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Oligonucleotide Synthesis

Gene Synthesis & Molecular Biology

Sanger Sequencing

Next Generation Sequencing

Genotyping & Gene Expression

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Deep insights into the vast biodiversity and function of microbiota

 

 

INVIEW Metagenome is a complete next-generation sequencing (NGS) solution for metagenomics analysis and taxonomic profiling of microbial communities in their natural environment..

Thanks to its independence from target amplification, the product is ideal for thorough characterisation of low complexity metagenomes or for a broad overview of genera in complex communities. The service provides a valuable approach for studying unculturable microorganisms that were previously impossible to analyse.

 

 

 

 

 

 

 

Applications

 

  • Profiling of biological entities, such as viruses, which cannot be differentiated by 16S rRNA sequencing alone
  • Analysis of relative abundance of microbial species in natural habitat   
  • Observation of changes in relative abundance of microorganisms under varying conditions or stresses
  • Obtain relative abundance levels of microbial species that are difficult or impossible to grow in a laboratory setting
  • Quantify microorganisms through assessment of all genomic information in a community rather than of common markers like 16S rRNA only
  • Observe changes in the composition of a microbial community during varying environmental conditions
  • Profile the functional characteristics of a particular microbiome
  • Identify novel pathogens
  • Discover novel biomarkers and bioactive compounds

Highlights of the INVIEW Metagenome

 

  • Taxonomic profiling of bacteria, archaea and viruses with reduced bias due to independence from taxonomic gene markers such as 16S rRNA
  • Simultaneous next-generation sequencing of the genomes of all microorganisms in a given sample
  • Next-generation sequencing of whole genomes, rather than only specific loci like 16S rRNA

 

 

 

 

 

 

 

Product Specifications & Ordering

 

Starting material

Accepted starting material 

 

  • 100 ng gDNA (up to 100µl / concentration >1 ng/µl) from human sample material

 

Please note, that only S1-classified material is accepted for DNA isolation ordered online. More information about current classification of biological material can be found here (TRBA 466). Please contact us for further information on DNA isolation from other starting material such as environmental or industrial samples or material classified as S2.

 

Sequencing specifications

2 x 150 bp paired-end sequencing mode on Illumina

 

Recommended sequencing depth for selected samples

 

 

Bioinformatics analysis

Option 1:

  • Sequence quality assessment
  • Removal of poor quality bases, adapters, primers and others
  • Taxonomic profiling using NCBI database of bacterial, archaeal fungal, protozoan and viral genomes
  • Removal of host sequences (only applicable for human, mouse or rat samples)

 

Deliverables:

  • FastQ Files (sequences and quality scores)
  • Phylum, genus and species level OTU abundance tables (tsv) and graphs (png)
  • Interactive species level OTU abundance plot (html)
  • Species diversity indices (tsv) and plots (png)
  • Rarefaction curves (png)

 

 

Option 2:

  • Thorough assessment of sequence quality prior to metagenome annotation
  • Removal of poor quality bases, adapters and primers
  • Removal of host sequences
  • Taxonomic profiling using established pre-built MiniKrakenDB constructed from complete bacterial, archaeal fungal, protozoan and viral genomes in RefSeq
  • Screening for virulence factors and antibiotic resistance genes using MvirDB
  • KEGG functional profiling of microbial communities using the integrated gene catalogue of the human gut microbiome (IGC)

 

Deliverables:

Taxonomic profiling

  • FastQ Files (sequences and quality scores)
  • Phylum, genus and species level OTU abundance tables (.tsv) and graphs (.png)
  • Interactive species level OTU abundance plot (html)
  • Species diversity indices (.tsv) and plots (.png)
  • Rarefaction curves (.png)

Functional profiling

  • KEGG annotation tables (.tsv) and graphs (.png)
  • Correlation plots (.png)

Resistance profiling

  • Antibiotic resistance and virulence tables (.tsv) and graphs (.png)
  • Correlation plots (.png)

 

Delivery time

  • 12 days for up to 192 samples
  • 17 days for up to 500 samples

 

 

Literature

 

 

 

 

 

 

 

 

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Quality is important for us

Our products and services are produced and performed under strict quality management and quality assurance systems.

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