All animal procedures used in this experiment were reviewed and approved by the Institutional Animal Care and Use Committee of China Agricultural University (Beijing, China). The study was conducted at the China Agricultural University Animal Experimental Base (Hebei, China). The three protein sources used in this study were HWP (hydrolyzed wheat protein; JPC56, Joosten, Weert, The Netherlands), FSBM (fermented soybean meal; Yuanyao Biotechnology Co., LTD, Jiangsu, China) and ESBM (enzyme-treated soybean meal; HP300, Hamlet Protein, Horsens, Denmark).
Animals, diets, and experimental design
A total of 144 Duroc × Landrace × Large White weaned piglets, with an initial body weight (BW) of 7.75 ± 0.96 kg, were randomly assigned to 3 treatments with 6 replications of 8 piglets (4 barrows and 4 gilts) per pen. The whole experimental period lasted for 28 d, and contained phase 1 ( days 0-14) and phase 2 (days 15-28). The dietary treatments included (1) HWP diet: 15.90% JPC56 replacing soybean meal in phase 1 and 7.90% JPC56 replacing soybean meal in phase 2; (2) FSBM diet: 15.80% FSBM replacing soybean meal in phase 1 and 7.80% FSBM replacing soybean meal in phase 2; (3) ESBM diet: 15.10% HP300 replacing soybean meal in phase 1 and 7.50% HP300 replacing soybean meal in phase 2. The experimental diets had similar level of crude protein (CP, 18.0%). All diets were formulated to meet or exceed the nutrient requirements of National Research Council (NRC 2012) [17] for nursery pigs ranging from 7 to 11 kg (or 11 to 25 kg) BW and fed as mash (Table 1).
All piglets were housed in an commercial flat-deck pens with duckbill drinkers, adjustable feeders and plastic slatted floors. Feeds and water were provided ad libitum for piglets. The room temperature and relative humidity were maintained at 24°C to 26°C and 60% to 70%, respectively. Piglet were weighed individually after fasting on days 14 and 28 to calculate average daily gain (ADG), average daily feed intake (ADFI) and feed conversion ratio (FCR). Fecal score were determined by clinical signs of fecal consistency every day based on the methods described by Pan et al. [18] and a scoring system was applied to indicate the presence and severity of diarrhea as following: 1 = hard feces; 2 = slightly soft feces; 3 = soft, partially formed feces; 4 = loose, semiliquid feces; and 5 = watery, mucous-like feces.
Sample collection and preparation
All diet samples were collected and stored at 4°C for further chemical analysis. On days 14 and 28, fasting blood samples (approximately 10 mL) were collected from 1 piglet per pen (closest to the average body weight of each pen) via the jugular vein into vacutainer tubes (Greiner Bio-One GmbH, Kremsmunster, Austria). Serum samples were obtained by centrifugation at 3000 × g for 10 min at 4°C, and then stored at −20°C until analysis of serum parameters. From d 26 to 28, approximately 200 g of feces was collected from each pen for 3 d and stored at −20°C. Then the 3 d collection of feces was pooled by pen and dried at 65°C for 72 h to determine apparent total tract digestibility (ATTD) of nutrients. All samples were ground to pass through a 1-mm screen (40 mesh) before analysis. At the end of experiment, six fresh fecal samples (1 piglet per pen) in each treatment were rapidly frozen in liquid nitrogen, and then stored at −80°C for further analysis of intestinal bacteria, SCFAs and nitrogen metabolites.
Chemical analysis
Diets and feces were analyzed in duplicate for the contents of dry matter (DM, method 934.01) and crude protein (CP, method 990.03) according to the Association of Official Analytical Chemists (AOAC, 2006) [19]. Gross energy (GE) was determined by an Automatic Energy Analyzer (Parr 1281, Moline, IL, USA). The chromium (Cr) content in the diets and feces was analyzed using an Atomic Absorption Spectrophotometer (Z-5000; Hitachi, Tokyo, Japan) according to the procedure of Williams et al. [20]. ATTD was determined by the equation as follows: digestibility (%) = 100 – [(Crdiet × Nutrientfeces) / (Crfeces × Nutrientdiet)] × 100. The levels of advanced oxidation protein products (AOPP) and ferric reducing ability of plasma (FRAP) in serum were assessed using commercially available ELISA test kits (Zhongshang Boao Biotechnology Co., Ltd., Beijing, China). The contents of malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px), diamine oxidase (DAO) and endotoxin in serum were measured using assay kits according to the manufacturer’s protocols (Nanjing Jiancheng Bioengineering Institute, Jiangsu, China). Serum D-lactate level was measured by an ELISA kit (Luyuan Byrd Biotechnology Co., Ltd., Beijing, China). The levels of immunoglobulin G (IgG), immunoglobulin A (IgA) and immunoglobulin M (IgM) in serum were measured using commercially available kits (Leadman Biochemistry Co., Ltd., Beijing, China). The concentrations of interleukin-1β (IL-1β), interleukin-6 (IL-6) and tumour necrosis factor-α (TNF-α) in serum were determined using ELISA kits (Kangjia Hongyuan Biotechnology Co., Ltd., Beijing, China).
DNA extraction, PCR amplification, Illumina MiSeq sequencing and data analysis
Microbial DNA was extracted from the fecal samples using the DNA Kit (Omega Bio-tek, Norcross, GA, USA). The integrity of DNA was assessed by agarose gel electrophoresis. Isolated DNA was used as a template for amplification of the 16S rRNA gene V3-V4 region using universal primers 338F (5’-barcode-ACTCCTRCGGGAGGCAGCAG-3’) and 806R (5’-GGACTACCVGGGTATCTAAT-3’), where barcode is an eight-base sequence unique to each sample. After purification, amplicons were pooled and paired-end sequenced on the Illumina MiSeq platform (Illumina Inc., San Diego, CA, USA). Raw fastq files were demultiplexed, and quality-filtered using QIIME(version1.17). Operational taxonomic units (OTUs) were clustered with 97% similarity cutoff using UPARSE and chimeric sequences were removed using UCHIME. The Ribosomal Database Project (RDP) Classifier (http://rdp.cme.msu.edu/) was used to analyze the taxonomy of each 16S rRNA gene sequence with confidence greater than 70%. The Venn diagram was present based on the occurrence of shared and unique OTUs among different treatments. α-diversity including observed species, Chao, Ace, Shannon, Simpson, Good’s coverage was performed using MOTHUR (v.1.31.2). The Unifrac metric was used to calculate β-diversity and UPGMA tree was displayed by QIIME (v1.80) based on Unweighted UniFrac distances of the OTUs community. Principal component analysis (PCA) was conducted by R software (v3.1.1) according to the OTUs among different treatments. LefSe analysis was performed to identify the biomarkers for microbial communities from phylum to genus based on the relative abundance of annotated taxonomic profiling.
Predictive metabolic functions of microbial communities
Predictive metabolic functions of the bacterial community in the fecal samples were conducted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on 16S rRNA gene sequencing [21]. OUTs were used to predict functional profiling of microbial communities by referencing the Kyoto Encyclopedia of Genes and Genome (KEGG) orthology database [22].
Measurements of SCFAs and BCFAs by high performance ion chromatography
The fecal samples were prepared for analyzing SCFAs and BCFAs as previously described by He et al. [23]. Samples (0.5 g) were weighed and dissolved in 8 mL of ultrapure water. After ultrasound for 30 min, fecal samples were centrifuged at 3000 × g for 5 min. The supernatant was diluted (1:50) and then filtered through a 0.22 µm filter. Extracted sample solution (25 µL) was analyzed for SCFAs (acetate, propionate, butyrate), BCFAs (isobutyrate, valerate and isovalerate) using a high performance ion chromatography system (DIONEX ICS-3000, Thermo Fisher, Waltham, MA, USA). The SCFAs and BCFAs were separated by an AS11 analytical column (250 × 4 mm) and an AG11 guard column using potassium hydroxide. The concentration of SCFAs and BCFAs were expressed as mg/g of feces.
Analysis of ammonia nitrogen in feces
The content of ammonia nitrogen (NH3-N) was analyzed based on the method as described by Chen et al. [24]. In short, 0.5 g of samples was dissolved in 5 mL of ammonia-free water and centrifuged at 5000 × g for 15 min. Next, 19 mL of ammonia-free water and 1 mL of potassium sodium tartrate was added into 1 mL of collected supernatant in a 50-mL sterile tube, followed by the addition of 1.5 mL of Nessler’s reagent. The absorbance of final mixture was determined at 420 nm against ammonia-free water using a UV-vis Spectrophotometer (MAPADA, Shanghai, China).
Determination of biogenic amines by high performance liquid chromatography
The concentrations of biogenic amines (putrescine, cadaverine and spermine) were determined by high performance liquid chromatography (HPLC) as previously described by Li et al. [25] with modification. Briefly, 0.5 g of fecal samples was added into a 2-mL centrifuge tube and mixed with 1 mL of trichloroacetic acid. The mixture was centrifuged at 3600 × g for 10 min, the supernatants were then vortexed with the same volume of n-hexane for 5 min. The aqueous phase was extracted again in the same manner. Internal standard (20 mL) was added into the extracts, followed by the addition of 1.5 mL of saturated sodium bicarbonate, 1mL of dansyl chloride, and 1mL of sodium hydroxide. The mixture was subsequently heated at 60°C for 45 min with occasional shaking. Next, 100 μL of ammonia was added into the mixture and kept at 40°C in a water bath under N2 condition. Finally, the analyzed sample was produced by adding acetonitrile to the residue. Each sample (20 μL) was injected into Agilent HPLC 1200 series equipped with a reversed-phase ZORBAX 80 A Extend-C18 column (250 mm × 4.6 mm i.d.; 5 µm particle size, Agilent, Santa Clara, USA). The flow rate, wavelength and column temperature were set at 1.0 mL/min, 254 nm and 40°C, respectively. The concentration of biogenic amines were expressed as μg/g of feces.
Statistical analysis
Data analyses of growth performance, serum parameters, SCFA concentrations, and nitrogen metabolites were analyzed by One-Way ANOVA using the GLM procedure of SAS 9.4 (SAS Inst. Inc., Cary, NC), with results presented as mean ± SEM. Differences in the fecal score were determined by the χ2 contingency test. Microbiota diversity metrics were conducted from standardized OTU reads using R software (version 3.2.2). The relative abundance of fecal microbiota composition was analyzed by the Kruskal-Wallis method. Differences were considered significant at p < 0.05, and tendency was declared with 0.05 ≤ p < 0.10.