Glycoinformatics-assisted Glycan-related Metagenomics Analysis Service
Unveiling Microbial Worlds through Metagenomics Analysis with the Assisted of Glycoinformatics
In recent years, CD BioGlyco has expanded its capabilities on a global scale, offering researchers comprehensive support for
Glycoinformatics-assisted Glycomics Analysis. Glycan-related metagenomics analysis aims to study glycometabolism and related genes in microbial communities using metagenomics techniques. CD BioGlyco utilizes our extensive experience in glycoinformatics to offer a professional glycoinformatics-assisted glycan-related metagenomics analysis service.
Sample preparation and sequencing
We begin by extracting the total DNA of microorganisms from the glycan-related samples, selecting the method of DNA extraction based on the sample type and experimental purpose. The common extraction methods we used include chemical, mechanical, and thermal lysis. Following this, we proceed with DNA library construction, with polymerase chain reaction (PCR) library construction being a frequently utilized method. PCR amplification is employed to amplify the DNA samples into library fragments. Subsequently, we obtain DNA sequence information by sequencing the DNA fragments in the DNA library. We feed the prepared DNA library into a DNA sequencer for the sequencing reaction. Depending on the specifics of the experiment we choose different sequencing technologies, such as Sanger sequencing, 454 sequencing, Illumina sequencing, etc., which generates a large amount of sequencing data.
Data processing and analysis and results interpretation
Our experts perform quality control of sequencing data, including processing such as removing low-quality sequences, splice sequences, and contaminating sequences. Due to the limitation of sequencing technology, the sequences obtained are usually short fragments. Our experts use glycoinformatics tools to perform sequence comparison and sequence splicing. At the same time, we analyze the sequences obtained by comparing them with known databases for species annotation, and functional annotation. Subsequently, we integrate glycoinformatics data with glycan-related metagenomics data to find links between glycometabolism, gene expression, and methylation status. The transcriptome data are analyzed for differentially expressed genes and screened for genes with significant changes in expression levels under different glycometabolism states. Finally, based on the results of the analysis, we provide a detailed report and conclusions for you.
Publication
Technology: Metagenomics and CAZy database
Journal: BMC Bioinformatics
IF: 3.0
Published: 2021
Results: This article investigates the role of glycan-related genes in different environments through functional glycogenomics. The article determines the optimal parameters for identifying glycan-related genes through sequence alignment and uses these parameters to identify 86.73 million glycan-related genes in 198 different metagenome data. Among 12 different environments, human-related environments were found to have a higher proportion of glycan-related genes were higher, suggesting that these environments utilize glycan metabolism better than others. Moreover, the article classified and analyzed glycan-related genes for the GH and GT families, and found that genes of the general-GH and general-GT families were widely distributed across environments, whereas specific-GH genes and specific-GT families were more common in specific environments. This approach can help us better understand the glycometabolism process in the environment and provide new perspectives and methods for discoveries and research. The findings suggest that these genes play different roles in different environments, including participation in metabolism, signaling, and immunity. These findings contribute to a deeper understanding of the function and mechanism of action of glycan-related genes in different environments.
Fig.1 Identification strategy for glycan-related genes in environmental settings. (Takihara, et al., 2021)
Applications
- Glycoinformatics-assisted glycan-related metagenomics analysis can be used to research glycosylation modifications in gut microbial communities and explore their associations with host health, nutrient uptake, and immune function.
- Glycoinformatics-assisted glycan-related metagenomics analysis is used for microbial community optimization in biopharmaceutical and bioproduction processes, leading to improved product quality and yield, and the development of new biopharmaceutical products and biomaterials.
- The technique is used to analyze glycosylation structures and metabolites in microbial communities and to develop novel bioenergy production technologies.
Advantages
- In-depth interpretation of the results: We combine advanced data analysis algorithms and domain expertise to help you gain insight into the relationship between glycosylation structure and microbial community function, host interactions, and environmental adaptations.
- Interdisciplinary integration: Our experts integrate knowledge and techniques from different disciplines, including microbiology, bioinformatics, ecology, medicine, etc., to provide interdisciplinary perspectives and approaches to complex problems.
- The breadth of application: Our glycoinformatics-assisted glycan-related metagenomics analysis service has diverse applications in biomedicine, environmental science, agricultural production, and other fields. We offer research and application support across various disciplines.
Frequently Asked Questions
- How to identify genes and pathways associated with glucose metabolism?
- We use glyco-bioinformatics tools and techniques such as gene annotation and metabolic pathway analysis to analyze and interpret genomic data from microbial communities. Genes and pathways associated with glycometabolism can be identified by comparing known glycometabolism genes and pathways in the database.
- How does glycoinformatics-assisted glycan-related metagenomics analysis differ from traditional metabolomics approaches?
- While traditional metabolomics approaches focus on the analysis of metabolites, glycan-related metagenomics analysis emphasizes the genes and pathways associated with glycometabolism in microbial communities. It combines the techniques of glycoinformatics to enable a deeper understanding of the role of microbes in glycometabolism.
CD BioGlyco possesses expert teams in glycoinformatics research, utilizing a range of cutting-edge technologies to provide comprehensive support to clients through glycoinformatics-assisted glycan-related metagenomics analysis. Please feel free to contact us if you need more information.
Reference
- Takihara, H.; et al. Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. BMC bioinformatics. 2021, 22: 1-15.
For research use only. Not intended for any diagnostic use.
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