气候变化领域集成服务门户(CCPortal): Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico

CCPortal

DOI	10.1371/journal.pone.0291402
	Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico
	Cisneros-Martinez, Alejandro Miguel; Rodriguez-Cruz, Ulises E.; Alcaraz, Luis D.; Becerra, Arturo; Eguiarte, Luis E.; Souza, Valeria
发表日期	2024
ISSN	1932-6203
起始页码	19
结束页码	2
卷号	19 期号:2
英文摘要	Due to the enormous diversity of non-culturable viruses, new viruses must be characterized using culture-independent techniques. The associated host is an important phenotypic feature that can be inferred from metagenomic viral contigs thanks to the development of several bioinformatic tools. Here, we compare the performance of recently developed virus-host prediction tools on a dataset of 1,046 virus-host pairs and then apply the best-performing tools to a metagenomic dataset derived from a highly diverse transiently hypersaline site known as the Archaean Domes (AD) within the Cuatro Cienegas Basin, Coahuila, Mexico. Among host-dependent methods, alignment-based approaches had a precision of 66.07% and a sensitivity of 24.76%, while alignment-free methods had an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best overall performance (F1_score = 95.7%). However, when predicting the host of AD viruses, methods based on public reference databases (such as RaFAH) showed lower inter-method agreement than host-dependent methods run against custom databases constructed from prokaryotes inhabiting AD. Methods based on custom databases also showed the greatest agreement between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism. This highlights the value of including custom data when predicting hosts on a highly diverse metagenomic dataset, and suggests that using a combination of methods and qualitative validations related to the source environment and predicted host biology can increase the number of correct predictions. Finally, these predictions suggest that AD viruses infect halophilic archaea as well as a variety of bacteria that may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing, or marine, which is consistent with the specific environment and the known geological and biological evolution of the Cuatro Cienegas Basin and its microorganisms.
语种	英语
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:001158449800024
来源期刊	PLOS ONE
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/302128
作者单位	Universidad Nacional Autonoma de Mexico; Universidad Nacional Autonoma de Mexico; Universidad Nacional Autonoma de Mexico; Universidad Nacional Autonoma de Mexico
推荐引用方式 GB/T 7714	Cisneros-Martinez, Alejandro Miguel,Rodriguez-Cruz, Ulises E.,Alcaraz, Luis D.,et al. Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico[J],2024,19(2).
APA	Cisneros-Martinez, Alejandro Miguel,Rodriguez-Cruz, Ulises E.,Alcaraz, Luis D.,Becerra, Arturo,Eguiarte, Luis E.,&Souza, Valeria.(2024).Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico.PLOS ONE,19(2).
MLA	Cisneros-Martinez, Alejandro Miguel,et al."Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico".PLOS ONE 19.2(2024).