Fall 2020: Investigating Microbial Communities
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Introduction to topic and methods.
BIT 477/577 Fall 2020 Students
Module Learning Objectives (MOs)
- MO 1.1. Define next-generation or high-throughput sequencing (‘NGS’). (CO 5)
- MO 1.2. Define metagenomics. (CO 5)
- MO 1.3. List two applications of metagenomics in health, industry, or medicine. (CO 5)
- MO 1.4. Apply cloud-based tools to analyze shotgun sequencing data on the cloud using a WGS pipeline. (CO 4)
What is metagenomics?
Metagenomics is the study of complex microbial communities using genome sequencing technologies and bioinformatics. Sequencing technologies include:
a) Illumina sequencing by synthesis which conducts parallel sequencing and produces many short reads
b) PacBio and Oxford Nanopore long-read sequencing technology.
NGS vs. qPCR
When to choose WGS or PCR-Directed Sequencing
Table 1 from Schlebusch S, Illing N. Next generation shotgun sequencing and the challenges of de novo genome assembly. S Afr J Sci. 2012;108(11/12), Art. #1256, 8 pages. http://dx.doi.org/10.4102/
sajs.v108i11/12.1256 it is outdated, but is one of the only comparisons of read-length and cost I could find for different NGS methods. Other cool stuff in this paper too.
Next generation shotgun sequencing and the challenges of de novo genome assembly | Schlebusch
- Here is a previous paper from my lab that I used as a reference to conduct qPCR and NGS for my research on the effects of nitrification inhibitors on soil microorganisms. It was pretty hard since I had to essentially teach myself the techniques due to COVID.
Xia, Q., Chen, H., Yang, T., Miller, G., & Shi, W. (2019). Defoliation management and grass growth habits modulated the soil microbial community of turfgrass systems. PloS One, 14(6), e0218967. doi:10.1371/journal.pone.0218967
I found this paper to be helpful context for our first reading assignment!
Kucharska K, Rybarczyk P, Holowacz I, Lukajtis R, Glinka M and Kaminski M. (2018). Pretreatment of Lignocellulosic materials as substrates for fermentation processes. Molecules, 23(11), 2937; https://doi.org/10.3390/molecules23112937
Another paper that might help with the 1st reading assignment:
Luo, G., De Francisci, D., Kougias, P. G., Laura, T., Zhu, X., & Angelidaki, I. (2015). New steady-state microbial community compositions and process performances in biogas reactors induced by temperature disturbances. Biotechnology for Biofuels, 8, 3. https://doi.org/10.1186/s13068-014-0182-y
Here’s a paper on application of metagenomics in clinical diagnosis and treatment:
Chiu, C.Y., Miller, S.A. Clinical metagenomics. Nat Rev Genet 20, 341–355 (2019). https://doi.org/10.1038/s41576-019-0113-7
I found this article on viral metagenomics. It discusses utilizing virus particles and proteins in samples to identify the virus present. It’s available in PDF form
https://onlinelibrary.wiley.com/doi/abs/10.1002/rmv.532
Here’s a post in a blog where someone talks about his lab’s effort to assemble a bacterial genome using Nanopore and their frustration when they got only 65% completeness. This fact generated a huge discussion on Twitter on what is better to use: Illumina, PacBio or Nanopore? The take- home message from the discussion was that hybrid Illumina/ PacBio or Illumina/ Nanopore data is the best approach for getting good genomes, combining accuracy with long reads. https://microbe.net/2018/03/21/the-lady-or-the-tiger-nanopore-illumina-and-pacbio/
Here’s a cool article about soil metagenomics and some approaches for analyzing soil microbial communities, as well as some challenges soil microbiologists face
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748112/
This is an article summarizing what metagenomics is and some tools that are used to analyze environment samples! Potential challenges are also discussed
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905821/
KBase
MO 1.4. KBase -the U.S. Department of Energy Systems Biology Knowledge Base, is a free open source software and data platform that allows users to upload data, analyze public data and share/publish workflows and conclusions. Data import can be conducted by three methods: local computer file upload (limited to 20GB), through GLOBUS or from the Web.