Aquaculture Microbiome Testing Analysis

Optimize Aquatic Health with Rapid Microbial Insights

Unlock precise aquaculture microbiome testing insights to safeguard aquaculture systems and aquatic ecosystems using Cosmos-Hub, a dedicated microbiome analysis platform designed for research labs.

From pond sediments to fish gut samples, Cosmos-Hub equips aquaculture scientists with a powerful, no-code solution to process your metagenomics and metabolomics  data in just hours..

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Cosmos-Hub Aquaculture Microbiome Analysis Platform

The Cosmos-Hub platform is built to streamline microbiome research in aquaculture, offering laboratory teams an end-to-end solution for managing complex microbial data. By removing coding barriers and automating quality checks, the platform frees researchers to focus on discovery rather than analysis overhead.

Cosmos-Hub integrates strain-level taxonomic resolution, antimicrobial resistance tracking, and functional pathway predictions, empowering researchers to detect both fish pathogens, beneficial microbes, and those influencing intestinal microbiome and respiratory microbiome marine mammals before they impact production.

Key benefits for aquaculture research labs include:

  • Simplified processing of diverse sample types: water, sediment, host-associated, fish gut microbiome, feed-related microbiota

  • Rapid, reproducible results within hours of data upload, ideal for time-sensitive investigations

  • Scalable workflows that support both small pilot experiments and enterprise-level aquaculture monitoring  programs

  • Comparative dashboards for tracking microbial changes across species, locations, treatments, or seasons

  • Integrated detection of pathogens, probiotics, antimicrobial resistance genes, and virulence factors

  • Compatibility with both short- and long-read sequencing data, ensuring versatility for different projects

With Cosmos-Hub, aquaculture researchers can generate high-resolution microbial profiles that inform water quality management, disease prevention strategies, feed optimization, and probiotic validation.

The platform transforms complex sequencing information into data-driven decisions on the microbial composition of aquatic organisms that strengthen aquatic research outcomes.

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Why Aquaculture Microbiome Analysis Matters

The success of aquaculture operations hinges on microbial balance in water, sediment, and host organisms. Disruptions can lead to disease outbreaks, reduced yield, and economic losses. Microbiome analysis empowers aquaculture professionals to take a proactive approach, identifying imbalances before they become visible problems.
As the world’s fastest-growing protein sector, aquaculture demands fast, reliable insights into microbial communities impacting fish, shellfish, and the surrounding environment.

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Example Sample Types for Aquaculture Microbiome Studies 

  • Tank water and biofilm samples
  • Sediment from pond, marine, or RAS systems
  • Skin, gill, or gut microbiota of fish and shellfish
  • Feed-associated microbial content 
  • Probiotic or antimicrobial treatment impact studies
  • Disease outbreak diagnostics and routine surveillance
A drone shot of fish nets

How Cosmos-Hub supports Aquaculture Health Management

 

Fast, no-code processing of 16S or metagenomic sequencing data


 

Detects pathogens and beneficial microbes with strain-level resolution

 

Compares microbial profiles across sites, life stages, or treatment periods

 

 

Tracks AMR genes and virulence factors impacting fish health

Relevant Pipelines

All of Your Microbiome Studies. One Easy Platform.

Microbiome Profiling

Microbiome Profiling 

 

Industry-leading bioinformatics pipelines thhat let you analyze different types of sequencing data for multiple applications.

 

 
Popular Features
Import fastq's directly via UI or CLI 
Analysis of 16S, ITS & Shotgun data
Short & long-read compatibility 

 

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Statistics Toolbox

Statistical Analysis 

 

Comparative analysis workflows that leverage your study metadata to create virtual cohorts and analyze them with the latest statistical tools and visualizations.

 
Popular Features
Interactive charts & visualizations 
Univariate statistics like LeFSe, Wlicoxon Rank-Sum & PERMANOVA
Multivariate statistics like MaAsLin2 & MaAsLin3
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Integrated Data Management

Study Management 

 

A study dashboards that provides integrated storage of raw data, profiling data, and study metadata for secure and easy access. 

 

 
Popular Features
Easy-to-navigate dashboard
Upload and edit metadata directly
Single-sample reporting & visualization 

 

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Cosmos-Hub Atlas

Cosmos-Hub Atlas

 

A curated database of over 40,000 microbiome samples, with metadata, that users can compare their samples against. 

 

 
Popular Features
Standardized profilings
Curated metadata
Results shared in 2-3 days 
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AI Co-Pilot

AI Co-Pilot 

 

Cosmos-Hub's AI Co-Pilot, RITAi, supports the interpretation of results generated in the software by allowing researchers to make queries like when using their favorite GPT.

 
Popular Features
Publication insights with complete references  
Species Wizard
Support on how to use the Hub 
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Metabolomics (Coming Soon)

Metabolomics Module (Coming Soon) 

Cosmos-Hub is going multi-omics! In 2025, users will be able to import metabolomics data from any provider and conduct their analysis.

 

 
Popular Features
Support for targeted and untargeted metabolomics 
Additional statistics and visualizations
Multi-Omics Support

 

coming soon

Ready to Dive Into Healthier Aquatic Ecosystems?

 Unlock the power of high-resolution microbiome analysis with Cosmos-Hub.

Aquaculture Microbiome Testing FAQs