Microbiome Analysis

Highly Accurate Microbiome Studies

About Microbiome Analysis

Approximately half of all cells within the human body are microbial cells, and most of these microbes are part of the gut microbiome. Recent research suggests a close relationship between the composition of the gut microbiome and the occurrence of a variety of diseases, as well as the response towards pharmaceutical drugs. While many microbes cannot be detected by routine culture-dependent techniques, next-generation sequencing allows the detection of all microbes present in a microbiome sample and their functional properties.

Applications of microbiome analysis are diverse and include:

  • disease monitoring
  • microbial biomarker detection
  • drug development
  • characterization of environmental microbiomes

CeGaT’s microbiome analysis products accurately detect the composition of microbial communities. This has been confirmed using microbial community standards. To achieve highest accuracy and data quality we suggest combining our specifically designed stool sampling kit and our well-established DNA isolation with our sophisticated sequencing service.

Our product portfolio comprises two types of analyses:

  • Metagenomic Profiling: Identification of all microbes down to the species level as well as their functional repertoire (shotgun analysis).
  • Bacterial Profiling: Identification of Bacteria and Archaea down to the genus level (16S analysis).

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We are happy to discuss sequencing options and find a solution specifically tailored to your clinical study or research project.

You help us by specifying sample information including starting material, number of samples, preferred library prep option, preferred sequencing depth and required bioinformatics.

Turnaround time

The turnaround time (TAT) highly depends on the batch size, the starting material, and the requested bioinformatics level.

Delivery

Your sequencing data will be available for download from one of our servers (FTAPI or SFTP). Upon request, as well as for large sample batches, data can also be delivered via external hard drive or uploaded to your own server.

Storage

The original samples and, if applicable, the isolated nucleic acids will be stored at CeGaT for a period of 3 months after data delivery.

Data will be irrevocably deleted after 5 months.

Bioinformatics

Raw sequencing data are automatically processed in order to facilitate immediate genetic evaluation.

Included in delivery are demultiplexed, and adapter trimmed FASTQ files.

Further options for bioinformatic analyses are available:

Metagenomic Profiling bioinformatic analysis:

  • Mapping against microbiome database (DAA format) *
  • Taxonomic and functional classification using MEGAN6 (MEGAN format) *
  • Generation of taxonomic abundance tables including sequence counts and relative abundances down to the species level (XLSX and BIOM format)
  • Generation of microbial function tables including sequence counts and relative abundances of functional genes classified using the KEGG database (XLSX format)
  • Generation of barplots showing relative abundances down to the species level (PNG format)
  • Generation of a detailed project report (PDF format)

Bacterial Profiling bioinformatic analysis:

  • Mapping against 16S database (RMA format) *
  • Taxonomic classification using MEGAN6 (MEGAN format) *
  • Generation of taxonomic tables including sequence counts and relative abundances down to the genus level (XLS and BIOM format)
  • Generation of barplots showing relative abundances down to the genus level (PNG format)
  • Generation of a detailed project report (PDF format)

* These files can be interactively explored and further analyzed using MEGAN6, a user-friendly and open source software for analyzing microbiome data.

Technical Information

At CeGaT, paired-end sequencing is performed on state-of-the-art Illumina Sequencing Systems.

  • Metagenomic Profiling: 2 x 100 bp on NovaSeq 6000
  • Bacterial Profiling: 2 x 250 bp on MiSeq

If customers require sequencing parameters other than those presented in our product portfolio, please let us know! We can provide further solutions.

We are pleased to offer you our specifically designed stool sampling kit which provides convenient and unbiased self-collection of fecal material combined with our DNA isolation service. Please also reach out to us to discuss sampling and DNA extraction of various starting material.

Explore our Microbiome Analysis product portfolio

Metagenomic Profiling

Target gene
Whole genome (shotgun analysis)

Detectable microbes
Bacteria, Archaea, Fungi, Protozoa, Viruses

Lowest detectable taxonomic level
Species

Detection of microbial functions
Yes

Sequencing technology
Illumina

Read length
2 × 100 bp

Output
10 M clusters

Data format
FASTQ

Potential application
Identification of specific microbial species and functions associated with the response towards immune checkpoint inhibitors

Bacterial Profiling

Target gene
16S rRNA gene (V3-V4)

Detectable microbes
Bacteria, Archaea

Lowest detectable taxonomic level
Genus

Detection of microbial functions
No

Sequencing technology
Illumina

Read length
2 × 250 bp

Output
25,000 clusters

Data format
FASTQ

Potential application
Detection of general changes in bacterial community composition and diversity during antibiotic intake

We recommend using our specifically designed stool sampling kit for convenient and unbiased self-collection of fecal material. All products can be combined with our DNA isolation service and tailored data analysis.

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Further
Reading