Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota
Despite the convenience and noninvasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. Using chickens as a model, we collected 1,026 samples from 206 animals, including duodenum, jejunum, ileum, cecum and feces samples. Most taxa in the small intestine (94.10-94.82%) and ceca (99.57%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 26.69 and 2.36% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes and Proteobacteria members in ceca could mirrored that observed in fecal samples well (ρ = 0.68-0.79 and 0.66-0.79, respectively, P < 0.05). Enterotype-like clustering was performed in GI tract and all sites were clustered into 2 or 3 enterotype-like clusters. Feces from different clusters reflected the GI microbiota with different efficacies, giving a new insight into observing efficacy of feces as a gut proxy. Our results provide evidences that the good potential of feces to identify most taxa in chicken guts, but microbial structure analyses using feces as a proxy for gut should be interpreted with caution.
- Downloaded 1,205 times
- Download rankings, all-time:
- Site-wide: 9,039 out of 94,912
- In microbiology: 575 out of 8,320
- Year to date:
- Site-wide: 36,536 out of 94,912
- Since beginning of last month:
- Site-wide: 57,911 out of 94,912
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!