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

IF 13.8 1区生物学 Q1 MICROBIOLOGY Microbiome Pub Date : 2024-10-02 DOI:10.1186/s40168-024-01903-z

Tetsuro Kawano-Sugaya, Koji Arikawa, Tatsuya Saeki, Taruho Endoh, Kazuma Kamata, Ayumi Matsuhashi, Masahito Hosokawa

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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.

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单个扩增基因组目录揭示了人类微生物群中动员群和抵抗群的动态变化。

背景：元基因组组装基因组（MAGs）的增加促进了我们对人类微生物组功能特征和分类分配的了解。相比之下，通过单细胞基因组测序获得的单个扩增基因组（SAGs）可以捕捉到单个基因组的内容，包括MGEs：我们介绍了首个来自人类口腔和肠道微生物组的大量 SAG 数据集（bbsag20），其中包括 17,202 个中等质量以上的 SAG，且未进行共组装。该数据集揭示了312种口腔和647种肠道细菌系的多样性，显示了与MAGs不同的分类组成。此外，SAGs 还显示了口腔细菌向肠道转移的细胞级证据。我们还发现了携带抗生素耐药基因（ARGs）的广泛宿主范围的 MGEs，这些基因在 MAGs 中未检测到：结论：SAGs 和 MAGs 在分类组成上的差异表明，将这两种方法结合起来将有效扩大基因组目录。通过连接单个样本中的移动基因组和耐药性基因组，SAGs可以细致地描绘出MGEs上ARGs的动态网络，准确定位潜在的ARGs库及其在微生物群落中的传播模式。视频摘要。

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来源期刊

Microbiome MICROBIOLOGY-

CiteScore

21.90

自引率

2.60%

发文量

198

审稿时长

4 weeks

期刊介绍： Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.