Choir Performance

https://www.youtube.com/watch?v=gJTBGtZIHFg

Nucleotide Hits

Nucleotide Hits is based on particular DNA sequences from the 16S ribosome of the six most abundant orders present in subject B. The six most abundant orders present within subject B included; Clostridiales, Bacteroidales, Bifidobacteriales, Erysipelotrichales, Lactobacillales and Burkholderiales.
Days 17 through 25 were selected for subject B. This period was chosen as no irregularities in the data sets were observed during this time. The melodies were randomly generated to create the songs for this relationship. The chord progressions were based on the list of the above relative abundance orders of bacteria. The chords were randomly selected and was based on Robert Palmers song “Addicted to Love”.

 

Home is where the biome is

The relationship between the sensitivity of the human microbiome to the environment was assessed in this piece. It is important to note that only data from subject A was utilized during this analysis. Three time intervals were chosen to determine whether or not the relationship indicated any significance. Firstly a period was selected before the subject travelled, which included days 53 through 60. Secondly a period was selected where the subject was traveling abroad which included days 113 through 120. It is of importance to note that there was a period during travel where subject A was unwell, but this time period was not explored as a relationship due to the fact that it could not be compared to a time period where subject A was not traveling and unwell. Lastly a period was selected after the subject had returned from said travels which encompassed days 138 through 146.

The relative abundances of the bacterial families clearly indicated a shift in the composition of the orders present within the microbiome.

The four most abundant bacterial families over all three time periods were selected, namely: Actinomycetales, Bifidobacteriales, Coriobacteriales, and Lactobacillales. Bacterial data used were selected from high abundance bacteria over the selected time period. The bacterial names also possessed the appropriate quantity of syllables needed to add lyrics to 4/4 time. This meant that once the music had been written the names of the bacteria were suitable for use as lyrics. The chord progression was randomly generated based on Elton John’s “Rocket Man”.

Sam and Ella

The effect of an enteric infection caused by Salmonella was assessed in this relationship. LAB attached itself to the lining of the gut, were it is usually found in abundance. When a Salmonella infection occurs, the two organisms are now forced to compete for the same binding sites on the gut lining. During Subject B’s infection there were significant quantities of LAB found in the subjects stool samples as a result. The quantity of LAB was compared to that of Salmonella, within the stool samples by observing the amount of LAB present. The more LAB present within the sample would indicate that Salmonella is outcompeting the LAB for binding sites in the GIT. This selection indicates that one pathogenic organism has the ability to change the entire composition of the microbiome. The competition between Salmonella and LAB was clearly demonstrated in the change of pitch. As the pitch increases the relative abundance of LAB also increased. Days 150, 151, 153, 155, 156, 157, 158 and 159 were selected as they were the only days that illness was reported by the subject in the corresponding metadata files, it is important to note that only data pertaining to subject B was utilised for this analysis. The relative abundance OTUs of Lactobacillales was used to create a melody, revealing a clear pattern created over two bars in 4/4 time. This meant that a melody made up of 8 notes was generated in order to make a repetitive tune that would be simpler to learn. Again, random chords were chosen, in this instance based on an American folk song titled “Saint James Infirmary”.

Selected relationships

After analysing the data we have decided to explore the following relationships:

Carl and Wildene will be exploring the dynamics between Salmonella and lactic acid bacteria (LAB) of subject B during the period of his enteric infection.

Sam will be exploring the microbial diversity of subject A during normal daily life (the most abundant orders present).

Heinrich will be exploring the microbial diversity of subject B during normal daily life (the most abundant orders present).

Megan will be exploring the effects of on the microbiome during travel of subject A.

The dynamics between Salmonella and lactic acid bacteria (LAB) will be examined in order to convey to the children that some microorganisms are pathogenic (Salmonella), but that there are groups of organisms that are beneficial to your health and well-being (LAB).

The microbial diversities of subject A and B during normal daily life will be compared with one another to show that the microbial diversities of any two people differ from one another and that each person's microbiome is unique.

The effect of travel on the microbiome will indicate how a change in diet and geographical location influences diversity levels.

We have asked Peter Larsen to help us explore these relationships and to import selected data points into Impro-Visor to see if they are viable options for the conversion process.

Ethical consent

As part of our project we had to submit several ethical forms which proved especially difficult for us as we are used to working with microbes which, luckily, have no problem being experimented on. So as we are planning on using children to illustrate our findings we had several problems which we faced with regard to several long winded forms for committees, departments, the school principles, the parents and the children.

The main problem was the consent forms for the children. As they are in primary school we had to find a way to explain to them what exactly we were planning on doing which included telling them what the human microbiome is.

We actually had a lot of fun coming up with the idea of telling the children that we were going to have them sing songs about the tiny animals which live inside their bodies. However, to make sure they weren’t terrified of the idea of millions of tiny creatures all over their bodies we added that they were responsible for keeping their bodies healthy and happy. And we are pretty sure if we tell them they are singing about faecal matter (poo) that they will be more than thrilled to take part in our study!

Impro-Visor

This week we have started to analyze the data Lawrence David has sent from his study and downloaded the Impro-Visor program (http://sourceforge.net/projects/impro-visor/) used in the Microbial bebop study. Impro-Visor will allow us to convert datasets into sheet music which we will need to teach the choir our songs. 

In order to use the data in Impro-Visor we will have to normalize the data points of interest and then assign musical notes to each of the selected data points. The data points will be selected on the basis of what relationships we choose to investigate. 

This coming week each of us will identify one relationship and normalize the data points needed to import into Impro-Visor. 

We have also decided, after another skype meeting with Jack Gilbert and Peter Larsen, that to make the interaction with the school children more educational, we will be making them perform a small play while they are singing. A short interactive story explaining what happened to the subjects in terms of the relationships we have chosen to explore would probably be the most fun and educational for the children. If you have any suggestions or tips for us please feel free to leave a comment below.

We would also like to thank Peter for creating a small musical piece to show us that this project might actually work out in the end! 

Peter created and sent us a short song using Impro-Visor of the data obtained from Lawrence's data sets. Although the song is virtually composed, it demonstrates exactly what we aim to do with our project, but in an acapella fashion.

https://soundcloud.com/carlbruce/testingmicrobiomedata (melody = 6 most abundant orders, notes = caloric intake, chords = fiber)

Do Gut Bacteria Rule Our Minds?

Very interesting article exploring the importance of the role of gastrointestinal microbiota: https://ucsf.box.com/shared/static/pdz2z4b5fdvwlpr9hfdh.pdf 

Meet the team

(From the left): 

Sam Delport

Carl Bruce

Megan Cousins

Heinrich Kreuger

Wildene Le Roux

The Stellenbosch Microbiome Musical

As final year students at Stellenbosch University, we were given the instruction in our last semester as undergrad students to design and carry our own practical for our microbiology module relating to microbial ecology. So as any savvy undergrad students would do, we immediately started scouring through various scientific articles and journals in order to find something we could use as a base for our practicals during the seven week peroid we have to carry out our experiments. 

One article we found online immediately caught our attention: "Microbial Bebop: Creating Music from Complex Dynamics in Microbial Ecology" (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058119). The concept of translating complex data sets into a sonic format in order to involve the non-scientific public seemed to us like an ingenious idea. In order to gain a better comprehension of how the data was converted into music, we emailed one of the authors, associate professor at Chicago University, Jack Gilbert, and set up a skype meeting.

 
During our skype meeting, Jack assisted our group immensely by helping us in formulating exactly what we will be basing our practicals on for the semester. He suggested that we use the data from the paper "Host lifestyle affects human microbiota on daily timescales" (http://genomebiology.com/2014/15/7/R89) in order to generate music from the microbiomes of the two subjects studied in the paper. During our skype meeting with Jack, Peter Larsen (the creator of the microbial bepop sofware) also joined in and further helped guide our group in explaining what would be needed to create the music.

Our next step was to contact one of the authors of "Host lifestyle affects human microbiota on daily timescales" in order to find out if they would be willing for us to use the data they collected in their study in our experient. We contacted one of the authors, an associate professor at Duke University, Lawrence David, to find out. In the skype meeting with Lawrence, we explained to him what we are planning to do and he gave us the go ahead to use the data collected in their study. He also sent us data sets generated for their original study in order to help us with the handling of the data. 

With the data we have assembled we aim to generate sheet music by using Peter Larsen's microbial bebop sofware to sonically explore the unique microbiomes of the subject's involved in Lawrence David's study. 

After the generation of the sheet music, we will be approaching a local primary school choir to convey the differences and similarities of the two individual's microbiomes in an acapella musical. In this manner we hope to involve the local community, the non-scientific public as well as the youth in science. 

The group will be updating this blog weekly in order to track our progress and hopefully generate greater public interest in science.