---
title: "Metabarcoding"
search_description: "IGATech’s metabarcoding services provide accurate identification and analysis of microbial and environmental biodiversity, supporting ecological research, conservation, and environmental monitoring. Uncover community dynamics with our advanced sequencing."
published: 2025-02-10 13:11:18.491284+00:00
locale: "en"
---

# Metabarcoding

[Contact us](https://igatechnology.com/igatech/contacts/#contact-form)

## Technologies

![AVITI Element Biosciences](/media/images/0.width-500.png)

### AVITI Element Biosciences

The AVITI System by Element Biosciences is a benchtop sequencer designed for high performance, cost efficiency, and flexibility. It features dual independent flow cells for parallel or independent operation, enabling flexibility in throughput from low to full. The system utilizes Avidity Sequencing™ technology, ensuring over 90% of reads exceed Q30 quality, with minimal errors, low duplication rates, and reduced AT/GC bias. It supports easy data conversion to FASTQ files, offers compatibility with numerous assays, and provides cost-effective sequencing. This is our ideal companion for dedicated and fast-turnaround run set-up. For more detailed information, you can visit their website directly at [https://www.elementbiosciences.com/products/aviti](https://www.elementbiosciences.com/products/aviti).

![NovaSeq X Plus](/media/images/Illumina_NovaSeq_XPlus_Left_561x375.width-500.png)

### NovaSeq X Plus

The NovaSeq X Plus is a powerful and scalable ultra-high-throughput sequencing system that supports the broadest range of applications and study sizes. Unrivaled data quality using Illumina's proven SBS chemistry has made the NovaSeq X Plus the instrument of choice for all major genome centers and leading institutions throughout the world. Producing up to 25 billion reads \(7.5 Tbp\) per flowcell, yielding up to 120 human genomes in about 2 days at full capacity.

![Nucleic acids extraction](/media/images/DNA_extraction.width-500.png)

### Nucleic acids extraction

DNA and RNA extraction is routinely performed at IGATech, providing support to our customers directly from raw material. Relying on automated systems and consolidated protocols we can help you in accelerating the path to analyzed data. We also work with non standard substrates, such as [plants](https://igatechnology.com/genomics-research-services/?area=plant) and [food](https://igatechnology.com/agrigenomics-solutions/). Our expertise in the isolation of high molecular weigth DNA for long-molecule sequencing applications will also be a specialized complement for [*de novo*](http://igatechnology.com/genomics-research-services/?area=plant#denovo) applications*.* Pleas [enquire](https://igatechnology.com/igatech/contacts/) to obtain further details*.*

![Metagenomics](/media/images/Metagenomics.width-500.png)

### Metagenomics

The area of research which investigates the taxonomical composition and activity of complex biological substrates. While traditional sequencing of cultured microorganisms could not provide a picture of the diversity of natural substrates, shotgun sequencing has opened the possibility of an unbiased fingerprinting and metabolic activity profiling of diverse communities, ranging from soil samples to the human intestinal flora. Several techniques provide scalable solutions. See [metagenomics](https://igatechnology.com/genomics-research-services/plantanimal/metagenomics/) - [metabarcoding](https://igatechnology.com/genomics-research-services/plantanimal/metabarcoding/).

![Amplicon Sequencing](/media/images/Amplicon_Seq.width-500.png)

### Amplicon Sequencing

With NGS increasing read length and base quality, amplification of one or many loci can be adopted as sequencing template. Whether interested to analyze the diversity of a single amplification product or to discover variability on limited set of interesting genes, Amplicon-Seq is a system that can provide adequate resolution and flexibility while maintaining a very affordable price to cope with large scale experiments/surveys. See [Metabarcoding](https://igatechnology.com/genomics-research-services/plantanimal/metabarcoding/) - [Metagenomics](https://igatechnology.com/genomics-research-services/plantanimal/metagenomics/) - [Clinical Genotyping](https://igatechnology.com/genomics-research-services/clinical-genotyping/)

![Nanopore Sequencing](/media/images/1.width-500.jpg)

### Nanopore Sequencing

Nanopore sequencing is empowering many applications by the ability to analyze DNA, RNA and their modifications with no limitation on sequence length. This is of particular importance when the goal is to resolve hard-to-sequence or repetitive regions that have so far hampered the possibility to decode structural and epigenetic variation. Also, direct RNA sequencing and full-length cDNA sequencing are providing unprecedented insight into the real strucure and abundance of transcripts isoforms.

## Integrative Approach for Biodiversity Assessment

DNA metabarcoding is the targeted sequencing of taxonomically informative genetic markers, which allows **biodiversity** to be **measured rapidly**, **cheaply**, **comprehensively**, **repeatedly** and **verifiably**.

### Short-read sequencing

Designed to resolve complex communities in diverse matrices, ranging from bacteria, archaea, and fungi to plants and animals. We use Illumina and Element Biosciences platforms with read lengths of up to 300 bp, providing high-quality data for your research and utilize a variety of markers to achieve precise identification and analysis. This highly customized service allows for the use of numerous marker genes and different primer sets, tailored to meet your specific research needs. Additionally, we offer the creation of custom databases for comprehensive analysis, ensuring you gain the most accurate and detailed insights into your samples.

### Long-read sequencing

Leveraging full-length gene coverage offers unparalleled advantages, including comprehensive coverage, superior resolution of complex communities, and the ability to capture extensive genetic variation. With duplex basecalling, which involves reading both amplicon strands, we reach sequencing accuracies of ~Q30, achieving quality parallel to short-read sequencing.
 Long-read sequencing is available for commonly used markers like 16S, ITS, and 18S, and can be customized for any marker gene of interest. This flexibility enables detailed microbial community studies and eDNA research, providing deeper insights into community diversity and ecosystem dynamics.

The foremost advantage of metabarcoding approach is the possibility of the simultaneous characterization of whole communities/mixed substrates from unsorted bulk samples \(total DNA\) or potentially degraded DNA from environmental samples \(eDNA\) for which species identification is not practical.

![1S9A6359\_Moment\_Moment](/media/images/1S9A6359_Moment_Moment.width-1500.jpg)

### Efficient and non-lethal way to detect species

- **Ecosystem Monitoring** - look for bioindicator species or determine species present in microfauna such as fish, mammals and birds and record changes in ecosystem composition
- **Marine and Freshwater Biology** - identify microalgae and larvae present in water samples and survey organisms ignored by traditional approaches
- **Feeding Ecology** - identify prey species by analysing DNA from the predator's faeces
- **Food Quality, Provenance and Security** - providing assurance in food authenticity and detection of food fraud by identification of plants, fungi, and animal species present in food products
- **Food Safety** - surveliance of microbes present in the food chain

**From barcoding single individuals to metabarcoding biological communities**

The simple idea of using short DNA fragment as a barcode for identifying species transformed the traditional approach for the study of biodiversity. The use of affordable Next-Gen sequencing technologies has opened a new world of possibilities in DNA-based surveys of biodiversity. This amplicon-seq based approach is most advanced in the field of microbiology, where molecular taxonomy has a long tradition, and analyses regularly use high-throughput sequencing to characterize markers for estimates of taxonomic as well as functional diversity. Amplified ‘barcode’ genes are now also increasingly being used to identify fungi, plants, invertebrates and vertebrates present in DNA mixtures and the method has wide applications in **biodiversity conservation**, **environmental management**, **invasion biology**, the **study of trophic interactions**, **food safety and integrity** **evaluation** and**human health**.

###

Our **sequencing and bioinformatics analysis services** is tailored to your research needs. Whether you require raw demultiplexed sequences or a complete bioinformatics analysis, we deliver high-quality results.

### IGATech workflow

- DNA isolation from appropriately preserved samples \(different DNA isolation protocols are adapted, depending on the starting biological material\)
- Metabarcoding library construction for the target taxonomic group\(s\) -   **bacteria,** **plants**, **animals**, **protists**, and/or**metazoans**
- Sequencing on NovaSeq \(Illumina\) or AVITI \(Element Biosciences\) platforms
- Qualitative metrics of sequencing data \(multiQC\)

### **KEY DELIVERABLES**

- **Raw Reads and Quality Control Reports**: sequencing data in FASTQ format along with detailed quality control reports.
- **Feature Tables**: Obtain read clustering and frequencies of OTUs \(Operational Taxonomic Units\) or ASVs \(Amplicon Sequence Variants\) across all samples.
- **Taxonomic Classification**: Visualize taxonomic abundances through barplot graphs, heatmaps, and Krona charts, available in PNG, JPEG, or PDF formats.
- **Alpha and Beta Diversity Metrics**: Explore diversity metrics with PCoA plots and rarefaction curves.
- **Phylogenetic Tree**: Gain insights into the evolutionary relationships within your samples.
- **Statistical Analyses**: Identify significant differences in microbial communities between different sample groups.
- **Custom Databases**: Build tailored databases for refined analyses.
- **Summary of Methods**: Receive a comprehensive summary of the methods applied in your analysis.

Our team is dedicated to providing accurate and insightful data to support your research endeavors. Contact us today to learn more about how we can assist you!

**Tailored Consultancy**

For every project we want to make sure that the outcome will meet your expectations

We also provide full support on study design to ensure correct sequencing and bioinformatics strategies are used to meet your project goals.  Our expert will consult with you about your specific requirements. Any **metadata**attached to samples will be used to perform statistical analysis in our default analysis pipelines. **Sample DNA extraction** can be part of our workflow.

## Terms & Conditions

- [Privacy Information.pdf](/documents/12/Privacy_Information_rev00.pdf)
- [Human samples clearance.pdf](/documents/13/__Human-samples_clearance.pdf)
- [Shipping and Packaging Guidelines.pdf](/documents/9/SHIPPING_AND_PACKAGING_GUIDELINES.pdf)
- [rev05 Terms and Conditions.pdf](/documents/137/__M12_01_rev05_Terms_and_Conditions.pdf)