Namco: A microbiome explorer

Dietrich, A.; Matchado, M. S.; Zwiebel, M.; Ölke, B.; Lauber, M.; Lagkouvardos, I.; Baumbach, J.; Haller, D.; Brandl, B.; Skurk, T.; Hauner, H.; Reitmeier, S.; List, M.

doi:10.1101/2021.12.15.471754

bioRxiv · 10.1101/2021.12.15.471754

Namco: A microbiome explorer

Dietrich, A.·Matchado, M. S.·Zwiebel, M.·Ölke, B.·Lauber, M.·Lagkouvardos, I.·Baumbach, J.·Haller, D.·Brandl, B.·Skurk, T.·Hauner, H.·Reitmeier, S.·List, M.

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Abstract

16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows for studying microbial diversity, taxonomic profiling, phylogenetics, functional and network analysis. While a plethora of tools have been developed for the analysis of 16S rRNA gene data, only a few platforms offer a user-friendly interface and none comprehensively covers the whole analysis pipeline from raw data processing down to complex analysis. We introduce Namco, an R shiny application that offers a streamlined interface and serves as a one-stop solution for microbiome analysis. We demonstrate Namcos capabilities by studying the association between a rich fibre diet and the gut microbiota composition. Namco helped to prove the hypothesis that butyrate-producing bacteria are prompted by fibre-enriched intervention. Namco provides a broad range of features from raw data processing and basic statistics down to machine learning and network analysis, thus covering complex data analysis tasks that are not comprehensively covered elsewhere. Namco is freely available at https://exbio.wzw.tum.de/Namco/. Impact statementAmplicon sequencing is a key technology of microbiome research and has yielded many insights into the complexity and diversity of microbiota. To fully leverage these data, a wide range of tools have been developed for raw data processing, normalization, statistical analysis and visualization. These tools are mostly available as R packages but cannot be easily linked in an automated pipeline due to the heterogeneous characteristics of microbiome data. Instead, user-friendly tools for explorative analysis are needed to give biomedical researchers without experience in scripting languages the possibility to fully exploit their data. Several tools for microbiome data analysis have been proposed in recent years which cover a broad range of functionality but few offer a user-friendly and beginner-friendly interface while covering the entire value whole value chain from raw data processing down to complex analysis. With Namco(https://exbio.wzw.tum.de/namco/), we present a beginner-friendly one-stop solution for microbiome analysis that covers upstream analyses like raw data processing, taxonomic binning and downstream analyses like basic statistics, machine learning and network analysis, among other features.

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Dietrich, A., Matchado, M. S., Zwiebel, M., Ölke, B., Lauber, M., Lagkouvardos, I., Baumbach, J., Haller, D., Brandl, B., Skurk, T., Hauner, H., Reitmeier, S., List, M.. 2021-12-16. Namco: A microbiome explorer. https://doi.org/10.1101/2021.12.15.471754

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