Namco: a microbiome explorer

Alexander Dietrich; Monica Steffi Matchado; Maximilian Zwiebel; Benjamin Ölke; Michael Lauber; Ilias Lagkouvardos; Jan Baumbach; Dirk Haller; Beate Brandl; Thomas Skurk; Hans Hauner; Sandra Reitmeier; Markus List

doi:10.1099/mgen.0.000852

Namco: a microbiome explorer

Alexander Dietrich, Monica Steffi Matchado, Maximilian Zwiebel, Benjamin Ölke, Michael Lauber, Ilias Lagkouvardos, Jan Baumbach, Dirk Haller, Beate Brandl, Thomas Skurk, Hans Hauner, Sandra Reitmeier, Markus List

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows the study of 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 Namco’s 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/.

Original language	English
Article number	000852
Journal	Microbial Genomics
Volume	8
Issue number	8
DOIs	https://doi.org/10.1099/mgen.0.000852
State	Published - 2022

Keywords

bioinformatics pipeline
data visualization
microbial co-occurrence networks
microbial functional profiling
microbiome data analysis

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10.1099/mgen.0.000852

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abstract = "16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows the study of 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 Namco{\textquoteright}s 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/.",

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year = "2022",

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AU - Dietrich, Alexander

AU - Matchado, Monica Steffi

AU - Zwiebel, Maximilian

AU - Ölke, Benjamin

AU - Lauber, Michael

AU - Lagkouvardos, Ilias

AU - Baumbach, Jan

AU - Haller, Dirk

AU - Brandl, Beate

AU - Skurk, Thomas

AU - Hauner, Hans

AU - Reitmeier, Sandra

AU - List, Markus

PY - 2022

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N2 - 16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows the study of 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 Namco’s 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/.

AB - 16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows the study of 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 Namco’s 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/.

KW - bioinformatics pipeline

KW - data visualization

KW - microbial co-occurrence networks

KW - microbial functional profiling

KW - microbiome data analysis

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JO - Microbial Genomics

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Namco: a microbiome explorer

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Keywords

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