Microbiome Bioinformatics Services

Bioinformatics is the application of computer resources to analyze and interpret data from biological and clinical sources. At Microbiome Insights, our team is ready to analyze sequencing data and to offer consultation for a new or a follow-up study. Our end-to-end services allow our clients to consult with our team for insights on study design and to analyze and interpret results. These are cases where we can highlight what we can do and incorporate the expertise of our team.

We have assisted clients that:

are new to microbiome analysis,
run pilot studies and need further advice,
look for data and support on a grant proposal or writing a paper,
need assistance with large cohort studies.

In each case, our team is ready to answer questions and share insights based on our experience with more than 400 studies.

We ensure quality while working for a timely delivery. Efficiency and speed are our guiding principles, and we are continually improving in that sense.

Bioinformatics Services

Standard Bioinformatic Report

Amplicon Sequencing

Some of the highlights of the report include the samples’ taxonomic composition at various taxonomic levels, alpha and beta diversity, and multivariate analysis. This service also includes differential abundance testing.

Taxonomic and functional profiling of metagenomes

We provide high-resolution taxonomic profiles and functional profiles of deeply sequenced metagenomes. Profiles are analyzed observing the same principles that guide the analysis of amplicons. Our main metagenomics pipeline is based on tools developed to characterize human microbiomes — specifically HUMAnN2, MetaPhlAn2, and StrainPhlAn form the Huttenhower lab — but we can also accommodate approaches better suited to studying environmental microbiomes.

Shallow Shotgun Metagenome Analysis

Our “shallow” metagenomics sequencing pipeline (~1.5 M reads per sample) uses a k-mer-based taxonomic classification approach that leverages new databases containing >20,000 species-level archaeal and bacterial genomes. To obtain functional profiles, we map quality-controlled sequencing reads to the SEED Subsystems database, which organizes functional potential information into discrete, interpretable hierarchies.

Machine-learning-based Modelling

Our team is capable of integrating microbiome sequencing data to create machine learning methods to study host-microbe interactions. Using known labels (traits) of a dataset, we are able to train a model to recognize feature characteristics associated with the trait and create a comprehensive analysis or method to understand this relationship.

Multi-omics Integration Analysis

Dealing with the multiple dimensions and features of microbiome data can be challenging. Our team has expertise in how to approach multi-omics data and use integration analysis to gain valuable insights on such complex data structures.

Custom Bioinformatics Analysis

Our bioinformaticians are available to understand your particular requirements and support with custom reporting to address your needs.

Sample Bioinformatic Reports

Download a sample report

For Shotgun Metagenome Sequencing

Click here

Download a sample report

For Amplicon Sequencing

Click here

Frequently Asked Questions

When is it beneficial to use Shotgun Metagenomic Sequencing?

While amplicon sequencing provides a good basis for relative abundance of the genus/phyla level per amplicon as well as alpha and beta diversity, your research may require investigation at the species level and/or at the functional level. If so, this is a good option for your study.

Will I only see bacteria?

No. Using shotgun metagenomics you will see anything that can be amplified in this sample. This refers to all DNA that can be amplified in the sample, including non-microbes.

Can I use Shotgun Metagenomics for viral analysis?

This test is not optimized for virome work, but we can assess the nature of your study to see what would be applicable.

What do you use for Shotgun Metagenomic Sequencing?

We have access to both the Illumina Nextseq and Illumina Hiseq for shotgun metagenomic sequencing. In particular, we can run your samples on the 1) Nextseq Medium, 2) Nextseq High, 3) HiSeq rapid run 2×100, or the 4) HiSeq rapid run 2×250.

NextSeq Medium	MAX 31	HiSeq rapid run 2×100	MAX 48

Total reads per run (M)	260	Total reads per run (M)	600

NextSeq High	MAX 96	HiSeq rapid run 2×250	MAX 120

Total reads per run (M)	800	Total reads per run (M)	600

What is the best option for me?

In choosing the right platform for you, we would need to assess the sample type, number of samples, and desired number of reads per sample (coverage). With this we can determine how to achieve the best combination for your samples.

Each platform has a maximum number of samples per lane. We can either determine pricing by the total cost per lane divided by the number of desired samples OR we can determine the optimal number of samples to place in each lane based on the total number of reads per lane divided by the desired coverage per sample.

How do you prepare your libraries?

Whole DNA is prepared for sequencing using the Illumina Nextera XT DNA Library prep kit. Samples are barcoded and mixed together for sequencing. The mix is then sequenced using Illumina technologies for either high-output or medium-output.

How are sequences processed after sequencing?

Paired reads are concatenated and then processed to remove adaptors, barcodes, and low-quality reads, as well as contaminant sequences (typically host DNA). Sequences are then compared to phylogenetic and functional databases to obtain taxonomic and functional profiles.

Bioinformatics Services

Standard Bioinformatic Report

Taxonomic and functional profiling of metagenomes

Shallow Shotgun Metagenome Analysis

Machine-learning-based Modelling

Multi-omics Integration Analysis

Custom Bioinformatics Analysis

Sample Bioinformatic Reports

Download a sample report

Download a sample report

Frequently Asked Questions

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