Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing

Abstract Background Rabbit can produce meat, fur and leather, and serves as an important biomedical animal model. Understanding the microbial community of rabbits helps to raise rabbits healthily and better support their application as animal models. Results In this study, we selected 4 healthy Belg...

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Autores principales:	Xiaofen Hu, Fei Wang, Shanshan Yang, Xu Yuan, Tingyu Yang, Yunxiao Zhou, Yong Li
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Rabbit microbial community whole body sites 16S rRNA gene Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a94ca4d61c73443d8436c971104f656b
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spelling	oai:doaj.org-article:a94ca4d61c73443d8436c971104f656b2021-11-14T12:08:48ZRabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing10.1186/s12866-021-02377-x1471-2180https://doaj.org/article/a94ca4d61c73443d8436c971104f656b2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12866-021-02377-xhttps://doaj.org/toc/1471-2180Abstract Background Rabbit can produce meat, fur and leather, and serves as an important biomedical animal model. Understanding the microbial community of rabbits helps to raise rabbits healthily and better support their application as animal models. Results In this study, we selected 4 healthy Belgium gray rabbits to collect the microbial samples from 12 body sites, including skin, lung, uterus, mouth, stomach, duodenum, ileum, jejunum, colon, cecum, cecal appendix and rectum. The microbiota across rabbit whole body was investigated via 16S rRNA gene amplicon sequencing. After quality control, 46 samples were retained, and 3,148 qualified ASVs were obtained, representing 23 phyla and 264 genera. Based on the weighted UniFrac distances, these samples were divided into the large intestine (Lin), stomach and small intestine (SSin), uterus (Uter), and skin, mouth and lung (SML) groups. The diversity of Lin microbiota was the highest, followed by those of the SSin, Uter and SML groups. In the whole body, Firmicutes (62.37%), Proteobacteria (13.44%) and Bacteroidota (11.84%) were the most predominant phyla. The relative abundance of Firmicutes in the intestinal tract was significantly higher than that in the non-intestinal site, while Proteobacteria was significantly higher in the non-intestinal site. Among the 264 genera, 35 were the core microbiota distributed in all body sites. Sixty-one genera were specific in the SML group, while 13, 8 and 1 were specifically found in the Lin, SSin and Uter groups, respectively. The Lin group had the most difference with other groups, there were average 72 differential genera between the Lin and other groups. The functional prediction analysis showed that microbial function within each group was similar, but there was a big difference between the intestinal tracts and the non-intestinal group. Notably, the function of microorganism in uterus and mouth were the most different from those in the gastrointestinal sites; rabbit’s coprophagy of consuming soft feces possibly resulted in little differences of microbial function between stomach and large intestinal sites. Conclusion Our findings improve the knowledge about rabbit microbial communities throughout whole body and give insights into the relationship of microbial communities among different body sites in health rabbits.Xiaofen HuFei WangShanshan YangXu YuanTingyu YangYunxiao ZhouYong LiBMCarticleRabbitmicrobial communitywhole body sites16S rRNA geneMicrobiologyQR1-502ENBMC Microbiology, Vol 21, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Rabbit microbial community whole body sites 16S rRNA gene Microbiology QR1-502
spellingShingle	Rabbit microbial community whole body sites 16S rRNA gene Microbiology QR1-502 Xiaofen Hu Fei Wang Shanshan Yang Xu Yuan Tingyu Yang Yunxiao Zhou Yong Li Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing
description	Abstract Background Rabbit can produce meat, fur and leather, and serves as an important biomedical animal model. Understanding the microbial community of rabbits helps to raise rabbits healthily and better support their application as animal models. Results In this study, we selected 4 healthy Belgium gray rabbits to collect the microbial samples from 12 body sites, including skin, lung, uterus, mouth, stomach, duodenum, ileum, jejunum, colon, cecum, cecal appendix and rectum. The microbiota across rabbit whole body was investigated via 16S rRNA gene amplicon sequencing. After quality control, 46 samples were retained, and 3,148 qualified ASVs were obtained, representing 23 phyla and 264 genera. Based on the weighted UniFrac distances, these samples were divided into the large intestine (Lin), stomach and small intestine (SSin), uterus (Uter), and skin, mouth and lung (SML) groups. The diversity of Lin microbiota was the highest, followed by those of the SSin, Uter and SML groups. In the whole body, Firmicutes (62.37%), Proteobacteria (13.44%) and Bacteroidota (11.84%) were the most predominant phyla. The relative abundance of Firmicutes in the intestinal tract was significantly higher than that in the non-intestinal site, while Proteobacteria was significantly higher in the non-intestinal site. Among the 264 genera, 35 were the core microbiota distributed in all body sites. Sixty-one genera were specific in the SML group, while 13, 8 and 1 were specifically found in the Lin, SSin and Uter groups, respectively. The Lin group had the most difference with other groups, there were average 72 differential genera between the Lin and other groups. The functional prediction analysis showed that microbial function within each group was similar, but there was a big difference between the intestinal tracts and the non-intestinal group. Notably, the function of microorganism in uterus and mouth were the most different from those in the gastrointestinal sites; rabbit’s coprophagy of consuming soft feces possibly resulted in little differences of microbial function between stomach and large intestinal sites. Conclusion Our findings improve the knowledge about rabbit microbial communities throughout whole body and give insights into the relationship of microbial communities among different body sites in health rabbits.
format	article
author	Xiaofen Hu Fei Wang Shanshan Yang Xu Yuan Tingyu Yang Yunxiao Zhou Yong Li
author_facet	Xiaofen Hu Fei Wang Shanshan Yang Xu Yuan Tingyu Yang Yunxiao Zhou Yong Li
author_sort	Xiaofen Hu
title	Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing
title_short	Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing
title_full	Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing
title_fullStr	Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing
title_full_unstemmed	Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing
title_sort	rabbit microbiota across the whole body revealed by 16s rrna gene amplicon sequencing
publisher	BMC
publishDate	2021
url	https://doaj.org/article/a94ca4d61c73443d8436c971104f656b
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Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing

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