Details of all animals, diets, reagents, kits, instruments, software, and service providers used in this protocol are provided in the Table of Materials. All animal studies were performed following the National Institutes of Health (NIH) Guidelines for the Care and Use of Laboratory Animals and received approval from the Experimental Animals Committee of Shandong Provincial Hospital (ethical approval no. 2022–007, approved on January 24, 2022).
CAUTION: Animal blood, fecal samples, and tissues should be handled as potentially biohazardous materials. All procedures involving live animals, biological samples, sharps, organic solvents, and chemical assay reagents should be performed in accordance with institutional biosafety, animal care, and chemical safety regulations. Animal carcasses, tissues, blood-contaminated materials, and fecal samples should be collected in designated biohazard waste containers and disposed of through the institutional animal facility or biosafety office. Needles, gavage needles, capillary tubes, and other sharps should be discarded immediately after use in approved sharps containers. Organic solvent waste, including methanol, acetonitrile, and formic acid-containing solutions, should be collected in labeled chemical waste containers and disposed of through the institutional hazardous chemical waste program. Waste from biochemical and oxidative stress assays should be collected and disposed of in accordance with the manufacturer’s safety data sheets and institutional chemical safety rules.
Experimental animals
Six-week-old male C57BL/6J mice (n = 4 per group) were maintained under specific pathogen-free (SPF) conditions with a 12 h light/dark cycle at 22 ± 2 °C and 50–60% relative humidity. Animals had ad libitum access to food and water, with a maximum of five mice housed per cage. The control mice were fed a standard chow diet consisting of 70% carbohydrates, 20% protein, and 10% fat (kcal). To establish the MASLD mouse model, mice were fed a high-fat diet for 8 weeks containing 20% carbohydrates, 20% protein, and 60% fat (kcal). All diets were stored at 4 °C and replenished twice per week. Mice were randomly assigned to experimental groups using a random number generator, and sample size (n = 4 per group) was determined based on previous studies using similar high-fat diet–induced mouse models and preliminary experiments. All treatments were administered at the same time each day to minimize circadian variation.
Microalgae oil was extracted and purified by the Shandong Academy of Agricultural Sciences, with a purity of approximately 99%. The microalgae oil was stored at −30 °C protected from light. Before administration, the oil was prepared with an emulsifier and thoroughly mixed to ensure homogeneity. Specifically, DHA-rich microalgae oil was emulsified in sterile 0.5% carboxymethylcellulose sodium containing 0.5% Tween-80 in normal saline. The microalgae oil and emulsifier vehicle were mixed at a ratio of 1:9 (v/v) and vortexed for 2 min immediately before gavage to obtain a uniform suspension. Mice in the microalgae oil-treated group received the preparation once daily by oral gavage using a sterile feeding needle at a dose of 10 µL/g body weight. The gavage volume was adjusted daily according to body weight to ensure dose consistency. Mice in the control group received an equivalent volume of sterile normal saline under the same conditions. The saline used was 0.9% sodium chloride injection.
Probiotic treatment consisted of a composite formulation containing Lactobacillus plantarum (DY-1), Lactobacillus acidophilus (KDB-03), Lactobacillus casei (KDB-LC), and Bacillus coagulans (GIM 1.645). The four strains were mixed at an equal viable-cell ratio of 1:1:1:1. Each strain contributed 2.5 × 107 CFU/mL to the final formulation, yielding a total bacterial concentration of 1 × 108 CFU/mL. The probiotic mixture was synthesized by the Shandong Academy of Agricultural Sciences and is not commercially available. Probiotic treatment consisted of a composite probiotic fermentation broth containing Lactobacillus plantarum DY-1, Lactobacillus acidophilus KDB-03, Lactobacillus casei KDB-LC, and Bacillus coagulans GIM 1.645. The bacterial concentration of the formulation was 1 × 108 CFU/mL. The probiotic fermentation broth was stored at 4 °C before use. Mice in the probiotic-treated group received the probiotic formulation once daily by oral gavage at a dose of 0.01 mL/g body weight throughout the experimental period.
Individual strains were cultured under appropriate conditions and harvested at the mid-log growth phase (OD₆₀₀ ≈ 0.6), then combined at the indicated ratio. Bacterial cultures were centrifuged to remove the supernatant, and the pellets were resuspended in sterile phosphate-buffered saline (PBS). The freshly prepared bacterial suspension was kept on ice prior to administration to preserve viability. The final bacterial concentration was adjusted to 1 × 108 CFU/mL before administration. Mice in the probiotic group received the formulation by oral gavage at a dose of 0.01 mL/g body weight once daily throughout the experimental period. No antibiotic pretreatment was applied prior to probiotic administration. To reduce experimental bias, outcome assessment was performed by blinded investigators where applicable. MASLD was confirmed through blood biochemical analysis.
Blood analysis
At the end of the experimental period, mice were fasted overnight (12 h) with free access to water before glucose measurement and terminal blood collection. Mice were deeply anesthetized with isoflurane using an anesthesia vaporizer until loss of pedal reflex was confirmed. Terminal blood samples were collected by retro-orbital bleeding. After blood collection, mice were euthanized by cervical dislocation while under deep anesthesia, and death was confirmed by cessation of respiration and heartbeat. Blood was allowed to clot at room temperature and then centrifuged at 3,000 × g for 10 min to obtain serum. Serum samples were aliquoted and stored at −80 °C until analysis. Serum glucose, total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-c), high-density lipoprotein cholesterol (HDL-c), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) were measured using an automatic biochemical analyzer, following the manufacturer's instructions. These parameters were quantified using enzymatic colorimetric assays with standard reagent kits integrated into the analyzer system. All biochemical parameters were normalized to the serum volume and expressed in the units specified by the manufacturer.
Oxidative stress assays
Oxidative stress biomarkers were measured using kits, including those for malondialdehyde, superoxide dismutase, and catalase. Assays were conducted following the manufacturer’s instructions. Briefly, liver tissues were homogenized in ice-cold buffer and centrifuged to obtain supernatants for analysis. Malondialdehyde (MDA) levels were determined using a thiobarbituric acid reactive substances (TBARS) assay; superoxide dismutase (SOD) activity was measured by its ability to inhibit superoxide-mediated reactions; and catalase (CAT) activity was quantified by monitoring the decomposition rate of hydrogen peroxide. Measurements were performed using a microplate reader, and values were calculated using standard curves or the formulae provided in the kits. Oxidative stress markers were normalized to liver tissue weight and expressed according to the manufacturer’s specifications.
16S rRNA sequencing and microbiome analysis
Fecal samples were collected at the end of the experimental period directly from individual mice under sterile conditions, immediately frozen in liquid nitrogen, and stored at −80 °C until DNA extraction. Microbial DNA was extracted using a commercial kit according to the manufacturer’s protocol. The V3–V4 region of the bacterial 16S rRNA gene was amplified using primers 341F/806R. PCR amplification was performed in a 25 µL reaction system containing template DNA, 2x PCR master mix, and 0.2 µM of each primer. The amplification program consisted of initial denaturation at 95 °C for 3 min, followed by 25 cycles of 95 °C for 30 s, 55 °C for 30 s, and 72 °C for 45 s, with a final extension at 72 °C for 10 min. Amplicon libraries were constructed and sequenced on an Illumina MiSeq platform using a paired-end 2 × 250 bp strategy by a commercial sequencing service provider. Library quality was assessed prior to sequencing, and pooled libraries were loaded at the manufacturer’s recommended cluster density. Low-quality reads with ambiguous bases, insufficient length, or an average quality score below Q20 were removed before downstream analysis.
Raw sequencing reads were processed using QIIME 2 version 2019.420. Briefly, paired-end reads were demultiplexed, quality-filtered, denoised, merged, and chimera-filtered using DADA2 with default parameters unless otherwise specified. Non-singleton amplicon sequence variants (ASVs) were retained for downstream analysis. Taxonomic assignment was performed using the Greengenes database version 13_8 implemented in QIIME221. Given the inherent resolution limitations of 16S rRNA gene sequencing, particularly when using the Greengenes database, taxonomic annotations were interpreted exclusively at the genus level. Species-level classification was not considered reliable and therefore was not used in any downstream analyses, statistical comparisons, or biological interpretations. All microbial features were collapsed to the genus level prior to visualization and analysis.
Alpha-diversity metrics (Chao1, Observed species, Shannon, Simpson, Faith’s PD, and Pielou’s evenness) were used. Statistical comparisons of alpha diversity between groups were performed using appropriate non-parametric tests (e.g., Kruskal–Wallis test). The Jaccard distance and Bray-Curtis dissimilarity were used as beta diversity metrics. Principal Coordinate Analysis (PCoA) plots, non-metric multidimensional scaling (NMDS), and linear discriminant analysis effect size (LEfSe) were used to illustrate changes in microbiome communities, with an LDA score threshold of 2.0. Permutational multivariate analysis of variance (PERMANOVA) was used to assess statistical significance in beta diversity. Data visualization and statistical analyses were performed using the GenesCloud platform (https://www.genescloud.cn).
Microbial functional profiles were inferred from 16S rRNA sequencing data rather than directly measured by shotgun metagenomic or transcriptomic sequencing. Based on the normalized pathway or functional group abundance table, predicted functional units were mapped to commonly used databases, including KEGG, MetaCyc, and COG. KEGG pathway abundance was summarized according to its hierarchical functional categories, with level 2 pathway classifications used for downstream comparison. The average abundance of each pathway category was calculated using R software.
Untargeted metabolomics analysis of liver samples
Liver tissues were rapidly excised immediately after death confirmation, immediately frozen in liquid nitrogen, and stored at −80 °C prior to analysis. Approximately 50 mg of frozen liver tissue was homogenized in ice-cold methanol:water (4:1, v/v) supplemented with internal standards. The tissue-to-extraction solvent ratio was 1:10 (w/v). Samples were vortexed for 1 min, sonicated on ice for 10 min, and then incubated at −20 °C for 30 min to improve protein precipitation. The homogenates were thoroughly mixed, subjected to sonication on ice, and centrifuged at 12,000 × g for 15 min at 4 °C. The supernatants were carefully collected, evaporated under a mild nitrogen flow, and reconstituted in 50% methanol for subsequent analysis.
Quality control (QC) samples were generated by pooling equal volumes from each sample and were analyzed intermittently throughout the run to evaluate analytical stability and reproducibility. Untargeted metabolomics analysis was performed using an ultra-high-performance liquid chromatography system coupled to high-resolution mass spectrometry, operated by a commercial service provider. Metabolites were separated on a reverse-phase C18 column using a binary solvent system consisting of water with 0.1% formic acid and acetonitrile with 0.1% formic acid. The injection volume was 2 µL, the column temperature was maintained at 40 °C, and the flow rate was set at 0.30 mL/min. A gradient elution program was used to achieve broad metabolite separation. Mass spectrometric detection was conducted in both positive and negative electrospray ionization modes across an m/z range of 70–1,000 to achieve broad metabolite coverage. The ion spray voltage was set to 3.5 kV in positive mode and −2.5 kV in negative mode. The capillary temperature was maintained at 320 °C, and data were acquired in full-scan MS mode with data-dependent MS/MS acquisition for metabolite annotation. Raw data were processed using dedicated metabolomics software (MassLynx v4.1) for feature detection, alignment, and normalization. Metabolite identification was performed based on accurate mass, retention time, and MS/MS fragmentation patterns by comparison with public databases, including the Human Metabolome Database (HMDB) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) (v2023), where applicable.
Multivariate and pathway analysis
Processed metabolomics data were subjected to multivariate statistical analyses, including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), to visualize metabolic differences among experimental groups. Differential metabolites were identified based on a combination of variable importance in projection (VIP) scores (>1.0) and statistical significance (p < 0.05). Identified metabolites were further mapped to metabolic pathways using KEGG pathway enrichment analysis to elucidate biological processes associated with DHA-rich microalgae oil supplementation.
Statistical analysis
The data were presented as mean ± SEM and analyzed using one-way analysis of variance (ANOVA) followed by Tukey’s multiple comparisons test. Statistical significance was defined as p < 0.05. Enrichment analysis of liver metabolites was performed using R (version 4.4.1). Pairwise associations between microbial genera and liver metabolites were analyzed using Spearman rank correlations. Only significant correlations (false discovery rate, FDR < 0.05) with |ρ| ≥ 0.6 were included in the integrative network analyses. Microbiome and metabolomics data processing were conducted as described above, including the use of the GenesCloud platform and quality control procedures.