Mouse strains and treatments
Eight- to ten-week-old male C57BL/6J mice weighing 20–22 g were purchased from Shanghai SLAC Laboratory Animal Co Ltd. (Shanghai, China). All mice were maintained under 12-hour light/dark cycles at 22 °C with unlimited access to a standard rodent diet and water and were housed under specific pathogen-free (SPF) conditions (free of known bacteria, including Helicobacter spp., viral and parasitic pathogens). Mice were allowed to acclimate for at least one week before experiments. All animal experiments were conducted under the“3R”principle (reduction, replacement and refinement) and were approved by the Animal Ethics Committee of Shanghai Jiao Tong University School of Medicine (SYXK 2013-0050, Shanghai, China). A lithogenic diet-induced mouse model of CGS was used in this study. Mice were fed a standard chow diet (normal diet, ND, containing 0.02% cholesterol) or a lithogenic diet (LD, containing 15% butter fat, 1.25% cholesterol and 0.5% cholic acid) for 8 weeks (n = 12 mice/group)[54]. To determine the effect of Lactobacillus reuteri CGMCC 17942 (LR) and Lactobacillus plantarum CGMCC 14407 (LP), the mice fed an LD received 200 µL of bacterial suspension of either LP or LR at a dosage of 109 colony-forming units (CFU)/day for 8 weeks. The ND group and LD group received an equal volume of normal saline, which served as the control. In some experiments, the intestinal-specific FXR inhibitor Gly-β-MCA (10 mg/kg) and the global FXR antagonist Z/E-guggulsterone (10 mg/kg) were orally administered along with LR and LC for 8 weeks[12].
Probiotic preparations
LP and LR were incubated with de Man–Rogosa–Sharpe liquid medium (MRS broth, BD, USA) under anaerobic conditions at 37 °C for 24 hours to reach the early stationary phase. The cultures were centrifuged at 5000 × g for 5 min at 4 °C, and bacterial cells were resuspended in sterilized saline solution (109 cells/200 µL) and stored at -80 °C as a stock solution. Each aliquot was thawed for 1 hour to room temperature before it was administered to each mouse by oral gavage. To determine the number of bacterial cells, serial dilutions of the bacterial suspensions were inoculated on fresh MRS agar plates under anaerobic conditions.
Sample collection
The mice were treated for 8 weeks after a week of adaptation. The body weight and food intake of the mice were checked once a week[52]. At the beginning of the 8th week after the start of LP and LR administration, fecal samples were collected from these mice and stored in liquid nitrogen for RNA extraction and subsequent quantification of the strain.
At the end of the 8th week, the mice were fasted for 5 hours but allowed free access to water. Blood samples were collected by heart puncture and centrifuged at 400 × g for 20 min at 4 °C for subsequent biochemical analysis. The animals were sacrificed by exsanguination after being anaesthetized with pentobarbital. The liver, gallbladder, and ileum were harvested. Half of these tissues were immediately snap-frozen in liquid nitrogen, and the other half were fixed in formalin.
Histology
Fresh liver and gallbladder specimens were fixed in 4% neutral paraformaldehyde at room temperature for 24 h. Paraffin-embedded sections (4 µm) were stained with hematoxylin and eosin (H&E) and assessed using a 20 × objective over 5 separate fields by two expert liver pathologists who were blinded to the treatment groups to identify the percentage of hepatocytes involved by steatosis, and subsequently the steatosis score was determined using the NAS histologic scoring system.
Hepatic lipid accumulation was measured by oil red O (ORO) staining as described previously[55]. Frozen liver sections (6 µm) were stained with ORO lipid stain (Abcam, USA) and assessed in the same way to identify the percentage of hepatocytes involved by steatosis.
Bile acid analysis
Ten microliters of serum was accurately measured, 300 µL of ethanol was added for precipitation, and the sample was vortexed for 60 seconds and centrifuged at 12000 × g at 4 °C for 10 min. The supernatants were further diluted with 100 µL of methanol to reconstitute the sample and vortexed for 30 s. Bile acid concentrations were determined using liquid chromatography-mass spectrometry (LC-MS) (Waters Corp., Milford, USA) with an electrospray ionization source. Chromatographic separation was archived on an Acquity UPLC® BEH C18 column (100 mm inner diameter, 1.7 µm; Waters Corp.). The mobile phase consisted of a mixture of 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile (B). Gradient elution was applied for the following phases: 0 ~ 4 min, 25% B; 4 ~ 9 min, 25 ~ 30% B; 9 ~ 14 min, 30 ~ 36% B; 14 ~ 18 min, 36 ~ 38% B; 18 ~ 24 min, 38 ~ 50% B; 24 ~ 32 min, 50 ~ 75% B; 32 ~ 35 min, 75 ~ 100% B; 35 ~ 38 min, 100 ~ 25% B. The flow rate was 0.25 mL/min.
Immunofluorescence
The immunofluorescence of FGF15 was evaluated on paraffin-embedded Ileum tissue sections. Briefly, after dewaxing and hydration, the antigen of sections was retrieved with citrate solution (Sangon Biotech (Shanghai) Co., Ltd, Shanghai, China). The sections were permeabilized in 0.3% Triton X-100 (Sangon Biotech (Shanghai) Co., Ltd, Shanghai, China) for 10 min, and nonspecific binding was blocked by immunostaining blocking buffer (Sangon Biotech (Shanghai) Co., Ltd, Shanghai, China) for 1 h at room temperature. Tissue sections were incubated with primary antibodies against FGF15 (1:100, Santa, USA) overnight at 4 °C. After washing, the sections were incubated with goat anti-mouse or goat anti-rabbit IR-Dye 594 CW-labeled secondary antibodies (1:1000, Cell Signaling Technology, USA) for 1 h at room temperature. The nuclei were stained with DAPI (5 mg/ml, Yeasen Biotech Co., Ltd, Shanghai, China). Finally, the sections were imaged with a Leica TCS SP8 confocal microscope.
Western blotting
Total proteins from liver and ileum tissues were extracted as previously described[56]. Total proteins (40 µg per lane) were separated by 10% SDS-PAGE and then electrotransferred to nitrocellulose membranes. The membranes were incubated with primary antibodies against FXR (NR1H4, 1:1000, Abcam, USA), SREBP2 (1:1000, Abcam, USA), CYP7A1 (1:1000, Abcam, USA), CYP8B1 (1:1000, Abcam, USA), CYP7B1 (1:1000, Proteintech Group, USA), CYP27A1 (1:1000, Proteintech Group, USA) and β-actin (1:1000, Cell Signaling Technology, USA) overnight at 4 °C. After washing with 0.1% Tween 20 phosphate buffer solution (PBST) three times, the membranes were incubated with goat anti-mouse or goat anti-rabbit IR-Dye 700 or 800 CW-labeled secondary antibodies for 1 hour at 37 °C and imaged with an Odyssey infrared scanner (LI-COR, Lincoln, NE, USA). Quantification was performed using the LI-COR software Image Studio.
RNA extraction and quantitative real-time polymerase chain reaction
Total RNA from liver and ileum tissues was extracted using TRIzol (Invitrogen, CA, USA) homogenization followed by isopropanol incubation as previously described, and the purity of RNA products was determined to be between 1.8 and 2.0 according to the 260/280 ratio. One thousand ng of RNA was subjected to reverse transcription to generate complementary DNA using a commercial PrimeScript™ RT reagent kit (Takara, Japan). The synthesized cDNA was used for quantitative polymerase chain reaction (qPCR) to determine the relative expression of targeted genes using gene-specific, intron-spanning primers (Table 1). qPCR was performed in 20 µL reactions using Hieff® qPCR SYBR Green Master Mix (Yeasen Biotech, Shanghai, China) to analyze mRNA transcripts. All reactions were performed using the ABI Prism 7900HT Sequence Detection System (Applied Biosystems, CA, USA). The fold changes in the expression of each target gene were compared to the housekeeping gene β-actin using the 2−ΔΔCT method and are represented as the fold change relative to the control group. Each target gene analyzed in the tissues was analyzed in triplicate in experiments that were repeated three times.
Table 1
PCR Genes Primers Sequences
Gene (mouse) | Primer sequences |
Fxr Forward | 5’- AGCATTACCAAGAACGCCGTGTAC − 3’ |
Reverse | 5’- GCTGTCGTCCTCATTAGCTGTCTG − 3’ |
Fgf15 Forward | 5’- CGGTCGCTCTGAAGACGATTGC − 3’ |
Reverse | 5’- TACATCCTCCACCATCCTGAACGG − 3’ |
Fgfr4 Forward | 5’- GCCCCTGTACGTGATTGTGG − 3’ |
Reverse | 5’- ATCCATTTGACTGGCAGGCG-3’ |
Shp Forward | 5’- TCCTAGCCAAGACAGTAGCCTTCC − 3’ |
Reverse | 5’- TACCGCTGCTGGCTTCCTCTAG − 3’ |
Ibat Forward | 5’- ACCACTTGCTCCACACTGCTT − 3’ |
Reverse | 5’- CGTTCCTGAGTCAACCCACAT − 3’ |
Mrp3 Forward | 5’- TGAGATCGTCATTGATGGGC − 3’ |
Reverse | 5’- AGCTGAGAGCGCAGGTCG − 3’ |
Mrp4 Forward | 5’- TTAGATGGGCCTCTGGTTCT − 3’ |
Reverse | 5’- GCCCACAATTCCAACCTTT − 3’ |
Mdr2 Forward | 5’- GGATGGTGACTGTGGGCTGAT − 3’ |
Reverse | 5’- GGCTGTTCTCCCTTCTCATGG − 3’ |
Bsep Forward | 5’- GCTGCCAAGGATGCTAATGC − 3’ |
Reverse | 5’- CTACCCTTTGCTTCTGCCCA − 3’ |
Cyp7a1 Forward | 5’- GCTAAGACGCACCTCGTGATCC − 3’ |
Reverse | 5’- CCGCAGAGCCTCCTTGATGATG − 3’ |
Cyp8b1 Forward | 5’- GGCAAGAAGATCCACCACTACAGC − 3’ |
Reverse | 5’- TCAGGCGATAGAGGAAGCGTACC-3’ |
Cyp27a1 Forward | 5’- ATTAAGGAGACCCTGCGCCT − 3’ |
Reverse | 5’- AGGCAAGACCGAACCCCATA − 3’ |
Cyp7b1 Forward | 5’- TGGCTTCCTTATCTTGGCATGGC − 3’ |
Reverse | 5’- TCGCTGATAATCGGCTGCTGAAC − 3’ |
Fecal DNA extraction and microbiota sequencing
Fecal samples were collected within 15 min of defecation and stored in liquid nitrogen within 1 hour. DNA extraction was performed with the QIAamp DNA Stool Kit (Qiagen, California, USA). The bacterial 16S ribosomal RNA (rRNA) gene was PCR amplified using primers binding to the V3-V4 regions. The resulting amplicons were purified by gel extraction (AxyPrep DNA GelExtraction Kit, Axygen Biosciences, Union City, California, USA) and then quantified and sequenced on the Illumina MiSeq platform (Illumina, San Diego, USA) with paired-end 300-nucleotide reads. The 16S rRNA sequencing data were analyzed by the Quantitative Insights Into Microbial Ecology platform (V.1.9.1). Sequence files and metadata for all samples used in this study have been deposited in the GenBank Sequence Read Archive database.
Bioinformatics and statistical analysis
The raw 16S rRNA gene sequencing reads were demultiplexed, quality-filtered by fastp version 0.20.0 and merged by FLASH version 1.2.7[57, 58] with the following criteria: (1) No contaminant sequences; (2) The 300 bp reads were truncated at any site receiving an average quality score of < 20 over a 50 bp sliding window, and the part of truncated reads shorter than 50 bp and the part of reads containing ambiguous characters were both discarded; (3) Only overlapping sequences longer than 10 bp were assembled according to their overlapped sequence. The maximum mismatch ratio of overlap region is 0.2. Reads that could not be assembled were discarded; (4) Samples were distinguished according to the barcode and primers, and the sequence direction was adjusted, exact barcode matching, 2 nucleotide mis-match in primer matching. Operational taxonomic units (OTUs) with 97% similarity cutoff[59] were clustered using UPARSE version 7.1, and chimeric sequences were identified and removed. The taxonomy of each OTU representative sequence was analyzed by RDP Classifier version 2.2 against the 16S rRNA database using confidence threshold of 0.7[60].
Principal coordinate analysis (PCoA) based on Bray-Curtis dissimilarity were performed to provide an overview of gut microbial dynamics in response to LD and LR/LP treatments. Similarities of gut microbiota between samples were compared by ANOSIM and Adonis based on Bray-Curtis in phylum level. Statistical comparison of the relative abundance in different groups were analyzed by Kruskal-Wallis H test and using Welch’s t test (with 95% confidence intervals, P-value < 0.05, multiple testing P values were adjusted with FDR). The relationship between the top 50 abundance of Species levels and the incidence and grade of CGS and the serum BAs, the serum biochemical values and the CGS-related mRNA expressions were analyzed by Spearman’s correlation analysis, the Spearman’s correlation coefficient │R│≥0.1 and * 0.01 < P ≤ 0.05, ** 0.001 < P ≤ 0.01, *** P ≤ 0.001.
Reagents
Z/E-Guggulsterone was purchased from MCE (MCE, USA). Primary antibodies against CYP7A1, CYP8B1 and FXR were purchased from Abcam (Abcam, USA). β-actin was purchased from Cell Signaling Technology (CST, USA). The primary antibodies against CYP7B1, CYP27A1 and FGFR4 were from Proteintech Group (Proteintech Group, USA). The primary antibodies against FGF15 and all the other reagents were from Sigma-Aldrich Chemical (MO, USA).
Statistical analysis
Data were presented as the mean ± SEM. Statistical analysis was performed using GraphPad Prism 7.0 (GraphPad, La Jolla, CA). Two groups were compared by an unpaired t-test. A P value < 0.05 was considered statistically significant.