Cattle studies
To obtain the CtM animals, male cattle were orchiectomized by a veterinarian (both testicles were removed). Prior to sample collection, the cattle were examined for symptoms of diarrhea, and antibiotic and other medication treatment within 1 month of sampling. Rectal material and the blood were sampled from 45 healthy animals: juvenile (male, CtM, and female; mean age: 11.9 ± 1.1 months; n = 5 of each) and postpubescent (male, CtM, and female; mean age: 19.3 ± 1.5 months; n = 5 of each) Hanwoo, and postpubescent (male, CtM, and female; mean age: 12.1 ± 1.6 months; n = 5 of each) Holsteins. The rectal luminal content was collected by rectal enema using clean disposable latex gloves. The blood samples (5 ml) were collected from the jugular vein by a veterinarian and immediately centrifuged in BD Microtainer chemistry tubes (Becton Dickinson, Franklin Lakes, NJ, USA) for serum collection. The blood and muscle samples, and the luminal content of the rumen, ileum, cecum, and colon of the adult male (mean age: 31.2 ± 5.9 months) and CtM Hanwoo (mean age: 33.9 ± 1.4 months, n = 10 in each group) were collected from a local slaughterhouse (Gunwi-Gun, South Korea) under the supervision of the official veterinarian; the serum was collected from whole-blood samples as described above. The collected samples were transported to the laboratory on dry ice and stored at − 80 °C until use.
Mouse studies
C57BL/6J mice were purchased from the Japan SLC Inc. (Hamamatsu, Japan) and supplied by Central Lab. Animal Inc. (Seoul, South Korea). All mice were housed in individually ventilated cages in a temperature-controlled room with a 12 h light/12 h dark cycle, and given sterilized bedding and food and water ad libitum. At the end of the experiments, mice were fasted (6 h), anesthetized by isoflurane inhalation, and euthanized by cardiac exsanguination. To sample the intestinal (luminal) contents, the target regions of the intestinal tract were flushed with sterile phosphate-buffered saline (PBS).
Castrated male mouse studies
To obtain the CtM animals, 4-week-old male mice were castrated by orchiectomy. For the Sham groups, age-matched male mice underwent a sham operation (i.e., the muscle layer and skin incision). After the surgery, both groups were given antibiotics (enrofloxacin) and an analgesic (Repellent). To reverse the effect of enrofloxacin on the gut microbiota, the Sham and CtM mice underwent FMT (the fecal samples were collected from the strain-, age-, and sex-matched non-operated donors,
n = 10) once a day for 2 continuous days prior to the dietary intervention. Subsequently, the mice were provided either a LFD (10% fat; D12450H, Research Diets, New Brunswick, NJ, USA) or a HFD (45% fat; D12451, Research Diet). For the antibiotic-treated groups, the HFD-fed mice were given a combination of ampicillin (1 g/l), neomycin (1 g/l), metronidazole (1 g/l), and vancomycin (0.5 g/l) in drinking water for 5 weeks (
n = 6 per group; Fig.
4a). The antibiotic cocktail was renewed every 4 d.
Mouse FMT studies
Non-castrated male mice (6-week-old) were maintained on LFD for 10 weeks. Prior to FMT, the mice received an antibiotic cocktail in drinking water. After a 12 h washout period, the mice were subjected to FMT (once a day for 3 continuous days) and fed HFD for 4 weeks. Fecal pellets from the Sham-HFD and CtM-HFD mouse donors (
n = 6 in each group) were freshly collected and transferred immediately to an anaerobic chamber (Bactron II-2, Sheldon Manufacturing) filled with an atmosphere of 5% H
2, 5% CO
2, and 90% N
2. The pellets were resuspended in sterile and reduced PBS (100 mg feces/ml PBS), vortex-mixed for 3 min, and sieved through a 70 ∝m cell strainer. The fecal suspension (inoculum) was kept in Hungate anaerobic culture tubes and administered to the recipient mice (Sham-R and CtM-R,
n = 5 in each group; Fig.
5a).
BCAA-enriched diet feeding studies
Non-castrated male mice (7-week-old) were acclimated on HFD for 1 week. The mice were fed HFD (0% BCAA) or a customized isocaloric BCAA-HFD (3% and 5% BCAA) for 8 weeks (
n = 6 in each group; Fig.
6a). The amount of each BCAA in the BCAA-enriched HFD is set out in Additional file 2: Supplementary Table S2.
DNA extraction and 16S rRNA gene sequencing
Bacterial genomic DNA was extracted from the intestinal luminal content of cattle and mice using a method involving the Repeated Bead-Beating plus column (QIAamp DNA stool mini kit; Qiagen, Valencia, CA, USA).[43] In preparation for the GS-FLX sequencing of the rectal samples from the juvenile and postpubescent cattle, a fragment of the 16S rRNA gene spanning the hypervariable V1–V2 regions was amplified by polymerase chain reaction (PCR) using bacterial universal primers 8F (5′-X-GAG TTT GAT CMT GGC TCA G-3′) and 338R (5′-TGC TGC CTC CCG TAG GAG T-3′); 10 b sample-specific barcodes (designated as X) were added to the 5′ primer terminus to tag the PCR products. In preparation for the Illumina MiSeq sequencing of the gastrointestinal samples from the adult Hanwoo and mice, a fragment of the 16S rRNA gene spanning the hypervariable V3–V4 regions was amplified by PCR using the forward primer 5′-TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG-3′ and the reverse primer 5′-GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3′. The PCR was performed in a C 1000 thermal cycler (Bio-Rad, Hercules, CA, USA). The PCR conditions were as follows: initial denaturation at 96 °C for 6 min; followed by repeated cycles of denaturation at 94 °C for 1 min, annealing at 50 °C for 30 s, and extension at 72 °C for 90 s; and a final extension step at 72 °C for 10 min. For the PCR of DNA extracted from the rectum, rumen, cecum, and colon contents, 18 repeated cycles were used; for the PCR of DNA extracted from the ileum content, 25 repeated cycles were used. Three PCR reactions with the same template were pooled and the products were purified using the QIAquick PCR purification kit (Qiagen). Equimolar amounts of the purified amplicons were then combined in a single tube. For the GS-FLX sequencing, the amplicons were pyrosequenced by Macrogen (Seoul, Republic of Korea) using the Genome Sequencer FLX Titanium (Roche, Branford, CT, USA). For the Illumina MiSeq sequencing, a 16S V3–4 PCR product library was prepared using the Nextera XT Index (Illumina). The library was then sequenced using an Illumina MiSeq platform and the paired-end 2 ⋅ 300 bp reagent kit, according to the manufacturer’s instructions.
Evaluation of contaminating DNA
Possible DNA contamination of all reagents used for DNA extraction and sequencing was investigated. PCR analysis for the presence of contaminating bacterial 16S rRNA genes (in a 30 cycle reaction) revealed no apparent contamination of any reagent used.
Sequence analysis
To generate the GS-FLX sequencing datasets, the raw sequences were preprocessed using the QIIME software package 1.9.0 [44] to exclude poor-quality sequences and/or sequencing errors. Briefly, raw sequences containing more than one ambiguous base call, with errors in the barcode or primer regions, with average quality scores < 25, or shorter than 200 bp were removed. To generate the Illumina MiSeq sequencing datasets, paired-end reads (forward and reverse fastq files) were joined and quality-filtered using the QIIME software. Chimeric sequences were excluded from the quality-filtered sequence sets using USEARCH software (version 7.0.1090). Unless noted otherwise in the text, default parameters were used. UCLUST software (version 1.2.21) clustered OTUs (at 97% sequence similarity) using the open reference OTU picking method. Singleton OTUs were excluded from further analyses. A representative sequence was selected for each OTU and aligned with reference sequences deposited in the Greengenes database using PyNAST (version 1.2.2). A phylogenetic tree of the aligned sequences was then constructed using Fasttree. Overviews of the 16S rRNA gene sequence datasets are provided in supplemental tables, as follows: the GS-FLX–generated datasets: the juvenile Hanwoo (15 samples) in Additional file 2: Supplementary Table S3; postpubescent Hanwoo (15 samples) in Additional file 2: Supplementary Table S4; and postpubescent Holstein (15 samples) in Additional file 2: Supplementary Table S5. The Illumina MiSeq-generated datasets: the adult Hanwoo (60 samples) in Additional file 2: Supplementary Table S6; castrated or sham-operated male mice (72 samples) in Additional file 2: Supplementary Table S7; FMT recipient mice (22 samples) in Additional file 2: Supplementary Table S8; and BCAA-HFD–fed mice (36 samples) in Additional file 2: Supplementary Table S9.
For phylogenetic analysis of abundant OTUs assigned to the family Peptostreptococcaceae, representative sequences were aligned with those of closely related species using the multiple sequence alignment program CLUSTAL W (Bioedit 7.2.5) [45]. A phylogenetic consensus tree was reconstructed using MEGA version 7 [46] and the neighbor-joining algorithm [47] based on 1000 randomly chosen bootstrap replications.
Metabolite extraction
Both extracellular and intracellular extracts of intestinal luminal contents, serum, and muscle were prepared for metabolite profiling as follows: the luminal contents (250–500 mg) of the ileum, cecum, and colon were extracted into 1 ml water using the MM400 mixer mill (Retsch®, Haan, Germany) at a frequency of 30 s− 1 for 5 min. After sonication (10 min) and centrifugation (12,578 ⋅ g, 4 °C, 10 min), the supernatant was filtered through a 0.2 ∝m polytetrafluoroethylene (PTFE) filter and concentrated using a speed-vacuum concentrator. For the serum extractions, 1 ml methanol was added to 200 ∝l of the serum, and then extracted by sonication and shaking for 10 min. After centrifugation (12,000 rpm, 4 °C, 10 min), the supernatant was filtered through a 0.2 ∝m PTFE filter and dried using a speed-vacuum concentrator. The muscle samples (5 g) were finely chopped before extraction, following which 10 ml methanol was added; the samples were then sonicated (10 min) and agitated (1 h). After centrifugation (12,000 rpm, 4 °C, 10 min), the supernatant was filtered through a 0.2 ∝m PTFE filter and dried using a speed-vacuum concentrator.
Metabolite profiling and data processing
The dried samples were oximated in 50 ∝l methoxyamine hydrochloride (20 mg/ml in pyridine) for 90 min at 30 °C, silylated in 50 ∝l N-methyl-N-(trimethylsilyl) trifluoroacetamide for 30 min at 37 °C, and analyzed by GC-TOF-MS, as previously described [48]. The analysis was performed using an Agilent 7890 gas chromatography system (Agilent Technologies, Palo Alto, CA, USA), an Agilent 7693 auto-sampler (Agilent Technologies), and a Pegasus HT TOF MS (LECO, St. Joseph, MI, USA) system.
The GC-TOF-MS data were acquired and preprocessed using the LECO Chroma TOF™ software (version 4.44; LECO Corp., St. Joseph, MI, USA) and converted to the NetCDF format (*.cdf) using the LECO Chroma TOF™ software. After conversion, peak detection, retention time correction, and alignment were assessed using MetAlign 3.0 (http://www.metalign.nl). Data were exported to an Excel file. Multivariate statistical analyses were conducted using the SIMCA-P+ program (version 12.0, Umetrics, Umea, Sweden). The datasets were auto-scaled and mean-centered in a column-wise fashion. The discriminant variables were selected based on the variable importance in projection (VIP) value (VIP > 0.7).
BCAA quantification
BCAA levels were determined in the serum samples from cattle and mice, and from the intestinal luminal contents from cattle. The BCAA concentrations were quantified using the BCAA assay kit (Sigma, St. Louis, MO, USA). A standard curve was constructed for each experiment using a leucine standards series (MAK003D, Sigma). The BCAA levels were then calculated based on the standard curves.
Hormone measurements
Serum samples from cattle and mice were prepared as described above. The concentrations of serum testosterone and 17β-estradiol were determined by enzyme-linked immunosorbent assay (ELISA) using a testosterone ELISA kit (Enzo Life Sciences, Farmingdale, NY, USA) and a 17β-estradiol high sensitivity ELISA kit (Enzo Life Sciences), respectively. Concentration of the serum insulin was determined by using a mouse ultrasensitive insulin ELISA kit (ALPCO, Salem, NH, USA).
Analysis of gastrointestinal urease activity
Urease activity was assayed in the ruminal and ileal luminal contents of the adult Hanwoo. The luminal contents were suspended in 10 volumes of PBS. The samples were homogenized in an assay buffer using a bead-beating method. After centrifugation, urease activity in the clear lysate solutions was determined by using a urease activity assay kit (MAK120, Sigma). A standard curve was constructed for each experiment using a series of ammonium chloride standards (MAK120C, Sigma). The amount of urease enzymatic activity in the samples was calculated according to the manufacturer’s instructions.
Ammonia and urea measurements
The ammonia levels in the rumen and ileum of the adult Hanwoo were determined using the urease activity assay kit as described above. Ammonia levels in the mouse serum were determined using an ammonia assay kit (AA0100, Sigma), according to the manufacturer’s instructions. A standard curve was constructed for each experiment using a series of ammonium sulfate standards (A0978, Sigma). To determine urea levels in the mouse serum, a urea assay kit (MAK006) was used. A standard curve for each experiment was constructed using a series of urea standards (MAK006F, Sigma).
Glucose tolerance test
Glucose tolerance test was performed using overnight (16 h)-fasted mice by an intraperitoneal injection of glucose (1 g/kg body weight). Blood glucose concentrations were measured with an Accu-Check glucometer (Roche) before (0 min), and 15, 30, 60, and 120 min after glucose injection.
Intramuscular fat image analysis
Striploin muscle images were size-normalized. The sizes of intramuscular fat areas were calculated using the i-Solution image analyzer (IMT i-Solution Inc., Vancouver, BC, Canada).
Statistics
The statistical analyses were performed using GraphPad Prism version 5.0 for Windows (GraphPad Software, La Jolla, CA, USA). Comparisons between two samples were made using the non-parametric Mann-Whitney U test and the unpaired Student’s t-test (one-tailed). Comparisons between multiple samples were conducted by the analysis of variance (ANOVA), followed by Tukey’s post-hoc test (*p<0.05, **p<0.01, and ***p<0.001). The statistical significance for the observed variations was assessed using the PERMANOVA function with 999 permutations. The lines, boxes, and whiskers in the box plot diagrams represent the median, first and third quartiles, and min-to-max distribution of replicate values, respectively. The values and scattered dots in the bar graphs represent the means ± SEM and the individual replicates, respectively.