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One of the “tricks” used in Peter Reinhart's Whole Grain Breads is to soak various whole grains in water, at room temperature, for 12–24 hours. For example, in his “Multigrain Stuan” formula, he calls for leaving 2 oz whole wheat flour, 6 oz mixed grains, .14 oz salt, and 6 oz milk, buttermilk, yogurt, soy milk, or rice milk out, covered lightly in plastic wrap, at room temperature, for 12–24 hours.

As to which grains to use, there is a note to see the comment. The comment talks about which grains to cook vs. use uncooked. It mentions using brown rice, cooked.

But rice can contain B. cereus spores, which are heat-stable and will survive cooking; and it seems like this room-temperature soaker would be a nice environment for them to grow. The pH isn't low enough (less than 4.3) to stop them, for example. And B. cereus produces heat-stable toxins, which would assumably survive baking.

Is there something I'm unaware of that makes this recipe safe?

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Baking at 180ºC should be a killer, or not. –  BaffledCook Apr 1 '12 at 8:10
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If you use yogurt (or cultured buttermilk) it sounds like the creator of the recipe is trying to get the Lactobacillus in the yogurt to start metabolizing some of the components of the mixture. Otherwise, it sounds like they want some random yeast to start the fermentation for the bread. There is definitely a risk of other potentially pathogenic organisms growing also as there is a source of moisture and food with those ingredients and a suitable temperature.

For buttermilk or yogurt specifically: From a safety standpoint, you would need to consider what the load of pathogenic bacteria is compared to the intentionally inoculated Lactobacillus as the Lactobacillus may interfere with the germination of B. cereus due to creation of an acidic pH.

In general: As per http://smas.chemeng.ntua.gr/miram/files/publ_77_13_1_2004.pdf it takes approximately 20 hours for a 2-log increase in concentration of B. cereus (1 bacteria dividing into 100 offspring), and as per http://www.cdc.gov/mmwr/pdf/wk/mm4310.pdf it takes 10^5 B. cereus per gram of food for symptomatic illness, so your initial concentration in the ingredients (assuming the growth conditions in the first paper) would need to be 10^3 per gram overall of viable organisms to get to the toxic level in this time frame (potentially meaning that your ingredients carrying B. cereus in and of themselves would need to be relatively close to the toxic range to start since not everything would be presumed to be contaminated). Since it takes time for spores to germinate, if we are talking about no viable organisms and spores only it would take an awful lot.

Regardless, I trust cultured organisms (yogurt, yeast, etc.) more than the naturally-occurring ones I might find at home (particularly since I work at a hospital and might track some nasty stuff home with me). I would inoculate it with some trusted microorganisms if I was making the recipe.

With that said, the standard caveat of if it smells bad after letting it sit out it probably should be thrown out would apply. Also, although I have a degree in biochemistry I am not a microbiologist, toxicologist, or pathologist.

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The stated aim is actually for some enzymes present in the flour to start work, if I remember correctly. But those papers you give explain clearly how it can be relatively safe, thank you. –  derobert Aug 22 '12 at 20:36
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