Stool genomic dna kit

Fecal DNA was extracted using the CWBIO Stool Genomic DNA Kit (CWBIO, China) according to the manufacturer’s protocol, and the concentration was measured by Nanodrop Lite (Thermo). The quantitative PCR assays were performed using the LightCycler 480 SYBR Green Master Mix (Roche (USA) 04887352001). The primers used for PCR are listed in Table S3.

Total bacterial DNA was isolated from fecal with Stool Genomic DNA Kit (CWBIO, Beijing, China) according to the manufacturer’s instructions. DNA quantification was conducted by a NanoDrop 2,000 (Thermo Fisher Scientific, Waltham, United States).

500 μL of TE (10 Tris-EDTA, pH 8.0 Tris-HCl 0.1 mol/L) was added to homogenize the samples. Samples were stored at − 20 °C until analysis. Metagenomic DNA was extracted from the zebrafish intestinal samples using a CWBIO Stool Genomic DNA Kit (CW2092, CWBIO, China). We assessed the quality of the metagenomic DNA by 0.8% agarose gel electrophoresis before sequencing. Isolated metagenomic DNA was stored at − 20 °C and used as the template for further analysis.

Shotgun metagenome sequencing was performed based on the method of a previous study [15 (link)]. Briefly, total faecal genomic DNA was extracted using the Stool Genomic DNA Kit (CW2092S; CWBIO) according to the manufacturer’s instructions.
DNA concentrations were measured using a NanoDrop 2000 system (Thermo Fisher Scientific), and the DNA molecular size was estimated by agarose gel electrophoresis. The DNA library was constructed using the TruSeq DNA Sample Preparation Kit (Illumina, San Diego, CA, United States). Libraries were sequenced using the 150 base pair paired-end strategy on the Illumina X-ten platform at Novogene Bioinformatics Technology Co., Ltd. A total of 274.5 GB original sequencing data were obtained from 44 samples (6.2G per sample, ranged from 4.8 to 8.7 G) and deposited in the Sequence Read Archive (PRJNA799832), where 6.1 ± 0.41 G for IPA group, 6.5 ± 0.66 G for NIPA group, 6.0 ± 1.13 G for HC group.

Microbial genomic DNA in cecum content was extracted using the Stool Genomic DNA kit (CWBIO, China). High-throughput sequencing and analysis were performed by the Beijing Genomics Institute (Shenzhen, China). All the qualified DNA was used to construct a library. Paired-end reads were generated with the Illumine HiSeq/MiSeq platform, and the reads with sequencing adapters, N base, poly base, and low quality were filtered. Species composition and abundance analysis was then carried out.