A systematic review on application of next-generation sequencing on microbes isolated from cultured species

Abstract

Background This study employs NGS for analyzing microbes in cultured species. It follows PRISMA guidelines to systematically investigate NGS’s role in identifying pathogens from cultured species. Methods Following PRISMA guidelines, Scopus and ScienceDirect were systematically searched for studies on next-generation sequencing (NGS) from 2012 to 2023. Articles lacking relevant data or keywords were excluded. Quality limitations were acknowledged. To reduce bias, ROBINS-I tool was used to assess bias across seven domains. Data were organized in a matrix table, facilitating detailed analysis and visualization. This systematic approach ensured a transparent, comprehensive review of NGS in microbiology. Results 956 and 200 articles were available and reviewed from Scopus and ScienceDirect, respectively, using keywords such as next generation sequencing, cultured species and microbes. Only 6 articles are related to this topic and within 10 years of publication to ensure up to date information. Three of them are reported from China, one from Mexico, one from Australia and one from United States of America. Most of the articles reported they are using Illumina platform more than Nanopore platform. 4 out of 6 articles of them are using Illumina while 2 out of 6 articles are using nanopore platform. The microbes identified using those next generation sequencing are microsporidia Enterocytozoan hepatopenaei (EHP), fathead minnow calicivirus (FHMCV), mud crab reovirus (MCRV), white spot syndrome virus (WSSV), and fungal species such as Pneumocystis jirovecii. Conclusions In conclusion, Illumina sequencing is more commonly employed platform for identifying pathogens in cultured species compared to Nanopore sequencing. China stands out as the leading contributor to NGS research in this context. However, it’s important to acknowledge potential limitations in the study due to the quality of the articles reviewed and the risk of bias assessment.