Abstract
The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.
Highlights
The microbiome is defined as a characteristic microbial community occupying a reasonably welldefined habitat which has distinct physio-chemical properties
Programmatic access to the data for cross-database complex queries is available via a RESTful application programming interface (API) (Mitchell et al, 2020), and a free service is available for users to submit raw metagenomics sequence data and associated metadata to the European Nucleotide Archive (ENA) followed by analysis using MGnify pipelines
Open-source bioinformatics workflows for processing raw multi-omics data have been developed based on production-quality workflows at the two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL)
Summary
The microbiome is defined as a characteristic microbial community occupying a reasonably welldefined habitat which has distinct physio-chemical properties. Programmatic access to the data for cross-database complex queries is available via a RESTful application programming interface (API) (Mitchell et al, 2020), and a free service is available for users to submit raw metagenomics sequence data and associated metadata to the European Nucleotide Archive (ENA) followed by analysis using MGnify pipelines While this platform does not yet support metabolomics and proteomics data analysis, it provides an intuitive way to enable cross-project sequence-based comparisons. We provide a perspective and review some challenges faced since the inception of the NMDC and the implementation of solutions to support standardization and cross-study, cross-sample microbiome comparisons We believe these challenges and the proposed solutions are applicable to any large-scale bioinformatics or scientific data portal development. We focus on challenges in 1) architecture considerations; 2) microbiome workflow selections; 3) Metadata to standardize and manage workflow data products
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
