Microbiome Bioinformatics & Data Analysis

Bioinformatics is an interdisciplinary field of science that combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological and clinical data.

At Microbiome Insights, our bioinformatics team has extensive experience working with clients to conduct the analysis for over 770 microbiome studies.

We have assisted clients with everything from basic reports with taxonomic and functional profiling to very comprehensive, complex bioinformatic analysis, including multi-omics integration analysis and machine learning-based modeling.

We are focused on quality of data and quality of our analysis, and work with our clients to interpret their data.

You can count on us if you:

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

In each case, our team is ready to answer questions and share insights based on our experience. Contact us here to start a conversation.

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

Our expertise includes:

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 modeling

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 on how to approach multi-omics data and use integration analysis to gain valuable insights on such complex data structures..

Additional advanced and customized microbiome bioinformatics analysis

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

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For Amplicon Sequencing

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Download a sample report

For Shotgun Metagenome Sequencing

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Learn more about Bioinformatics

Amplicon workflows

Pedro Dimitriu, Senior Director of Bioinformatics at Microbiome Insights Inc., provides an overview of generic amplicon workflow and distills the main concepts that underpin the process, as well as an overview of mothur workflow. In the video, Dr. Dimitriu also discusses taxonomic classification, as well as the features and examples of classifiers.

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Introduction to Metagenomics

Pedro Dimitriu, Senior Director of Bioinformatics at Microbiome Insights Inc., demystifies the complex topic of microbiome and shares the latest research in the field. He discusses common microbiome myths, facts, terminology and shares practical tips on how to plan and conduct a microbiome study.

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Frequenty Asked Questions

What is the required data format for this service?

Raw sequencing data should be provided to MBI in FASTQ format. We can also work with previously analyzed data which may be in various formats e.g. excel or .csv format.

How much does this service cost?

Our bioinformatics service is billed hourly, with a 4 hour minimum. You can request a quote here: https://microbiomeinsights.com/inquiry/ and a member of our team will be in touch with you shortly.

What is the turnaround time for this service?

The turnaround time will vary according to your project goals and complexity. On average you can expect to receive a report within 2 – 4 weeks.

Need a Microbiome Sequencing Partner?

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Our expertise includes:

Standard bioinformatic report (amplicon sequencing)

Taxonomic and functional profiling of metagenomes

Shallow shotgun metagenome analysis

Machine-learning-based modeling

Multi-omics integration analysis

Additional advanced and customized microbiome bioinformatics analysis

Download a sample report

Download a sample report

Download a sample report

Learn more about Bioinformatics

Amplicon workflows

Introduction to Metagenomics

Frequenty Asked Questions

Request Pricing for Bioinformatics

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