Answer two of Hanage’s questions listed below.  Provide support for your answer. Do the results presented in Figure 5 detect differences that matter? Do the results presented in Figure 5 show correlation or causation?  

Answer questions 30-32 using the prompt below. You are working in a research lab that studies the effects of diet on the gut microbiome.  You are particularly interested in the complex interactions between the host, diet and microbiota in individuals with inflammatory bowel syndrome (IBS).  In order to study this relationship you design an experiment comparing the short chain fatty acid concentrations in fecal samples from healthy individuals to individuals with one of two types of IBS diseases: (1) ulcerative colitis (UC) or (2) Crohn’s Disease (CD).  Results for butyrate concentrations are shown below. Figure 4: Quantification of butyrate concentrations in healthy individuals (control) and those with ulcerative colitis (UC) and Crohn’s Disease (CD)

[a] is a common microbe (that we discussed in class) that is associated with vaginal dysbiosis and is part of the bar colored [b] in Figure 2.b.  For full credit, Include the genus and species name in the first blank and use the provided figure key to name the color in the second blank.

Answer the following questions based on your knowledge of the vaginal microbiome and the data provided in the figure. How is lactic acid produced in the vaginal microbiome? What is the importance of lactic acid in the vaginal microbiome? Which two Community State Types produce the most lactic acid? Why is one of these Community State Types less protective against dysbiosis than the other?  Explain your answer.

Below is Figure 4 from Duran-Pinedo et al. (2014) “Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis”. Figure 4. GO enrichment analysis summarized and visualized as a scatter plot using REVIGO. (a) Summarized GO terms related tobiological processes in periodontitis. (b) Summarized GO terms related to biological processes in health. (c) Summarized GO termsrelated to molecular function in periodontitis. (d) Summarized GO terms related to molecular function in health. GO terms arerepresented by circles and are plotted according to semantic similarities to other GO terms (adjoining circles are most closely related).Circle size is proportional to the frequency of the GO term, whereas color indicates the log10 P value (red higher, blue lower). Identify one GO term that is related to biological processes in periodontitis from the figure. Which panel did you identify this GO term in? Explain the role that this GO term likely plays in periodontitis.

Name one microbe that is part of the RED complex commonly associated with periodontitis.  You must write the full genus and species name for full credit.

Answer two of Hanage’s questions listed below.  Provide support for your answer. Do the results presented in Figure 5 detect differences that matter? Do the results presented in Figure 5 show correlation or causation?  

Dental caries occur when the host’s immune response begins to destroy the gums and soft tissues surrounding the infected tooth.

Answer questions 10 – 19 using the figure below. Figure 1: An individual’s vaginal microbiome was sampled daily for 70 days.  A. The relative species abundance was determined using 16S sequencing for every day of sampling.  B. The relative transcript abundance was analyzed for four individual time samples labeled T1-T4 using RNAseq.

Answer questions 30-32 using the prompt below. You are working in a research lab that studies the effects of diet on the gut microbiome.  You are particularly interested in the complex interactions between the host, diet and microbiota in individuals with inflammatory bowel syndrome (IBS).  In order to study this relationship you design an experiment comparing the short chain fatty acid concentrations in fecal samples from healthy individuals to individuals with one of two types of IBS diseases: (1) ulcerative colitis (UC) or (2) Crohn’s Disease (CD).  Results for butyrate concentrations are shown below. Figure 4: Quantification of butyrate concentrations in healthy individuals (control) and those with ulcerative colitis (UC) and Crohn’s Disease (CD)