{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T02:25:06Z","timestamp":1793931906313,"version":"4.8.0"},"reference-count":48,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,2,9]],"date-time":"2025-02-09T00:00:00Z","timestamp":1739059200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"STI2030\u2014Major Projects","award":["2023ZD04064"],"award-info":[{"award-number":["2023ZD04064"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The disease caused by Salmonella pullorum has been demonstrated to exert a deleterious effect on the performance of poultry, giving rise to elevated mortality and considerable economic losses within the breeding industry. However, there is a paucity of research investigating the relationship between cecal gene expression and different isomer and Salmonella pullorum infection, and research on the relationship between intestinal microbiota and Salmonella pullorum infection is also limited. In this study, mRNA-Seq and metagenomic sequencing were performed on the cecal tissues and fresh feces of individuals who tested positive (n = 4) and negative (n = 4) for Salmonella pullorum, with the aim of exploring the chickens infected with Salmonella pullorum from two perspectives: the gene transcription level and the microbial level. The mRNA sequencing results revealed 1560 differentially expressed genes (DEGs), of which 380 genes were found to be up-regulated and 1180 genes were down-regulated. A number of genes were reported to be associated with immunity, including AQP8, SLC26A3, CBS, IFI6, DDX60, IL8L1 and IL8L2. Furthermore, a total of 1047 differentially expressed alternative splicings (DEASs) were identified through alternative splicing analysis, including CBS, SLC6A9, ILDR2, OCRL, etc. The joint analysis of DEGs and DEASs revealed 70 genes that exhibited both differentially expressed alternative splicings and differential expression, including CTNND1, TPM1, SPPL2A, etc. The results of metagenomic sequencing demonstrated that the abundances of Bacteroides, Firmicutes, and Verrucobacteria underwent a significant alteration subsequent to the infection of Salmonella pullorum. In summary, the present study conducted a preliminary exploration of the genetic basis of chickens infected with Salmonella pullorum. TPM1 and SPPL2A were found to be differentially expressed by mRNA-Seq, and differences in alternative splicing events. Furthermore, metagenomic sequencing revealed significant changes in the microbial communities of Bacteroidetes, Firmicutes, and Verrucobacteria during infection with Salmonella pullorum.<\/jats:p>","DOI":"10.3390\/ijms26041448","type":"journal-article","created":{"date-parts":[[2025,2,10]],"date-time":"2025-02-10T04:44:03Z","timestamp":1739162643000},"page":"1448","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Application of mRNA-Seq and Metagenomic Sequencing to Study Salmonella pullorum Infections in Chickens"],"prefix":"10.3390","volume":"26","author":[{"given":"Xiaohuan","family":"Chao","sequence":"first","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhexia","family":"Fan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiongwen","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chutian","family":"Ye","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaomeng","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruina","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuya","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7940-1303","authenticated-orcid":false,"given":"Xiquan","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9240-8756","authenticated-orcid":false,"given":"Cheng","family":"Fang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingbin","family":"Luo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Animal Science, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1111\/age.13079","article-title":"Identification of candidate genes associated with slaughter traits in F2 chicken population using genome-wide association study","volume":"52","author":"Liu","year":"2021","journal-title":"Anim. 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