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Metagenomics

At the Intersection of Genes and Their Environment, Unveil the Complexity of Microscopic Ecosystems.

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Accelerate Biomarker Discovery with GENXMAP

Metagenomics-Genxmap

Metagenomics is an approach that analyzes genetic material directly extracted from environmental samples, allowing the study of microbial community diversity and functionality without the need to cultivate individual species.

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  1. 1 Comprehensive Profiling: Enables the simultaneous examination of thousands of microbial species, providing an overview of community structure and function.

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  1. 2 Functional Insights: Predicts functional capabilities based on genetic information, facilitating the understanding of metabolic processes.

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  1. 3 Multiple Applications: Used in various fields such as environmental science, agriculture, and medicine, playing a key role in the study of human health.

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  1. 4 Technological Advancements: Advances in sequencing, such as high-throughput sequencing, enhance the analysis of complex samples.

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With GENXMAP, you benefit from deep expertise in metagenomics, helping you maximize data quality and gain valuable insights into the composition and functions of microbial communities in your samples.

High-Resolution Metagenomics for Comprehensive Microbial Profiling

Service Details

    • Research Objectives Identification:

      • You will explain your scientific objectives to clarify the purpose of your study, whether it's analyzing microbial diversity, identifying pathogens, or characterizing microbial communities in a specific sample.

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    • Sample Type Identification:

      • You will specify the types of samples you wish to analyze (feces, soil, water, tissues, etc.), allowing us to adapt the preparation and sequencing process accordingly.

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    • Methodology Selection:

      • Based on your objectives, we will advise you on the most appropriate method for metagenomic analysis, such as sequencing specific genes (e.g., 16S or 18S rRNA) or using a comprehensive metagenomic approach (Shotgun).

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    • Sequencing Platform Choice:

      • We will discuss the available options based on the complexity of the sample and the required resolution level (Illumina, MiSeq, Oxford Nanopore Technology).

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    • Project Planning and Customization:

      • Targeted or Whole Sequencing: If necessary, we will design a specific panel to target particular genes or groups of interest, or opt for a global approach to analyze genetic diversity in its entirety.

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    • Enrichment Strategy and Sample Preparation: 

      • We will define the preparation steps, including pre-extraction, DNA purification, and enrichment of target regions. This is particularly important if rare or difficult-to-capture microbial populations are present.

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    • Budget and Timeline Estimation:

      • Budget Validation: We will provide a clear cost estimate based on the selected methodology, sample number, required coverage, and additional bioinformatics analyses.​

      • Timeline Planning: An estimated timeline for sample preparation, sequencing, and bioinformatics analysis will be provided, with regular checkpoints to track progress.

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    • Ongoing Support and Follow-Up:
      Once the project is underway, we will guide you through the entire process, from raw data collection to bioinformatics support for interpreting the results, with customized reports and recommendations for next steps.

  • High-Throughput Sequencing (Next-Generation Sequencing - NGS)


    GENXMAP utilizes the following platforms:

    • NovaSeq (Illumina)

    Advantages:

    • Rapid and accurate sequencing of large amounts of DNA from various environmental or biological sources.

    • Provides high coverage and depth for precise detection of microorganisms present.

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    • MiSeq (Illumina)

    Advantages:

    • High Precision: Illumina's sequencing-by-synthesis technology is known for its low error rate, ideal for analyses requiring high accuracy, such as genetic variation studies.

    • Rapid Turnaround: Quick run times enable timely results for urgent projects.

     

    • Oxford Nanopore Technology

    Advantages:

    • Long Reads: ONT allows for the generation of very long reads (up to several hundred kb), which is valuable for studying complex genomic regions, whole genomes, and full transcripts without fragmentation.

    • Real-Time Data: Immediate analysis as sequencing occurs, providing instant insights.

    • Step 0 >> Sample Reception Control:

      • Visual evaluation of quantity and quality.

      • Report and client decision "Go / No-Go" for the continuation of the process.

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    • Step 1 >> Sample Preparation:

      • DNA/RNA Extraction: Optimized protocols ensure high-quality extraction, even from challenging samples (FFPE tissues, rare cells, etc.).

      • Quantification and Quality Assessment: Check the quantity and quality of extracted DNA/RNA using spectrophotometers (Nanodrop), Qubit, or fragment analyzer (Qiaxcel).

      • Targeted Enrichment: If necessary, enrichment techniques are applied to focus on specific regions of interest (e.g., resistance genes, 16S rRNA genes, etc.) before sequencing. Enrichment concentrates the analysis on specific genome areas.

      • Library Preparation: Once DNA is extracted and potentially enriched, it is fragmented, and necessary adapters are added for sequencing. This process creates a sequencing library ready for analysis on the selected platform.

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    • Step 2 >> Sequencing Launch:

      • Based on the chosen technology (Illumina, Oxford Nanopore), sequencing is carried out on the appropriate platform.

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    • Step 3 >> Real-Time Quality Control:

      • Monitoring of the sequencing process to ensure no technical errors and maintain the quality of the generated data.

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    • Step 4 >> Data Analysis:

      • Taxonomic Identification: Using databases like QIIME, MetaPhlAn, or Kraken to identify the species in the sample and provide a detailed taxonomic profile.

      • Functional Analysis: In addition to taxonomic identification, a functional analysis is performed to determine the genes and metabolic pathways in the sample, including resistance genes, enzymes, or other points of interest.

      • Sequence Assembly: The obtained sequences are assembled and analyzed using specialized software to reconstruct the genomes of microorganisms in the sample. This step processes and structures raw data.

      • For more details, please refer to our "Bioinformatics & Biostatistics Analysis" page.

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    • Step 5 >> Validation and Interpretation:

      • Data Interpretation: Our bioinformatics experts and partners analyze the results to provide in-depth interpretation. This analysis highlights complex relationships between microorganisms and identifies potential biomarkers or therapeutic targets.

      • Detailed Reports: A comprehensive report is generated, including visualizations of the results (graphs, phylogenetic trees, heatmaps, etc.), conclusions on microbial diversity, and recommendations for the next steps based on project objectives.

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    • Step 6 >> Result Delivery:

      • Result Formats: Provision of raw files (FASTQ), assemblies, taxonomic results, functional analyses, and metadata.

      • Detailed Report: Includes a summary of results, visualizations (charts, phylogenetic trees), biological interpretation, and recommendations for the next steps.

      • Delivery Methods: Accessible via a secure online platform, email delivery, or a results presentation meeting.

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    • Follow-Up and Support: 

      • Post-delivery assistance for clarifications, revisions, or additional analyses.

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    • Delivery Timeframes:

      • Typically between 3 to 6 weeks, depending on the complexity of the project.

    • 16S rRNA Sequencing

    • 18S rRNA Sequencing

    • Shotgun Sequencing

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    • Sample Enrichment:
      Before sequencing, specific regions of the genome may be enriched (e.g., resistance genes or functional regions of interest) to improve coverage of those regions.

Diverse Applications

Sequencing and Analysis of Microbial Community Genomes from Environmental Samples enable in-depth studies of biodiversity, precise environmental monitoring, and a comprehensive exploration of industrial microbiology.

16S rRNA Gene Sequencing

  • Objective: Identify and compare bacterial and archaeal communities based on the 16S ribosomal RNA gene, a highly conserved component of the ribosome.

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Applications:

  • Microbial diversity and taxonomy in environmental samples (soil, water, etc.).

  • Gut microbiome analysis.

  • Detection of pathogens in clinical samples.

  • Environmental monitoring and bioremediation.

18S rRNA Gene Sequencing

  • Objective: Study eukaryotic microorganisms (e.g., protists, fungi, algae) by targeting the 18S ribosomal RNA gene.

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Applications:

  • Eukaryotic microbiome studies.

  • Biodiversity assessments in natural and artificial ecosystems.

  • Parasitology and environmental health studies.

Métagénomique Shotgun

  • Objective: Sequence all DNA present in a sample, providing a comprehensive view of all organisms present and their functional potential.

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Applications:

  • Comprehensive profiling of microbial communities, including bacteria, archaea, fungi, viruses, and eukaryotes.

  • Functional genomics and analysis of metabolic pathways.

  • Detection of rare or novel organisms.

  • Discovery of antibiotic resistance genes and other functional traits.

GENXMAP, your trusted partner to support you in your research.

Optimized and Transparent Services

  • Our Go/No-Go processes allow you to track the progress of your project in real-time. At each stage, you validate the transition to the next, ensuring complete control and maximum transparency throughout the entire process.

  • Our optimized timelines ensure fast and efficient execution of each project while meeting your specific requirements. This system ensures proactive time management, minimizing delays and maximizing productivity to deliver results that align with your expectations.

  • Our tailored processes are designed to meet the unique needs of each project, offering flexibility and personalized follow-up. This system ensures rigorous control while delivering accurate results that align with your expectations.

  • Our detailed analyses guarantee reliable and in-depth results tailored to each study. With cutting-edge tools and proven methodologies, we provide a precise understanding of genetic data, while adhering to the highest standards of quality and scientific rigor.

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