miaverse – microbiome analysis framework within the SummarizedExperiment ecosystem

Author(s): Tuomas Borman,Leo M Lahti

Affiliation(s): University of Turku



Microbiome refers to a collection of microbes and their genetic material in a certain habitat. It has a pivotal role in human health and disease, yet the underlying mechanisms are still often unclear. The research relies on sequencing data to elucidate microbial composition and function, additionally, the adoption of multiomics approach is becoming increasingly common. Recent years have seen rapid expansion in microbiome research, driven by technological advancements. The swift evolution of the field has resulted in a lack of established best practices. Moreover, previous technologies are suboptimal for larger, more complex datasets and fail to fully exploit the capabilities of the Bioconductor ecosystem. The miaverse framework is addressing these challenges. It is built upon the TreeSummarizedExperiment data container, which is optimized for microbiome analytics. This data container extends the SummarizedExperiment class by incorporating support for phylogenetic trees, linking the field of microbiome to other application domains that use similar containers. This design choice facilitates interoperability with methods in related fields, such as single-cell analysis, thereby enhancing the broader toolkit available within the SummarizedExperiment ecosystem. The miaverse framework encompasses the mia* packages, providing methods for common operations in microbiome downstream analysis, including analysis, simulation, and visualization. In addition to methods, it features a comprehensive online book titled Orchestrating Microbiome Analysis (OMA), aimed at disseminating best practices in microbiome data science. The framework is designed to foster the development of efficient workflows that are standardized, transparent, and reproducible, providing a robust and versatile toolset for microbiome research. Available within Bioconductor, the open-source miaverse framework is continuously expanding as more methods support the TreeSummarizedExperiment data container. We anticipate that the use of the SummarizedExperiment ecosystem will continue to grow in popularity and has the potential to become widely adopted in microbiome research.