Fruit Flies and another Pan Integrale

Pan Integrale: 100% whole wheat sourdough loaves @ 85% hydration

Fruit Flies

It's fruit-fly season again.  I've seen the odd little flying critter skating around my sourdough dish.  I leave my sourdough out on the counter most of the year at room temperature, but recently I thought I might reconsider that plan.

In the past when fruit-flies became a problem, I'd block off the air hole to my culture with gauze and put a fruit-fly trap beside the container (also containing sourdough).  I was finding the flies could get through the gauze, but that they would not generally attempt it if they had easier access to the trap.

Why the concern now?

Recently I found a reference to an article that drew my curiosity.  Vogel et. al. "Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs" (2011) Microbial Cell Factories. 10 (Suppl 1) 56  discusses how, although there are many different lactobacillus bacteria in sourdough, over time the predominant species will be Lactobacillus sanfranciscensis, which was first isolated in the famous San Francisco sourdough cultures.  It occurs to me now that this really shouldn't be too surprising for Darwinists: since this tiny bacteria does so many good things for sourdough, of course we are going to be selecting for it in our culture, and we are going to be providing them with an environment where they can thrive.  We have learned to select them through the way we refresh our sourdoughs -- even long before we knew what they were, we could see their effects.

Vogel et al wrote, 

"With the exception of one report by Groenevald et al, who allotted isolates from fruit flies exhibiting 97% rDNA sequence homologies as L. sanfranciscensis, this species has only been isolated from sourdoughs…"

This caught my attention: a sourdough lactobacillus species shares DNA with fruit flies?  

Er, no.  

I googled Groenewald's article, Groenewald et al "Identification of Lactic Acid Bacteria from Vinegar Flies based on Phenotypic and Genotypic characteristics" (2006, Dec) American Journal of Enology and Viticulture 57(4) pp 519-525.  What Vogel meant was, Groenevald et al isolated some bacteria from the gut of a fruit fly that was captured in a winery.  They apparently wanted to see what it had been eating (and/or leaving behind after it ate!).  I've only read the abstract of Groenevald et al's article, and it had this to say of the 30 odd species of fruit-fly gut bacteria they found there:

"The majority of isolates belonged to the species Lactobacillus planetarium, but Lactobacillus paracasei, Lactobacillus sanfranciscensis, Leuconostoc mesenterioides subsp. mesenteries, Lactobacillus lactis subs. lactis, Enterococcus faecalis and Pediococcus pentosaceus were also identified…"

This again is not entirely surprising.  Fruit flies are attracted to the fermenting fruit, and they are going to ingest some of the bacteria that abounds on that fruit.  And the bacteria they eat are going to live in their gut (just as they live in ours).  Even more so, because unlike humans, fruit flies do not cook their fermented products in a hot oven.

I recalled some of the early experiments with sourdough, long before scientists had any idea of what was causing bread to rise.  They did not understand how sourdough worked, in the beginning.  How did ground-up grains ferment?  What was causing it?  An early idea was that fruit flies were carrying the unseen element in on their feet.  This had to be rigorously controlled for, in experiments.  And the scientists found that indeed, the fermentation happens even without fruit flies.  

But in fact, fruit flies can help it along.  These little buggers can fly away with a few bacteria in their gut and poop it into the next batch when no one is looking.  And if it was only L. sanfranciscensis, maybe no one would complain.  But when I read that Groenewald found "Enterococcus faecalis", I wrinkled my nose in disgust -- anything with a name based on 'faeces' can't be too wonderful, I thought.  But when I looked up the wiki, Enterococcus faecalis (which is considered prebiotic) it doesn't sound as bad as E. faecium (which could be pathogenic).

So let's look closely at all the species named by Groenewald:

1. Lactobacillus planetarium

This LB has been found in many fermented products.  Wen-hua et al found it in Sauerkraut, for example, where it grows rapidly, and produces acid quickly and prevents the growth of E. coli and staphylococcus.  Though Wen-hua felt it prevented the growth of E. coli and staphylococcus, Okoro's team did not find that this particular LB inhibited their growth.

It can produce conjugated linoleic acid (CLA), which has garnered a lot of interest lately for its anticancer properties and as a weight control supplement. It also produces teichoic acids,  which some have claimed has anti-inflammatory effects.

2. Lactobacillus paracasei 

This is one of the LB species that has supposed probiotic effects, but currently the science hasn't proved its worth.  Studies are ongoing for its ability to suppress the common cold, but the European Food Safety Authority has so far rejected its claim as a probiotic.

Nevertheless, Aronsson et al showed that it may alter fat storage by altering levels of Angiopoietin-Like 4 Protein (ANGPTL4), which has also been studied extensively recently for their anti-tumor growth ability.

3. Lactobacillus sanfranciscensis

The famous sourdough bread Lacto Bacillus.  This LB has been studied extensively, because it is so important to our bread-making culture.  For example, its growth under various environmental influences is well documented and mathematically modelled by Ganzle et al.

4. Leuconostoc mesenterioides subsp. mesenteries

Bergey's Manual of Systematic Bacteriology v3 (which I found earlier on Google Books, but the link doesn't seem to be working any longer) discusses Leuconostoc bacteria; there are 10 species, and 3 subspecies for Leuconostoc mesenteries.  The subspecies found in our fruit fly is subsp. mesenteries; it ferments the sugars in fruit (and is important for the beginning stages of fermenting vegetables like sauerkraut and kimchi) and this little bacteria can make dextran from sucrose.  It has been a problem in the sugar cane industry, where it can make the sweet stuff a bit sour tasting.

Usually subsp. mesenteries likes a middle range pH (grows at 6.5, not at 4.8), but it is found in most acidic leavened breads like idli, doss and tef (p. 628).  Its optimal temperature range is 20-30 degrees C, but grows even in cultures with a temperature of 5 degrees F. 

5. Lactobacillus lactis subsp. lactis

Another nonpathogenic LB bacterium. Commonly used to start cheese fermentation, and well-known to geneticists (this is the subspecies that is best used for soft cheeses).  This one lives in the gut of most animals that consume it: you've got it too.

6. Enterococcus faecalis 

This species has been studied widely because it is resistant to vancomycin (was the first bacteria to be found resistant to that potent antibiotic), and the fear is, it may transfer its resistance genes to other bacteria that can cause lots of troubles in hospitals.  "Enterococci are members of the healthy human intestinal flora, but are also leading causes of highly antibiotic-resistant, hospital acquired infection" (Shankar et. al., "Modulation of virulence within a pathogenicity island in vancomycin-resistant Enterococcus facecalis" Nature, (2002, June) 417, pp 746-750

In the GI tract, this is fairly benign, but if it gets in the bloodstream, or in the urinary tract, you could have a problem -- especially if you are already ill.  That is why hospitals everywhere are trying to be diligent about handwashing, and infection control.  Despite what I said above about its dangers compared to E. faecium, it can still cause a lot of problems, including death from bacteremia if the patient is already ill.   Noskin G. et. al. "Enterococcus faecium and Enterococcus faecalis Bacteremia: Acquisition and Outcome" (1995) Clinical Infectious Diseases. 20(2) pp 296-301

7. Pediococcus pentosaceus 

This species of bacteria is used to ferment sausages, for it helps preservation by providing compounds (e.g. Pediocin A) that give its environment a broad-band anti-bacterial coverage.  It forms many different volatile compounds and flavour molecules, in addition to providing lactic and acetic acids.  Some of the volatile compounds that have been identified: 

"aliphatic and aromatic hydrocarbons, aldehydes, ketones, alcohols, phenyls, carboxylic acids, esters, nitrogen compounds, sulphur compounds, chloride compounds, terpenes and furans,"

but it is unknown whether this bacteria is the one producing all of them, in this complex interaction.

Johansson, G. "Lipolysis, proteolysis and formation of volatile components during ripening of a fermented sausage with Pediococcus pentosaceus and Staphylococcus xylosus as starter cultures" Meat Science (1994) 38(2) pp 203-218.  P. pentosaceus has also been used to ferment cheese and wine.

The final verdict on Fruit Flies:
So, do I need to refrigerate my sourdough?

Not based on what I've learned.

The stuff that fruit flies drag in on their feet (and elsewhere on their tiny bodies) may not be totally benign, but many of the bacteria turn out to be beneficial and prebiotic or probiotic and often important in fermentation.  Sure, it sounds disgusting.  But most of the best parts of life are bound up with goo and ooze.  It is where life itself began.  Embrace the root of it all.  And let the tiny flies have a teensy bit of sourdough.  How much can they eat?  Remember, you are baking your bread, and most of these bacteria won't survive the heat of the oven.  They will leave behind things that are beneficial though, including enhanced flavours.

Remember, our ancient ancestors didn't refrigerate their sourdough.  They had to battle fruit flies for their food.  But they made bread, flies or no -- and they survived.  They may have placed their starter in a cool spot, perhaps in caves or underground or root cellars.  A place with a more or less constant cool temperature year round would have been ideal for keeping sourdough viable and dependable -- but it wouldn't have kept the fruit flies away.  I'll try to do keep mine coolish -- but only refrigerate when I go away for a week or two at a time.


Today's Bread:
A Tartine-style Pan Integrale again.  This one was very good.  I needed both loaves mostly for myself, to get me through a 3-day weekend of work.  We were short-handed over Father's Day weekend.  I used a stiff starter and 85% hydration and I refrigerated the dough overnight while proofing.  The loaves kept their shape in the oven and plumped up nicely.  Taste was very good.

Notes to Myself

• Don't worry too much about fruit flies.  But don't eat raw sourdough that has been left out, either.  
• This was one of my best breads yet.  I had tossed a few sesame seeds in the bottom of the banneton and they roasted nicely atop the loaf, complementing the flavour of the whole wheat quite nicely.
• The second loaf began to stale on the 3rd day.