A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome

Abstract

Background: The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.

Results: We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.

Conclusions: The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.

Fig. 1

Overview of the Single Amplified Genome catalog bbsag20 for human oral and fecal bacteria. a Overview of samples, assembled genomes, MGEs, and ARGs in the bbsag20 dataset. SAGs and MAGs were categorized as high-quality (HQ), medium-quality (MQ), or low-quality (LQ). b Assembly statistics for both SAGs and MAGs. Gray dots indicate the average values. Genome completeness and contamination show all fecal MAG, fecal SAG, and oral SAG data. Metrics for high- or medium-quality genomes include quality (defined as completeness minus 5 × contamination), total length, contig count, CDS count, GC content, N50, tRNA repertoire, and rRNAs

Fig. 2

Taxonomy of bbsag20 for human oral and fecal bacteria. a, (left) Venn diagram visualizing the species found by fecal MAGs, fecal SAGs, and oral SAGs. (right) Phylogenetic tree representing 811 species obtained from all medium- or high-quality 17,202 SAGs and 869 MAGs. The colored strips show the presence of genomes in each method. b A list of the 12 species consistently present in both the oral and fecal microbiomes of the participants. The number of SAGs obtained is shown in different colors depend on samples. c ANI heatmap for Streptococcus salivarius across SAGs from saliva (salmon) and feces (green). d ANI heatmap for Streptococcus sp001556435 across SAGs from saliva (salmon) and feces (green)

Fig. 3

Detailed examination of mobilomes and resistomes in human-associated microbiomes at single-cell resolution. a Determination of the host spectrum of plasmids and phages. To avoid redundant counts, similar plasmids or phage sequences were grouped into clusters. The predicted host numbers are depicted in histograms, distinguishing between SAGs and MAGs across different taxonomic ranks. b Distribution of ARGs in MGEs. ARG (class) presence and genetic context are visualized as pie charts. The x-axis labels detail the medical condition associated with each sample (Healthy; BC, breast cancer; CRC, colorectal cancer; LC, lung cancer; IBS, irritable bowel syndrome; UC, ulcerative colitis). c Comparison of ARGs (subclass) in MGEs among participants. Six resistomes in the gut microbiome (QLF001, QLF003, QLF010, QLF027, QLF033, and QLF055, marked with stars in c) are presented. d A network diagram depicted the links between the plasmid and its host genome at the species level in QLF055. Lines represent the connections between bacterial hosts and plasmids