*2.6. Liver Histology and Morphometric Assessment*

The largest lobe of the fresh liver from each mouse in the different treatment groups was fixed in paraformaldehyde at room temperature and embedded in paraffin. Fivemicrometer-thick sections of the liver tissue were cut, dewaxed, stained with hematoxylineosin (H&E), dehydrated, and sealed with neutral gum. To determine possible histopathological changes, the slides were then observed under an upright optical microscope (Nikon, Shanghai, China) for routine morphological evaluation and image acquisition (Servicebio Technology Co., Ltd., Wuhan, China).

#### *2.7. DNA Extraction and High throughput Metagenomic Sequencing*

Total DNA was extracted from fecal samples by using the QIAamp® DNA Stool Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction, and purity and integrity of DNA were determined by 0.8% agarose gel electrophoresis. The concentration of DNA was determined by NanoDrop 2000 (Novogene Company, Beijing, China). The V3-V4 region of the 16s ribosomal RNA (rRNA) gene was amplified as previously described [24]. The shotgun metagenomic sequencing was performed by Illumina HiSeq 2500 instrument (Novogene, Beijing, China). About 150 bp paired-end gene fragments were obtained by sequencing, and a sequencing library with the length of the DNA fragments of 300 bp was prepared.

#### *2.8. Bioinformatics for Amplification and Shotgun Metagenomic Sequencing Analysis*

According to the quality scores, the sequences were filtered by using the sliding window approach. The low-quality sequences for which the average quality score over a 50-nt sliding window dropped below 30 were removed from the raw sequences. The QIIME (v1.9) platform was used for bioinformatics analysis [27]. The Operational Taxonomic Units (OTU) were selected by QIIME (default settings). OTUs were classified with a 97% threshold identity. An RDP Classifier was used to obtain the taxonomy against the RDP database using the representative [28]. The metagenomic reads were trimmed using Sickle software and subsequently aligned to the mouse genome (GRCm38.p6) to remove the host DNA fragments for subsequent analysis. For metagenomic species annotation, MetaPhlan2 software for taxonomic classification was employed [29]. HUMAnN2 was performed for metagenomic functional features and metabolic-pathway annotation based on the UniRef90 database [29].

#### *2.9. Statistical Analysis and Figure Construction*

The statistical analyses were performed using R. Data are presented as mean ± standard error (SE). The differential abundances of the genera were tested using the Wilcoxon rank-sum test and the Kruskal–Wallis test, and *p* < 0.05 were considered to be significantly different genera. Principal coordinate analysis (PCoA) was performed using the "ade4" package. The package "ggplot2" was used for generating line charts, box plots, and bar charts. The heatmap was constructed using the "pheatmap" package. The *p*-value was filtered and corrected by the "DESeq2" package in the bubble diagram. The microbial ecological networks were inferred by Spearman's rank correlation coefficient from the metagenomic sequencing data and visualized in Cytoscape (Version 3.7.1).

#### **3. Results**

#### *3.1. The Granules Form of JSRS*

The morphology of JSRS granules is shown in Figure S1A. The SEM images of JSRS samples showed that the starch granules were mainly semi-oval or bell-shaped. The particle size of starches was about 10 μm, which was similar to our previous finding [26].
