Reconstruction of Metagenome-Assembled Microbial Genomes from a Micro-biome (Poster)

dc.contributor.authorPapudeshi, Bhavya
dc.description.abstractMicrobiome/host interactions describe characteristics that affect the host health; shotgun metagenomics sequences microbiome samples, allowing us to analyze its taxonomic and metabolic potential. Reconstruction of metagenome fragments into genomes (called metagenome-assembled genomes) that facilitates linking function to taxa within microbial symbionts. Reconstruction of genomes sort assembled sequences into bins, characteristic of a genome. However, the microbial community composition, including taxonomic and phylogenetic diversity may influence genome reconstruction. We determine the optimal reconstruction method for four microbiome projects with variable sequencing platforms, diversity, and environment using a set of parameters to select for optimal assembly and binning tools. We evaluated 3 assemblers (IDBA, MetaVelvet, and SPAdes) and 2 binning tools (GroopM and MetaBat) for four projects (105 metagenomes). We find that SPAdes assembled more contigs (143,718 ± 124) of longer length (N50 = 1632 ± 108 bp), incorporated the most sequences (19.65 %), and low chimera levels (microbial richness and evenness were maintained across assembly). SPAdes assembly was responsive to biological and technological variations within the projects. MetaBat binning tool produced bins, characteristic of a genome with less GC variation (standard deviation 1.49), low species richness (4.91 ± 0.66), and higher genome completeness (40.92 ± 1.75). MetaBat extracted 115 bins of which 66 bins were identified as quality reconstructed metagenome-assembled genomes with a genus specific sequences. In conclusion, we present a set of biologically relevant parameters to select for optimal assembly and binning tools. SPAdes and MetaBat tools reconstructed quality metagenome-assembled genomes for the four projects included in this study.en
dc.description.sponsorshipThis research is based upon work supported by the National Science Foundation under grant No. ABI-1458641 to Indiana University.en
dc.identifier.citationPapudeshi, B. (2018). Reconstruction of Metagenome-Assembled Microbial Genomes from a Micro-biome (Poster). Plant and Animal Genomics 2018, San Diego, CA. Retrieved from
dc.publisherPlant and Animal Genomics 2018en
dc.rightsExcept where otherwise noted, the contents of this presentation are copyright of the Trustees of Indiana University. This license includes the following terms: You are free to share -to copy, distribute and transmit the work and to remix -to adapt the work under the following conditions: attribution -you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work.en
dc.subjectNCGAS, Microbiome, Genomicsen
dc.titleReconstruction of Metagenome-Assembled Microbial Genomes from a Micro-biome (Poster)en


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