Analysis of prospective microbiology research using third-generation sequencing technology

Abstract

Microbes are ubiquitous in human life. In years past, the study of microbes has only focused on single-bacteria cultures and qualitative analyses. The development of sequencing technology has greatly enhanced progress in microbiology research and more and more evidence shows that human symbiotic microbes, especially intestinal microbes, are closely related to human health. Second-generation sequencing technology is currently mainstream in microbiology research because of its high throughput, high accuracy and low cost. However, with the deepening complexity of research, the disadvantages of second-generation technology, i.e. short read length (< 450 bp), lead to subsequent challenges in data analysis and genome assembly, and limit the applicability to future research. In this context, the third-generation sequencing technology comes into being. The third-generation of sequencing (TGS) technology is also called single molecule sequencing. It directly carries out real-time sequencing of single DNA molecules without PCR amplifications. TGS technology significantly increases read length up to 2-10 kb or even 2.2 Mb. Because of its advantages of long read and no preference for GC, TGS provides a new method for full-length gene sequencing that facilitates the assembly of complete and reliable genome maps in microbes and that further reveals the diversity of microbial structures and functions. This review summarizes the technical characteristics and principles of TGS, and then mainly analyzes its applications and progress in 16S/18S rRNA gene sequencing, complete bacterial genome mapping and metagenomics research.

Advances in artificial intelligence-based microbiome for PMI estimation

“…Many complex environmental and artificial factors can potentially affect the succession of microorganisms. Second, NGS has the limitation of short reads and low accuracy of species identification ( Yakun et al, 2019 ); consequently, most studies have predominantly targeted amplification of the V3 and V4 regions of the 16S rRNA gene, and these fragments only provide an approximate picture of the bacterial phyla ( Verma et al, 2018 ). Accurate detailed taxonomy annotation of microorganisms requires full-length amplification of DNA.…”