--- title: Next-Gen Sequencing Technologies in Microbiology description: With several NGS platforms available and a variety of applications to choose from, here we outline some of the more popular technologies and their potential use in microbial research. image: https://blog.genewiz.com/hubfs/GWZ%20BLOG-HERO%20Microbial%20research%20blog.png --- [![GENEWIZ](https://blog.genewiz.com/hubfs/GENEWIZ%20Brand%20Assets/GENEWIZ%20Logos/2025-04%20Current%20GENEWIZ%20Logos/GENEWIZ_Full-Color_Logo_PublicWeb_200x63.svg "GENEWIZ")](https://www.genewiz.com/) - Close Search [GENEWIZ Blog Homepage](https://blog.genewiz.com/) # Next-Gen Sequencing Technologies in Microbiology [By GENEWIZ .](https://blog.genewiz.com/author/genewiz) October 29, 2026 0 Comments ![](https://blog.genewiz.com/hubfs/GWZ%20BLOG-HERO%20Microbial%20research%20blog.png) Understanding microbial diversity and function is increasingly critical in many fields, from healthcare, to farming, food production, and environmental science. Studying microbial diversity can be challenging, with many different microbial species and subspecies present. Next-Generation Sequencing (NGS) methods have revolutionized microbial research, allowing for the identification and characterization of individual microorganisms and complex microbial populations. With several NGS platforms available and a variety of applications to choose from, we discuss some of the more popular technologies and their potential use in microbial research. ## Microbial Genome Discovery and Characterization For the discovery of novel microbial genomes or further characterization of poorly annotated genomes, whole genome sequencing (WGS) is the gold standard. *De novo* WGS does not require a reference genome; instead, it uses random fragmentation of the genome, deep sequencing, and assembly of the overlapping sequences to generate a new reference sequence. High-throughput short-read sequencing instruments, including Illumina, are typically used. For improved quality and better resolution of complex regions of the genome and structural variations, the use of long-read sequencing platforms, including Oxford Nanopore or PacBio is recommended. A combination of short- and long-read sequencing can also be used. ## Microbial Detection To check for the presence of specific organisms, polymerase chain reaction (PCR) is frequently used for rapid identification. When PCR tests are unavailable or when more detailed classification is needed, targeted sequencing of 16S rRNA (bacteria), 18S rRNA (eukaryotes), or ITS (fungi) is ideal. Whole genome sequencing (WGS) provides more detailed analysis and can be used to gain insights into virulence factors, drug resistance mechanisms, and other genetic traits. Choose whole genome sequencing for sub-species/strain resolution and PCR/Microarray or targeted 16S, 18S, or ITS sequencing for genus/species resolution. ## Species Classification For higher-level classification and genus-level sequencing, specific targeted NGS assays are ideal. However, depending on the organism and complexity, even sequencing the entire 16S region with long-read technologies may not always lead to species-level taxonomic resolution. Additionally, targeted sequencing methods may not offer insights into the functional capabilities of microbes. When a deeper understanding of microbial characteristics is required, such as strain-level identification to assess pathogenicity (e.g., influenza strains) or to detect low-level mutations, WGS is the preferred approach, especially if reference genomes are available. Depending on the genome size, time constraints, cost, and desired accuracy, either short-read sequencing platforms or long-read technologies may be used. Choose whole genome sequencing for sub-species/strain resolution and targeted 16S, 18S and ITS sequencing for genus/species resolution. ## Microbial Transcriptomics To better understand the gene expression and functional profile of a microbe under specific conditions, RNA Sequencing (RNA-Seq) is the preferred approach. This allows for a deeper investigation into active functions when microorganisms adapt to environmental changes, including host-pathogen interactions. RNA-Seq traditionally requires a reference genome; however, when more detailed information is needed or no reference genome exists, *de novo* transcriptome assembly can be performed. Choose RNA-Seq or whole transcriptome for sub-species/strain resolution and RNA-Seq or targeted 16S, 18S and ITS sequencing for genus/species resolution. ## Whole Genome Metagenomics Microbial population structure and evolution can be studied using whole genome metagenomics, which analyzes the total microbiome. Whole genome metagenomics involves sequencing all genetic material in a sample, offering a comprehensive view of the microbiome by directly assembling and analyzing individual genomes from mixed microbial communities. This method provides information on the total genomic DNA from all organisms in a sample, eliminating the need to isolate and grow microorganisms, and providing more precise classification and mutation monitoring. Choose short or long-read whole genome metagenomics for genus/species resolution. ## Metatranscriptomics Metatranscriptomics is used to obtain a functional profile of whole microbiomes and study gene expression in microbial populations, especially those that may be difficult to isolate or cultivate from their natural environment. Depending on the experimental purpose, RNA-Seq, targeted 16S for prokaryotes, or targeted ITS2 for fungi can be chosen when cost and time are significant factors. Whole transcriptome sequencing can also be used to obtain a more detailed profile of gene expression using large-scale, high-throughput shotgun sequencing of transcripts from all microbial communities in a specific environmental sample. 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