Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes
Abstract
1. Introduction
2. Materials and Methods
2.1. Mice and Sample Collection
2.2. Power Analysis
2.3. DNA Extraction
2.4. RNA Extraction
2.5. Metagenomic Library Preparation
2.6. Metatranscriptomic Library Preparation
2.7. Meta-Omic Preprocessing, Assembly, Binning, and Analyses
2.8. Phylogenomics, Pangenome Construction and Differential Analyses
2.9. Data Analyses and Figures
3. Results
3.1. Metagenomic, Metatranscriptomic, and Taxonomic Summary
3.2. Candidate Phyla Radiation Taxa Demonstrate Strain-Level Differences Between Vendors
3.3. Distinct Source-Dependent MAGs Within Multiple Taxonomies
3.4. Functional Differences Between Source-Dependent GM
3.5. Supplier-Origin GMs Indicate Variable Levels of Enzymatic Activity Associated with Eukaryotes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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McAdams, Z.L.; Busi, S.B.; Gustafson, K.L.; Bivens, N.; Franklin, C.L.; Wilmes, P.; Ericsson, A.C. Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes. Appl. Microbiol. 2024, 4, 1600-1615. https://doi.org/10.3390/applmicrobiol4040109
McAdams ZL, Busi SB, Gustafson KL, Bivens N, Franklin CL, Wilmes P, Ericsson AC. Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes. Applied Microbiology. 2024; 4(4):1600-1615. https://doi.org/10.3390/applmicrobiol4040109
Chicago/Turabian StyleMcAdams, Zachary L., Susheel Bhanu Busi, Kevin L. Gustafson, Nathan Bivens, Craig L. Franklin, Paul Wilmes, and Aaron C. Ericsson. 2024. "Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes" Applied Microbiology 4, no. 4: 1600-1615. https://doi.org/10.3390/applmicrobiol4040109
APA StyleMcAdams, Z. L., Busi, S. B., Gustafson, K. L., Bivens, N., Franklin, C. L., Wilmes, P., & Ericsson, A. C. (2024). Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes. Applied Microbiology, 4(4), 1600-1615. https://doi.org/10.3390/applmicrobiol4040109