A Cazals","year":"2022","journal-title":"Genet Sel Evol GSE"},{"issue":"1","key":"pone.0270012.ref018","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1017\/S0950268803001274","article-title":"Faecal shedding and intestinal colonization of Salmonella enterica in in-bred chickens: the effect of host-genetic background","volume":"132","author":"PA Barrow","year":"2004","journal-title":"Epidemiol Infect"},{"issue":"2","key":"pone.0270012.ref019","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1111\/j.1365-2052.2010.02090.x","article-title":"Genome-wide SNP analysis identifies major QTL for Salmonella colonization in the chicken: Major QTL for Salmonella colonization in the chicken","volume":"42","author":"MS Fife","year":"2011","journal-title":"Anim Genet"},{"issue":"1","key":"pone.0270012.ref020","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1186\/1471-2164-13-198","article-title":"A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state","volume":"13","author":"T Thanh-Son","year":"2012","journal-title":"BMC Genomics"},{"issue":"1","key":"pone.0270012.ref021","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/s00251-008-0340-0","article-title":"Differential mRNA expression of the avian-specific toll-like receptor 15 between heterophils from Salmonella-susceptible and -resistant chickens","volume":"61","author":"JR Nerren","year":"2009","journal-title":"Immunogenetics"},{"issue":"3\u20114","key":"pone.0270012.ref022","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.vetimm.2008.02.010","article-title":"Toll-like receptor gene expression in cecum and spleen of advanced intercross line chicks infected with Salmonella enterica serovar Enteritidis","volume":"123","author":"B Abasht","year":"2008","journal-title":"Vet Immunol Immunopathol"},{"issue":"3\u20114","key":"pone.0270012.ref023","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.vetmic.2009.01.024","article-title":"Expression profile of toll-like receptors within the gastrointestinal tract of 2-day-old Salmonella enteriditis-infected broiler chickens","volume":"137","author":"KM MacKinnon","year":"2009","journal-title":"Vet Microbiol"},{"issue":"4","key":"pone.0270012.ref024","doi-asserted-by":"crossref","first-page":"1038","DOI":"10.3382\/ps.2011-01939","article-title":"Loxoribine pretreatment reduces Salmonella Enteritidis organ invasion in 1-day-old chickens","volume":"91","author":"CL Swaggerty","year":"2012","journal-title":"Poult Sci"},{"issue":"3","key":"pone.0270012.ref025","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1080\/03079457.2011.565310","article-title":"Protein tyrosine kinase and mitogen-activated protein kinase signalling pathways contribute to differences in heterophil-mediated innate immune responsiveness between two lines of broilers","volume":"40","author":"CL Swaggerty","year":"2011","journal-title":"Avian Pathol J WVPA"},{"issue":"5","key":"pone.0270012.ref026","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1111\/1751-7915.13621","article-title":"Gut microbiota composition before infection determines the Salmonella super- and low-shedder phenotypes in chicken","volume":"13","author":"F Kempf","year":"2020","journal-title":"Microb Biotechnol"},{"key":"pone.0270012.ref027","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.freeradbiomed.2014.10.575","article-title":"Regulation of iNOS function and cellular redox state by macrophage Gch1 reveals specific requirements for tetrahydrobiopterin in NRF2 activation","volume":"79","author":"E McNeill","year":"2015","journal-title":"Free Radic Biol Med"},{"issue":"2","key":"pone.0270012.ref028","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1084\/jem.192.2.237","article-title":"Antimicrobial actions of the NADPH phagocyte oxidase and inducible nitric oxide synthase in experimental salmonellosis. II. Effects on microbial proliferation and host survival in vivo","volume":"192","author":"P Mastroeni","year":"2000","journal-title":"J Exp Med"},{"issue":"9","key":"pone.0270012.ref029","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/S1286-4579(01)01428-9","article-title":"Inducible nitric oxide synthase and Salmonella infection","volume":"3","author":"BJ Cherayil","year":"2001","journal-title":"Microbes Infect"},{"issue":"4","key":"pone.0270012.ref030","doi-asserted-by":"crossref","first-page":"1997","DOI":"10.1128\/IAI.70.4.1997-2009.2002","article-title":"Host Immune Response to Salmonella enterica Serovar Typhimurium Infection in Mice Derived from Wild Strains","volume":"70","author":"G Sebastiani","year":"2002","journal-title":"Infect Immun"},{"issue":"7","key":"pone.0270012.ref031","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/sj.gene.6363924","article-title":"Genetic regulation of host responses to Salmonella infection in mice","volume":"3","author":"MF Roy","year":"2002","journal-title":"Genes Immun"},{"issue":"12","key":"pone.0270012.ref032","doi-asserted-by":"crossref","first-page":"1833","DOI":"10.1111\/cmi.12476","article-title":"Low-oxygen tensions found in Salmonella-infected gut tissue boost Salmonella replication in macrophages by impairing antimicrobial activity and augmenting Salmonella virulence","volume":"17","author":"J Jennewein","year":"2015","journal-title":"Cell Microbiol"},{"key":"pone.0270012.ref033","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.freeradbiomed.2017.12.032","article-title":"Nitric oxide synthase 2 enhances the survival of mice during Salmonella Typhimurium infection-induced sepsis by increasing reactive oxygen species, inflammatory cytokines and recruitment of neutrophils to the peritoneal cavity","volume":"116","author":"S Yadav","year":"2018","journal-title":"Free Radic Biol Med"},{"issue":"14","key":"pone.0270012.ref034","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1016\/j.micinf.2008.08.008","article-title":"Salmonella enterica serovar Enteritidis dam mutant induces low NOS-2 and COX-2 expression in macrophages via attenuation of MAPK and NF-\u03baB pathways","volume":"10","author":"M Cristina Cerquetti","year":"2008","journal-title":"Microbes Infect"},{"issue":"5","key":"pone.0270012.ref035","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1084\/jem.20121946","article-title":"Nitric oxide\u2013mediated regulation of ferroportin-1 controls macrophage iron homeostasis and immune function in Salmonella infection","volume":"210","author":"M Nairz","year":"2013","journal-title":"J Exp Med"},{"key":"pone.0270012.ref036","first-page":"35","article-title":"Association of INOS, TRAIL, TGF-beta2, TGF-beta3, and IgL genes with response to Salmonella enteritidis in poultry","volume":"1","author":"M Malek","year":"2003","journal-title":"Genet Sel Evol GSE"},{"issue":"6","key":"pone.0270012.ref037","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1080\/03079457.2012.739680","article-title":"The effects of polymorphisms in IL-2, IFN-\u03b3, TGF-\u03b22, IgL, TLR-4, MD-2, and iNOS genes on resistance to Salmonella enteritidis in indigenous chickens","volume":"41","author":"R Tohidi","year":"2012","journal-title":"Avian Pathol J WVPA"},{"key":"pone.0270012.ref038","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.vetimm.2017.11.002","article-title":"Chicken macrophages infected with Salmonella (S.) Enteritidis or S. Heidelberg produce differential responses in immune and metabolic signaling pathways","volume":"195","author":"H He","year":"2018","journal-title":"Vet Immunol Immunopathol"},{"issue":"4","key":"pone.0270012.ref039","doi-asserted-by":"crossref","first-page":"e0247938","DOI":"10.1371\/journal.pone.0247938","article-title":"Efficacy of a nanoparticle vaccine administered in-ovo against Salmonella in broilers","volume":"16","author":"K Acevedo-Villanueva","year":"2021","journal-title":"PloS One"},{"issue":"10","key":"pone.0270012.ref040","doi-asserted-by":"crossref","first-page":"e106188","DOI":"10.15252\/embj.2020106188","article-title":"TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria","volume":"40","author":"F Breyer","year":"2021","journal-title":"EMBO J"},{"issue":"3","key":"pone.0270012.ref041","doi-asserted-by":"crossref","first-page":"151487","DOI":"10.1016\/j.ijmm.2021.151487","article-title":"The role of the blood group-related glycosyltransferases FUT2 and B4GALNT2 in susceptibility to infectious disease","volume":"311","author":"A Galeev","year":"2021","journal-title":"Int J Med Microbiol IJMM"},{"issue":"6202","key":"pone.0270012.ref042","doi-asserted-by":"crossref","first-page":"1254009","DOI":"10.1126\/science.1254009","article-title":"Innate lymphoid cells regulate intestinal epithelial cell glycosylation","volume":"345","author":"Y Goto","year":"2014","journal-title":"Science"},{"issue":"7","key":"pone.0270012.ref043","doi-asserted-by":"crossref","first-page":"e1007915","DOI":"10.1371\/journal.ppat.1007915","article-title":"Std fimbriae-fucose interaction increases Salmonella-induced intestinal inflammation and prolongs colonization","volume":"15","author":"A Suwandi","year":"2019","journal-title":"PLoS Pathog"},{"issue":"4","key":"pone.0270012.ref044","doi-asserted-by":"crossref","first-page":"e94863","DOI":"10.1371\/journal.pone.0094863","article-title":"Faecal microbiota composition in adults is associated with the FUT2 gene determining the secretor status","volume":"9","author":"P Wacklin","year":"2014","journal-title":"PloS One"},{"issue":"11","key":"pone.0270012.ref045","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1038\/nrg.2017.63","article-title":"Human genetic variation and the gut microbiome in disease","volume":"18","author":"AB Hall","year":"2017","journal-title":"Nat Rev Genet"},{"issue":"1","key":"pone.0270012.ref046","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/s12915-019-0699-4","article-title":"The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health","volume":"17","author":"JL Waters","year":"2019","journal-title":"BMC Biol"},{"key":"pone.0270012.ref047","doi-asserted-by":"crossref","first-page":"601089","DOI":"10.3389\/fimmu.2020.601089","article-title":"From Chickens to Humans: The Importance of Peptide Repertoires for MHC Class I Alleles","volume":"11","author":"J. Kaufman","year":"2020","journal-title":"Front Immunol"},{"issue":"3","key":"pone.0270012.ref048","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/s00251-003-0566-9","article-title":"Chicken MHC class I and II gene effects on antibody response kinetics in adult chickens","volume":"55","author":"H Zhou","year":"2003","journal-title":"Immunogenetics"},{"issue":"8","key":"pone.0270012.ref049","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1007\/s00251-002-0495-z","article-title":"Association of MHC class I and class II gene polymorphisms with vaccine or challenge response to Salmonella enteritidis in young chicks","volume":"54","author":"W Liu","year":"2002","journal-title":"Immunogenetics"},{"issue":"5","key":"pone.0270012.ref050","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1016\/j.chom.2011.04.012","article-title":"Invasive Bacterial Pathogens Exploit TLR-Mediated Downregulation of Tight Junction Components to Facilitate Translocation across the Epithelium","volume":"9","author":"TB Clarke","year":"2011","journal-title":"Cell Host Microbe"},{"issue":"3","key":"pone.0270012.ref051","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1080\/10409238.2018.1458071","article-title":"Functions of the sirtuin deacylase SIRT5 in normal physiology and pathobiology","volume":"53","author":"S Kumar","year":"2018","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"pone.0270012.ref052","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.3389\/fimmu.2020.01882","article-title":"Control of Gut Inflammation by Modulation of Purinergic Signaling","volume":"11","author":"M Vuerich","year":"2020","journal-title":"Front Immunol"},{"issue":"Pt A","key":"pone.0270012.ref053","doi-asserted-by":"crossref","first-page":"107055","DOI":"10.1016\/j.intimp.2020.107055","article-title":"Implications of CD39 in immune-related diseases","volume":"89","author":"J Zeng","year":"2020","journal-title":"Int Immunopharmacol"},{"issue":"2","key":"pone.0270012.ref054","doi-asserted-by":"crossref","first-page":"775","DOI":"10.3390\/biom5020775","article-title":"Extracellular adenosine generation in the regulation of pro-inflammatory responses and pathogen colonization","volume":"5","author":"MS Alam","year":"2015","journal-title":"Biomolecules"},{"issue":"1","key":"pone.0270012.ref055","doi-asserted-by":"crossref","first-page":"289","DOI":"10.3945\/ajcn.113.080549","article-title":"Single-nucleotide polymorphisms in SLC22A23 are associated with ulcerative colitis in a Canadian white cohort","volume":"100","author":"A Serrano Le\u00f3n","year":"2014","journal-title":"Am J Clin Nutr"},{"key":"pone.0270012.ref056","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.3389\/fimmu.2020.01080","article-title":"Cytotoxic Granule Trafficking and Fusion in Synaptotagmin7-Deficient Cytotoxic T Lymphocytes","volume":"11","author":"M Sleiman","year":"2020","journal-title":"Front Immunol"},{"issue":"7","key":"pone.0270012.ref057","doi-asserted-by":"crossref","first-page":"E1697","DOI":"10.3390\/cells9071697","article-title":"In Silico Evaluation of Putative S100B Interacting Proteins in Healthy and IBD Gut Microbiota","volume":"9","author":"M Orsini","year":"2020","journal-title":"Cells"},{"issue":"11","key":"pone.0270012.ref058","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.3390\/pathogens10111512","article-title":"The Interplay between Salmonella and Intestinal Innate Immune Cells in Chickens","volume":"10","author":"A Ijaz","year":"2021","journal-title":"Pathogens"},{"issue":"3","key":"pone.0270012.ref059","doi-asserted-by":"crossref","first-page":"101639","DOI":"10.1016\/j.psj.2021.101639","article-title":"Bacillus coagulans protect against Salmonella enteritidis-induced intestinal mucosal damage in young chickens by inducing the differentiation of goblet cells","volume":"101","author":"S Xie","year":"2022","journal-title":"Poult Sci"},{"issue":"1","key":"pone.0270012.ref060","doi-asserted-by":"crossref","first-page":"skz396","DOI":"10.1093\/jas\/skz396","article-title":"Effects of inulin supplementation on intestinal barrier function and immunity in specific pathogen-free chickens with Salmonella infection","volume":"98","author":"J Song","year":"2020","journal-title":"J Anim Sci"},{"issue":"7","key":"pone.0270012.ref061","doi-asserted-by":"crossref","first-page":"e0131474","DOI":"10.1371\/journal.pone.0131474","article-title":"High Incubation Temperature and Threonine Dietary Level Improve Ileum Response Against Post-Hatch Salmonella Enteritidis Inoculation in Broiler Chicks","volume":"10","author":"Filho AL de Barros Moreira","year":"2015","journal-title":"PLoS ONE"},{"issue":"1","key":"pone.0270012.ref062","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.jcpa.2008.10.002","article-title":"Expression of mucins and trefoil factor family protein-1 in the colon of pigs naturally infected with Salmonella typhimurium","volume":"140","author":"CH Kim","year":"2009","journal-title":"J Comp Pathol"},{"issue":"3","key":"pone.0270012.ref063","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1111\/jpn.13063","article-title":"Effect of Mucine 4 and Fucosyltransferase 1 genetic variants on gut homoeostasis of growing healthy pigs","volume":"103","author":"D Luise","year":"2019","journal-title":"J Anim Physiol Anim Nutr"},{"issue":"1\u20114","key":"pone.0270012.ref064","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1159\/000075742","article-title":"Linkage and comparative mapping of the locus controlling susceptibility towards E. COLI F4ab\/ac diarrhoea in pigs","volume":"102","author":"CB J\u00f8rgensen","year":"2003","journal-title":"Cytogenet Genome Res"},{"key":"pone.0270012.ref065","doi-asserted-by":"crossref","first-page":"89","DOI":"10.3389\/fimmu.2018.00089","article-title":"The Role of Cytochromes P450 in Infection","volume":"9","author":"E Stavropoulou","year":"2018","journal-title":"Front Immunol"},{"key":"pone.0270012.ref066","article-title":"Intestinal cytochromes P450 regulating the intestinal microbiota and its probiotic profile","volume":"23","author":"EEV Bezirtzoglou","year":"2012","journal-title":"Microb Ecol Health Dis"},{"issue":"28","key":"pone.0270012.ref067","doi-asserted-by":"crossref","first-page":"16828","DOI":"10.1016\/S0021-9258(19)84781-6","article-title":"Molecular cloning and characterization of a chromosomal gene for human eosinophil peroxidase*","volume":"264","author":"K Sakamaki","year":"1989","journal-title":"J Biol Chem"},{"key":"pone.0270012.ref068","doi-asserted-by":"crossref","first-page":"214","DOI":"10.3389\/fvets.2017.00214","article-title":"Differential Levels of Cecal Colonization by Salmonella Enteritidis in Chickens Triggers Distinct Immune Kinome Profiles","volume":"4","author":"CL Swaggerty","year":"2017","journal-title":"Front Vet Sci"},{"issue":"4","key":"pone.0270012.ref069","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1078\/1438-4221-00263","article-title":"Membrane ruffling and invasion of human and avian cell lines is reduced for aflagellate mutants of Salmonella enterica serotype Enteritidis","volume":"293","author":"RM La Ragione","year":"2003","journal-title":"Int J Med Microbiol"},{"issue":"3","key":"pone.0270012.ref070","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.clim.2004.07.014","article-title":"Targeting of the actin cytoskeleton during infection by Salmonella strains","volume":"114","author":"DG Guiney","year":"2005","journal-title":"Clin Immunol Orlando Fla"},{"key":"pone.0270012.ref071","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.3389\/fmicb.2020.01512","article-title":"Validation of Droplet Digital Polymerase Chain Reaction for Salmonella spp","volume":"11","author":"C Villamil","year":"2020","journal-title":"Quantification. Front Microbiol"},{"issue":"8","key":"pone.0270012.ref072","doi-asserted-by":"crossref","first-page":"3050","DOI":"10.1128\/JCM.40.8.3050-3052.2002","article-title":"Real-Time PCR Detection of Salmonella in Suspect Foods from a Gastroenteritis Outbreak in Kerr County, Texas","volume":"40","author":"LT Daum","year":"2002","journal-title":"J Clin Microbiol"},{"issue":"1","key":"pone.0270012.ref073","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinforma Oxf Engl"},{"issue":"2","key":"pone.0270012.ref074","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"S Anders","year":"2015","journal-title":"Bioinformatics"},{"issue":"12","key":"pone.0270012.ref075","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"key":"pone.0270012.ref076","article-title":"topGO: Enrichment Analysis for Gene Ontology [Internet]","author":"A Alexa","year":"2021","journal-title":"Bioconductor version: Release (3.12)"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0270012","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T17:35:42Z","timestamp":1660757742000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0270012"}},"subtitle":[],"editor":[{"given":"Michael H.","family":"Kogut","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,8,17]]},"references-count":76,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2022,8,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0270012","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,17]]}}}