{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T11:19:21Z","timestamp":1790680761826,"version":"4.1.0"},"reference-count":57,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,6,6]],"date-time":"2023-06-06T00:00:00Z","timestamp":1686009600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020051","name":"Jiangsu Agriculture Research System","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Coccidiosis is an intestinal parasitic disease caused by\n                      <jats:italic>Eimeria<\/jats:italic>\n                      protozoa, which endangers the health and growth of animals, and causes huge economic losses to the poultry industry worldwide every year. Studies have shown that poultry gut microbiota plays an important role in preventing the colonization of pathogens and maintaining the health of the host. Coccidia infection also affects host gene expression. However, the underlying potential relationship between gut microbiome and host transcriptome during\n                      <jats:italic>E. tenella<\/jats:italic>\n                      infection in chickens remain unclear.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In this study, metagenomic and transcriptome sequencing were applied to identify microbiota and genes in cecal contents and cecal tissues of infected (JS) and control (JC) chickens on day 4.5 postinfection (pi), respectively.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      First, microbial sequencing results of cecal contents showed that the abundance of\n                      <jats:italic>Lactobacillus, Roseburia<\/jats:italic>\n                      sp. and\n                      <jats:italic>Faecalibacterium<\/jats:italic>\n                      sp decreased significantly after\n                      <jats:italic>E. tenella<\/jats:italic>\n                      infection (\n                      <jats:italic>P<\/jats:italic>\n                      &amp;lt; 0.05), while the abundance of\n                      <jats:italic>Alistipes<\/jats:italic>\n                      and\n                      <jats:italic>Prevotella pectinovora<\/jats:italic>\n                      increased significantly (\n                      <jats:italic>P<\/jats:italic>\n                      &amp;lt; 0.05). Second, transcriptome sequencing results showed that a total of 434 differentially expressed mRNAs were identified, including 196 up-regulated and 238 down-regulated genes. These differentially expressed genes related to inflammation and immunity, such as\n                      <jats:italic>GAMA, FABP1, F2RL1 and RSAD2<\/jats:italic>\n                      , may play an important role in the process of host resistance to coccidia infection. Functional studies showed that the enriched pathways of differentially expressed genes included the TGF-beta signaling pathway and the ErbB signaling pathways. Finally, the integrated analysis of gut microbiome and host transcriptome suggested that\n                      <jats:italic>Prevotella pectinovora<\/jats:italic>\n                      associated with\n                      <jats:italic>FABP1<\/jats:italic>\n                      ,\n                      <jats:italic>Butyricicoccus<\/jats:italic>\n                      porcorum and\n                      <jats:italic>Colidextribacter<\/jats:italic>\n                      sp. associated with\n                      <jats:italic>RSAD2<\/jats:italic>\n                      were involved in the immune response upon\n                      <jats:italic>E. tenella<\/jats:italic>\n                      infection.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      In conclusion, this study provides valuable information on the microbiota and key immune genes after chicken\n                      <jats:italic>E. tenella<\/jats:italic>\n                      infection, with the aim of providing reference for the impact of coccidia infection on cecal microbiome and host.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcimb.2023.1191939","type":"journal-article","created":{"date-parts":[[2023,6,6]],"date-time":"2023-06-06T12:40:15Z","timestamp":1686055215000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":29,"title":["Comprehensive analysis of gut microbiome and host transcriptome in chickens after Eimeria tenella infection"],"prefix":"10.3389","volume":"13","author":[{"given":"Hailiang","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianqiang","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liyue","family":"Dong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guojun","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Genxi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaizhou","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongsheng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenhua","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,6,6]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2013a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0194825","article-title":"At-Hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota","volume":"13","author":"Baldwin","year":"2018","journal-title":"PloS One"},{"key":"B3","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/B978-0-12-386471-0.00007-9","article-title":"The SerpinB1 knockout mouse a model for studying neutrophil protease regulation in homeostasis and inflammation","volume":"499","author":"Benarafa","year":"2011","journal-title":"Methods Enzymol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1186\/s13567-020-00837-2","article-title":"Re-calculating the cost of coccidiosis in chickens","volume":"51","author":"Blake","year":"2020","journal-title":"Vet. 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