Gut microbiome sequencing results in type 2 diabetes under p53 deficiency
Data files
Sep 06, 2026 version files 199.79 MB
-
CD_N_1_R1.fastq.gz
5.45 MB
-
CD_N_1_R2.fastq.gz
4.79 MB
-
CD_N_2_R1.fastq.gz
4.07 MB
-
CD_N_2_R2.fastq.gz
4.67 MB
-
CD_N_3_R1.fastq.gz
4.30 MB
-
CD_N_3_R2.fastq.gz
4.74 MB
-
CD_N_4_R1.fastq.gz
6.79 MB
-
CD_N_4_R2.fastq.gz
5.99 MB
-
CD_N_5_R1.fastq.gz
5.07 MB
-
CD_N_5_R2.fastq.gz
4.40 MB
-
CD_p53_1_R1.fastq.gz
3.43 MB
-
CD_p53_1_R2.fastq.gz
4.46 MB
-
CD_p53_2_R1.fastq.gz
3.87 MB
-
CD_p53_2_R2.fastq.gz
4.47 MB
-
CD_p53_3_R1.fastq.gz
4.73 MB
-
CD_p53_3_R2.fastq.gz
5.28 MB
-
CD_p53_4_R1.fastq.gz
5.40 MB
-
CD_p53_4_R2.fastq.gz
4.64 MB
-
CD_p53_5_R1.fastq.gz
4.30 MB
-
CD_p53_5_R2.fastq.gz
4.95 MB
-
HFD_N_1_R1.fastq.gz
3.75 MB
-
HFD_N_1_R2.fastq.gz
4.57 MB
-
HFD_N_2_R1.fastq.gz
5.91 MB
-
HFD_N_2_R2.fastq.gz
5.05 MB
-
HFD_N_3_R1.fastq.gz
4.45 MB
-
HFD_N_3_R2.fastq.gz
5.35 MB
-
HFD_N_4_R1.fastq.gz
4.33 MB
-
HFD_N_4_R2.fastq.gz
5.38 MB
-
HFD_N_5_R1.fastq.gz
4.33 MB
-
HFD_N_5_R2.fastq.gz
5.26 MB
-
HFD_p53_1_R1.fastq.gz
5.35 MB
-
HFD_p53_1_R2.fastq.gz
5.99 MB
-
HFD_p53_2_R1.fastq.gz
5.12 MB
-
HFD_p53_2_R2.fastq.gz
5.85 MB
-
HFD_p53_3_R1.fastq.gz
5.34 MB
-
HFD_p53_3_R2.fastq.gz
5.70 MB
-
HFD_p53_4_R1.fastq.gz
5.31 MB
-
HFD_p53_4_R2.fastq.gz
5.74 MB
-
HFD_p53_5_R1.fastq.gz
5.94 MB
-
HFD_p53_5_R2.fastq.gz
5.27 MB
-
README.md
8.74 KB
Abstract
The p53 protein has been identified as a critical regulator of metabolic processes in a variety of diseases, including obesity, diabetes, liver disease, and cardiovascular disease. However, the precise function and mechanism of action of p53 in the regulation of glucose-lipid metabolism through the enterohepatic axis remain to be fully elucidated.The present study investigated the effects of p53 deficiency on type 2 diabetic mice and demonstrated that p53 deficiency resulted in more severe impairment of glucose tolerance and insulin tolerance. Furthermore, the study revealed that p53 can influence hepatic glucose metabolism via the PI3K/AKT pathway. Additionally, p53 deletion has been observed to modify intestinal function and the intestinal microenvironment, thereby correlating with intestinal function and microbiota composition in T2DM mice. Specifically, p53 knockdown mice exhibited impaired ileal digestion, absorption, and colonic secretion after a HFD (HFD). Additionally, the richness and diversity of their intestinal flora were reduced, and these mice exhibited symptoms such as obesity, fat infiltration, defecation abnormalities, and severe abnormalities of glucose and insulin tolerance. The expression levels of β-catenin and c-Myc proteins were found to be elevated in mice fed a HFD, while the expression of these proteins was diminished in mice with p53 knockdown, compared to those on a normal diet. The experimental results suggest that p53 affects insulin secretion through PI3K/AKT signaling pathway and regulates the distribution of intestinal flora through Wnt signaling pathway, which in turn affects the development of type 2 diabetes mellitus.
Dataset DOI: 10.5061/dryad.2280gb641
Description of the data and file structure
The mice were placed in clean cages, and after natural defecation, fecal samples were collected with sterile tweezers. 0.1 g of fecal samples were placed in sterile EP tubes and frozen in a -80°C refrigerator.The microbial DNA was extracted from the fecal samples according to the MagPure Soil DNA LQ Kit (D635601, Magen, Guangzhou, China), and the extracted microbial DNA was amplified using 16S rDNA universal primers. The amplification procedure was as follows: 95°C pre-denaturation for 5 min, 95°C denaturation for 30 s, 55°C annealing for 30 s, 72°C elongation for 1 min for 30 cycles, and 72°C elongation for 10 min. Five microliters of PCR products were analyzed by 1.5% agarose gel electrophoresis. Subsequently, the PCR products were sent to a sequencing company for sequencing using Illumina MiSeq.Alpha and Beta diversity analyses were performed using QIIME2 software to assess the diversity and composition of the microbial community.
Files and variables
File: CD_N_1_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed normal diet, biological replicate 1.
File: CD_N_1_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed normal diet, biological replicate 1.
File: CD_N_2_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed normal diet, biological replicate 2.
File: CD_N_3_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed normal diet, biological replicate 3.
File: CD_N_2_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed normal diet, biological replicate 2.
File: CD_N_4_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed normal diet, biological replicate 4.
File: CD_N_3_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed normal diet, biological replicate 3.
File: CD_N_4_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed normal diet, biological replicate 4.
File: CD_N_5_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed normal diet, biological replicate 5.
File: CD_p53_1_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed normal diet, biological replicate 1.
File: CD_N_5_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed normal diet, biological replicate 5.
File: CD_p53_1_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed normal diet, biological replicate 1.
File: CD_p53_2_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed normal diet, biological replicate 2.
File: CD_p53_3_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed normal diet, biological replicate 3.
File: CD_p53_4_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed normal diet, biological replicate 4.
File: HFD_N_1_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed high-fat diet, biological replicate 1.
File: CD_p53_5_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed normal diet, biological replicate 5.
File: HFD_N_1_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed high-fat diet, biological replicate 1.
File: HFD_N_2_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed high-fat diet, biological replicate 2.
File: HFD_N_3_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed high-fat diet, biological replicate 3.
File: HFD_N_4_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed high-fat diet, biological replicate 4.
File: HFD_N_3_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed high-fat diet, biological replicate 3.
File: HFD_p53_2_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed high-fat diet, biological replicate 2.
File: HFD_p53_1_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed high-fat diet, biological replicate 1.
File: HFD_p53_5_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed high-fat diet, biological replicate 5.
File: HFD_p53_5_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed high-fat diet, biological replicate 1.
File: HFD_p53_2_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed high-fat diet, biological replicate 2.
File: CD_p53_2_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed normal diet, biological replicate 2.
File: HFD_N_2_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed high-fat diet, biological replicate 2.
File: HFD_p53_3_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed high-fat diet, biological replicate 3.
File: HFD_p53_4_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed high-fat diet, biological replicate 4.
File: HFD_p53_4_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a p53KD mouse fed high-fat diet, biological replicate 4.
File: CD_p53_3_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed normal diet, biological replicate 3.
File: HFD_N_5_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a control mouse fed high-fat diet, biological replicate 5.
File: CD_p53_4_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed normal diet, biological replicate 4.
File: HFD_N_4_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed high-fat diet, biological replicate 4.
File: CD_p53_5_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed normal diet, biological replicate 5.
File: HFD_p53_3_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed high-fat diet, biological replicate 3.
File: HFD_p53_1_R1.fastq.gz
Description: Paired-end RNA-seq read 1 (R1) from feces of a p53KD mouse fed high-fat diet, biological replicate 1.
File: HFD_N_5_R2.fastq.gz
Description: Paired-end RNA-seq read 2 (R2) from feces of a control mouse fed high-fat diet, biological replicate 5.
Code/software
First, the raw data were subjected to merging and filtering through the following steps: (1) Removal of primer sequences and balance base sequences from RawData using cutadapt (v1.9) with parameters: '-g R1 -G R2 -n1 -O 17 -m 100'; (2) Merging each pair of paired-end reads into a single, longer tag based on sequence overlap using FLASH (v1.2.8) with parameters: '-m 10 -M 100 -x 0.25 -t 1 -z'; (3) Sliding-window quality scanning of sequencing reads, with a default window size of 100 bp; when the average quality score within a window fell below 20, the read was truncated from the start of the window to the 3' end using fqtrim with parameters: '-P 33 -w 100 -q 20 -l 100 -m5 -p 1 -V -o trim.fastq.gz'; (4) Removal of sequences shorter than 100 bp after truncation; (5) Removal of sequences containing >5% ambiguous bases (N) after truncation; (6) Removal of chimeric sequences using Vsearch (v2.3.4) with default parameters. Subsequently, length filtering and denoising were performed by calling DADA2 via qiime dada2 denoise-paired. Downstream diversity analyses and taxonomic annotation were then conducted using QIIME2 (version 2019.7). Based on the obtained species abundance profiles, differential analysis among multiple groups with biological replicates was performed using the Kruskal–Wallis test.