Microbiome Profiling at Biomcare

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Collecting the right samples – the right way

Every project starts with the collection of samples, and getting this right is essential for the success of the project.
Key questions include which samples to collect? How many samples to collect? How to collect, store and transport the samples?

At Biomcare we are happy to discuss these questions and help identify the optimal design.

Sample shipment and sequencing

When collaborating with Biomcare, we provide you with a sample sheet and shipment guide, for simple tracking and shipment of samples. Samples to be shipped to Biomcare must be collected in tubes labeled with IDs that start with a letter e.g. S1, S2, S3, etc.

While we are happy to answer practical questions, organization and payment of transportation is not included in Biomcare services.

When your samples arrive at the sequencing facility, they are scanned and registered in the in-house database for safe sample tracking. Therefore, it is of key importance that you return the above-mentioned sample sheet to Biomcare before your samples are shipped. The samples are then processed with DNA extraction, library preparation, and sequencing as requested. We generally have a turnaround time in the laboratory of 6-10 weeks depending on project size and type of sequencing selected. However, we cannot guarantee this timeline is met and we recommend you discuss with us at an early stage if your project has a specific deadline. When the raw sequencing data is generated, it is transferred to your project folder on Biomcares server and we proceed with data evaluation.

From raw data to microbiome profiles

When we receive raw sequencing data, the first thing we do is assess the quality of the data. If the evaluation raises concerns that indicate fundamental issues with the samples or the performed sequencing, we will discuss these concerns with you before we proceed. After quality assessment, data is quality filtered to remove low quality reads and base pairs, and microbiome profiles are generated. The exact process selected for quality filtering and microbiome profiling depends on the type of data as well as the type of sample. You will receive a report describing the data generation, quality evaluation, filtering, and microbiome profiling; as well as an assessment of the resulting microbiome profiles.

"All of us rely on our body’s microbiome to function properly. We have more microbial cells living inside our bodies than human cells. These bacteria protect us from infection and are particularly essential to digestion.

For example, your body literally cannot break down certain types of plant fibers without an assist from the bacteria in your gut."

Bill Gates

Telegraph, October 2019

Extracting the key results

Evaluating the microbiome community and diversity

Microbiome profiles are large tables with taxonomic or functional information on the microbiome in each sample of the project. Tables with taxonomic information on detected microorganisms and their abundance (relative or absolute) in each sample, can be overwhelming and are only informative after extensive processing and statistical analysis. Which processing and analyses to perform depends on the project design and the questions that the project aims to answer. At Biomcare we start with a detailed evaluation of the data. We perform normalizations, filter samples, calculate diversity measures and generate a range of plots to support data assessment.

We then move to the statistical analysis, starting at the broader community level to access multivariable clustering, explanatory variables, dispersion, and association with alpha diversity. While these analyses might not answer the key question(s), they are important to understand the data and guide downstream models e.g. covariates inclusion and feature selection.

Detecting the relevant indicator species and functions

While some projects are interested in the overall patterns of the microbiome, most are interested in detecting specific features of the microbiome that associate with a specific testing condition. While this is the key question of most microbiome projects it is also the most difficult to perform and it requires detailed consideration of the project design and aim. At Biomcare we do not work with one-fits-all solutions, simply because this will not give the best results and will in many instances provide wrong results. We have an extensive toolbox of statistical models and approaches to choose from and we will select a subset of models that are optimal and which together can provide high quality results. We select and assess not one, but several models, because this increases the confidence of the results and helps decrease possible limitations of each model.

Our toolbox includes a range of models, both univariate and multivariate, such as ANOVA-based models, simple correlations, chi-square or Wilcoxon rank sum tests, generalized linear models, robust regression, reference taxa-based methods (ANCOM/DACOMP), ensemble methods, and machine learning.

Communication and reports pave the way for a successful project

When we have performed the requested analysis, you will receive an email with login information to your private project folder at Biocare’s server. All data, both raw and processed, will be available for download, together with all resulting plots, tables, and reports.

At Biomcare we generate several reports that guide you through each step of data generation, processing, and analysis. These reports include a number of figures, and each figure will be available as single plots in your project folder for individual use in presentations or publications.

Communication is essential for a successful project

In addition to generating the reports, we invite you to a face-to-face meeting at Biomcares location to discuss the results. We will walk you through the performed analysis and answer your questions to ensure you are confident with the provided results. If the discussion identifies additional analysis that could be informative, Biomcare will perform these analyses at no extra cost. We further support with modifications to the generated illustrations such as changes of labels and colors, and support with the generation of joint figure panels where requested. For each project, Biomcare accommodates requests for modifications up to ca. six hours of work, after which an hourly rate takes effect. Biomcare will of course inform you before any work that requires extra payment is initiated.