Illumina Sequencing and Metabolomic Analysis Explored the Effects of the Mixed Silage of Rice Straw and Chinese Cabbage Waste on Fecal Microorganisms and Metabolites in Hu Sheep
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Diet, Experimental Animals, and Feeding
2.2. Sample Collection and Measurement
2.2.1. Growth Performance
2.2.2. Fecal Sample Collection
2.2.3. 16S rRNA Microbial Community Analysis
2.2.4. Untargeted Metabolomics Based on Liquid Chromatography-Mass Spectrometry and Data Processing
2.3. Data Analysis
3. Results
3.1. Growth Performance
3.2. Fecal Microbiota Structure
3.3. Fecal Metabolomics
3.4. KEGG Enrichment Analysis
3.5. Analysis of Differential Metabolites and Fecal Microbial Correlations
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Items | Treatment 1 | |
---|---|---|
Control | Silage | |
Ingredients (% of DM) | ||
Peanut seedling | 30 | - |
Corn husk | 15 | - |
Sorghum shell | 5 | - |
Mixed Silage | 0 | 50 |
Corn | 34 | 34 |
Soybean meal | 7 | 5.5 |
Bran | 7.5 | 8 |
Corn gluten meal | - | 1 |
NaHCO3 | 0.5 | 0.5 |
Premix contained 2 | 0.5 | 0.5 |
Salt | 0.5 | 0.5 |
Total | 100 | 100 |
Nutrient composition (% of DM) | ||
Digestive energy/DE (MJ/kg) 3 | 13.52 | 14.73 |
Metabolizable energy/ME (MJ/kg) 4 | 18.93 | 20.62 |
Crude protein, CP | 15.08 | 15.11 |
Ash | 4.36 | 12.33 |
Neutral Detergent Fiber, NDF | 47.64 | 48.23 |
Acid Detergent Fiber, ADF | 23.71 | 27.17 |
Ca | 0.48 | 0.45 |
P | 0.38 | 0.39 |
Metabolites | Group 1 | VIP 2 | p | FC 3 | Trend | Mode | |
---|---|---|---|---|---|---|---|
Control | Silage | ||||||
Amino acids, peptides, and analogues | |||||||
DL-Alanine | 0.079 | 0.242 | 1.403 | 0.018 | 3.071 | Up | ESI+ |
Glycine | 0.003 | 0.011 | 1.637 | 0.001 | 3.633 | Up | ESI+ |
LEVODOPA | 0.004 | 0.008 | 1.430 | 0.013 | 1.950 | Up | ESI+ |
N,N-Dimethylglycine | 0.012 | 0.003 | 1.277 | 0.042 | 0.268 | Down | ESI+ |
Ala-Ile | 0.065 | 0.027 | 1.119 | 0.045 | 0.407 | Down | ESI− |
Arginine | 0.053 | 0.004 | 1.299 | 0.006 | 0.079 | Down | ESI− |
D-ASPARTATE | 0.644 | 0.093 | 1.375 | 0.002 | 0.145 | Down | ESI− |
gamma-Glutamylleucine | 0.083 | 0.027 | 1.407 | 0.001 | 0.328 | Down | ESI− |
L-Histidine | 0.055 | 0.007 | 1.147 | 0.046 | 0.136 | Down | ESI− |
L-Phenylalanine | 1.630 | 0.474 | 1.165 | 0.040 | 0.291 | Down | ESI− |
L-Valine | 0.077 | 0.018 | 1.197 | 0.022 | 0.231 | Down | ESI− |
N-Acetylglutamic acid (NAG) | 0.641 | 0.230 | 1.220 | 0.012 | 0.359 | Down | ESI− |
N-Isobutyrylglycine | 1.345 | 0.017 | 1.206 | 0.015 | 0.012 | Down | ESI− |
N-Tigloylglycine | 0.861 | 0.003 | 1.199 | 0.025 | 0.004 | Down | ESI− |
Benzoic acids and derivatives | |||||||
2-Hydroxyhippuric acid | 0.544 | 0.007 | 1.199 | 0.028 | 0.013 | Down | ESI− |
5-Methoxysalicylic acid | 0.018 | 0.005 | 1.135 | 0.049 | 0.277 | Down | ESI− |
Butylparaben | 0.231 | 0.063 | 1.144 | 0.019 | 0.275 | Down | ESI− |
Bile acids, alcohols, and derivatives | |||||||
Cholic Acid | 0.015 | 0.009 | 1.419 | 0.011 | 0.578 | Down | ESI+ |
Glycochenodeoxycholate | 0.014 | 0.001 | 1.274 | 0.045 | 0.040 | Down | ESI+ |
GLYCOCHOLATE | 0.005 | 0.002 | 1.411 | 0.011 | 0.441 | Down | ESI+ |
Carbohydrates and carbohydrate conjugates | |||||||
N-Acetylneuraminic acid | 0.018 | 0.133 | 1.487 | 0.006 | 7.483 | Up | ESI+ |
D-SACCHARIC ACID | 0.166 | 0.053 | 1.425 | 0.001 | 0.318 | Down | ESI− |
N-Acetylmannosamine | 8.252 | 2.333 | 1.232 | 0.010 | 0.283 | Down | ESI− |
N-Acetylmuramic Acid | 0.636 | 0.141 | 1.425 | 0.001 | 0.222 | Down | ESI− |
Carbonyl compounds | |||||||
Acetophenone | 0.243 | 0.035 | 1.627 | 0.001 | 0.145 | Down | ESI+ |
4-Hydroxybenzaldehyde | 0.844 | 0.276 | 1.424 | 0.001 | 0.327 | Down | ESI− |
Eicosanoids | |||||||
Prostaglandin B1 | 0.007 | 0.079 | 1.272 | 0.007 | 11.976 | Up | ESI− |
Resolvin E1 | 0.011 | 0.054 | 1.376 | 0.002 | 4.752 | Up | ESI− |
Fatty acids and conjugates | |||||||
3,3-Dimethylglutaric acid | 0.642 | 0.110 | 1.577 | <0.001 | 0.172 | Down | ESI− |
3-Methylglutaric acid | 0.050 | 0.224 | 1.154 | 0.032 | 4.455 | Up | ESI− |
Arachidic acid | 0.322 | 1.498 | 1.126 | 0.016 | 4.655 | Up | ESI− |
Lauric acid | 0.061 | 0.027 | 1.224 | 0.006 | 0.454 | Down | ESI− |
Isoflav-2-enes | |||||||
Daidzein | 0.176 | 0.050 | 1.147 | 0.024 | 0.283 | Down | ESI− |
Genistein | 2.530 | 0.442 | 1.376 | 0.002 | 0.175 | Down | ESI− |
Pyrimidine 2′-deoxyribonucleosides | |||||||
2′-Deoxyuridine | 0.002 | 0.006 | 1.564 | 0.003 | 3.150 | Up | ESI+ |
Thymidine | 0.018 | 0.051 | 1.330 | 0.030 | 2.752 | Up | ESI+ |
Tetrahydrofuran lignans | |||||||
Enterolactone | 0.018 | 0.110 | 1.118 | 0.029 | 6.082 | Up | ESI− |
matairesinol | 0.163 | 0.015 | 1.202 | 0.010 | 0.091 | Down | ESI− |
Others | |||||||
Benzothiazole | 1.248 | 1.073 | 1.295 | 0.033 | 0.860 | Down | ESI+ |
Metaxalone | 0.003 | 0.001 | 1.319 | 0.029 | 0.219 | Down | ESI+ |
9-Fluorenone | 5.195 | 0.812 | 1.172 | 0.017 | 0.156 | Down | ESI− |
Abietic acid | 0.005 | 0.016 | 1.135 | 0.034 | 3.514 | Up | ESI− |
Biotin | 0.038 | 0.082 | 1.157 | 0.047 | 2.143 | Up | ESI− |
Bis(4-hydroxyphenyl)methane | 0.028 | 0.074 | 1.168 | 0.022 | 2.634 | Up | ESI− |
cirsimaritin | 0.033 | 0.002 | 1.508 | <0.001 | 0.074 | Down | ESI− |
delta7-Dafachronic acid | 0.090 | 0.047 | 1.104 | 0.048 | 0.525 | Down | ESI− |
Ecgonine | 0.381 | 0.062 | 1.137 | 0.050 | 0.162 | Down | ESI− |
Piceatannol | 0.010 | 0.059 | 1.393 | 0.001 | 6.047 | Up | ESI− |
Pseudouridine | 1.798 | 0.457 | 1.160 | 0.033 | 0.254 | Down | ESI− |
Resveratrol | 0.071 | 0.172 | 1.129 | 0.031 | 2.420 | Up | ESI− |
santin | 0.019 | 0.085 | 1.286 | 0.009 | 4.525 | Up | ESI− |
URIDINE | 1.502 | 0.455 | 1.120 | 0.043 | 0.303 | Down | ESI− |
3-Hydroxyphenylacetic acid | 0.108 | 0.021 | 1.519 | <0.001 | 0.199 | Down | ESI− |
adrenosterone | 0.044 | 0.001 | 1.329 | 0.002 | 0.025 | Down | ESI− |
3-Indoxyl sulphate | 2.911 | 0.004 | 1.160 | 0.042 | 0.001 | Down | ESI− |
Epinephrine | 0.190 | 0.000 | 1.203 | 0.024 | 0.002 | Down | ESI− |
Isobutyric acid | 0.085 | 0.019 | 1.208 | 0.020 | 0.220 | Down | ESI− |
Bisphenol A | 0.003 | 0.045 | 1.409 | 0.001 | 16.963 | Up | ESI− |
Glabranine | 1.708 | 0.069 | 1.608 | <0.001 | 0.040 | Down | ESI− |
Stearamide | 0.022 | 0.010 | 1.365 | 0.016 | 0.448 | Down | ESI+ |
Chrysin | 0.027 | 0.001 | 1.553 | <0.001 | 0.045 | Down | ESI− |
Ferulic acid | 0.005 | 0.012 | 1.375 | 0.023 | 2.257 | Up | ESI+ |
afzelechin | 0.020 | 0.116 | 1.388 | 0.002 | 5.671 | Up | ESI− |
3-(2-Hydroxyethyl)indole | 0.073 | 0.001 | 1.171 | 0.035 | 0.019 | Down | ESI− |
D-(+)-Tryptophan | 0.459 | 0.165 | 1.162 | 0.041 | 0.360 | Down | ESI− |
Equol | 0.072 | 0.003 | 1.478 | <0.001 | 0.043 | Down | ESI− |
Dihydrojasmonic Acid | 0.306 | 0.128 | 1.269 | 0.011 | 0.419 | Down | ESI− |
13-HPODE | 2.260 | 4.175 | 1.091 | 0.034 | 1.847 | Up | ESI− |
Vanillin | 0.025 | 0.005 | 1.362 | 0.003 | 0.192 | Down | ESI− |
Formononetin | 0.069 | 0.003 | 1.522 | <0.001 | 0.045 | Down | ESI− |
2-Hydroxyphenylacetic acid | 0.060 | 0.004 | 1.318 | 0.003 | 0.060 | Down | ESI− |
2′-Deoxyinosine | 0.029 | 0.065 | 1.360 | 0.021 | 2.221 | Up | ESI+ |
Uric acid | 0.671 | 0.083 | 1.165 | 0.038 | 0.124 | Down | ESI− |
4-Pyridoxic acid | 0.060 | 0.026 | 1.294 | 0.042 | 0.426 | Down | ESI+ |
Cytosine | 0.045 | 0.099 | 1.520 | 0.004 | 2.218 | Up | ESI+ |
Acetylcholine | 0.151 | 0.030 | 1.295 | 0.043 | 0.200 | Down | ESI+ |
4-Methyl-2-oxovaleric Acid | 1.376 | 0.415 | 1.162 | 0.013 | 0.302 | Down | ESI− |
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Li, C.; Lu, Z.; Qi, R.; Zhang, Z.; Lu, Y.; Zafar, M.H.; Yang, K.; Wang, M. Illumina Sequencing and Metabolomic Analysis Explored the Effects of the Mixed Silage of Rice Straw and Chinese Cabbage Waste on Fecal Microorganisms and Metabolites in Hu Sheep. Fermentation 2024, 10, 233. https://doi.org/10.3390/fermentation10050233
Li C, Lu Z, Qi R, Zhang Z, Lu Y, Zafar MH, Yang K, Wang M. Illumina Sequencing and Metabolomic Analysis Explored the Effects of the Mixed Silage of Rice Straw and Chinese Cabbage Waste on Fecal Microorganisms and Metabolites in Hu Sheep. Fermentation. 2024; 10(5):233. https://doi.org/10.3390/fermentation10050233
Chicago/Turabian StyleLi, Chuang, Zhiqi Lu, Ruxin Qi, Zhenbin Zhang, Yue Lu, Muhammad Hammad Zafar, Kailun Yang, and Mengzhi Wang. 2024. "Illumina Sequencing and Metabolomic Analysis Explored the Effects of the Mixed Silage of Rice Straw and Chinese Cabbage Waste on Fecal Microorganisms and Metabolites in Hu Sheep" Fermentation 10, no. 5: 233. https://doi.org/10.3390/fermentation10050233
APA StyleLi, C., Lu, Z., Qi, R., Zhang, Z., Lu, Y., Zafar, M. H., Yang, K., & Wang, M. (2024). Illumina Sequencing and Metabolomic Analysis Explored the Effects of the Mixed Silage of Rice Straw and Chinese Cabbage Waste on Fecal Microorganisms and Metabolites in Hu Sheep. Fermentation, 10(5), 233. https://doi.org/10.3390/fermentation10050233