Accurate Detection of Microbes

Recent research suggests a close relationship between the composition of the human microbiome and the occurrence of a variety of diseases, as well as the response towards pharmaceutical drugs. According to recent findings, this has been particularly shown for the gut microbiome, but it can also be extended to other body sites (e.g., skin, oral, nasal). Furthermore, microorganisms are involved in many biochemical reactions in the environment and thus represent important constituents of environmental ecosystems. Understanding microbial functions in specific microbiomes or host-microbe relationships, especially for microbes, which are difficult to cultivate, offers great potential for new therapeutic discoveries.

Mapping-based metagenomic profiling allows the accurate detection of microbes (bacteria, archaea, fungi, protozoa, viruses, etc.) down to the species level. This has been validated using microbial community standards. During Shotgun analysis, DNA fragments are sequenced. Accordingly, functional genes coding for enzymes related to specific metabolic pathways can also be analyzed.

Shotgun metagenomic sequencing is the best choice when microbiomes need to be thoroughly characterized, including accurate identification of microbial species and their functional repertoire.

Applications of Shotgun Metagenomic Sequencing are diverse and include:

• Disease monitoring
• Microbial biomarker detection
• Drug development
• Characterization of environmental microbiomes
• Discovery of new microbial species (de novo assembly)

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:

• 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)

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