3
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

      Preprint

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Culture-independent analyses of microbial communities have advanced dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1,262 metagenomes) and IBD (1,635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4,077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.

          Related collections

          Author and article information

          Contributors
          (View ORCID Profile)
          (View ORCID Profile)
          (View ORCID Profile)
          (View ORCID Profile)
          (View ORCID Profile)
          (View ORCID Profile)
          (View ORCID Profile)
          (View ORCID Profile)
          (View ORCID Profile)
          Journal
          bioRxiv
          November 21 2020
          Article
          10.1101/2020.11.19.388223
          430f82d9-9f20-4546-9ea9-3881782ba6a3
          © 2020
          History

          Microbiology & Virology
          Microbiology & Virology

          Comments

          Comment on this article