Abstract
Background 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 few platforms offer a user-friendly interface and none comprehensively cover the whole analysis pipeline from raw data processing down to complex analysis.
Results We introduce Namco, an R shiny application that offers a streamlined interface and serves as a one-stop solution for microbiome analysis. We demonstrate Namco’s capabilities by studying the association between rich fibre diet and the gut microbiota composition. Namco helped to prove the hypothesis that butyrate-producing bacteria are prompted by fibre-enriched intervention.
Conclusion 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/.
Competing Interest Statement
Dr. Markus List receives consulting fees from mbiomics GmbH outside this work.
10. Abbreviations
- ABC
- ATP-Binding Cassette
- AST
- Aspartate Aminotransferase
- ASV
- Amplicon Sequence Variants
- BMI
- Body Mass Index
- GDPR
- General Data Protection Regulation
- KO
- KEGG Orthology
- IM
- Intervention Meals
- M
- non-intervention Meals
- MDS
- Multi-Dimensional Scaling
- NMDS
- Non-metric Multidimensional Scaling
- OTU
- Operational Taxonomic Units
- SCFA
- Short Chain Fatty Acid