Exploring Gut Microbiota Alterations with Trimethoprim-Sulfamethoxazole and Dexamethasone in a Humanized Microbiome Mouse Model
Abstract
:1. Introduction
2. Materials and Methods
2.1. Reagents
2.2. Mice
2.3. Sample Preparation for High-Throughput Sequencing
2.4. High-Throughput Sequencing
2.5. Taxonomic Assignment and Distribution
2.6. Predicted Functional Analysis
2.7. Read Quality and Sample Statistics and Taxonomic Distribution across All Samples
3. Results
3.1. HuM1Rag and HuM2Rag Are Unique Microbiome Lines
3.2. Predicted Functional Analysis between HuM1Rag and HuM2Rag Mice Pre–Treatment
3.2.1. TMP-SMX Significantly Altered the Microbiome of HuM1Rag Mice
3.2.2. HuM1Rag Mice Did Not Recover to Original Microbial Composition Post-Treatment with TMP-SMX
3.2.3. TMP-SMX Altered the Microbiome of HuM2Rag Mice
3.2.4. HuM2Rag Mice Microbiome Recovered from TMP-SMX Treatment
3.2.5. Predicted Functional Analysis of HuM1Rag Revealed Significant Pathways Affected by TMP-SMX Treatment
3.2.6. Predicted Functional Analysis from TMP-SMX Treatment of HuM2Rag Revealed Fewer Pathways Altered when Compared to HuM1Rag Mice
3.2.7. Dexamethasone Significantly Alters the Microbiome of HuM1Rag
3.2.8. HuM1Rag Mice Did Not Recover to Original Microbial Composition from Dexamethasone Treatment
3.2.9. HuM2Rag Showed Overall Recovery from Dexamethasone Treatment
3.2.10. HuM2Rag Mice Recovered from Original Microbial Composition Post-Treatment Dexamethasone
3.2.11. Predicted Functional Analysis of HuM1Rag Revealed Significant Pathways Affected by Dexamethasone Treatment
3.2.12. Predicted Functional Analysis of HuM2Rag Revealed Dexamethasone Treatment Had Fewer Pathways Altered Compared to HuM1Rag Mice
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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ASV | Hum1Rag (n = 17) | Hum2Rag (n = 17) |
---|---|---|
Lachnospiraceae_NK4A136_group | 18% ± 11% | 18% ± 13% |
Lactobacillus | 17% ± 16% | 3% ± 7% |
Faecalibaculum | 15% ± 13% | 14% ± 26% |
Bifidobacterium | 13% ± 6% | 4% ± 3% |
Blautia | 13% ± 12% | 5% ± 4% |
Dubosiella | 12% ± 9% | 17% ± 10% |
Turicibacter | 8% ± 6% | 16% ± 10% |
Romboutsia | 3% ± 3% | 5% ± 4% |
Ileibacterium | 1% ± 1% | 17% ± 11% |
ASV | Pre-txt (n = 7) | 1 wk Post txt (n = 7) | 3 wk Post txt (n = 7) |
---|---|---|---|
Faecalibaculum | 17% ± 13% | 16% ± 20% | 7% ± 6% |
Lachnospiraceae_NK4A136_group | 15% ± 13% | 5% ± 3% | 16% ± 11% |
Blautia | 14% ± 15% | 2% ± 1% | 4% ± 2% |
Dubosiella | 13% ± 10% | 18% ± 8% | 14% ± 9% |
Bifidobacterium | 11% ± 3% | 19% ± 8% | 8% ± 4% |
Lactobacillus | 11% ± 11% | 12% ± 6% | 13% ± 6% |
Turicibacter | 9% ± 7% | 15% ± 13% | 2% ± 2% |
Muribaculaceae | 6% ± 8% | 12% ± 3% | 25% ± 8% |
Lachnospiraceae_UCG-001 | 5% ± 3% | 3% ± 2% | 11% ± 10% |
ASV | Pre-txt (n = 6) | 1 wk Post txt (n = 6) | 3 wk Post txt (n = 6) |
---|---|---|---|
Turicibacter | 24% ± 14% | 11% ± 3% | 12% ± 7% |
Faecalibaculum | 21% ± 31% | 4% ± 3% | 2% ± 2% |
Lachnospiraceae_NK4A136_group | 14% ± 9% | 24% ± 12% | 16% ± 11% |
Ileibacterium | 14% ± 11% | 3% ± 6% | 3% ± 2% |
Dubosiella | 14% ± 11% | 21% ± 9% | 22% ± 9% |
Blautia | 5% ± 3% | 5% ± 2% | 4% ± 3% |
[Eubacterium]_xylanophilum_group | 3% ± 2% | 11% ± 7% | 2% ± 2% |
Muribaculaceae | 3% ± 7% | 19% ± 8% | 33% ± 6% |
Bifidobacterium | 3% ± 3% | 2% ± 2% | 6% ± 5% |
ASV | Pre-txt (n = 6) | 1 wk Post txt (n = 6) | 3 wk Post txt (n = 6) |
---|---|---|---|
Lachnospiraceae_NK4A136_group | 20% ± 8% | 34% ± 19% | 26% ± 10% |
Bifidobacterium | 18% ± 10% | 10% ± 9% | 7% ± 7% |
Faecalibaculum | 16% ± 15% | 12% ± 14% | 7% ± 6% |
Muribaculaceae | 12% ± 14% | 8% ± 6% | 21% ± 8% |
Blautia | 12% ± 8% | 8% ± 5% | 9% ± 5% |
Dubosiella | 10% ± 10% | 3% ± 2% | 6% ± 3% |
Lachnospiraceae_UCG-001 | 5% ± 4% | 14% ± 10% | 12% ± 6% |
Lachnoclostridium | 5% ± 2% | 4% ± 2% | 4% ± 2% |
Incertae_Sedis | 4% ± 3% | 6% ± 2% | 7% ± 2% |
ASV | Pre-txt (n = 6) | 1 wk Post txt (n = 6) | 3 wk Post txt (n = 6) |
---|---|---|---|
Faecalibaculum | 22% ± 33% | 4% ± 4% | 1% ± 1% |
Ileibacterium | 17% ± 16% | 1% ± 2% | 3% ± 3% |
Lachnospiraceae_NK4A136_group | 16% ± 12% | 36% ± 13% | 25% ± 16% |
Dubosiella | 14% ± 12% | 13% ± 11% | 16% ± 13% |
Turicibacter | 13% ± 8% | 7% ± 3% | 8% ± 3% |
Lachnoclostridium | 6% ± 4% | 7% ± 1% | 6% ± 5% |
Blautia | 5% ± 4% | 9% ± 6% | 5% ± 4% |
Lachnospiraceae_UCG-001 | 4% ± 4% | 11% ± 11% | 10% ± 9% |
Muribaculaceae | 2% ± 5% | 11% ± 9% | 26% ± 17% |
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Green, G.B.H.; Cox-Holmes, A.N.; Backan, O.; Valbak, O.; Potier, A.C.E.; Chen, D.; Morrow, C.D.; Willey, C.D.; McFarland, B.C. Exploring Gut Microbiota Alterations with Trimethoprim-Sulfamethoxazole and Dexamethasone in a Humanized Microbiome Mouse Model. Microorganisms 2024, 12, 1015. https://doi.org/10.3390/microorganisms12051015
Green GBH, Cox-Holmes AN, Backan O, Valbak O, Potier ACE, Chen D, Morrow CD, Willey CD, McFarland BC. Exploring Gut Microbiota Alterations with Trimethoprim-Sulfamethoxazole and Dexamethasone in a Humanized Microbiome Mouse Model. Microorganisms. 2024; 12(5):1015. https://doi.org/10.3390/microorganisms12051015
Chicago/Turabian StyleGreen, George B. H., Alexis N. Cox-Holmes, Olivia Backan, Olivia Valbak, Anna Claire E. Potier, Dongquan Chen, Casey D. Morrow, Christopher D. Willey, and Braden C. McFarland. 2024. "Exploring Gut Microbiota Alterations with Trimethoprim-Sulfamethoxazole and Dexamethasone in a Humanized Microbiome Mouse Model" Microorganisms 12, no. 5: 1015. https://doi.org/10.3390/microorganisms12051015
APA StyleGreen, G. B. H., Cox-Holmes, A. N., Backan, O., Valbak, O., Potier, A. C. E., Chen, D., Morrow, C. D., Willey, C. D., & McFarland, B. C. (2024). Exploring Gut Microbiota Alterations with Trimethoprim-Sulfamethoxazole and Dexamethasone in a Humanized Microbiome Mouse Model. Microorganisms, 12(5), 1015. https://doi.org/10.3390/microorganisms12051015