{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T17:42:44Z","timestamp":1793036564167,"version":"4.5.0"},"reference-count":70,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2017,12,22]],"date-time":"2017-12-22T00:00:00Z","timestamp":1513900800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100004722","name":"Stiftelsen Lars Hiertas Minne","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004722","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008584","name":"Stiftelsen L\u00e4ngmanska Kulturfonden","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008584","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004063","name":"Knut och Alice Wallenbergs Stiftelse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005753","name":"Kungliga Fysiografiska S\u00e4llskapet i Lund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005753","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003788","name":"Helge Ax:son Johnsons Stiftelse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003788","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2018,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches,\n                    <jats:italic>Struthio camelus<\/jats:italic>\n                    , and high\u2010throughput 16S\n                    <jats:styled-content style=\"fixed-case\">rRNA<\/jats:styled-content>\n                    sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of\n                    <jats:italic>Gammaproteobacteria<\/jats:italic>\n                    and fewer\n                    <jats:italic>Clostridia<\/jats:italic>\n                    relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable:\n                    <jats:italic>Bacteroidetes<\/jats:italic>\n                    was the most highly correlated phylum between all three gut sections and both methods, whereas\n                    <jats:italic>Actinobacteria<\/jats:italic>\n                    , for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.12744","type":"journal-article","created":{"date-parts":[[2017,12,5]],"date-time":"2017-12-05T06:30:44Z","timestamp":1512455444000},"page":"424-434","source":"Crossref","is-referenced-by-count":147,"title":["Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling"],"prefix":"10.1111","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9998-3689","authenticated-orcid":false,"given":"Elin","family":"Videvall","sequence":"first","affiliation":[{"name":"Department of Biology Lund University Lund Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Strandh","sequence":"additional","affiliation":[{"name":"Department of Biology Lund University Lund Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anel","family":"Engelbrecht","sequence":"additional","affiliation":[{"name":"Directorate Animal Sciences Western Cape Department of Agriculture Elsenburg South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Schalk","family":"Cloete","sequence":"additional","affiliation":[{"name":"Directorate Animal Sciences Western Cape Department of Agriculture Elsenburg South Africa"},{"name":"Department of Animal Sciences Stellenbosch University Matieland South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlie K.","family":"Cornwallis","sequence":"additional","affiliation":[{"name":"Department of Biology Lund University Lund Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2017,12,22]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2014.07.020"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep10189"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.3920\/BM2013.0082"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00191-16"},{"key":"e_1_2_8_6_1","unstructured":"Andrews S.(2010)FastQC: A quality control tool for high throughput sequence data. 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