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Plenty of studies demonstrate that antibiotics can disrupt gut ecosystem leading to dysbiosis. Little is known about the microbial variation of appendix and its up\/downstream intestine after antibiotic treatment. This study aimed to investigate the microbiome and mucosal morphology of jejunum, appendix, and colon of rats in health and dysbiosis. A rodent model of antibiotic-induced dysbiosis was employed. Microscopy was used to observe mucosal morphological changes. 16S rRNA sequencing was performed for identifying bacterial taxa and microbiome structure. The appendices of dysbiosis were found enlarged and inflated with loose contents. Microscopy revealed the impairment of intestinal epithelial cells. High-throughput sequencing showed the Operational Taxonomic Units changed from 361\u2009\u00b1\u200933, 634\u2009\u00b1\u200918, 639\u2009\u00b1\u200919 in the normal jejunum, appendix, colon to 748\u2009\u00b1\u200998, 230\u2009\u00b1\u200911, 253\u2009\u00b1\u200916 in the disordered segments, respectively. In dysbiosis,\n                    <jats:italic>Bacteroidetes<\/jats:italic>\n                    translocated inversely from the colon and appendix (0.26%, 0.23%) to the jejunum (13.87%\u2009\u00b1\u20090.11%); the relative abundance of all intestinal\n                    <jats:italic>Enterococcaceae<\/jats:italic>\n                    increased, while\n                    <jats:italic>Lactobacillaceae<\/jats:italic>\n                    decreased. Several bacterial clusters were found correlated to the normal appendix, whereas nonspecific clusters correlated to the disordered appendix. In conclusion, species richness and evenness reduced in the disordered appendix and colon; similar microbiome patterns were shared between the appendix and colon regardless of dysbiosis; site-specific bacteria were missing in the disordered appendix. Appendix is likely a transit region involving in upper and lower intestinal microflora modulation. The limitation of this study is all the data were derived from rats. We must be cautious about translating the microbiome results from rats to humans.\n                  <\/jats:p>","DOI":"10.1007\/s00284-023-03224-0","type":"journal-article","created":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T10:03:13Z","timestamp":1678096993000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Microbiome Structure and Mucosal Morphology of Jejunum Appendix and Colon of Rats in Health and Dysbiosis"],"prefix":"10.1007","volume":"80","author":[{"given":"Chenyi","family":"Shao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaobo","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongying","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinhui","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunhao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shenmin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baowei","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3014-8359","authenticated-orcid":false,"given":"Li","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,3,6]]},"reference":[{"issue":"4","key":"3224_CR1","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1016\/j.chom.2017.03.010","volume":"21","author":"C Tropini","year":"2017","unstructured":"Tropini C, Earle KA, Huang KC, Sonnenburg JL (2017) The gut microbiome: connecting spatial organization to function. 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