Massively parallel single-cell sequencing of genetic loci in diverse microbial populations
Lan, F.; Saba, J.; Ross, T. D.; Zhou, Z.; Krauska, K.; Anantharaman, K.; Landick, R.; Venturelli, O. S.
Show abstract
Single cell genetic heterogeneity is ubiquitous in microbial populations and an important aspect of microbial biology. However, we lack a broadly applicable and accessible method to study this heterogeneity at the single cell level. Here, we introduce a simple, robust, and generalizable platform for quantitative and massively parallel single cell sequencing of target genetic loci in microbes using ultrahigh-throughput droplet microfluidics (Droplet Targeted Amplicon Sequencing or DoTA-seq). Using DoTA-seq, we elucidate the highly diverse single cell ON/OFF states of the phase-variable capsule synthesis operons in the prevalent human gut species Bacteroides fragilis. In addition, we quantify the shifts in antibiotic resistance gene abundances in different species in a 25 member human gut microbial community in response to antibiotics. By sequencing tens of thousands of single-cells derived from a human fecal sample, we identify links between plasmid replicons and the taxonomic lineages of their associated hosts. In sum, DoTA-seq is an accessible and broadly applicable tool for profiling single-cell genetic variation in microbiomes.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Investigating the dynamics of microbial consortia in spatially structured environments 96%
- Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes 96%
- Fragmented micro-growth habitats present opportunities for alternative competitive outcomes 96%
Similar papers in this journal
- Targeted Genome Editing of Bacteria Within Microbial Communities 98%
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models 96%
- Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota 96%
Similar papers in this journal
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.