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:
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- 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
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- 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