I found some slightly mouldy bread in the cupboard, cut off the mould and made toast. And I thought about bread and microbes.
For flavour, not as a raising agent, I make sour dough. My method is simple: I mix rye flour with water in a glass, cover it with cling film and put it on the countertop for a week or so. Lactic acid bacteria soon colonise the mix, lowering the pH to make the environment cosy for themselves and deter any other opportunistic microbes.
When the sour dough smells like vinegar I make bread dough with it, adding a second microbe: yeast fungus. The yeast eats sugar in the flour that the lactic acid bacteria haven’t had time to gobble up, and then it emits carbon dioxide gas, causing the bread to rise. (Rubbery gluten protein in the flour makes sure tenacious bubbles form instead of the gas seeping out of the dough.)
Then I bake the bread, which kills off the bacteria and yeast. After 50 minutes at 225 C, the bread is sterile. And delicious! But after a week or so, the bread gets recolonised by microbes, unwelcome ones. This time its another group of fungi, blue-green mould. Tastes awful, so I cut those bits off.
And my toast? I ate it all, sending it straight into the greatest throng of microbes it had ever encountered: the symbiont bacteria in my gut.