Bacteria section (#16)

* started editing bacteria section

* finish first sweep of edits to bacteria section

* final polish

* finished bacteria section

book/basics/how-sourdough-works.tex

@@ -323,11 +323,12 @@ so that they could penetrate the tissue of the plants.
 
 \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.
+The other most dominant microbial antagonists in your sourdough are bacteria.
+In fact, they are so dominant that they outnumber the yeast in your dough 100
+to 1. Whereas yeast provide leavening power, bacteria create the distinct
+flavours for which sourdough has been named. These are due to the acidic
+byproducts that result from bacterial feeding. As an added bonus, these acids
+can significantly increase the shelf life of sourdough breads.
 \cite{shelflife+acidity}
 
 \begin{figure}
@@ -336,97 +337,103 @@ is responsible for increasing the shelf life of sourdough breads.
   \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.
+There are two predominant types of acid produced in sourdough bread: lactic and
+acetic. In terms of flavor, lactic acid has clear dairy notes, while acetic
+acid tastes of vinegar (of which it is, in fact, the primary ingredient!) These
+acidic byproducts are produced by both \emph{homofermentative} and
+\emph{heterofermentative} lactic acid bacteria.
 
-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.
+\emph{Homofermentative} means that, during fermentation, the bacteria produce
+a single compound: in this case, lactic acid. \emph{Heterofermentative}, on
+the other hand, means that other compounds are also produced: in this case,
+not only lactic acid, but also acetic acid, as well as ethanol and even some
+carbon dioxide, two byproducts ordinarily associated with yeast. One quite
+famous strain of lactic acid bacteria, \emph{Fructilactobacillus sanfranciscensis},
+derives its name from the equally famous San Francisco style sourdough bread.
+The first isolated culture came from a bakery in this city, hence the name.
 
-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.
+Yeast and bacteria both compete for the same food source: sugar. Some scientists
+have reported that bacteria consume mostly maltose, while yeast prefer glucose.
+Others have reported that bacteria feed on the byproducts of yeast and vice
+versa. This makes sense, as nature generally does a superb job of composting
+and breaking down biological matter \cite{lactobacillus+sanfrancisco}.
 
-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.
+I have yet to find a proper source that clearly describes the symbiosis between
+yeast and bacteria, but my current understanding is that they both co-exist and
+sometimes benefit each other, but not always. Yeast, for example, tolerate the
+acidic environment created by the surrounding bacteria and are thus protected
+from other pathogens. Meanwhile, however, other research demonstrates that both
+types of microorganisms produce compounds that prevent the other from
+metabolizing food---an interesting observation, by the way, as it could help to
+identify additional antibiotics or fungicides \cite{mold+lactic+acid+bacteria}.
 
-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.
+In the past, I've tried cultivating mushrooms and observed the mycelium
+attempting to defend itself against the surrounding bacteria; both types of
+microorganisms actively produced compounds to combat each other. And yet,
+after a while, the fight seemed to reach a standstill, as the mycelium had
+fully grown around the bacterial patch, preventing it from spreading further.
+I imagine a similar scenario could be playing out in our sourdough starters,
+although, given that the sourdough environment tends to be more liquid, this
+fight would have to take place everywhere in the dough and not just in an
+isolated patch. More research on this topic is required to better understand
+the details of the relationship between yeast and bacteria.
+
+One other interesting trait of sourdough bacteria worth mentioning is their
+ability to break down and consume the proteins in your dough. If you've baked
+sourdough before, chances are you've experienced this first hand. You'll recall
+from the \emph{Enzymatic reactions} section that protease breaks down the
+gluten network in your dough, resulting in a sticky mess if left unbaked for
+too long. The bacteria, too, consume and break down the gluten in your
+dough through a process called \emph{proteolysis}.
+
+This, to me, was a great riddle when I first started working with sourdough.
+On the one hand, it makes the dough stickier. On the other, it makes the dough
+more extensible and easier to work with. As the gluten is reduced, the dough
+becomes easier for the microorganisms to inflate, allowing it to rise. This
+could be likened to the level of effort required to inflate a thick rubber tire
+versus a thin and fragile balloon. The latter would be easy to blow up with
+your mouth, while the former would not.
+
+Unsurprisingly, proteolysis is further accelerated by the protease enzyme
+previously discussed, which aids in the breakdown of gluten into smaller,
+more easily metabolized amino acids.
+
+This, to me, is the amazing process of fermentation. When you eat sourdough
+bread, you are not merely consuming flour and water but the end result of
+complex biological processes accomplished by the bacteria and yeast. Because
+of the added bacterial component, sourdough bread typically contains less
+gluten than a pure yeast-based dough \cite{proteolysis+sourdough+bacteria}.
+Furthermore, the homofermentative bacteria metabolize the ethanol produced by
+the yeast and other heterofermentative lactic acid bacteria. In both cases,
+most of the resulting compounds are organic acids. Every natural resource in
+your sourdough bread is recycled by the microorganisms inside, who are all
+trying to eat whatever is available for as long as possible, and with each
+feeding, they become more adept at utilizing these resources.
+
+Depending on which flavour profile you prefer, you can select for one organic
+acid or another. Acetic aacid production requires oxygen, and by depriving
+your sourdough starter of it, you can boost the population of homofermentative
+lactic acid bacteria. 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 strains you've cultured in your starter. Generally, they work best at the
+temperature used to create your starter because you've already selected for
+bacteria that thrive under that condition.
+
+In one noteworthy experiment, scientists examined the lactic acid bacteria
+found on corn leaves. They lowered the ambient temperature from 20-25°C to around
+5-10°C and afterward observed varieties of the bacteria that had never been
+seen before \cite{temperature+bacteria+corn}, confirming that there is, in
+fact, a large variety of bacterial strains living on the leaves of the plant.
+
+Incidentally, you could perform a similar experiment by kicking off a sourdough
+starter at a lower temperature. In theory, the microbiome should adapt, as the
+microorganisms that thrive the most at lower temperatures will start to become
+dominant. It would be interesting to see if this could actively influence the
+taste of the resulting bread.
+
+One last footnote worth mentioning: Some sources say that fermenting at a
+lower temperature can increase acetic acid production, while fermenting at a
+warmer temperature can boost lactic acid production. I could not verify this
+in my own tests. More research is needed on the topic.