Exploring strain diversity of dominant human skin bacterial species using single-cell genome sequencing

Abstract

To understand the role of the skin commensal bacterial community in skin health and the spread of pathogens, it is crucial to identify genetic differences in the bacterial strains corresponding to human individuals. A culture-independent genomics approach is an effective tool for obtaining massive high-quality bacterial genomes. Here we present a single-cell genome sequencing to obtain comprehensive whole-genome sequences of uncultured skin bacteria from skin swabs. We recovered 281 high-quality (HQ) and 244 medium-quality single-amplified genomes (SAGs) of multiple skin bacterial species from eight individuals, including cohabiting group. Single-cell sequencing outperformed in the genome recovery from the same skin swabs, showing 10-fold non-redundant strain genomes compared to the shotgun metagenomic sequencing and binning approach. We then focused on the abundant skin bacteria and identified intra-species diversity, especially in 47 Moraxella osloensis derived HQ SAGs, characterizing the strain-level heterogeneity at mobile genetic element profiles, including plasmids and prophages. Even between the cohabiting individual hosts, they have unique skin bacterial strains in the same species, which shows microdiversity in each host. Genetic and functional differences between skin bacterial strains are predictive of in vivo competition to adapt bacterial genome to utilize the sparse nutrients available on the skin or produce molecules that inhibit the colonization of other microbes or alter their behavior. Thus, single-cell sequencing provides a large number of genomes of higher resolution and quality than conventional metagenomic analysis and helps explore the skin commensal bacteria at the strain level, linking taxonomic and functional information.

Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics

“…3 e), SAG had fewer CDSs per genome (1469 CDSs) than MAG (2108 CDSs), which is consistent with the lower genome completeness of SAG compared to MAGs. SAGs obtained using SAG-gel had a similar number of CDSs (2470, 2329, and 1875 CDSs) to MAGs in humans [17] , [100] , soil [16] , and mammal-associated samples [13] , respectively. In mammals, SAGs obtained using WGA-X also had 2025 CDSs [15] .…”

“…However, these shortcomings in genome amplification for single-cell genomics have been addressed by WGA-X, an improved whole-genome amplification enzyme [12] , [15] , or microfluidic droplets, which use droplets or gel capsules for cell isolation and genome amplification [10] , [13] , [14] , [96] , [98] , [99] . SAGs derived from human skin using SAG-gel [100] were comparable in genome completeness (85.7%) to those of human-associated MAGs. Depending on the sample type, SAGs with genome completeness similar to that of MAGs were obtained ( Fig.…”

“…Although not included in this review, various databases have been developed for gut bacteria and other organisms [91] , [108] , [109] , [110] , [111] , [112] , [113] , [114] . Single-cell genomics should be utilized to acquire genomes of known species at the strain level from human-associated samples [17] , [34] , [100] and to identify the genomes of novel species in environmental samples where metagenomic binning is not feasible.…”

Tools for microbial single-cell genomics for obtaining uncultured microbial genomes

“…The genomic information obtained from these single cells is then sequenced, producing SAGs that are theoretically free from contamination or admixture with other organisms. This approach offers several advantages, such as the ability to link bacterial core genes in their genomes to exogenous mobile genetic factors such as plasmids and phages, the recovery of conserved genes such as 16S rRNA genes, and other genes often missing in conventional MAGs (Arikawa et al 2021 ; Ide et al 2022b ). SAGs are collected individually, so their data quality is not affected by sample diversity or the presence of closely related microbes.…”

Single Amplified Genome Catalog Reveals the Dynamics of Mobilome and Resistome in the Human Microbiome

“…This advantage is attributed to efficient whole-genome amplification and deep single-cell sequencing by coupling in-gel and well-formatted reactions. Thus far, we have applied our method to various microbiomes, not only from human-associated samples but also from environmental samples, enabling us to reach novel implications such as strain heterogeneity, including MGEs 14,[21][22][23][24] .…”