8.4 Try it Question 1 - What has more impact on human microbial variation, diet or individuality

Diet is suggested to play an important role in shaping the human gut microbiome. However, other factors that are specific to an individual such as their physical fitness, metabolism, and genotype are also suspected to play a strong role. Here we will explore the impact of diet and individuality on the human gut microbiome.

Approach: Plot high level taxa (Phyla) for all timepoints and subjects and compare the plots to determine which factor has a stronger effect on microbiome composition.

8.4.1 Step 1A: Plot high-level taxonomy (Phylum level) for each timepoint using the plot_bar() function.** Specifically, your plot should show Phyla diversity across all 5 timepoints.

  • Refer to the “Explore 16S rRNA Data with phyloseq” tutorial for help using the plot_bar() function.
  • Ensure your plot has a title
  • Remember, the BD diet includes timepoints 1 and 2, the HD diet includes timepoints 3 and 4, and the WO diet includes timepoint 5.
  • Use the following code as a template:
plot_bar(miso, "fill in the blank", fill = "fill in the blank", title = "choose a name for your graph") + 
geom_bar(aes(color = fill in the blank, fill = fill in the blank), stat = "identity", position = "stack")
1A-1. Paste figure 1A below.


1A-2. Does the gut microbiome at the phyla-level look similar for the two samples within the baseline diet treatment (timepoints 1&2)?


1A-3. Does the gut microbiome at the phyla-level look similar for the two samples within the homogenous diet treatment (timepoints 3&4)?


1A-4. Does the gut microbiome at the phyla-level look different between diet treatments (timepoints 1 & 2 vs. 3 & 4 vs 5?)


1A-5 Based on what you wrote above, conclude the effect of diet on the gut microbiome at the level of phylum.


8.4.2 Step 1B: Plot high-level taxonomy (Phylum level) for each individual, using only normalized homogenized diet “HD” timepoints to minimize contribution of diet to the analysis using the plot_bar() function.

misoHD = subset_samples(miso, diet == "HD")
plot_bar(misoHD, "fill in the blank", fill = "fill in the blank", title = "choose a name for your graph") + 
geom_bar(aes(color = fill in the blank, fill = fill in the blank), stat = "identity", position = "stack")
  • Specifically, your plot should show Phyla diversity across all 21 individuals at HD timepoints.
  • Refer to the “Explore 16S rRNA Data with phyloseq” tutorial for help using the plot_bar() function.
  • Check that your plot has a title
  • Use the command below to create a phyloseq object with only “HD” timepoints and fill in the template code to make your plot.
1B-1. Paste your Figure 1B below:


1B-2. How different is the gut microbiome between subjects?


1B-3. Based on this figure, what is the effect of the individual on the gut microbiome composition at the level of phylum? Remember, this figure contains data for subjects who were all eating the same homogenized diet. So, the effect of diet is controlled for here and we can see the effect of the individual, which encompasses their lifestyle, genetic factors, age, and unique biology.


8.4.3 Grading criteria

  • Download the assignment to your local computer as a .docx, complete it, and upload the assignment to your LMS (Blackboard, Canvas, Google Classroom).

8.4.4 Footnotes

8.4.4.2 Contributions and affiliations

  • Valeriya Gaysinskaya, Johns Hopkins University
  • Gauri Paul, Clovis Community College
  • Frederick Tan, Johns Hopkins University
  • Sayumi York, Notre Dame of Maryland University
All materials CC-BY unless noted otherwise.