Unlocking the Microbiome

Unlocking the Microbiome

End-to-End Metagenomics Services
Full Genome Sequencing, Genome Analysis and Phylogenetic Analysis
Industry Leading Bioinformatics using Next Generation sequencing technologies
Experience in 20+ sample types

Experience in 20+ sample types

World's largest curated database of microbial genomes

World's largest curated database of microbial genomes

User-friendly, interactive analysis software

User-friendly, interactive analysis software

50+ publications

50+ publications

Advice and Recommendations

METAGENOMICS ANALYSIS EXPERTSYour study deserves the best!

Next generation sequencing is used to rapidly analyze the variety of microbial communities and determine the significance of individual species in metagenomics. We provide a range of metagenomics services, ranging from targeted tests (16S for prokaryotes and ITS2 for fungi) to whole genome analysis.

Over the years, CosmosID has used metagenomic analysis to support countless organizations to publish new studies, develop new products & therapeutics as well as help diagnose over 1500 patients using an industry-leading bioinformatics pipeline and high-quality sequencing. Our goal is to provide our clients with affordable solutions, a seamless customer experience and the highest resolution microbiome data!
  • Customers in 25+ countries
  • 4x award-winning bioinformatics pipeline
  • CLIA/GCP/HIPAA Compliance
  • 12+ years experience

Your study deserves the best!


Sahar El Aidy, PhD – Assistant Professor – University of Groningen

CosmosID has added great value in helping me understand the role that microbiota composition plays in certain disorders and they provide great interactions with customers when further questions on analyses are raised.


Jennifer Wargo, PhD & Nadim Ajami, PhD – MD Anderson Cancer Center (PRIME TR)

“Aside from the excellent quality of sequencing data CosmosID generates, their project management skills are exceptional. Our group has benefited immensely from CosmosID’s personalized service and flexibility to work under tight timelines – in the past few months, which have brought new challenges to all, CosmosID have helped us regain the pace of our translational microbiome studies. Their user interface for data analysis is also a great tool for teams that need bioinformatics and analytic support.”


Christopher Belnap, PhD – CEO – Resilient Biotics

“CosmosID offers a suite of sequencing services that we have utilized to generate high quality metagenomic and transcriptomic data for deep microbiome-host analyses. Hitting appropriate sequence depth, data quality, and timely completion of projects are critical factors that we evaluate when working with a sequencing provider. CosmosID has provided exemplary customer service and has worked with us to complete custom sequencing projects in order to generate critical time-sensitive data.”

Need Metagenomics Analysis?

Most scientists working in the microbiome field are in uncharted territory. You’re not alone and we’re here to help! By combining over 12 years of experience, a CLIA/GCP facility and unrivaled bioinformatics, CosmosID supports industry, academia & clinicians
with standardized and validated metagenomics analysis so they can so they can analyze all of the genes present in a microbial community and unlock the microbiome with confidence!


The CosmosID pipeline was developed to address many challenges in modern-day bioinformatics by achieving better taxonomic resolution than traditional kmer and assembly-based approaches, yet maintaining computational efficiency and being able to achieve species, sub-species and strain-level resolution with less sequencing depth.
Multi-kingdom identification for every sample, every time
Precision filtering for confidence thresholds
fastQC results for data quality reporting
Exportable abundance values, charts & visualizations including sunburts, bubble charts & stacked bar graphs
Unlimited comparative analysis software, complete with Heatmaps, 3D PCA, Alpha Diversity plots & Beta Diversity PCoA

Sequencing Services

At CosmosID, we offer a range of sequencing services that cover a range of metagenomic approaches. Our sequencing services cover a range of different sample types and have been extensively researched.
Amplicon Sequencing

Like many metagenomic approaches, amplicon sequencing offers unique advantages to microbiome researchers including cost-effectiveness and the creation of comprehensive taxonomic profiles.

Shallow Shotgun Sequencing

Shallow Shotgun Sequencing allows researchers to unlock the microbiome with better species level resolution than 16S sequencing whilst also maintaining cost effectiveness. This makes it a powerful choice for large cohort studies that focus on human health, such as the gut microbiome.

Deep Shotgun Sequencing

In deep shotgun sequencing, whole DNA is extracted from a sample then exposed to random fragmentation prior to Next Generation Sequencing to gain an exponential amount of metagenomics data and advantages alongside it.

Bacterial Isolate Sequencing

Whole Genome Sequencing of bacterial isolates offers unique advantages over traditional typing methods. Unlike PCR, this technology identifies the complete genetic makeup of an organism and offers unprecedented insight into the different types of microbial diversity .

Exceptional Bioinformatics

Through unrivaled sensitivity and precision, the CosmosID metagenomics pipeline is validated to return strain-level resolution of bacteria, viruses, phages, fungi, protists, bacterial MAGs as well as AMR & Virulence genes. The power of the platform has been demonstrated in 3 key community challenges:

1st Place 

Janssen Pharmaceuticals‘ Mosaic – Strain’ Challenge


1st Place

PrecisionFDA ‘Pathogen Detection’ Challenge


1st Place

PrecisionFDA ‘Biothreat Challenge’


ENQUIRE NOWUnlock the Microbiome

From quotes to samples submission forms and a free account on the CosmosID Metagenomics App, we can help! Get in touch today.
Experience in 20+ sample types

Experience in 20+ sample types

Human, Environmental, food & more
Microbial Genomes to Multi-kingdom, strain-level, bioinformatics

Microbial Genomes to Multi-kingdom, strain-level, bioinformatics

Stored on our user-friendly software

Contact Us Now