Mothur workflow

Input:
-521 single reads fastq files
-metadata

Output:
-Shared file (OTUs)
-taxonomy file
-Unifrac scores
Mothur produced...
a unifrac unweighted score, show the significance of the distance between the two
groups, monozygous and the dizygous.

Unlike QIME2, no visualization data was produced.

Goodrich et. al. 2014
The taxonomy classification for in mothur yielded
different results.

Goodrich et. al. 2014

Limitations
Overall
● 521 of 1081 samples
analyzed
○ Single-end reads
● No categorization of
unrelated individuals
(UN) available in
metadata
● Request all 1081 samples and
analyze these
● Request information on
unrelated individuals and
account for this group
QIIME2
● QIIME2 possessed
updates that made
specific steps different
from QIIME
○ Denoising with
DADA2
● Use for single- or paired-end
reads
● Must have computing
resources available
mothur
● Not equipped for single-
end reads
● Does not output data for
plotting unweighted
UniFrac scores
● Use for paired-end reads only
● Use alternative tool for
producing visualizations
● Must have computing
resources available
Conclusions
● QIIME2 and mothur produced considerably different results
○ QIIME2 was more similar to the results reported in the paper
● The ideal tool depends on the dataset available
● The training data dictates the ability to make accurate and specific
classifications
● All methods are computationally demanding
● A better study could incorporate:
○ Paired-read data
○ Consistent computational resources
○ Metadata for unrelated (UN) individuals
References
1. Gilbert, J. A. et al. Current understanding of the human microbiome. Nature Medicine 24, 392–400 (2018).
2. Goodrich, J. K. et al. Human Genetics Shape the Gut Microbiome. Cell 159, 789–799 (2014).
3. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7,
335–336 (2010).
4. Schloss, P. mothur. (2017). Available at: https://www.mothur.org/wiki/MiSeq_SOP. (Accessed: November 30, 2018).