Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling
Valery V Panyukov1,2, Sergey S Kiselev2,3, Olga N Ozoline2,3
1Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia.
International Journal of Molecular Sciences
|February 7, 2020
Summary
This study introduces alignment-free k-mer methods for precise microbial taxonomic profiling. These methods successfully distinguished Escherichia coli phylogroups and identified strain-specific barcodes in human microbiomes.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Comparative analysis of natural metagenomes necessitates advanced taxonomic profiling methods.
- Alignment-free k-mer approaches offer high resolution, identifying species and strains.
Purpose of the Study:
- To evaluate genus-specific k-mers for distinguishing eight Escherichia coli phylogroups.
- To assess the presence of unique 22-mers in human microbiomes from healthy individuals and Crohn's disease patients.
Main Methods:
- Utilized k-mer analysis on 124 Escherichia coli genomes to identify unique sequences.
- Inferred phylogenetic trees using k-mer distances and compared them with traditional gene-based methods.
- Analyzed human microbiome samples for the presence of specific E. coli 22-mers.
Main Results:
- Phylogenetic trees from k-mer analysis (18-mers and 22-mers) showed high concordance with gene-based trees.
- Strain-specific k-mer "barcodes" were proposed for rapid phylotyping.
- All E. coli groups were detected in human microbiomes, with significant differences in abundance in some samples.
Conclusions:
- Alignment-free k-mer analysis is a robust method for high-resolution microbial phylotyping.
- The findings highlight significant intraspecies heterogeneity of E. coli in the human gut microbiome.
- Further research can explore the role of this heterogeneity in microbial community homeostasis.
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