Metabarcoding

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.

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. 

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.

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

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)
• Bioinformatics analysis of the sequencing data (standard bioinformatics pipeline includes demultiplexing and quality filtering, read clustering in OTUs/ASVs, taxon assignment, read count per taxon, and the generation of rarefaction curves).
• Beta-diversity across samples and estimation of
• Possibility to build custom databases for refined analyses.
• Curated tables of taxonomic annotation and relative abundance accompanied by barplot graphs, heatmaps, and Krona charts for each sample in PNG/JPEG or PDF format
• Corrected list of unique sequences (ASV) found in the sample and their absolute counts (FASTA)
• Boxplot or Violin plot: To compare alpha diversity among groups of samples
• Principal Coordinates Analysis (PCoA) in PDF format
• Heatmap: Similarity or dissimilarity among samples
• Data delivery -  a detailed scientific report including tables and graphs that summarize variation within and among different samples, raw data and the summary of the methods applied are delivered through our server

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.