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Sample GSM5983702

Query DataSets for GSM5983702

Status

Public on Apr 02, 2022

Title

Sample type

SRA

Source name

fecal

Organism

human feces metagenome

Characteristics

tissue: fecal
treatment: In-vitro co-fermentation of feces and satsuma orange flavonoids for 24 h

Treatment protocol

The fresh fecal samples were immediately collected, weighed and diluted in anaerobic, sterile phosphate-buffered saline (PBS, pH 7, 0.10 M) to prepare 10% fecal homogenate suspensions (w/v). Each culture consisted of sterilized VIS medium (5 mL) fecal suspension (500 μL), and CPFE sample (0.10 g/mL, 500 μL).

Growth protocol

Anaerobic fermentation (10% H2, 10% CO2 and 80% N2) at 37 °C was performed in an anaerobic workstation (DG250, Don Whitley Scientific, Bingley, UK). After 24 h, fecal fermentation suspension (1 mL) was collected.

Extracted molecule

genomic DNA

Extraction protocol

Genomic DNA was extracted from the fecal fermentation suspension with a QIAamp PowerFecal DNA extraction kit, according to the manufacturer’s instructions.
16S rDNA gene high-throughput sequencing of the V3-V4 region was performed by Biomarker Bio-Tech Co., Ltd. (Beijing, China), with an Illumina MiSeq platform.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Data processing

Library strategy: 16S rDNA DNA-seq
Total DNA extracted from the sample
Using FLASH v1.2.7 software, the reads of each sample were spliced by overlapping, and the obtained splicing sequence was the original Tag data (Raw Tags)
Using Trimmomatic v0.33 software to filter the spliced Raw Tags to obtain high-quality Tag data (Clean Tags)
Using UCHIME v4.2 software to identify and remove chimera sequences to obtain final effective data (Effective Tags)
Use Usearch software to cluster effective data at the 97% similarity level to obtain OTU. By comparing the representative sequences of OTUs with the Silva (bacteria) taxonomy database, the species classification information corresponding to each OTU can be obtained, and then the community composition of each sample can be counted at each level (phylum, class, order, family, genus, species). The QIIME software was used to generate species abundance tables at different taxonomic levels, and then the R language tool was used to draw the community structure map of the samples at each taxonomic level.
Assembly: V3-V4 region of the 16S rDNA gene
Supplementary files format and content: tab-delimited text file includes OTU relative abundance of each sample

Submission date

Mar 30, 2022

Last update date

Apr 02, 2022

Contact name

zuorui xie

E-mail(s)

xiezuorui2020@outlook.com

Organization name

ZFM

Street address

Zhejiang Gongshang University