• Unfermented beans do not produce cocoa flavor on roasting.
• Produces acids, alcohols, & heat that penetrate the testae.
• Metabolic activity stops. Kills the embryo.

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• Allows the diffusion of metabolites in & out of seed.
• Which triggers complex biochemical reactions in the cotyledon.
• Initiates chemical reactions that will form the precursors.

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• No evidence that microbial enzymes penetrate testae.
• Rather enzymes inside the beans are activated by microbial metabolites.
• Exact role of microbes in final product is not understood.

Plesse note that unless otherwise stated, I created all figures and take full responsibility for their content.

• Cacao to cocoa workflow was made by the author using the R package DiagrammeR and adapted from Aprotosoaie, Luca, & Miron (2015) Flavor Chemistry of Cocoa and Cocoa Products—An Overview. Comprehensive Reviews in Food Science and Food Safety 15:73-91.
  
• Images of pre and post fermented testae & fermented beans were modified from Brillouet & Hue (2017) Fate of proanthocyanidins and anthocyanins along fermentation of cocoa seeds (Theobroma cacao L.). Journal of Applied Botany and Food Quality 90:141-146. Figures 1 & 5.
• Photos on the cacao to cocoa slide credits: left photo entitled Cocoa beans in a cocoa pod by Keith Weller (Kbh3rd) was obtained from Wikimedia Commons licensed under CC-0. Original file; right photo was obtained from this website (original credit could not be ascertained).
• Close-up photo of cacao beans entitled bean in pod Cocoa beans in cocoa pod at El Trapiche in Costa Rica by Aude was obtained from Wikimedia Commons licensed under CC BY-SA 3.0. Original file
• Images from the Mystery of Lambic Beer were modified from the original publication by Jacques De Keersmaecker.
• Figure of parenchyma cells was modified from the paper by Elwers, Zambrano, Rohsius, Lieberei (2010) Histological features of phenolic compounds in fi ne and bulk cocoa seed (Theobroma cacao L.). Journal of Applied Botany and Food Quality 83:182-188. Figure 3.

Credits continue on the next slide

• The Sankey diagram was made using the Sankey Diagram Generator using data from da Veiga Moreira, de Figueiredo Vilela, Santos, Lima, Schwan (2018). Volatile compounds and protein profiles analyses of fermented cocoa beans and chocolates from different hybrids cultivated in Brazil. Food research international 109:196-203. Table 1.
• Timeline of succession and metabolite developement was reproduced from De Vuyst &Weckx (2016). The cocoa bean fermentation process: from ecosystem analysis to starter culture development. Journal of Applied Microbiology 121:5-17. Figure 1.

Images on the History of fermentation slidecome from the following references:

• McGovern, Zhang, Tang, Zhang, Hall, Moreau, Nuñez, Butrym, Richards, Wang, Cheng, Zhao, Wang (2004). Fermented beverages of pre- and proto-historic China. Proceedings of the National Academy of Sciences. 101:17593-17598. Figure 1.
• Henderson, Rosemary, Hall, Gretchen, Hurst, Jeffrey, McGovern (2007). Chemical and archaeological evidence for the earliest cacao beverages. Proceedings of the National Academy of Sciences. 104:18937-18940. Figure 2.
• McGovern, Mirzoian, Hall (2009). Ancient Egyptian herbal wines. Proceedings of the National Academy of Sciences. 106:7361-7366. Figures 1 & 2.
• Boethius (2016). Something rotten in Scandinavia: The world’s earliest evidence of fermentation. Journal of Archaeological Science 66 (2016) 169-180. Figure 10.

Here is the recipe I used to make the chemical collage.

1. Get a list of compound names, e.g., from a paper.
   
2. Put the names into a single column text file, say compounds.txt.
   
3. Upload the file to PubChem Identifier Exchange Service. Under Input ID List select Synonyms from the drop-down menu and the Choose File radio button. Upload the file. Under Operator Type select Same CID from the drop down. For Output IDs select CIDs and for Output Method choose the two column option. Then hit Submit Job.
   
4. Download the resulting file. This will have the CID to Compound name. Delete the compound name so there is a single column of CIDs. Save a new file with the csv file extension.
   
5. Upload file to the PubChem Download Service. Select PubChem Compound, under Choose a format select Image then hit the Download button. You should get a directory of .png image files, one for each CID.

6. Once I had .png files for all of the compounds I did some cropping in Gimp.
7. Then I used an online tool called Photo Collage to put all the images together and Inkscape to add text and finalize the image. Finally I used this tool to compress the image.

• reveal.js An HTML Presentation Framework in R Markdown.
  
• DiagrammeR an R package for flow charts.
  
• treemap an R package for treemap visualization.