Medical Microbiome-Metagenome Unit (M3U)
Scientific & Technical Manager Microbiome-MetagenomePD Dr. Torsten Hain |
Scientific & Technical Manager CulturomicsPD Dr. Can Imirzalioglu |
Description
The M3U technology module for culturomics, microbiome, and metagenomics at the Institute of Medical Microbiology of the Justus-Liebig-University Giessen provides 16S rRNA and metagenome sequencing for an extensive variety of medical and environmental microbiome samples using Illumina for short-read sequencing as well as Oxford Nanopore Technologies (ONT) long-read sequencing devices.
Next-generation (NGS) and third-generation DNA sequencing are revolutionary technologies, which empower the rapid and low-cost generation of high-throughput data for microbiome and metagenome research. As a technology module for culturomics, microbiome, and metagenomics, we provide 16S rRNA sequencing for an extensive variety of medical and environmental microbiome samples using Illumina for short-read sequencing as well as Oxford Nanopore Technologies (ONT) long-read sequencing devices. Our vast experience with cultivation of bacteria, DNA extraction, quality control, preparation, DNA sequencing, and bioinformatics analysis of microbiome and metagenomic samples, gives us the opportunity to offer efficient state-of-the-art workflows tailored to each project and scientific question. Furthermore, we consistently evaluate and implement newly launched sequencing chemistry or software tools to provide the best possible DNA sequencing strategies and results, such as the adaptive sampling approach by ONT. This innovative method, e.g. applied for metagenomics, enables target-specific enrichment or depletion of organisms or gene regions of interest.
Sequencing Devices
- MiSeq System (Illumina, San Diego, USA)
- NextSeq 500 System (Illumina, San Diego, USA)
- MinION Flongle (Oxford Nanopore Technologies, Oxford, UK)
- MinION Mk1b (Oxford Nanopore Technologies, Oxford, UK)
- MinION Mk1c (Oxford Nanopore Technologies, Oxford, UK)
- MinION PromethION 2 Solo (Oxford Nanopore Technologies, Oxford, UK)
Quality Control and Quantification
- Invitrogen Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, USA)
- Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA)
- Agilent Fragment Analyzer (Agilent Technologies, Santa Clara, USA)
- ABI StepOnePlus Real-Time PCR System (Thermo Fisher Scientific, Waltham, USA)
Robotics and Other Instruments
- Microlab STAR (Hamilton Company, Bonaduz, Switzerland)
- Microlab STARLET (Hamilton Company, Bonaduz, Switzerland)
- Automated LabElite Decapper (Hamilton Company, Bonaduz, Switzerland)
- Biometra TAdvanced Thermocycler (Analytik Jena, Jena, Germany)
- FastPrep-24 Lysis System (MP Biomedicals, Eschwege, Germany)
Software
- Microbiome pipeline based on mothur and the SILVA ribosomal RNA database
- Generation for highly interactive visualisations of your research data with M3P
- Automatic validation of identified taxonomy with the ribosomal RNA BLAST databases
Services
Project Planning
- Planning and preparation of high-throughput experiments
- Data management and storage
- Support with data submission
- Workflow programming
- Project related tool/database establishment
16S rRNA V4 Amplicon using Illumina Technologies
- Generation of short reads
- Identification of pathogenic and non-pathogenic bacteria to family and genus level
- Differential abundances between different conditions
16S rRNA Full Length Amplicon using ONT Technologies
- Possible validation of the short-read results
- Additional resolution of bacterial species level
Comparative Microbial Genome Analyses
- Comparative genome sequencing of bacterial isolates
Metagenome Analyses
- Generation of short-read and long-read metagenomic sequences
- Discovery of viral or fungal composition
- Antimicrobial resistance profiling
- Enrichment or depletion of targeted sequences using adaptive sampling
Other Services
- Classification of poly- and mono-microbial infections
- Methylation analyses
- Culturomics
- Support to interpret the data and results
Downloads/Links
spezifische Nutzungsordnung
Website