{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T21:52:39Z","timestamp":1768341159647,"version":"3.49.0"},"reference-count":80,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2023,12,18]],"date-time":"2023-12-18T00:00:00Z","timestamp":1702857600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32101243"],"award-info":[{"award-number":["32101243"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology"],"published-print":{"date-parts":[[2024,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Limited knowledge of bird microbiome in the all\u2010body niche hinders our understanding of host\u2013microbial relationships and animal health. Here, we characterized the microbial composition of the crested ibis from 13 body sites, representing the cloaca, oral, feather and skin habitats, and explored assembly mechanism structuring the bacterial community of the four habitats respectively. The bacterial community characteristics were distinct among the four habitats. The skin harboured the highest alpha diversity and most diverse functions, followed by feather, oral and cloaca. Individual\u2010specific features were observed when the skin and feathers were concentrated independently. Skin and feather samples of multiple body sites from the same individual were more similar than those from different individuals. Although a significant proportion of the microbiota in the host (85.7%\u201396.5%) was not derived from the environmental microbiome, as body sites became more exposed to the environment, the relative importance of neutral processes (random drift or dispersal) increased. Neutral processes were the most important contributor in shaping the feather microbiome communities (<jats:italic>R<\/jats:italic><jats:sup>2<\/jats:sup>\u2009=\u2009.859). A higher percentage of taxa (29.3%) on the skin were selected by hosts compared to taxa on other body habitats. This study demonstrated that niche speciation and partial neutral processes, rather than environmental sources, contribute to microbiome variation in the crested ibis. These results enhance our knowledge of baseline microbial diversity in birds and will aid health management in crested ibises in the future.<\/jats:p>","DOI":"10.1111\/mec.17238","type":"journal-article","created":{"date-parts":[[2023,12,18]],"date-time":"2023-12-18T09:46:31Z","timestamp":1702892791000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Structure, variation and assembly of body\u2010wide microbiomes in endangered crested ibis<i>Nipponia nippon<\/i>"],"prefix":"10.1111","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3234-0523","authenticated-orcid":false,"given":"Ying","family":"Zhu","sequence":"first","affiliation":[{"name":"Institute of Qinghai\u2010Tibetan Plateau, Provincial Key Laboratory for Alpine Grassland Conservation and Utilization on Qinghai\u2010Tibetan Plateau Southwest Minzu University Chengdu China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruifeng","family":"Ma","sequence":"additional","affiliation":[{"name":"Institute of Qinghai\u2010Tibetan Plateau, Provincial Key Laboratory for Alpine Grassland Conservation and Utilization on Qinghai\u2010Tibetan Plateau Southwest Minzu University Chengdu China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1897-2425","authenticated-orcid":false,"given":"Lei","family":"Hu","sequence":"additional","affiliation":[{"name":"Institute of Qinghai\u2010Tibetan Plateau, Provincial Key Laboratory for Alpine Grassland Conservation and Utilization on Qinghai\u2010Tibetan Plateau Southwest Minzu University Chengdu China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haiqiong","family":"Yang","sequence":"additional","affiliation":[{"name":"Emei Breeding Center for Crested Ibis Emei China"},{"name":"College of Veterinary Medicine, Sichuan Agricultural University Chengdu China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haizhou","family":"Gong","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Yangzhou University Yangzhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6446-9439","authenticated-orcid":false,"given":"Ke","family":"He","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A &amp; F University Hangzhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,12,18]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-022-02002-y"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-1-31"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-015-0653-0"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v067.i01"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1007028107"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2015.142"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1890\/11-0426.1"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.5"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168\u2010019\u20100749\u20108"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13730"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1224203"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1186\/1297-9716-45-36"},{"issue":"5","key":"e_1_2_11_14_1","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi G.","year":"2006","journal-title":"InterJournal, Complex Systems"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1550-8579(07)80061-1"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-7580.2008.01041.x"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/d41586\u2010020\u201003524\u20106"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00248\u2010017\u20101130\u20108"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/iob\/oby009"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-021-02315-7"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad3503"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15652-8"},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2022.01.009"},{"key":"e_1_2_11_24_1","unstructured":"Gehlenborg N.(2019).UpSetR: A more scalable alternative to Venn and Euler diagrams for visualizing intersecting sets. R package version 1.4. 0. In."},{"key":"e_1_2_11_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecolind.2019.05.038"},{"key":"e_1_2_11_26_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00105-16"},{"key":"e_1_2_11_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.09.053"},{"key":"e_1_2_11_28_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.191320.115"},{"key":"e_1_2_11_29_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1171700"},{"key":"e_1_2_11_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2537"},{"key":"e_1_2_11_31_1","doi-asserted-by":"publisher","DOI":"10.1111\/1365-2656.13531"},{"key":"e_1_2_11_32_1","doi-asserted-by":"publisher","DOI":"10.1111\/jav.01788"},{"key":"e_1_2_11_33_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-048X.2008.04650.x"},{"key":"e_1_2_11_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2017.11.002"},{"key":"e_1_2_11_35_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.321"},{"key":"e_1_2_11_36_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2015.11"},{"issue":"4","key":"e_1_2_11_37_1","first-page":"72","article-title":"Isolation, identification and drug susceptibility detection of Escherichia coli, Klebsiella pneumoniae and Clostridium perfringens from crested ibis","volume":"44","author":"Jiang J.","year":"2023","journal-title":"Progress in Veterinary Medicine"},{"key":"e_1_2_11_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1650"},{"key":"e_1_2_11_39_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.131029.111"},{"key":"e_1_2_11_40_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0179945"},{"key":"e_1_2_11_41_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.16398"},{"key":"e_1_2_11_42_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.14993"},{"key":"e_1_2_11_43_1","doi-asserted-by":"crossref","unstructured":"Lenth R. Singmann H. Love J. Buerkner P. &Herve M.(2018).Emmeans: Estimated marginal means. AKA Least\u2010Squares Means 2\u20131.","DOI":"10.32614\/CRAN.package.emmeans"},{"key":"e_1_2_11_44_1","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.83"},{"key":"e_1_2_11_45_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf4507"},{"key":"e_1_2_11_46_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.12.8228-8235.2005"},{"key":"e_1_2_11_47_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.0908-8857.2005.03479.x"},{"key":"e_1_2_11_48_1","doi-asserted-by":"publisher","DOI":"10.1161\/01.CIR.0000137969.87365.05"},{"key":"e_1_2_11_49_1","doi-asserted-by":"publisher","DOI":"10.1177\/1099800420941606"},{"key":"e_1_2_11_50_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes9080387"},{"key":"e_1_2_11_51_1","doi-asserted-by":"publisher","DOI":"10.1890\/09\u20101395.1"},{"key":"e_1_2_11_52_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1218525110"},{"key":"e_1_2_11_53_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature13786"},{"key":"e_1_2_11_54_1","unstructured":"Oksanen J.(2017).Vegan: Community ecology package.https:\/\/cran.r\u2010project.org\/web\/packages\/vegan\/"},{"key":"e_1_2_11_55_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.133"},{"key":"e_1_2_11_56_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0365-4"},{"key":"e_1_2_11_57_1","doi-asserted-by":"publisher","DOI":"10.1038\/307321a0"},{"key":"e_1_2_11_58_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-021-00913-1"},{"key":"e_1_2_11_59_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1801302115"},{"key":"e_1_2_11_60_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168\u2010019\u20100694\u20106"},{"key":"e_1_2_11_61_1","doi-asserted-by":"publisher","DOI":"10.1002\/jez.b.26"},{"key":"e_1_2_11_62_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ddmec.2012.12.003"},{"key":"e_1_2_11_63_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10123\u2010023\u201000372\u2010y"},{"issue":"4","key":"e_1_2_11_64_1","first-page":"17","article-title":"Preliminary preparation of Bifidobacterium chu microcapsules","volume":"33","author":"Shi W.","year":"2005","journal-title":"Journal of Northwest Science\u2010Tech University of Agriculture and for (Natural Science Edition)"},{"key":"e_1_2_11_65_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2016.11.010"},{"key":"e_1_2_11_66_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2005.00956.x"},{"key":"e_1_2_11_67_1","doi-asserted-by":"publisher","DOI":"10.1177\/0022034515606045"},{"key":"e_1_2_11_68_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-019-1413-y"},{"key":"e_1_2_11_69_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00004-19"},{"issue":"1","key":"e_1_2_11_70_1","first-page":"1","article-title":"Multi\u2010level comparisons of cloacal, skin, feather and nest\u2010associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks","volume":"5","author":"Veelen H. P. J.","year":"2017","journal-title":"Microbiome"},{"key":"e_1_2_11_71_1","doi-asserted-by":"publisher","DOI":"10.1111\/jav.02686"},{"key":"e_1_2_11_72_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00673"},{"key":"e_1_2_11_73_1","doi-asserted-by":"publisher","DOI":"10.3389\/fevo.2016.00090"},{"key":"e_1_2_11_74_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1474-919X.2000.tb07677.x"},{"key":"e_1_2_11_75_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41522-020-00176-2"},{"key":"e_1_2_11_76_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.geoderma.2023.116562"},{"key":"e_1_2_11_77_1","unstructured":"Yang Z. Wang X. Zhang S. Wang W. Chang X. Lu B. Ding H. &Fan G.(2004).Diagnosis and treatment of colibacillosis in crested ibis. Paper presented at the proceedings of the 10th symposium on infectious diseases of domestic animals."},{"key":"e_1_2_11_78_1","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00002-17"},{"key":"e_1_2_11_79_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-1-r1"},{"key":"e_1_2_11_80_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.723682"},{"key":"e_1_2_11_81_1","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.57"}],"container-title":["Molecular Ecology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mec.17238","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T06:32:42Z","timestamp":1730874762000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/mec.17238"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,18]]},"references-count":80,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,2]]}},"alternative-id":["10.1111\/mec.17238"],"URL":"https:\/\/doi.org\/10.1111\/mec.17238","archive":["Portico"],"relation":{},"ISSN":["0962-1083","1365-294X"],"issn-type":[{"value":"0962-1083","type":"print"},{"value":"1365-294X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,18]]},"assertion":[{"value":"2023-06-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-11-27","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-12-18","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e17238"}}