Long Read Sequencing for Human Microbiome

The human microbiome has attracted a great deal of interest from researchers and has become a model system for studying different microbial communities. Two of the most diverse human microbiomes are the gut and oral microbiomes, which contain hundreds of coexisting species, including bacteria and viruses. CD Genomics offers long read sequencing solutions to study the microbiomes in human gut and oral samples.

Introduction to Human Gut and Oral Microbiome

A comprehensive understanding of the microbial communities in which pathogens reside is important for predicting the progression of infections in clinical settings. The human microbiome consists of a vast array of microorganisms, including bacteria, viruses, fungi, and protozoa, which colonize many different ecological niches within the human body. Interspecific networks within the microbiome can modulate energy metabolic pathways and influence human health.

The human gut microbiome contributes to host metabolic and immune homeostasis, and microbial dysbiosis has been shown to be at the root of a variety of diseases, including metabolic and immune disorders, central nervous system pathologies, and cancer. Methodologically, most compositional and functional insights about the microbiome have been obtained based on shot-gun metagenomic sequencing data, which has dedicated supported profiling of microbiomes in terms of single-nucleotide polymorphisms (SNPs) and structural variations (SVs) for various populations. However, Such short-read sequencing data has limitations, particularly in assembly contiguity. Recent advances in long read sequencing technology provide unique opportunities to study changes and functions of the gut microbiome.

The human oral microbiome consists of more than 700 common taxonomic units at the species level and includes a large number of opportunistic pathogens involved in periodontal, respiratory, cardiovascular, and systemic diseases. Species-level identification of oral microorganisms is fundamental and a prerequisite for analyzing oral microbial communities. 16S rRNA genes are considered the gold standard for phylogenetic studies of microbial communities. Long read sequencing for 16S rRNA genes can provide a snapshot of microbial communities, revealing the phylogeny and abundance of microbial populations in different ecosystems.

Fig. 1. Oxford Nanopore Technology reads improved gut microbiome metagenomic assembly, empowered SVs detection and validations. (Zhang et al., 2020)

Solutions Offering at CD Genomics

In-depth analysis of genetic variation in the gut microbiome is necessary to understand its function and impact on host health and disease. CD Genomics leverages the long read length advantage provided by PacBio SMRT sequencing and ONT Nanopore sequencing to characterize structural variation (SV) in hundreds of gut microbiomes from healthy humans. of fine genetic variation in the healthy human gut microbiome. Our long read sequencing improves the quality of metagenome assembly and can reliably detect a large number of extended structural variant types (including, in particular, a large number of insertions and inversions). In addition, we attempt to explore the association between alterations in the human enterovirome and disease. Our long read sequencing solutions have been widely used for the assembly of genomes of sequential bacterial isolates, as well as the extraction of sufficient molecular weight, purity, and amount of DNA from fecal samples for metagenomic sequencing.

The gut microbiota has received increasing attention over the past decade, while the oral microbiota has been less well studied. At CD Genomics, we utilize the PacBio SMRT sequencing and ONT Nanopore sequencing platforms to sequence the full length of the 16S rRNA gene to explore the oral microbiota. Sequencing the entire 16S rRNA gene produces longer reads that give you a higher resolution of the organism and higher abundance estimates.

Advantages of Our Long Read Sequencing Solutions for Human Microbiome

• In human microbiome studies, long read sequencing data support improved metagenomic assembly and functional annotation and facilitate studies of the spread of antibiotic resistance genes in various environments.
• Long read sequencing increases the confidence of microbiome fingerprinting as improved metagenomic assembly results in more complete bacterial and viral genomes.
• Reads that are long enough can also cover a wide range of genomic regions, including different structural variants, enabling direct read-level verification of fingerprints.
• Long read sequencing provides longer sequences and reads generated by sequencing the entire 16S rRNA gene.
• Long read sequencing can establish higher abundance estimates and provide the ability to identify organisms with higher taxonomic and phylogenetic resolution.

CD Genomics is committed to providing long read sequencing technology to characterize the complex human intestinal and oral microbiomes with the goal of promoting human health. If you have any questions, please feel free to contact us. We look forward to working with you on projects of interest.

Related Services

PacBio SMRT Sequencing
Oxford Nanopore Sequencing
Microbial Whole-Genome Resequencing
Long-Read Metagenomics Sequencing
Full-Length 16S/18S/ITS Amplicon Sequencing