2.1 Research participants and sample collection
This study included stool samples from 104 SLE patients and 90 health controls from Affiliated Hospital of Nantong University during June 2017 to February 2019. Informed consent was obtained from each participant. All patients met the 2009 American College of Rheumatology (ACR) classification criteria for SLE [15]. Exclusion criteria were listed as follows: 1) Pregnancy or breast-feeding; 2) Recent or current medical disorder (cardiac, respiratory, gastrointestinal, neurological, endocrine, malignancy, etc); 3) History of probiotics within 2 weeks or antibiotics within 3 months before admission; 4) If on immunosuppressant, the dose must be stable for 4 weeks before the sample collection. The gender and age-matched healthy controls (N) were recruited from the Health Examination Centre of Affiliated Hospital of Nantong University. The inclusion of human participants and supporting documentation were approved by the Affiliated Hospital of Nantong University Ethics Committee (2017-K002). All fecal specimens of participants were collected in a sealed fecal storage box after defecation and stored at -80°C after collection.
2.2 Experimental animal and treatments
Fourty six-week-old female MRL/Lpr mice and ICR mice were bought from Shanghai Sushang Biological Technology Co., LTD. The mice were in the SPF environment of animal research center of Nantong University and were housed three to four per cage at 23–24 ℃ with a 12-h/12-h light/dark cycle with free access to food and water. This animal study was proved by the Institutional Animal Care and Use Committee of Nantong University (S20200313-014).
These mice were divided into five groups (8 mice/group): control ICR mice (N) and MRL/Lpr mice (S) were treated with saline. The dose of BBR in person is 0.3g-0.9g/day. According to Meeh-Rubner equation [16], MRL/Lpr mice (L, M and H) were treated with BBR in the daily amount of 60mg/kg, 120mg/kg and 180mg/kg. Urine was collected for 24 h and detected by the Bradford Protein Assay Kit (Solarbio, Beijing). After the appearance of lupus nephritis (Fig. 3B), mice were given saline or berberine orally. After 6 weeks, treatment, mice were sacrificed. Serum, faeces and organs samples were collected. The kidneys and colons were formalin-fixed and paraffin-embedded and sliced at 4 µm thickness for further staining. Serum antibody level (dsDNA, ANA, C3, C4) in mice was detected by ELISA (Jingmei Biotechnology, China). The entire progress was showed in Fig. 3A.
2.3 16S high-throughput (16S rRNA ) sequencing and short-chain fatty acid detection
16S rRNA sequencing of intestinal flora in intestinal faeces was completed in Sangon Biotech (Shanghai) Co., LTD. Microbial DNA was extracted by QIAamp® Fast DNA Stool Mini Kit (QIAGEN, Germany). The V3-V4 hypervariable regions of the microbiota 16S rRNA gene were amplified with primers 341F (5'-CCTACGGGNGGCWGCAG-3') and 805R (5'-GACTACHVGGGTATCTAATCC-3').
Data analyses were performed by the Sangon platform. The detection of intestinal metabolites, short-chain fatty acids, was carried out by Wuhan Huada Medical Laboratory Co. LTD (supplementary Fig. 1). Thermo Trace1300-Thermo TSQ9000 tandem mass spectrometry and SIM mode were used for forward detection. Tracefinder (Thermo Fisher Scientific, Waltham, MA, USA) was used for data processing. After calculation, the absolute content of target compounds in samples was obtained. The datasets used and analysed during the study are available from the corresponding author.
2.4 Extraction of total DNA of fecal sample and quantitative real-time Polymerase Chain Reaction (qRT-PCR).
The QIAamp® Fast DNA Stool Mini Kit (QIAGEN, Germany) was used to obtain the total DNA from the sample of faeces. The DNA sample was diluted with RNase free water (Beyotime, China) into 5ng/ul and performed the real-time quantitative PCR. According to the bacterial colony 16S rRNA V3 sequence, the specific primers of total bacteria, Bacteroides and Firmicutes were designed and synthesized by Biomics Biotechnology, China. Sequences and reaction systems were showed in supplementary Tables 1 and 2. The procedure was operated in the Roche cobas z 480.
2.5 Histo-morphological Staining
The colon and kidney sections were stained with hematoxylin-eosin (HE), periodic acid-Schiff (PAS) and Masson’s trichrome respectively (Solarbio, Beijing). HE staining monitored the histological change, PAS staining evaluated the inflammatory cell infiltration and Masson’s trichrome staining determined the degree of fibrosis. Pathological histology was observed by a biological microscope.
2.6 Immunofluorescence
Kidney slides were dewaxed and incubated with antigen retrieval solution and 3% H2O2 (Solarbio, China). The kidney tissues were blocked by gout serum (Maxim,China). For direct immunofluorescence, sections were labeled with anti-C3 antibody (ab11862, Abcam), anti-IgM antibody (ab150121, Abcam) and anti-IgG antibody (ab150083, Abcam) for 30–60 min at room temperature. DAPI was used to stain the cell nuclei. Immunofluorescence staining of colon sections were similar to the above steps, with antibodies like anti-ZO-1 antibody (ab216880, Abcam) and anti-occludin antibody (ab216327, Abcam).
2.7 Western blot
Total protein was extracted from colon tissues using protein lysate (RIPA: PMSF = 100:1, Beyotime, China) and determined by a BCA Protein Assay kit (Beyotime, China). Proteins blotted with antibodies to ZO-1 (ab216880, Abcam, China) and occludin (ab216327, Abcam, China). ß-actin (110007, CST, China) served as the internal control. An enhanced chemiluminescence kit (ECL, Millipore, USA) was used to display the blots.
2.8 Flow cytometry
Lymphocytes were isolated from the tissue homogenates of spleen and mesenteric lymph nodes (MLN). The following primary antibodies were used in the process: mouse BV510-CD3 (Cat. 100233, BioLegend), FITC-CD4 (Cat. 100405, BioLegend), APC-CD25 (Cat. 101909, BioLegend), PE-Cy7-CXCR5 (25-7185-82, eBioscience), PE-Foxp3 (12-5773-82, eBioscience), FITC-CD21 (Cat. 123407, BioLegend), PE-Cy7-CD23 (25-0232-82, eBioscience), Alexa Fluor 700-CD19 (Cat. 115527, BioLegend), BV785-CD25 (Cat. 102051, BioLegend), BV510-CD3 (Cat. 100353, BioLegend), APC-NK1.1 (17-5941-82, eBioscience). Cell subsets were analysed on a BD LSRFortossaTM flow cytometer (BD Biosciences, USA) with FACSDiva Software (BD Biosciences) and FlowJo Software (Tree Star Inc., USA).
2.9 Statistical Analysis
Quantitative data were expressed as mean ± S.E.M. Differences determined by two-tailed t-test were used for two-group comparisons and One-way ANOVA was used for multiple comparisons. P-values < 0.05 indicated the experimental results are reliable.