Fall 2019: Investigating the Microbial Communities in Mortality Composts (3/8) -- BIT 477/577 Metagenomics

Fall 2019: Investigating the Microbial Communities in Mortality Composts 3 Pipelines and computational resources. BIT 477/577 Fall 2019 Students and Carlos Goller Learning Objectives - To critically analyze a published tool. - To describe the importance of processing reads before use. - Examine different approaches used for processing reads. What pipelines are available? MG-RAST (Metagenomic Rapid Annotations using Subsystems Technology) - Suggests automatic phylogenetic and functional analysis of metagenomes - It is also a very large data repository for metagenomic data Nephele - Provides QIIME1, mothur, and DADA2 pipelines for amplicon data and the bioBakery pipeline for metagenome shotgun data. - Includes a quality control pipeline for demultiplexed samples - Some issues with Nephele may include low flexibility with the analyses that can be done one codex Microbiome platform for genomic analysis and data management. Key features include: - - Taxonomy analysis - Functional gene predictions and markers (identification of potential genes of interest such as AMRs) - Reporting capabilities to answer specific questions - It does not do QC or paired-reads, but interactive plot produced within minutes thereafter. CosmosID - - A bioinformatics platform that achieves strain-level analysis with industry-leading sensitivity and precision. - Helps identify and characterize isolated organisms for strain discovery and sub-typing - Emphasizes pathogens, antimicrobial resistance, and virulence - Expensive (but free 24 samples or 12 WGS samples upon signing up) - They work with Qiagen and they have CLC plug-in function Main points of article #2 Che et al. (2019). Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing. Microbiome. 7. Article number: 44. - Three wastewater treatment facilities: influent, activated sludge, and effluent - Comparing Nanopore (long read) and Ilumina (short read) readings - Cultivated species: took affluent + LB + antibiotics —> sequenced non-multidrug resistance - Illumina Centrifuge: analyze sequences, get standardized pipelines - Plots: the abundance of antimicrobial genes in different samples - Pathogens acquire multidrug resistance in wastewater treatments (plasmids facilitate this resistance acquisition) - Higher prevalence of plasmids with antimicrobial resistance genes found in the effluent - Combination of Nanopore + Illumina - Limitations: No percentage abundance given for species