Shotgun Metagenome Sequencing
Analyze the diversity of microbial communities and elucidate the role of constituent species
Service summary
- DNA extractions with Qiagen kits on QIAsymphony*
- Library preparation and sample indexing with Illumina DNA Prep Kit
- Fully automated library preparation on Hamilton NGS STAR
- QC check with Qubit Flex Fluorometer and Agilent TapeStation
- Sequencing with Illumina platforms, 20 million reads per sample (R1 + R2 = 40 million total)
- Species-specific or mixed-species samples accepted
- Turnaround time approx. 2 to 3 weeks**
- (*) For unextracted samples.(**) Turnover times are not guaranteed, may change according to your project.
Sample requirements
Accepted Sample Type
Recommended Amount
Shipment Method
Stool/Fecal
≥ 200 mg
*
Saliva
≥ 200 mg
*
Soil/Environmental
≥ 500 mg
*
Buccal Swab
Follow the kit manufacturer's instructions
*
Special notes:
- Compatible with a broad range of species: human, mammalian, plant, microbial, viral, etc.
- For other types of samples, and shipment conditions please discuss the details with our customer service.
How to evaluate the sample quality
We check your samples upon arrival; however, we still require our users to perform their own QC steps before the shipment of samples.
- Use fluorometric measurements (e.g., Qubit, Quant-iT) instead of absorbance measurements (Nanodrop, spectrophotometer)
- DNA should be in EB buffer (not EDTA or water), with high molecular weight.
- Ideally: A260/280 = 1.8–2.0, A260/230 = 2.0–2.2.
- If your samples do not meet these thresholds, please contact us before shipment.
Concentration
Fluorometric measurements (Qubit, Quant-it). At least 100 ng RNA recommend input. The protocol supports a broad range of RNA inputs, from 1 ng to 1000 ng. The protocol is optimized for 10–100ng RNA input from low-quality RNA (RIN≥2) samples or FFPE (DV200>55%) samples. Library performance can vary with lower input amounts and lesser quality RNA. Do not use absorbance measurements (Nanodrop, spectrophotometer).
RNA quality
Capillary electrophoresis (Fragment Analyzer, Bioanalyzer, TapeStation), RIN ≥7.0. Do not use gel electrophoresis. For FFPE samples we recommend using capillary electrophoresis to determine the DV200 value.
If you are not able to carry out these steps, or your samples are below the required thresholds, please get in touch.
What we do with your samples
Once your samples arrive at Phenome Omics, we perform a visual check to ensure the samples meet our requirements.
If samples fail the first quality control, we will contact you to discuss possible options. If you choose to proceed with suboptimal samples, it will be at your own risk. We will only make one attempt at library preparation, and charges for this step will still apply even if the prep is failed.
If samples pass visual control, we will inform you and queue them for library preparation.
Library preparation
Illumina DNA Prep enables a fast, robust, and flexible workflow for preparing sequencing-ready libraries from a wide range of DNA inputs.
Advantages:
- Works with various sample types (human, environmental, microbial)
- Normalized libraries ready for sequencing
- Consistent coverage across genomes, including GC-rich regions
- Supports detection of low-abundance species in complex microbial communities
Library QC and Sequencing
Library concentration and size is evaluated using Qubit and Agilent TapeStation.
QC-passed libraries are normalized, pooled, and queued for sequencing.
Sequencing performed on an Illumina platform, generating 20 million paired-end reads per sample (2 × 150 bp).
Expected Results
Shotgun metagenome sequencing provides comprehensive, unbiased profiling of microbial communities, including bacteria, archaea, viruses, and fungi. With deep sequencing and optimized library preparation, even rare species can be detected, and GC-rich organisms are well represented in the results.
Science & Innovation
Awards
Omics Library
Language
English
Contact Us
Shotgun Metagenome Sequencing
Analyze the diversity of microbial communities and elucidate the role of constituent species
Service summary
- DNA extractions with Qiagen kits on QIAsymphony*
- Library preparation and sample indexing with Illumina DNA Prep Kit
- Fully automated library preparation on Hamilton NGS STAR
- QC check with Qubit Flex Fluorometer and Agilent TapeStation
- Sequencing with Illumina platforms, 20 million reads per sample (R1 + R2 = 40 million total)
- Species-specific or mixed-species samples accepted
- Turnaround time approx. 2 to 3 weeks**
- (*) For unextracted samples.(**) Turnover times are not guaranteed, may change according to your project.
Sample requirements
Accepted Sample Type
Recommended Amount
Shipment Method
Stool/Fecal
≥ 200 mg
*
Saliva
≥ 200 mg
*
Soil/Environmental
≥ 500 mg
*
Buccal Swab
Follow the kit manufacturer's instructions
*
Special notes:
- Compatible with a broad range of species: human, mammalian, plant, microbial, viral, etc.
- For other types of samples, and shipment conditions please discuss the details with our customer service.
How to evaluate the sample quality
We check your samples upon arrival; however, we still require our users to perform their own QC steps before the shipment of samples.
- Use fluorometric measurements (e.g., Qubit, Quant-iT) instead of absorbance measurements (Nanodrop, spectrophotometer)
- DNA should be in EB buffer (not EDTA or water), with high molecular weight.
- Ideally: A260/280 = 1.8–2.0, A260/230 = 2.0–2.2.
- If your samples do not meet these thresholds, please contact us before shipment.
Concentration
Fluorometric measurements (Qubit, Quant-it). At least 100 ng RNA recommend input. The protocol supports a broad range of RNA inputs, from 1 ng to 1000 ng. The protocol is optimized for 10–100ng RNA input from low-quality RNA (RIN≥2) samples or FFPE (DV200>55%) samples. Library performance can vary with lower input amounts and lesser quality RNA. Do not use absorbance measurements (Nanodrop, spectrophotometer).
RNA quality
Capillary electrophoresis (Fragment Analyzer, Bioanalyzer, TapeStation), RIN ≥7.0. Do not use gel electrophoresis. For FFPE samples we recommend using capillary electrophoresis to determine the DV200 value.
If you are not able to carry out these steps, or your samples are below the required thresholds, please get in touch.
What we do with your samples
Once your samples arrive at Phenome Omics, we perform a visual check to ensure the samples meet our requirements.
If samples fail the first quality control, we will contact you to discuss possible options. If you choose to proceed with suboptimal samples, it will be at your own risk. We will only make one attempt at library preparation, and charges for this step will still apply even if the prep is failed.
If samples pass visual control, we will inform you and queue them for library preparation.
Library preparation
Illumina DNA Prep enables a fast, robust, and flexible workflow for preparing sequencing-ready libraries from a wide range of DNA inputs.
Advantages:
- Works with various sample types (human, environmental, microbial)
- Normalized libraries ready for sequencing
- Consistent coverage across genomes, including GC-rich regions
- Supports detection of low-abundance species in complex microbial communities
Library QC and Sequencing
Library concentration and size is evaluated using Qubit and Agilent TapeStation.
QC-passed libraries are normalized, pooled, and queued for sequencing.
Sequencing performed on an Illumina platform, generating 20 million paired-end reads per sample (2 × 150 bp).
Expected Results
Shotgun metagenome sequencing provides comprehensive, unbiased profiling of microbial communities, including bacteria, archaea, viruses, and fungi. With deep sequencing and optimized library preparation, even rare species can be detected, and GC-rich organisms are well represented in the results.
Science & Innovation
Awards
Omics Library
Language
English
Contact Us
Phenome Omics © 2026
Shotgun Metagenome Sequencing
Analyze the diversity of microbial communities and elucidate the role of constituent species
Service summary
- DNA extractions with Qiagen kits on QIAsymphony*
- Library preparation and sample indexing with Illumina DNA Prep Kit
- Fully automated library preparation on Hamilton NGS STAR
- QC check with Qubit Flex Fluorometer and Agilent TapeStation
- Sequencing with Illumina platforms, 20 million reads per sample (R1 + R2 = 40 million total)
- Species-specific or mixed-species samples accepted
- Turnaround time approx. 2 to 3 weeks**
- (*) For unextracted samples.(**) Turnover times are not guaranteed, may change according to your project.
Sample requirements
Accepted Sample Type
Recommended Amount
Shipment Method
Stool/Fecal
≥ 200 mg
*
Saliva
≥ 200 mg
*
Soil/Environmental
≥ 500 mg
*
Buccal Swab
Follow the kit manufacturer's instructions
*
Special notes:
- Compatible with a broad range of species: human, mammalian, plant, microbial, viral, etc.
- For other types of samples, and shipment conditions please discuss the details with our customer service.
How to evaluate the sample quality
We check your samples upon arrival; however, we still require our users to perform their own QC steps before the shipment of samples.
- Use fluorometric measurements (e.g., Qubit, Quant-iT) instead of absorbance measurements (Nanodrop, spectrophotometer)
- DNA should be in EB buffer (not EDTA or water), with high molecular weight.
- Ideally: A260/280 = 1.8–2.0, A260/230 = 2.0–2.2.
- If your samples do not meet these thresholds, please contact us before shipment.
Concentration
Fluorometric measurements (Qubit, Quant-it). At least 100 ng RNA recommend input. The protocol supports a broad range of RNA inputs, from 1 ng to 1000 ng. The protocol is optimized for 10–100ng RNA input from low-quality RNA (RIN≥2) samples or FFPE (DV200>55%) samples. Library performance can vary with lower input amounts and lesser quality RNA. Do not use absorbance measurements (Nanodrop, spectrophotometer).
RNA quality
Capillary electrophoresis (Fragment Analyzer, Bioanalyzer, TapeStation), RIN ≥7.0. Do not use gel electrophoresis. For FFPE samples we recommend using capillary electrophoresis to determine the DV200 value.
If you are not able to carry out these steps, or your samples are below the required thresholds, please get in touch.
What we do with your samples
Once your samples arrive at Phenome Omics, we perform a visual check to ensure the samples meet our requirements.
If samples fail the first quality control, we will contact you to discuss possible options. If you choose to proceed with suboptimal samples, it will be at your own risk. We will only make one attempt at library preparation, and charges for this step will still apply even if the prep is failed.
If samples pass visual control, we will inform you and queue them for library preparation.
Library preparation
Illumina DNA Prep enables a fast, robust, and flexible workflow for preparing sequencing-ready libraries from a wide range of DNA inputs.
Advantages:
- Works with various sample types (human, environmental, microbial)
- Normalized libraries ready for sequencing
- Consistent coverage across genomes, including GC-rich regions
- Supports detection of low-abundance species in complex microbial communities
Library QC and Sequencing
Library concentration and size is evaluated using Qubit and Agilent TapeStation.
QC-passed libraries are normalized, pooled, and queued for sequencing.
Sequencing performed on an Illumina platform, generating 20 million paired-end reads per sample (2 × 150 bp).
Expected Results
Shotgun metagenome sequencing provides comprehensive, unbiased profiling of microbial communities, including bacteria, archaea, viruses, and fungi. With deep sequencing and optimized library preparation, even rare species can be detected, and GC-rich organisms are well represented in the results.
Science & Innovation
Awards
Omics Library
Language
English
Contact Us
Phenome Omics © 2026