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Microbiome Sequencing Services


Microbiome sequencing is a method of decoding the genetic material of all the microorganisms in a sample: bacteria, virus, fungi and protists. There are two major methods that are used: whole genome shotgun sequencing (WGS) and amplicon sequencing. WGS is an unbiased method that detects all the genetic material in the sample. 

Amplicon sequencing targets a portion of the genetic material that is shared among the microorganisms but contains regions of variability that allow their identification. WGS can also identify functional genes in the sample whereas amplicon sequencing cannot.

Microbiome SequencingAdvantages of a Microbiome Sequencing Service

Identification of microorganisms in a sample by sequencing techniques and data analysis allows several advantages over traditional culturing approaches. Benefits of microbiome analysis services include:

  • Identification of non-cultivable bacteria
  • Detection of anaerobic bacteria
  • Profile hundreds of microorganisms in a single analysis
  • Estimate the relative abundance of microbes in a sample
  • Examine complex microbiomes and microbiota communities
  • Provide more efficient and accurate microbe classification when compared to traditional identification methods such as cloning or culturing
  • Identify bacteria that are low in abundance
  • More cost-effective microbiome characterization of multiplex microbial samples.

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Microbiome SequencingMicrobiome Sequencing Services & Solutions

CosmosID offers several microbiome profiling and sequencing solutions, including amplicon sequencing, WGS, isolate sequencing and metatranscriptomics. The CosmosID team has extensive experience in supporting the design and execution of metagenomics projects for both industry and academia for a wide range of applications, from microbial ecology to disease diagnoses and health interventions, using both human and non-human sample types.

From sample collection, to sample processing, data generation and raw data analysis, our expert scientists offer detailed information and analyses to help you gain insight into your microbiome.

We offer comprehensive data analysis and interpretation services that include taxonomic assignments, functional profiles, phylogenetic distance comparisons (alpha and beta diversity), as well as correlations of species abundance with environmental factors.

With a team of bioinformaticians experienced in developing customized pipelines and visualization tools to display the most relevant findings for your project, we provide an unparalleled level of end-to-end support. 

Our solutions are constantly evolving to match the ever changing needs in microbiome sequencing, and we work closely with our customers to ensure they get the most out of their data.

Amplicon Sequencing Service

Amplicon sequencing has been an important methodology for microbiologists and microbiome researchers for decades, enabling the generation of whole community analysis of bacteria or fungi in any complex sample. 

For bacteria, the 16S rRNA gene is amplified and for fungi the ITS gene is amplified. Both of these genes contain conserved regions which are used to target primers to them to amplify variable regions within that allow taxonomic identification and calculation of relative abundance.

The advantages of an amplicon-based approach are:

  • Cost-effectiveness
  • Can be advantageous for swabs and other low biomass samples
  • Well suited for taxonomic profiling in new, under-studied or exotic sample types
  • Well-suited for large cohort, biobanking and population-based studies
  • Well-suited for routine testing, including microbiome-based diagnostics.

Amplicon sequencing also has some drawbacks that should be considered, including:

  • Primer bias – different variable regions preferentially amplify certain bacterial species
  • Amplification bias
  • Identification of taxa with confidence to the genus level – species and strain level identification is usually not possible or not accurate
  • Lack of functional information – only the 16S rRNA gene is identified, leaving the rest of the genetic material unused

Whole Genome Sequencing Services

WGS offers higher taxonomic resolution and accuracy than amplicon sequencing. Here, shotgun sequencing of the entire sample is applied, meaning no amplification step is necessary. 

This removes both primer and amplification bias. Further, the entire genome, not only the 16S rRNA gene, can be identified, allowing examination of the functional potential of the microbial community and any virulence, pathogenic, or antimicrobial resistance genes it may contain. 

In addition, assembly of the myriad microorganisms can be done to create metagenome-assembled genomes, or MAGS, allowing association of specific genes with the organisms containing them. 

This can be done for bacteria, archaea, viruses, protists, and phages within a sample. WGS offers a more comprehensive and accurate overview of the microbiome than amplicon sequencing is capable of, providing more value for the cost. 

The general advantages of WGS are:

  • Unambiguous taxonomic classification
  • Highly accurate depiction of strain relatedness, pathogenesis and transmission
  • Functional characteristics like antimicrobial resistance, virulence, and metabolic capabilities

CosmosID offers two major types of WGS: shallow shotgun and deep sequencing.

Shallow Shotgun Sequencing

Shallow shotgun sequencing can provide all the information above at a lower cost due to sequencing of the samples at a lower depth. Typically, this is 3 – 6 million reads per sample. 

This is sufficient coverage to provide a comprehensive overview of the most dominant features of the community. However, if you are interested in low abundance or rare features, you may want to consider deep sequencing. 

Advantages of shallow shotgun sequencing include:

  • Cost-effectiveness
  • Well-suited for biobanking, large cohort & population studies
  • Well-suited for gut microbiome research
  • Well-suited for routine testing, including microbiome-based diagnostics
Deep Shotgun Sequencing: What are the advantages?

Deep shotgun sequencing provides higher read coverage than shallow. This may be anywhere from 10 million reads and higher, depending on the needs of the individual study. Price per sample increases with higher coverage depth.

Some additional advantages are:

  • Increased resolution and specificity as compared to shallow shotgun
  • Lower false-positive rates relative to amplicon sequencing
  • Increased identification accuracy, particularly of rare and low-abundance features


Through optimized RNA-based workflows for a range of different sample types, CosmosID offers metatranscriptomic services for both complex samples and microbial isolates for a range of study applications. Here, RNA is extracted from a microbiome sample in order to sequence and characterize the range of genes expressed.

The advantages are:

  • Direct study of gene expression, not simply genetic content
  • Untargeted profiling covering a range of expressed genes
  • Identification of active metabolic pathways
  • Combined metagenomic-metatranscriptomic analysis for assessment of microbial activity
  • Discover mechanisms behind observed gene expression

Custom Bioinformatics

CosmosID’s team of expert bioinformaticians and software developers have the unique ability to support custom bioinformatics and in silico studies. Example applications include:

  • Custom strain detection for LBP & Probiotic studies in metagenomic samples
  • Custom data mining and gene annotation
  • Intra-species, multi-strain analysis for low & high biomass samples
  • Biomarker Discovery & Patient Stratification
  • Machine Learning & custom tool development
  • Custom software development
  • Comprehensive In silico studies & retrospective analysis.

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