{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T16:59:23Z","timestamp":1785862763668,"version":"3.56.0"},"reference-count":75,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2020,12,26]],"date-time":"2020-12-26T00:00:00Z","timestamp":1608940800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The microbiota is extremely important for the animal\u2019s health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species, while the highest variability was found in the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.<\/jats:p>","DOI":"10.3390\/ani11010031","type":"journal-article","created":{"date-parts":[[2020,12,27]],"date-time":"2020-12-27T20:04:58Z","timestamp":1609099498000},"page":"31","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":53,"title":["Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8081-3332","authenticated-orcid":false,"given":"Elisa","family":"Cotozzolo","sequence":"first","affiliation":[{"name":"Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paola","family":"Cremonesi","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Biology and Biotechnology (IBBA)\u2014National Research Council (CNR), U.O.S. di Lodi, Via Einstein, 26900 Lodi, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6352-0036","authenticated-orcid":false,"given":"Giulio","family":"Curone","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Milano, Via dell\u2019Universit\u00e0 6, 26900 Lodi, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8500-7970","authenticated-orcid":false,"given":"Laura","family":"Menchetti","sequence":"additional","affiliation":[{"name":"Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40137 Bologna, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1270-1627","authenticated-orcid":false,"given":"Federica","family":"Riva","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Milano, Via dell\u2019Universit\u00e0 6, 26900 Lodi, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3901-2354","authenticated-orcid":false,"given":"Filippo","family":"Biscarini","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Biology and Biotechnology (IBBA)\u2014National Research Council (CNR), U.O.S. di Lodi, Via Einstein, 26900 Lodi, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4791-0514","authenticated-orcid":false,"given":"Maria Laura","family":"Marongiu","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Sassari, Via Vienna, 2, 07100 Sassari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3771-757X","authenticated-orcid":false,"given":"Marta","family":"Castrica","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Milano, Via dell\u2019Universit\u00e0 6, 26900 Lodi, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bianca","family":"Castiglioni","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Biology and Biotechnology (IBBA)\u2014National Research Council (CNR), U.O.S. di Lodi, Via Einstein, 26900 Lodi, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6731-4851","authenticated-orcid":false,"given":"Dino","family":"Miraglia","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6867-199X","authenticated-orcid":false,"given":"Sebastiano","family":"Luridiana","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Sassari, Via Vienna, 2, 07100 Sassari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriele","family":"Brecchia","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Milano, Via dell\u2019Universit\u00e0 6, 26900 Lodi, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,12,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1038\/ismej.2010.49","article-title":"Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores","volume":"4","author":"Liggenstoffer","year":"2010","journal-title":"ISME J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1111\/j.1574-6941.2011.01148.x","article-title":"Postnatal development of the rabbit caecal microbiota composition and activity","volume":"77","author":"Combes","year":"2011","journal-title":"FEMS Microbiol. 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