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Long Read Sequencing for Microbiome Research
Bacteria live in nearly every environment on Earth, with global microbial diversity estimated to exceed 1012 species. To obtain representative genomes, either sequencing of pure cultures or recovery of genomes directly from metagenomes are often used. Long read sequencing has become the method of choice for pure culture genomes and metagenomes. CD Genomics is a leading provider of customized solutions for long read sequencing, dedicated to comprehensively characterizing microbial diversity for a wide range of applications.
Microorganisms are a general term for tiny organisms that are difficult to see directly with the naked eye, including microorganisms with cellular structures such as eubacteria, archaea, fungi, actinomycetes, protozoa, and algae, as well as organisms without complete cellular structures such as viruses, mycoplasma, and chlamydia. Microorganisms are the most abundant and diverse life forms on Earth. They are found in every biosphere, including some of the most extreme places on Earth. Microorganisms are the most abundant and diverse life forms on Earth. However less than 1% of microorganisms have been identified, let alone sequenced. High-throughput short-read sequencing has been the method of choice for microbial research for many years, but it cannot resolve repetitive regions larger than the size of a library insert. Of the approximately 400,000 microbial strains for which sequencing data are available, most genomes are incomplete. To understand our evolving world, long-read sequencing can provide unbiased, accurate, and comprehensive information.
In general, microbial genomes are much smaller than those of plants and animals, making them ideal for genetic and physiological studies. CD Genomics offers comprehensive Microbial Genomics with Long-Read Sequencing services to sequence entire bacterial, fungal, or other microbial genomes.
Fig. 1. Taxonomic read composition, per-organism read-length distributions and genome assemblies in a defined 12-species bacterial mixture. (Moss et al., 2020)
Our Long Read Sequencing Solutions for Microbiome Research
CD Genomics is proud to offer long read sequencing solutions for microbial genomics research based on the PacBio SMRT sequencing and ONT Nanopore sequencing platforms. Our long read sequencing helps researchers identify organisms, assess microbial populations in environmental niches, catalog evolutionary pathways, and define genetic relatedness among microbial strains. Additionally, research is exploring the potential of using genomic signatures to determine antibiotic resistance and virulence. Its wide-ranging applications span all areas of our lives, such as ensuring food supply security, maintaining human health and well-being, combating the spread of disease, and protecting the environment.
We aim to enable microbiology researchers to comprehensively characterize microbial organisms, dissect complex microbial communities, and identify emerging pathogens with high accuracy, enabling scientists around the world to accelerate discovery, advance research and protect human, animal, and environmental health.
Our long read sequencing is used in the following areas of microbial research.
High-throughput bacterial genome sequencing can generate large amounts of high-quality data. Long read sequencing developments are making it easier to use genomics to analyze outbreaks and conduct broader public health surveillance. CD Genomics provides public health-oriented surveillance of healthcare pathogens, primarily involving the monitoring of their antimicrobial resistance (AMR), which may spread horizontally or clonally. We are committed to protecting public health with comprehensive long read genomic surveillance solutions that provide the complete information needed to accurately characterize and track all pathogens circulating in the community.
The microbiome of animals and plants plays a key role in their growth and health. Long-read sequencing technologies play an important role in exploring the biology of microbial symbionts, pathogens, microbiomes, and phytobiomes and their impact on crop yields, livestock health, and wildlife and natural habitat conservation. CD Genomics provides comprehensive long read sequencing solutions to analyze microbiota that influence animal and plant health, growth, and production, with the goal of increasing crop yields and promoting livestock health and production.
The human microbiome has attracted considerable interest from researchers and has become a model system for studying diverse microbial communities. Interspecific networks within the microbiome can modulate energy metabolic pathways and influence human health. The two most diverse human microbiota are the intestinal and oral microbiota, which harbor hundreds of coexisting species, including bacteria and viruses. CD Genomics provides long read sequencing solutions to study microbiota in human intestinal and oral samples.
One of the important goals of industrial biotechnology is to utilize cheap biomass resources. The traditional strategy is to use a single strain for microbial fermentation. However, cheap biomass often contains complex components and impurities that are difficult for individual microorganisms to utilize efficiently. CD Genomics provides long read sequencing solutions to study microbial communities used in food, environment, energy, chemical, and other industrial fields to meet the global demand for new therapies, environmental remediation, and efficient chemical production.
Advantages of Long Read Sequencing for Microbiome Research
- Entire viral genes or genomes can be phased, whether within a single host, within a community, or across a broad geographic area.
- Bacterial strains, serotypes, and plasmids can be resolved with great accuracy.
- Obtain reliably closed and highly accurate bacterial genomes.
- Ability to associate specific species with observed changes in metagenomic function or system outcomes.
- Generation of near-complete microbial genomes from pure cultures or metagenomes.
- Community function can be directly compared to different strains using high-quality metagenomic assembled genomes.
CD Genomics is committed to exploiting the potential of long read sequencing to ensure that our customers remain at the forefront of microorganisms research. If you have any questions, please feel free to contact us. We look forward to working with you on projects of interest.
Reference
- Moss, Eli L., Dylan G. Maghini, and Ami S. Bhatt. "Complete, closed bacterial genomes from microbiomes using nanopore sequencing." Nature biotechnology. 38.6 (2020): 701-707.
Related Services
PacBio SMRT Sequencing
Oxford Nanopore Sequencing
Microbial Whole-Genome Resequencing
Microbial Whole-Genome De Novo Sequencing
Long-Read Metagenomics Sequencing
Antibiotic Resistance Gene (ARG) Analysis
For research purposes only, not intended for personal diagnosis, clinical testing, or health assessment