Microbiome profiling services

Our microbiome sequencing approach utilises the 16S rRNA gene and internal transcribed spacer (ITS) regions as genetic markers, focusing on the hypervariable V3 and V4 regions for bacteria and ITS regions for fungi. This method, coupled with polymerase chain reaction (PCR) amplification and next-generation sequencing (NGS) using 2x300bp paired-end chemistry. Full length 16S rRNA or ITS can be done using Nanopore technology. This allows us to accurately identify and classify diverse microbial populations down to the genus or species level.

Each sample undergoes rigorous analysis, generating 0.1-0.2 million reads per sample for detailed comparative studies. By employing multiplexing approaches, we can analyse several amplicons from multiple samples in parallel, reducing the overall cost per sample.

Our end-to-end solutions

At Eurofins Genomics, we provide a comprehensive end-to-end solution for your 16S rRNA and fungal microbiome profiling needs along with bioinformatics analysis heling your microbiome study.

Sample requirements

• Submit 1-3 µg of RNA-free genomic DNA (NGS grade) with high molecular weight, NanoDrop A260/280 ratio >1.8, A260/230 = 2.0-2.2, and a concentration of ~50 ng/µl.
• Alternatively, soil, plant/human microbiome, water, stool or sludge samples can be shipped in cool packs to our facility.

Sample quality control (QC)

• Isolation of RNA-free, NGS-grade genomic DNA (gDNA) using validated DNA extraction kits.
• Quality assessment using agarose gel electrophoresis and NanoDrop spectrophotometry, with quantification performed using the Qubit 3.0 Fluorometer.

Illumina library preparation 

• Amplicon libraries prepared using 16S rDNA gene-specific primers and the Nextera XT Index Kit.
• Library validation using the Agilent 4200 TapeStation system.

Nanopore library preparation

• Amplicons generated using 16S, ITS, or 18S targeted primer sets and processed using the Oxford Nanopore Rapid DNA Sequencing Kit, 16S Barcoding Kit, or Native Barcoding Kit.
• Library quantification using the Qubit Fluorometer.

Sequencing

• Sequencing performed on the Illumina MiSeq platform using 2 × 300 bp paired-end chemistry.
• Sequencing also available on the Oxford Nanopore PromethION P2 Solo platform.

Deliverables

• Raw sequencing data provided as compressed FASTQ files for each sample.
• Comprehensive reports and datasets delivered via secure download link.
• Optional bioinformatics analysis services available for in-depth data interpretation.

Quick turnaround time

We understand the importance of timely results. Our standard turnaround time is 5-7 weeks after sample arrival and receipt of all necessary information, contingent on data size, project scope, technology selected, sample number, and complexity. This timeline assumes no biological or technical difficulties during processing.