Dataset Information

16S rRNA Gene Amplicon Sequencing of the Gut Microbiota of Chimaera phantasma (Silver Chimaera) Captured off Koshimoda in Suruga Bay, Japan.

ABSTRACT: The intestinal microbiota of Chimaera phantasma (silver chimera) (two females and one male) collected off Koshimoda in Suruga Bay in April to May 2022 were comprehensively analyzed. Bacteria belonging to the phylum Proteobacteria were the dominant species. Occupancy rates of other bacterial phyla differed greatly among the samples.

SUBMITTER: Ogita T

PROVIDER: S-EPMC10190657 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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16S rRNA Gene Amplicon Sequencing of the Gut Microbiota of Chimaera phantasma (Silver Chimaera) Captured off Koshimoda in Suruga Bay, Japan.

Ogita Tasuku T

Microbiology resource announcements 20230403 5

The intestinal microbiota of Chimaera phantasma (silver chimera) (two females and one male) collected off Koshimoda in Suruga Bay in April to May 2022 were comprehensively analyzed. Bacteria belonging to the phylum <i>Proteobacteria</i> were the dominant species. Occupancy rates of other bacterial phyla differed greatly among the samples. ...[more]

PMID: 37010408

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Project description:The gastrointestinal tract, the largest human microbial reservoir, is highly dynamic. The gut microbes play essential roles in causing colorectal diseases. In the present study, we explored potential keystone taxa during the development of colorectal diseases in central China. Fecal samples of some patients were collected and were allocated to the adenoma (Group A), colorectal cancer (Group C), and hemorrhoid (Group H) groups. The 16S rRNA amplicon and shallow metagenomic sequencing (SMS) strategies were used to recover the gut microbiota. Microbial diversities obtained from 16S rRNA amplicon and SMS data were similar. Group C had the highest diversity, although no significant difference in diversity was observed among the groups. The most dominant phyla in the gut microbiota of patients with colorectal diseases were Bacteroidetes, Firmicutes, and Proteobacteria, accounting for >95% of microbes in the samples. The most abundant genera in the samples were Bacteroides, Prevotella, and Escherichia/Shigella, and further species-level and network analyses identified certain potential keystone taxa in each group. Some of the dominant species, such as Prevotella copri, Bacteroides dorei, and Bacteroides vulgatus, could be responsible for causing colorectal diseases. The SMS data recovered diverse antibiotic resistance genes of tetracycline, macrolide, and beta-lactam, which could be a result of antibiotic overuse. This study explored the gut microbiota of patients with three different types of colorectal diseases, and the microbial diversity results obtained from 16S rRNA amplicon sequencing and SMS data were found to be similar. However, the findings of this study are based on a limited sample size, which warrants further large-scale studies. The recovery of gut microbiota profiles in patients with colorectal diseases could be beneficial for future diagnosis and treatment with modulation of the gut microbiota. Moreover, SMS data can provide accurate species- and gene-level information, and it is economical. It can therefore be widely applied in future clinical metagenomic studies.

Project description:BackgroundRabbit 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.ResultsIn 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.ConclusionOur 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.

Dataset Information

16S rRNA Gene Amplicon Sequencing of the Gut Microbiota of Chimaera phantasma (Silver Chimaera) Captured off Koshimoda in Suruga Bay, Japan.

Publications

16S rRNA Gene Amplicon Sequencing of the Gut Microbiota of Chimaera phantasma (Silver Chimaera) Captured off Koshimoda in Suruga Bay, Japan.

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