METAGENOME ANALYSIS

METAGENOME ANALYSIS

Overview - What is metagenomics?

Metagenomics, in contrast to Metataxonomics (16S rRNA analysis), is the study of the entire genetic content of all microbiota members in a natural habitat by utilisation of the whole genome sequencing technique. The field centers upon direct genetic analysis of microbial genomes isolated from various environments ranging from the human gut to geothermal hot springs.  Metagenomics is an alternative approach to targeted amplicon sequencing in the study of uncultured microbiota. By offering direct access to the entire genetic make-up of microbial communities, metagenomics can provide valuable molecular insights into novel enzymes and biocatalysts, as well as into genomic linkages between community function and structure. The metagenomics approach serves as a powerful tool for elucidating the relationship between host-associated microbial communities and host phenotype.

Applications - What are the advantages of metagenome sequencing?

Several distinct advantages are associated with the ability to sequence the entire genomic information of all organisms present in a complex sample:

  • Unbiased results free from influence of specific genomic loci 
  • Independence from taxonomically informative genetic markers
  • Ability to study highly diverged microbes, such as viruses
  • Close estimations of microbial diversity
  • Detection of abundance of microorganisms in various environments
  • Analysis of unculturable microorganisms
  • Information on composition as well as functional capabilities of an ecosystem
  • Investigation of function genes and gene clusters 

Workflow - Methods & technologies for metagenome sequencing

Metagenome analysis by next-generation sequencing (NGS) involves several distinct steps. Firstly, total DNA is extracted from the sample. Followingfragmenation, the DNA undergoes adapter ligation for final Illumina library preparation.. The libraries are analysed using paired-end reads to maximise coverage of the amplicons. The reads are sorted and assembled into contigs. For optional de novo genome assembly, genome binning is performed with the contigs in order to reconstruct complete genomes and to assign these assembled genomes to the closest possible taxonomy. Functional analysis can be performed additionally to detect open reading frames and associated gene functions.   

Workflow metagenome analysis

Examples of metagenomes

Human Metagenome

With regards to human health, metagenomics plays an important role in diagnosis, pathogen typing, virulence and antibiotic resistance detection, as well the development of new vaccines and culture media. The comprehensive analysis of complex human micro-florals, both commensal and pathological, has helped to better understand and manage human diseases such as obesity. An improved microbiota characterisation of the vagina, the gastrointestinal tract, the skin and the respiratory system has helped better understand how perturbation of microbial communities directly impacts the health of the host. Metagenomic sequencing can be additionally applied to aid the identification of biomarkers of well-being that correspond to a well-balanced microbiota. Inter-individual differences of the human microbiota are also of considerable importance for establishing personalised medicine as a future treatment. 

Metagenomics in cancer research

More than 15% of global cancer burden is due to microbes. Metagenomics in this field serves as an equitable approach for identifying, analysing and targeting the microbial diversity present in cancer tissue specimens. By generating a comprehensive metagenomic view of cancer microbiota, linkages between microorganisms and various types of cancers can be established. The identification of potential microorganisms associated with a particular cancer can greatly enhance drug target development and selection. 

Metagenomics and the human gut microbiome

More than 1000 microbial species live in the complex human intestine. Metagenomics contributes to studies of intestinal microbiome diversity and dysbiosis, as well as of the relationship between gut microbiota and health and disease. Functional metagenomics can help to identify novel functional genes, microbial pathways and antibiotic resistance genes, as well as to analyse co-evolution between microbiota and host.

Viral metagenomes

Viruses are the most abundant biological entities on the planet. Since there is no single gene that is common to all viral genomes, viruses cannot be investigated by commonly used methods such as amplicon sequencing and ribosomal DNA profiling. A collection of viral metagenomic studies shows that 60 to 99% of generated sequences are not homologous to known viruses, underlining the importance of metagenomic analysis for the virology field. Specifically, viral metagenomics has provided the means for virus discovery, characterisation of normal viral population in a healthy community, and identification of viruses that could pose a threat to human health.

Metagenomics in the food and pharmaceutical industries

Functional metagenomics has considerable potential in the food and pharma industries. The NGS approach can help identify exotic enzymes with valuable technological properties and with the ability to function under extreme conditions. Metagenomic sequencing can be used to discover novel bioactives, such as antimicrobials, as well as to address antibiotic resistance development. For quality control of food and medicines, the approach is a valuable tool for detection of proper ingredients, contamination, allergens, or spoilage in food.  

Environmental metagenomics

Metagenomes of microbial communities in the environment provide valuable information for the development of biofuels, environmental remediation, discovery of agrochemicals and improvement of agriculture practices. Environmental metagenomics contributes insights into the functional ecology of environmental communities that range from a body of water to air debris to a sample of dirt.

The microbial diversity in soil environments is greater than in any other microbial ecosystem. Analysis of the soil metagenome so far has helped uncover novel microbial resources including a number of microbial genes encoding novel enzymes or bioactive compounds.  
The field of metagenomics has helped research on community composition, adaptive strategies and biological functions of extremophiles. 

Metagenomics sequencing can potentially play a significant role in quality control, for example as a water quality assessment tool. 

Difference between genomics and metagenomics and 16S rRNA sequencing

The main difference between genomics and metagenomics is the nature of the sample. Genomics explores the complete genetic information of a single organism only, whereas metagenomics explores a mixture of DNA from multiple organisms and entities, such as viruses, viroids and free DNA. 
Amplicon sequencing, most frequently of the 16S rRNA or ITS genes, involves DNA extraction from all cells in a sample and then the targeting of a taxonomically informative genomic marker that is common to a specific group of interest. The resultant amplicons are sequenced and bioinformatically assessed to determine which microorganisms are present in the sample and in what relative abundance. 
In metagenomic next-generation sequencing, DNA is again extracted from all cells in a community. Rather than targeting a specific genomic locus for amplification, all DNA is sheared into fragments and independently sequenced by a shotgun sequencing approach. The resulting reads are aligned to various genomic locations for all genomes present in the sample, including non-microbes. 

Comparison between 16S analysis, metagenome analysis and whole genome sequencing

Scientific expertise: metagenome sequencing

GATC Biotech has many years of experience with metagenomics analysis. The sequencing infrastructure to generate the large volume of data needed to obtain meaningful results with fast turnaround times is well in place. The company has an optimised BioIT pipeline for the complex bioinformatics analysis involved in the process.  GATC Biotech’s protocols deal particularly well with metagenomes that contain unwanted host DNA. Such samples are handled with specialised techniques for selectively enriching microbial DNA prior to sequencing and with proprietary bioinformatics methods to filter host DNA and contaminant sequences during data processing. 
For the last several years, GATC Biotech has helped profile halophile viral communities, to identify novel bacteria with biodegradation capabilities, to construct dairy microbial genomes, to study gut metagenomes in diabetics, to explore DNA virsues on human skin and to study resistance elements in antibiotic-contaminated rivers. With many publications in the field of metagenomics, GATC Biotech is eager to participate and contribute to your research in molecular microbiology.

Metagenomic sequencing publications

Find here, a list of selected research articles supported by GATC Biotech ’s sequencing products, including metagenomics research articles .

Related products to metagenomic sequencing

GATC Biotech offers an all-inclusive solution for metagenomics sequencing. INVIEW METAGENOME is our standardised service for metagenomics projects. Although the focus on the product is on human microbiota samples, other kinds of starting material can be analysed on request. Molecular microbiologists can take advantage of quick delivery times and high quality data. We offer a complete package from DNA isolation to library preparation to Illumina sequencing to BioIT analysis in order to generate a comprehensive final data report for our customers. 

Are you profiling bacteria with a well-defined genetic marker like the 16S rRNA gene instead? Then try our INVIEW MICROBIOME PROFILING 2.0 for in-depth characterisation of complex microbial communities or INVIEW MICROBIOME HIGH SPECIFICITY for high resolution molecular characterisation of microbiomes based on full 16S rRNA gene sequencing. 

Are you exploring a novel organism without any reference genome sequence? Sequence the full genome without any gaps using PacBio’s Single Molecule Real Time technology with INVIEW DE NOVO GENOME 2.0 sequencing. 

If you have a limited number of samples and are only interested in a few specific genes, then see how Sanger sequencing services can propel your metagenomics project forward. 

Further reading on microbial sequencing

Banerjee, J. et al. Metagenomics: A new horizon in cancer research. Meta Gene 5, 84–89 (2015)

Sharpton, T.J. An introduction to the analysis of shotgun metagenomic data. Front Plant Sci. 5, 209 (2014)

Thomas, T. et al. Metagenomics - a guide from sampling to data analysis. Microb Inform Exp. 2,3 (2012)