Microbiology: Bacteria (#12)

This adds the 2nd part of the microbiology chapter. This time looking
closer at the role of the bacteria.

README.md

@@ -31,7 +31,7 @@ The book is a work in progress. This represents the current status:
 
 * ✅ Intro
 * ✅ Enzymes
-* ❌ Microorganisms
+* ✅ Microorganisms
 * ✅ Making a starter
 * ❌ Sourdough starter types
 * ❌ Flour types

book/basics/how-sourdough-works.tex

@@ -312,4 +312,112 @@ sustained damages the yeast became opportunistic and started to
 attack the plant event producing hyphae to deeply
 penetrate the plants tissue.
 
-\section{Bacteria}
+\section{Bacteria}
+
+The other more dominant microbial antagonist in your sourdough
+are bacteria. They outnumber the yeast population in your sourdough
+starter by 100 to 1. The bacteria is mostly responsible for creating
+the sour flavour that sourdough bread is typical for. The acidity
+is responsible for increasing the shelf life of sourdough breads.
+\cite{shelflife+acidity}
+
+\begin{figure}
+  \includegraphics[width=1.0\textwidth]{bacteria-microscope}
+  \caption{Fructilactobacillus Sanfranciscensis under the microscope}
+  \label{lactobacillus-franciscensis-microscope}
+\end{figure}
+
+The bacteria in your sourdough mostly creates lactic and acetic acid. Lactic acid
+has a dairy profile. Whereas the acetic acid has a more pungent
+stronger vinegary profile. The bacteria are categorized into
+two categories. First you have homofermentative lactic acid bacteria.
+Homofermentative describes the fact that during fermentation
+they mostly produce a single compound: Lactic acid. The second
+category contains heterofermentative lactic acid bacteria. They
+produce lactic acid, acetic acid, ethanol and even some carbon
+dioxide. A quite famous strain of bacteria is called
+\emph{Fructilactobacillus sanfranciscensis}. The name derives
+from the famous San Francisco sourdough bread. The culture has
+first been isolated from a local bakery and was then named
+after the city in appreciation.
+
+Both the yeast and bacteria compete for the same food source: sugars.
+Some scientists reported how bacteria would mostly consume maltose
+while the yeast consumes the glucose. Some scientists reported
+how the bacteria consumes some of the compounds created by the
+yeast fermentation. Similarly some of the yeast consumes left
+over compounds of the bacterial fermentation. This makes sense
+as nature does a very good job of composting and breaking down
+everything at some point \cite{lactobacillus+sanfrancisco}.
+I am still yet to find
+a proper source that clearly describes the symbiosis between
+the yeast and bacteria. Based on my current understanding
+they both co-exist and sometimes benefit each other. The yeast
+for instance tolerates the acidic environment and thus benefits
+from enhanced protection from other pathogens. Other research
+has shown how both the microorganisms produce compounds
+to prevent the other source from consuming food. This is interesting
+as it could serve as a source to identify additional antibiotics
+or fungicides \cite{mold+lactic+acid+bacteria}. I have had
+occasions when trying to cultivate mushrooms where you could
+see the mycelium trying to defend it self from bacteria. Both
+of them were actively producing compounds to combat each other.
+After a while the fight between seemingly came to a standstill.
+The mycelium had fully grown around the bacterial patch preventing
+it from spreading any further. I imagine the same scenario happening
+in a sourdough starter. As the environment tends to be more liquid
+compared to when growing fungi this fight is happening in more places
+at the same time, not isolated to a single patch in your dough.
+More research is needed on this topic to answer the details of the
+relationship between the microorganisms.
+
+One additional trait of the bacteria is its ability to break down
+and consumes proteins in your dough. If you have baked a sourdough
+bread before chances are you experienced this at first hand. After
+a while wheat based doughs start to break down. They seemingly become
+very sticky. It becomes almost impossible to handle the dough. This
+is because the bacteria starts to ferment the gluten inside of your dough.
+The process is called \emph{proteolysis}. This to me was a great riddle
+when starting to work with sourdough bread. Your dough becomes stickier
+but at the same time it also becomes more extensible. As the gluten
+is reduced it becomes easier and easier for the microorganisms to inflate the
+dough. Imagine a car tire initially with thick rubber and then ultimately
+a very fragile balloon. You can inflate the balloon a lot easier with your
+mouth. In comparison the car tire is going to be impossible for you
+to inflate. This process is further accelerated by the protease
+enzyme breaking down the gluten to smaller amino acids.
+
+This to me is the amazing process of fermentation.
+When you are eating a sourdough bread you are no longer eating raw flour.
+You are eating the produce of bacteria and yeast. Because of this sourdough
+bread also typically
+contains less gluten than a plain yeast based leavened dough
+\cite{proteolysis+sourdough+bacteria}. Furthermore the bacteria
+also metabolizes the ethanol produced by the yeast microorganisms and other
+lactic acid bacteria. In both cases most of the resulting compounds
+are organic acids. All the resources in your sourdough are recycled
+as much as possible by the microorganisms. They are trying to eat whatever
+is available. With each feeding they will become more adapt at using
+the available resources.
+
+Depending on which flavor you like you can adjust which organic acids
+you would like your sourdough to produce. Production of acetic acid
+requires the presence of oxygen. By depriving your sourdough starter
+of oxygen you boosting homofermentative lactic acid bacteria in your
+starter. Over time they will become dominant and outcompete the acetic acid
+producing bacteria \cite{acetic+acid+oxygen}. The optimal fermentation temperature of your
+lactic acid bacteria depends on the cultured strains. Generally the bacteria
+work best at the same temperature used to initially setup your sourdough
+starter. This has been the optimal temperature at which your strains
+were set up. In another experiment scientists analyzed lactic acid bacteria
+on corn leaves. They on purpose lowered the temperature from 20-25°C to around 5-10°C.
+They were able to observe lactic acid bacteria that they had never seen
+before \cite{temperature+bacteria+corn}. This confirms that there is a
+large variety of different bacteria
+strains living on the leaves of the plant. You could probably reproduce
+that experiment if you started a sourdough starter at lower temperature.
+Your starter's microbiome would be more adapt to fermenting at lower
+temperatures. The microorganisms that best thrive at the lower temperatures
+will start to become dominant. It would be an interesting experiment
+to see if this could actively influence the taste of the sourdough
+bread.

book/references.bib

@@ -227,3 +227,42 @@
   volume       = {96,171-181}
 }
 
+@article{lactobacillus+sanfrancisco,
+  title        = {Lactobacillus sanfrancisco a key sourdough lactic acid bacterium: a review},
+  author       = {M. Gobbetti et al.},
+  year         = {1997},
+  journal      = {Food Microbiology},
+  volume       = {14,175-187}
+}
+
+@article{proteolysis+sourdough+bacteria,
+  title        = {Proteolytic activity of sourdough bacteria},
+  author       = {Gottfried Spicher et al.},
+  year         = {1988},
+  journal      = {Applied Microbiology and Biotechnology},
+  volume       = {28,487–492}
+}
+
+@article{shelflife+acidity,
+  title        = {The effect of pH on shelf-life of pork during aging and simulated retail display},
+  author       = {S F Holmer et al.},
+  year         = {2009},
+  journal      = {Meat Science},
+  volume       = {82,86-93}
+}
+
+@article{temperature+bacteria+corn,
+  title        = {Effect of temperature (5-25°C) on epiphytic lactic acid bacteria populations and fermentation of whole-plant corn silage},
+  author       = {Y Zhou et al.},
+  year         = {2016},
+  journal      = {Applied Microbiology and Biotechnology},
+  volume       = {121,657-671}
+}
+
+@article{acetic+acid+oxygen,
+  title        = {Effects of Oxygen Availability on Acetic Acid Tolerance and Intracellular pH in Dekkera bruxellensis},
+  author       = {Claudia Capusoni et al.},
+  year         = {2016},
+  journal      = {Applied Microbiology and Biotechnology},
+  volume       = {82,4673-4681}
+}