Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacteria and DNA Extraction
2.2. Genome Sequencing, Assembly, and Functional Prediction
2.3. Pangenome and ANI Analysis
2.4. Phylogenetic Inference of B. longum subsp. longum Genomes
2.5. Gene Cluster Analysis
2.6. Detection of Virulence Factor and Antibiotic Resistance Genes
2.7. HMO Growth Conditions
2.8. Plasmid Prediction and Mobile Genetics Elements
3. Results
3.1. Bifidobacterium longum subsp. longum General Features
3.2. Evolutive Phylogenetic Inference
3.3. Predictive Genomics Analysis
3.3.1. Average Nucleotide Identity (ANI) Analysis
3.3.2. Bifidobacterium longum subsp. longum Pangenome
3.3.3. Glycosyl Hydrolase Prediction
3.3.4. Complex Carbohydrates Use Cluster
3.3.5. Plasmids and Mobile Elements
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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Díaz, R.; Torres-Miranda, A.; Orellana, G.; Garrido, D. Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota. Microorganisms 2021, 9, 1906. https://doi.org/10.3390/microorganisms9091906
Díaz R, Torres-Miranda A, Orellana G, Garrido D. Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota. Microorganisms. 2021; 9(9):1906. https://doi.org/10.3390/microorganisms9091906
Chicago/Turabian StyleDíaz, Romina, Alexis Torres-Miranda, Guillermo Orellana, and Daniel Garrido. 2021. "Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota" Microorganisms 9, no. 9: 1906. https://doi.org/10.3390/microorganisms9091906