Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design
2.2. Participants
2.3. Study Diets
2.4. Sample Collection and Processing
2.5. Protein Extraction and Sample Preparation
2.6. LC MS/MS Analysis
2.7. Database Search
2.8. Human Protein Data Analysis
2.9. Metaproteomic Data Analysis
2.10. Bioinformatics and Statistical Analysis
3. Results
3.1. Assay Reproducibility
3.2. Human proteins identified in fecal samples
3.3. Fecal Microbial Composition Based on Metaproteomics Analysis
3.4. Diet-Induced Significant Changes in GO Biological Processes
3.5. WG Induced Significant Enrichment in Bacterial Enzymes Involved in the Production of SCFA and the Degradation of Fatty Acids
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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PEPTIDE COUNTS Average (SEM) | ||||
---|---|---|---|---|
EC number | Enzyme Name | RG | WG | p value* |
Higher after WG Diet | ||||
1.1.1.- | Oxidoreductases Acting on the CH-OH group of donors with NAD(+) or NADP(+) as acceptor | 17.2 (4) | 25.2 (5.4) | 0.002584 |
1.1.1.1 | Alcohol dehydrogenase | 25.9 (11.8) | 35.1 (9.6) | 0.000514 |
1.1.1.157 | 3-hydroxybutyryl-CoA dehydrogenase | 23.1 (12.8) | 37.9 (13.7) | <0.000001 |
1.1.1.35 | 3-hydroxyacyl-CoA dehydrogenase | 18.1 (12.4) | 33.3 (11.7) | <0.000001 |
1.1.1.37 | Malate dehydrogenase | 21.4 (14.2) | 39 (11.9) | <0.000001 |
1.1.1.58 | Tagaturonate reductase | 12.7 (8.3) | 26.3 (9.5) | <0.000001 |
1.1.1.69 | Gluconate 5-dehydrogenase | 14.2 (7.3) | 23.9 (6.8) | 0.000272 |
1.1.1.86 | Ketol-acid reductoisomerase (NADP(+)) | 52.3 (19.3) | 60.8 (13.4) | 0.001469 |
1.17.7.4 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 21.7 (10.6) | 30.8 (7.2) | 0.0006 |
1.2.1.- | Oxidoreductases Acting on the aldehyde or oxo group of donors with NAD(+) or NADP(+) as acceptor | 189.1 (51.9) | 214.2 (44.2) | <0.000001 |
1.2.7.- | Oxidoreductases Acting on the aldehyde or oxo group of donors with an iron-sulfur protein as acceptor | 159.2 (64.8) | 185.8 (37.2) | <0.000001 |
1.3.8.1 | Butyryl-CoA dehydrogenase | 47.7 (16.4) | 61.9 (19) | <0.000001 |
2.2.1.1 | Transketolase | 22.3 (13.1) | 36.4 (13.1) | <0.000001 |
2.2.1.2 | Transaldolase | 20.8 (7.1) | 29.2 (13.7) | 0.001469 |
2.3.1.54 | Formate C-acetyltransferase | 36.1 (23.3) | 44 (24.1) | 0.002964 |
2.3.1.8 | Phosphate acetyltransferase | 17.3 (11.4) | 28.3 (8.8) | 0.000034 |
2.3.1.9 | Acetyl-CoA C-acetyltransferase | 48.7 (17.2) | 58.4 (10.5) | 0.000231 |
2.4.1.1 | Glycogen phosphorylase | 37.6 (13.6) | 48.4 (14.6) | 0.000041 |
2.5.1.47 | Cysteine synthase | 2.1 (3.1) | 11.9 (7.9) | 0.000231 |
2.5.1.49 | O-acetylhomoserine aminocarboxypropyltransferase | 5.3 (5) | 14.2 (6.2) | 0.000814 |
2.6.1.52 | Phosphoserine transaminase | 22.2 (5.9) | 30.3 (7.9) | 0.00225 |
2.7.1.92 | 5-dehydro-2-deoxygluconokinase | 16.8 (9.1) | 24.6 (7.1) | 0.003394 |
2.7.2.1 | Acetate kinase | 27.8 (9.2) | 37.4 (9.6) | 0.000272 |
2.7.2.3 | Phosphoglycerate kinase | 75.3 (30.6) | 107.3 (23.7) | <0.000001 |
2.7.7.27 | Glucose-1-phosphate adenylyltransferase | 22.9 (15.6) | 31.1 (10.2) | 0.001955 |
2.7.7.6 | DNA-directed RNA polymerase | 124.1 (30.9) | 136.3 (23.6) | 0.000004 |
2.7.7.8 | Polyribonucleotide nucleotidyltransferase | 28.8 (14.1) | 36.8 (11.6) | 0.002584 |
2.7.9.1 | Pyruvate, phosphate dikinase | 130.9 (35.2) | 168.9 (40.3) | <0.000001 |
3.5.-.- | Hydrolases Acting on carbon-nitrogen bonds, other than peptide bonds | 6.6 (6.2) | 15.1 (11.3) | 0.001271 |
3.6.3.14 | H(+)-transporting two-sector ATPase | 33.8 (13.4) | 47.1 (16.4) | <0.000001 |
3.6.5.3 | Protein-synthesizing GTPase | 93.8 (25.9) | 112.7 (30.6) | <0.000001 |
4.1.1.49 | Phosphoenolpyruvate carboxykinase (ATP) | 126.1 (50.6) | 157 (26.1) | <0.000001 |
4.1.2.13 | Fructose-bisphosphate aldolase | 65.2 (25.3) | 92.8 (20.9) | <0.000001 |
4.2.1.11 | Phosphopyruvate hydratase | 24.7 (13.6) | 32.9 (14.8) | 0.001955 |
4.2.1.17 | Enoyl-CoA hydratase (altronate dehydratase) | 15.2 (7.4) | 27.4 (7.8) | 0.000004 |
4.2.1.55 | 3-hydroxybutyryl-CoA dehydratase | 13.7 (7.2) | 23.8 (6.9) | 0.00014 |
4.4.1.11 | Methionine gamma-lyase | 5.4 (4.1) | 14.1 (6.4) | 0.001097 |
5.3.1.1 | Triose-phosphate isomerase | 43.2 (15) | 56.7 (12.2) | <0.000001 |
5.3.1.9 | Glucose-6-phosphate isomerase | 29.1 (11.8) | 42.1 (11.6) | <0.000001 |
5.4.2.2 | Phosphoglucomutase (alpha-d-glucose-1,6-bisphosphate-dependent) | 33.4 (15.7) | 50.7 (19.3) | <0.000001 |
5.4.2.8 | Phosphomannomutase | 13.7 (8.1) | 22.4 (9.6) | 0.000946 |
5.4.99.2 | Methylmalonyl-CoA mutase | 20.8 (15.4) | 28.6 (15.5) | 0.003394 |
6.3.1.2 | Glutamine synthetase | 24.9 (18.7) | 37.3 (20.5) | 0.000003 |
6.3.2.6 | Phosphoribosylaminoimidazolesuccinocarboxamide synthase purine | 20.8 (7) | 29.4 (11.2) | 0.001097 |
6.3.5.5 | Carbamoyl-phosphate synthase (glutamine-hydrolyzing) | 22.2 (9.5) | 36.4 (7.2) | <0.000001 |
Higher after RG Diet | ||||
1.11.1.1 | NADH peroxidase | 72.8 (29.4) | 57.8 (20.1) | <0.000001 |
3.2.1.23 | Beta-galactosidase | 46.3 (21.1) | 37.9 (14.4) | 0.001469 |
3.2.1.97 | Endo-alpha-N-acetylgalactosaminidase | 21.2 (20.8) | 7.4 (6.2) | <0.000001 |
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Pan, S.; Hullar, M.A.J.; Lai, L.A.; Peng, H.; May, D.H.; Noble, W.S.; Raftery, D.; Navarro, S.L.; Neuhouser, M.L.; Lampe, P.D.; et al. Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach. Microorganisms 2020, 8, 379. https://doi.org/10.3390/microorganisms8030379
Pan S, Hullar MAJ, Lai LA, Peng H, May DH, Noble WS, Raftery D, Navarro SL, Neuhouser ML, Lampe PD, et al. Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach. Microorganisms. 2020; 8(3):379. https://doi.org/10.3390/microorganisms8030379
Chicago/Turabian StylePan, Sheng, Meredith A. J. Hullar, Lisa A. Lai, Hong Peng, Damon H. May, William S. Noble, Daniel Raftery, Sandi L. Navarro, Marian L. Neuhouser, Paul D. Lampe, and et al. 2020. "Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach" Microorganisms 8, no. 3: 379. https://doi.org/10.3390/microorganisms8030379