Question

Read in the *microbiome* dataset that is posted on Moodle. The dataset contains (gut) microbial abundances of certain phyla of bacteria. The hypothesis is that body mass index (BMI) may be correlated to abundances of certain phyla is the reason for this dataset. The dataset has been simplified include only 25 subjects and the abundances of 4 of the most abundant phyla: bacteroidetes, firmicutes, proteobacteria, and actinobacteria. Let's do a few basic computations. Suppose I want to compute the average amount of actinobacteria for these subjects. Subset only actinobacteria abundances, and compute the average: ```{r} ``` Suppose now I want to compute the average abundance of each of the phyla. Subset each of the phyla, and put the abundances in a dataframe where each column containes each bacterial abundance. Then write a loop that will compute each average bacterial abundance. Display the result. ```{r} ``` Finally, use ggplot to create a visualization of abundances of each of the 4 phyla, broken down according to BMI. ```{r} ```

Answer 1

The student is asked to perform basic statistical analyses on a microbiome dataset to investigate potential correlations between BMI and microbial abundances. This requires calculating averages for bacterial phyla and visualizing them in relation to BMI, reflecting the broader scope of microbiome research on human health.

Step-by-step explanation:

The student's question involves conducting basic statistical analyses on a microbiome dataset to explore the relationship between body mass index (BMI) and microbial abundances within the human gut. The requested tasks include calculating the average abundance of actinobacteria and other bacterial phyla, then creating a visualization to illustrate the abundance of these phyla as it relates to BMI. This ties into studies conducted as part of the Human Microbiome Project, which seeks to understand the complexities of the microbial communities that inhabit the human body and their various roles in health, such as digestion, vitamin production, and even influencing mood and weight.

The gut microbiome is regarded as a 'forgotten organ' due to its significant role in human physiology, akin to multicellular organs like the liver. Understanding the relationships between microbiota and physiological traits such as BMI may offer insights into the impact of the microbiome on human health. These computations with the data can potentially shed light on whether certain phyla are correlated with BMI variations among individuals.