Data from: Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.
We demonstrate the benefits of using multiple sequencing technologies and proximity ligation in identifying unique biological facets of the cattle rumen metagenome, and we present data that suggests that each has a unique niche in downstream analysis. Our comparison identified biases in the sampling of different portions of the community by each sequencing technology, suggesting that a single DNA sequencing technology is insufficient to characterize complex metagenomic samples. Using a combination of long-read alignments and proximity ligation, we identified putative hosts for assembled bacteriophage at a resolution previously unreported in other rumen surveys. These host-phage assignments support previous work that revealed increased viral predation of sulfur-metabolizing bacterial species; however, we were able to provide a higher resolution of this association, identify potential auxiliary metabolic genes related to sulfur metabolism, and identify phage that may target a diverse range of different bacterial species. Furthermore, we found evidence to support that these viruses have a lytic life cycle due to a higher proportion of Hi-C intercontig link association data in our analysis. Finally, it appears that there may be a high degree of mobile DNA that was heretofore uncharacterized in the rumen and that this mobile DNA may be shuttling antimicrobial resistance gene alleles among distantly related species. These unique characteristics of the rumen microbial community would be difficult to detect without the use of several different methods and techniques that we have refined in this study, and we recommend that future surveys incorporate these techniques to further characterize complex metagenomic communities.
Datasets generated and/or analyzed during the current study are available in the NCBI SRA repository under Bioproject: PRJNA507739. Assemblies, bins, and ORF predictions are available on Figshare. A description of commands, scripts, and other materials used to analyze the data in this project are available in the GitHub repository: https://github.com/njdbickhart/RumenLongReadASM and also on Zenodo. Resources in this dataset:Resource Title: Availability of data and materials. File Name: Web Page, url: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1760-x#availability-of-data-and-materials The datasets generated and/or analyzed during the current study are available in the NCBI SRA repository under Bioproject: PRJNA507739. The assemblies, bins, and ORF predictions are available on Figshare. A description of commands, scripts, and other materials used to analyze the data in this project can be found in the following GitHub repository: https://github.com/njdbickhart/RumenLongReadASM and also on Zenodo.

本研究描述了一种方法，通过将长读长测序技术融入用于组装高度复杂的反刍动物瘤胃微生物群落的各种技术中，并与基于短读长的方法进行对比。长读长序列的比对和成簇配对染色体技术（Hi-C）的连接分析，支持了188种新型病毒-宿主关联的识别以及瘤胃微生物群落中噬菌体生命周期的确定。与短读长组装相比，长读长组装还识别出了94个抗微生物耐药基因，而短读长组装中仅有7个等位基因。我们展示了多种技术协同作用以提高对高度复杂瘤胃微生物群落生物特征的表征。我们证明了使用多种测序技术和邻近交联技术识别牛瘤胃宏基因组独特生物学方面的益处，并呈现了数据，表明每种技术都在下游分析中拥有独特的生态位。我们的比较揭示了不同测序技术对群落不同部分的采样偏差，表明单一的DNA测序技术不足以表征复杂的宏基因组样本。通过长读长比对和邻近交联技术的结合，我们以其他瘤胃调查中未曾报道的分辨率识别了组装的噬菌体的潜在宿主。这些宿主-噬菌体分配支持了先前揭示的病毒对硫代谢细菌物种捕食增加的研究；然而，我们能够提供更高分辨率的这种关联，识别与硫代谢相关的潜在辅助代谢基因，并识别可能针对多种不同细菌物种的噬菌体。此外，我们的分析表明，这些病毒可能具有裂解性生命周期，因为我们的分析中Hi-C跨片段连接关联数据的比例较高。最后，似乎存在大量先前未在瘤胃中表征的移动DNA，这些移动DNA可能在远缘相关物种之间穿梭抗微生物耐药基因等位基因。这些瘤胃微生物群落独特的特征，没有使用我们在本研究中精细化的多种方法和技术的组合是难以检测到的，我们建议未来的调查应纳入这些技术以进一步表征复杂的宏基因组群落。

本研究生成和/或分析的数据集可在NCBI SRA库下的Bioproject：PRJNA507739项目中获取。组装、分类单元和开放阅读框预测可在Figshare上获取。用于分析本项目中数据的命令、脚本和其他材料可在以下GitHub仓库中找到：https://github.com/njdbickhart/RumenLongReadASM，亦可在Zenodo上找到。该数据集中的资源：
资源标题：数据与材料的可用性。文件名：网页，网址：https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1760-x#availability-of-data-and-materials。本研究生成和/或分析的数据集可在NCBI SRA库下的Bioproject：PRJNA507739项目中获取。组装、分类单元和开放阅读框预测可在Figshare上获取。用于分析本项目中数据的命令、脚本和其他材料的描述可在以下GitHub仓库中找到：https://github.com/njdbickhart/RumenLongReadASM，亦可在Zenodo上找到。