Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese
Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada...
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ftpubmed:oai:pubmedcentral.nih.gov:5829075 2023-05-15T15:46:19+02:00 Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese Drovetski, Sergei V. O’Mahoney, Michael Ransome, Emma J. Matterson, Kenan O. Lim, Haw Chuan Chesser, R. Terry Graves, Gary R. 2018-02-27 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829075/ http://www.ncbi.nlm.nih.gov/pubmed/29487373 https://doi.org/10.1038/s41598-018-21892-y en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829075/ http://www.ncbi.nlm.nih.gov/pubmed/29487373 http://dx.doi.org/10.1038/s41598-018-21892-y © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. CC-BY Article Text 2018 ftpubmed https://doi.org/10.1038/s41598-018-21892-y 2018-03-04T01:44:16Z Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages. Text Branta canadensis Canada Goose PubMed Central (PMC) Canada Scientific Reports 8 1 |
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Article Drovetski, Sergei V. O’Mahoney, Michael Ransome, Emma J. Matterson, Kenan O. Lim, Haw Chuan Chesser, R. Terry Graves, Gary R. Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese |
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Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages. |
format |
Text |
author |
Drovetski, Sergei V. O’Mahoney, Michael Ransome, Emma J. Matterson, Kenan O. Lim, Haw Chuan Chesser, R. Terry Graves, Gary R. |
author_facet |
Drovetski, Sergei V. O’Mahoney, Michael Ransome, Emma J. Matterson, Kenan O. Lim, Haw Chuan Chesser, R. Terry Graves, Gary R. |
author_sort |
Drovetski, Sergei V. |
title |
Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese |
title_short |
Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese |
title_full |
Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese |
title_fullStr |
Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese |
title_full_unstemmed |
Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese |
title_sort |
spatial organization of the gastrointestinal microbiota in urban canada geese |
publisher |
Nature Publishing Group UK |
publishDate |
2018 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829075/ http://www.ncbi.nlm.nih.gov/pubmed/29487373 https://doi.org/10.1038/s41598-018-21892-y |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Branta canadensis Canada Goose |
genre_facet |
Branta canadensis Canada Goose |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829075/ http://www.ncbi.nlm.nih.gov/pubmed/29487373 http://dx.doi.org/10.1038/s41598-018-21892-y |
op_rights |
© The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/s41598-018-21892-y |
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Scientific Reports |
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