MICROBIOME AND ISOLATE SEQUENCING


We offer world-class microbiome and isolate sequencing and analysis services to industry and academia worldwide. Empowered by EzBioCloud database and analytics, our state-of-the-art sequencing laboratory caters quality and precision to innovate, accelerate and elevate your research. 

When you work with us, we take hurdles and facilitate the delivery of innovation, shorten the time of discovery and development of microbiota-based therapeutics and companion diagnostics, and ensure accurate strain authentication, safety assessment, and quantification of microbial load.

Metagenomics And Microbiome Profiling

Microbiomes play a crucial role in human health and wellness! They offer the opportunity to understand how microorganisms interact with the host to affect health and disease. It helps uncover the tight interplay the microbiome has with the environment to keep the ecosystem in balance. It became a treasure trove for discovery of exciting new biological insights and the possibility of developing transformative microbiota-based diagnostics and therapeutics. To be successful, microbiome study requires high accuracy and precision in biodiversity estimates, taxonomic classifications and reliability in metabolic and functional profiling. 

At EzBiome we offer fast, reliable and high-quality metagenomics and microbiome sequencing using expert-validated wet lab protocols and state of the art sequencing platforms paired with our industry leading bioinformatics powered by EzBioCloud’s cutting-edge genomics and informatics tools. Our reference database is validated by taxonomic experts, widely used (95,000+ citations) and includes the largest collection of species and subspecies (21,529 and 14,400 species and subspecies in 16S and genome databases, respectively) including 3,000+ new species offering broader taxonomic coverage than the competition. 


Additionally, we have an excellent team of microbiome experts who are ready to help you at every step of the process, including statistical recommendations on experimental design, choice of efficient sample collection and preservation method, bias-free nucleic acid extraction, selecting right sequencing approach, identifying database and bioinformatics platform, and selecting appropriate comparative statistical analyses to enable your research study to be better, well-controlled and increase the likelihood of desired outcome with more rigor and reliability.

Keep reading below to understand which methods to choose for your microbiome study

Selecting Your Microbiome Study Method


Amplicon (16S/ITS) Sequencing

Amplicon sequencing is a highly targeted method of next generation sequencing that enables researchers to perform ultra-deep sequencing of PCR products (amplicons) derived from specific genes of interest (16S/18S/ITS) to achieve efficient variant identification, taxonomic characterization and quantitation. It is suitable for most sample types of human, animal, natural environment and industrial samples, regardless of their level of biomass and/or background host DNA content (i.e., stool, skin, blood, tissue, saliva, BAL, soil, water, waste water, food, feed, dairy, produce, probiotics, raw materials, cosmetics etc.). However, it is specifically very useful for samples with low biomass and high host DNA content, as well as samples with highly diverse bacterial and fungal composition.

EzBiome 16S microbiome service offers you highly resolved species-level microbiome profiling with the most extensive taxonomic coverage. Our database includes species with validly published names, candidates, potential new species (> 3000 new species) and uncultured phylotypes. It offers great coverage on the human microbiome: >96% species-level identification can be achieved. You can also predict KEGG-based 16S functional profiles using >10,000 species genomes making our predictions far more accurate and insightful than the competition.


Therefore, together with our high quality bias-free amplicon sequencing and the most extensive and curated EzBioCloud reference database, we offer highly resolved and precise species-level taxonomic profiling, with comprehensive prediction of functional landscape to take your microbiome research to the next level.

Shallow And Deep Shotgun Sequencing

Shotgun sequencing is a method where long strands of DNA (such as entire chromosomes and entire genomes) are randomly shredded (“shotgunning”) into smaller DNA fragments, so that they can be sequenced individually. Once sequenced, these small fragments are then assembled together into contigs by computer programs that find overlaps in the genetic code, and the complete sequence of the bacterial genome is generated. Now, instead of one genome, if you directly sequence the entire assemblage of genomes from a metagenome using such a shotgun approach, the resulting output is termed a shotgun metagenomic sample. By this method, you are literally sequencing thousands of genomes simultaneously from a given metagenome in one assay and get the opportunity to reconstruct all genomes, genomic fragments or genes to infer multi-kingdom taxonomic composition of communities and their functions. Whereas targeted 16S rRNA or targeted amplicon sequencing relies on amplification and sequencing of one target region, shotgun metagenomics is actually target free, it is aimed at sequencing entire genomes of every organism present in a sample and gives a more accurate, and unbiased biological representation of a sample. Like amplicon sequencing, shotgun sequencing is also suitable for most sample types of human, animal, natural environment and industrial samples, regardless of their level of biomass and/or background host DNA content. Based on its operational utility, cost and intended research outcome, we offer two types of shotgun sequencing approaches, namely (a) Shallow shotgun sequencing (2M to 5 M reads/samples) and (b) Deep shotgun sequencing (20M – >100M reads/sample). Shallow shotgun sequencing is particularly attractive for moderate to high biomass samples with low host DNA background (i.e., stool, urine, probiotics, drinking water, etc), whereas deep shotgun sequencing is critical for samples with high biomass and low-moderate host DNA content (i.e., skin, blood, tissue, saliva, BAL, soil, waste water, food, feed, dairy, etc.)

EzBiome shallow and deep shotgun microbiome service offers highly resolved subspecies-level microbiome profiling with the most extensive taxonomic coverage. Our database includes species with validly published names, candidates, potential new species (> 3000 new species) and uncultured phylotypes. 


Therefore, together with our high quality bias-free shotgun sequencing, most extensive and curated EzBioCloud reference database, we offer highly resolved and precise multi-kingdom taxonomic profiling, with comprehensive community characterization and direct functional gene and pathway annotation.

Isolate Whole Genome Sequencing

Whole-genome sequencing (WGS) is considered as one of the most accurate and rapid methods for precise microbial identification and advanced characterization. WGS significantly improves identification with most accurate species delineation and highly resolved taxonomic inference based on genomic attributes. It can resolve taxonomic inconsistency of any cultivated bacteria, including novel species or strain, not attained by any existing methods.

Additionally, WGS provides the opportunity to investigate entire genetic makeup of an isolate genome for antimicrobial resistance and virulence genotyping, precise molecular subtyping (i.e., multilocus sequence typing, molecular serotyping, single nucleotide polymorphism etc.), and carry out high-resolution evolutionary and functional analysis.


EzBiome Isolate WGS service offers you a high-throughput one stop solution for generating draft-genomes and/or complete genomes of hundreds or thousands of bacterial isolates simultaneously. Just send your isolate cell pellet or gDNA and receive comprehensive cloud analysis of the isolate whole genome including precise taxonomic assignment, general genome info, completeness, information about antibiotics resistance gene and virulence factors, etc. assembly, annotation and comparative analysis with 4 randomly chosen genomes. Contig info, CDS, neighbor report by TNA, Genome browser/map, GC skew/ratio, EggNog, COG, Blast, Publication-ready images, FASTA, export in excel, png, etc.

Genome Report For Industrially Important Strains (GRIIS)


Genome Report For Industrially Important Strains (GRIIS)

GRIIS (Genome Report for Industrially Important Strains) analyzes the strain used in a product to verify its safety by identifying the correct strain, toxic genes, and antibiotic resistance genes. In addition, the final product test confirms the presence and quality of single or mixed strains contained in the product. 

GRIIS Essential

GRIIS Essential is a service for the master seed of probiotic products. The whole genome of the core resource strain is subjected to genome completion through a combination of PacBio and Illumina sequencing instruments. Identify the subject’s biological information and perform genome-based bacterial identification using a verified database from EzBiome, Inc.

GRIIS Composition

GRIIS Composition is a service to assess accurate composition and potential contamination, if any, in probiotic products.

Biomarker Discovery

We study the link between microbiome and chronic diseases using our proprietary Precision Microbiome Discovery Platform to identify microbes and/or functions that play key roles in health and diseases with unprecedented accuracy and precision. Our pipeline significantly shortens the time for discovery and development of candidate biomarkers for microbiota-based therapeutics and companion diagnostics for microbiome-related diseases.

EzBiome and ChunLab Inc. are extensively working on microbiota-based discovery and development of therapeutics and companion diagnostics for microbiome-related diseases leveraging our precision microbiome discovery platform. To this end, microbiota samples of ≧20 diseases are being collected and sequenced by building an extensive collaborative network with major hospitals in Korea. We offer collaborative research and development services to identify new therapeutic targets and/or markers for companion diagnostics by co-researching on the following areas of research.

Category
Diseases
Metabolic

Obesity, Diabetes

Oncology

Gastric cancer, Breast cancer, Liver cancer, Thyroid cancer

Gastroenterology

Irritable bowel syndrome, Inflammatory bowel disease, Necrotizing enterocolitis (infant)

Liver

Non-Alcoholic Steatohepatitis, Liver cirrhosis

Kidney

Nephropathy

Endocrine system

Hyperthyroidism, Hypothyroidism

CNS

Autism Spectrum Disorder, Alzheimer’s Disease, Epilepsy

Obstetrics

Preterm birth

Gynecology

Vaginosis

Infection

Multi-drug resistant pathogen infection

Dentistry

Periodontal disease

Contact Our Experts

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