INVIEW Microbiome High Specificity

Overview
Specifications

High throughput microbial classification down to the species-level

INVIEW Microbiome High Specificity applies an amplicon-based targeted resequencing method based on PacBio’s SMRT sequencing technology.

INVIEW Microbiome High Specificity is a next-generation sequencing service that offers characterization of microbial communities down to the species level based on full-length 16S rRNA gene profiling. The product combines library preparation, sequencing with PacBio long read technology and reliable BioIT analysis for better separation of species in microbiomes that are difficult to resolve.

Specific applications of INVIEW Microbiome High Specificity include

Identification of disease-causative agents and pathogens
Species-level chacterisation of bacteria that are unculturable or biochemically unidentifiable
Routine detection of medically important bacteria
Reference identification for unusual strains

Highlights of INVIEW Microbiome High Specificity

Excellent taxonomical resolution due to high throughput full-length 16S amplicon sequencing
Classification of microbial communities down to species level

INVIEW Microbiome High Specificity is a sample-to-data package that offers

Processing of up to 10 samples per run in parallel
Amplification of whole 16S rDNA by PCR
Use of validated primers (V1-V8)
Purification of PCR products
Barcoding of PCR products, pooling and standard adapter ligation
Library purification and QC
Sequencing using PacBio technology
Expert BioIT analysis for a comprehensive Data Analysis Report
Available under ISO17025 accreditation

Accepted starting material for INVIEW Microbiome High Specificity

>10 ng DNA with at least 10e3 bacterial/fungal genomes per sample and PCR amplification
DNA isolation available as additional service for sand, soil, sludge, stool, urine culture, blood culture, milk, yoghurt (<3.5% fat), buccal swap, skin swap and tracheal fluid

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 strating material or material classified as S2.

Specifications

Sequencing Technology

PacBio SMRT-Sequencing

Bioinformatics analysis

Quality filtering of sequencing reads
Removal of chimeras
Ribosome Database Project-based OTU assignment (BLAST)
Determination Shannon and Simpson diversity indices
Combined OTU analysis
Filtering and consolidation

Deliverables

Raw data (fastq, bas.h5, metadata.xml)
Sorted "Reads of Insert" (fastq)
Non-chimeric and quality filtered sequences (fasta)
Sequences w/ and w/o OTU assignment (fasta)
Read statistics (tsv)
OTU tables (tsv) and OTU distribution plots (png)
Shannon diversity index tables (tsv)
Simpson diversity index tables (tsv)
Diversity index plots (png)
Comprehensive Data Analysis Report (pdf)

Sequencing data delivered

All raw sequencing data (.fastq)
Tables listing all genera present in the analysed sample and the respective read counts
Diversity indices
Data delivery in common file types (.tsv, .txt), which can be handle with standard software for further analysis or visualisation
Visualisation of relative species abundance

Delivery time