Microbiome Profiling

Streamline Microbiome Profiling with Cosmos-Hub

Cosmos-Hub allows researchers to import their raw sequencing data directly into the platform and run a number of available bioinformatics pipelines for microbiome analysis.

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Short-Read ITS Amplicon Profiling with Cosmos-Hub

Introduction to Short-Read Amplicon Profiling

The internal transcribed spacer (ITS) region is the primary DNA marker for fungal community profiling, offering high discriminatory power across diverse environments and host-associated niches. Targeted ITS sequencing provides a fast, cost‑effective view of fungal community composition and complements 16S/18S surveys when the research focus is detection, baselining, or surveillance of fungal taxa. On Cosmos‑Hub, ITS workflows are optimized for production studies, from environmental monitoring to food, agriculture, and clinical applications.
ITS Workflow Infographic

Microbiome Profiling

Streamline Microbiome Profiling with Cosmos-Hub

Cosmos-Hub allows researchers to import their raw sequencing data directly into the platform and run a number of available bioinformatics pipelines for microbiome analysis.
Microbiome Profiling
 

In just a few easy steps, users can run industry-leading bioinformatics pipelines for a wide range of different data types:

  • Import data from their computer, from Illumina BaseSpace, directly from NCBI SRA or via Command Line Import (CLI).
  • Select the type of data they’d like to import: Shotgun, 16S or ITS
  • Select from 1 of 9 different host genomes to run automated host read depletion
  • Upload your study metadata
  • Choose your pipeline and primers
 

In just a few easy steps, users can run industry-leading bioinformatics pipelines for a wide range of different data types:

  • Import data from their computer, from Illumina BaseSpace, directly from NCBI SRA or via Command Line Import (CLI).
  • Select the type of data they’d like to import: Shotgun, 16S or ITS
  • Select from 1 of 9 different host genomes to run automated host read depletion
  • Upload your study metadata
  • Choose your pipeline and primers
Microbiome Profiling

Cosmos‑Hub ITS Pipeline Overview 

 

Cosmos‑Hub implements a short‑read ITS workflow using the QIIME framework and closed‑reference operational taxonomic units (OTU) clustering at 97% sequence identity against the UNITE database to deliver stable, well‑annotated fungal groupings for large studies. Raw reads (paired- or single-end FASTQs) are adapter‑ and quality‑trimmed, paired‑end overlaps are merged, unmerged reads are appended, and sequences are converted for OTU picking and taxonomy assignment, ensuring predictable behavior and reproducibility across cohorts and timepoints. UNITE’s community‑curated taxonomy and species hypotheses provide consistent fungal labels and traceability.

Our cloud-based platform addresses common challenges with implementing ITS pipelines through automated quality control, customizable workflows, and sequencing platform-agnostic design. Users can upload study metadata and select appropriate quality thresholds while the system handles complex bioinformatics processing across large datasets. This approach eliminates technical barriers while maintaining the analytical rigor that makes the Cosmos-Hub the preferred platform for ITS-based microbiome studies.

Databases and Outputs

  • UNITE reference taxonomy for fungal ITS ensures consistent naming and compatibility with the broader fungal informatics community.

  • Downloadable taxonomy tables (including read count, OTU sequence, relative abundance) and read/quality metrics enable audit‑ready reporting and external analytics when needed.

  • One‑click Comparative Analysis supports alpha/beta diversity, PCA/ordination, heatmaps, stacked bars, and differential abundance (LEfSe) for study‑level insights across locations, materials, or timepoints.

Parallels to the Cosmos-Hub 16S experience

The ITS analysis page mirrors 16S navigation and visualization options, so researchers can move between bacterial and fungal profiles with the same upload pathways (desktop, Illumina BaseSpace, NCBI SRA), grouping tools, color/order controls, and export behaviors without re‑learning the interface. This consistency is especially useful for mixed‑kingdom programs and lab networks supporting many teams, instruments, and sites under a unified SOP.

Learn more
Why Choose Cosmos-Hub for Short-Read Amplicon Analysis?
 
The ITS analysis pipeline is a streamlined, cloud-based tool that accepts raw sequencing data to generate taxonomic tables for single-samples and mixed-cohorts. This pipeline seamlesslessly integrates into the other microbiome bioinformatic pipelines within the platform, which is especially useful for mixed‑kingdom programs and lab networks supporting many teams, instruments, and sites under a unified SOP.
 
Finally, the Cosmos-Hub Support team provides personalized guidance for primer selection, quality parameter optimization, and technical troubleshooting to ensure successful project completion.
 
 

Applications and sample types
Human skin and scalp microbiome analysis.

Human skin and scalp microbiome analysis
Soil and rhizosphere microbiomes tracking beneficial and pathogenic fungi across seasons, cultivars, and agronomic inputs.

Soil and rhizosphere microbiomes tracking beneficial and pathogenic fungi across seasons, cultivars, and agronomic inputs
Food, fermentation, and spoilage investigations where rapid fungal ID supports root‐cause analysis and corrective actions.

Food, fermentation, and spoilage investigations where rapid fungal ID supports root‑cause analysis and corrective actions
Built environments and wastewater monitoring programs requiring scalable, routine fungal surveillance and trending.

Built environments and wastewater monitoring programs requiring scalable, routine fungal surveillance and trending
Clinical and public health investigations where mycobiome baselines, dysbiosis patterns, or environmental exposure signals are required at cohort scale.

Clinical and public health investigations where mycobiome baselines, dysbiosis patterns, or environmental exposure signals are required at cohort scale
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Industrial QC analysis in yeast production for nutritional applications (bread etc)

Ready to unlock the microbiome?

 

Complete your fungal amplicon study effortlessly with a single, integrated platform containing taxonomic processing, data storage, and advanced statistics toolbox for publication-ready results.

Need high-quality sequencing services to create your data?

ITS library preparation and short‑read sequencing are available through Cmbio in the US and EU, with end‑to‑end logistics and direct delivery into Cosmos‑Hub to streamline turnaround and minimize handoffs. 

Contact Us

Want to run a few samples and test the pipelines?

 Contact us below and a member of the team will reach out to arrange a call to discuss your project.