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I’ve found many sources about the positive effects of kefir for the digestive system. However I haven’t found any information about the fermenting process.

What is the exact biology (chemistry?) behind the process of milk becoming kefir?

What do the kefir grains exactly consume from the milk? And what do they defecate? What happens inside the microbes?

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    $\begingroup$ I think this can be answered to some degree with links to some deeper references. In my opinion no need to close it. $\endgroup$ – Chris Mar 12 '15 at 20:20
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The fermentation is relatively complex, as quite a number of different bacterial species and yeast live in the Kefir grains. These are made of of the polysaccheride kefiran which immobilizes the bacteria (in contrast for example to yoghurt). The microbes live symbiotic on this matrix.

According to the references a number of different microorganisms has been found, these include mainly Lactic acid bacteria, followed by yeasts and acetic acid bacteria. The species include: Lactobacillus paracasei, Lactobacillus parabuchneri, Lactobacillus casei, Lactobacillus kefiri, Lactococcus lactis, Acetobacter lovaniensis, Kluyveromyces lactis, Kazachstania aerobia, Saccharomyces cerevisiae and Lachancea meyersii.

In brief the lactobacilli break down lactose to produce lactic acid, while the yeasts make alcohol and carbon dioxide while the acetobacter species make acetic acid. This consumes the lactose and the fat content of the milk making it suitable for lactose intollerant people. It also lowers the pH of the kefir. The exact mixture is hard to identify as this contains strongly on the exact composition of the kefir grains.

If you are interested further, I recommend you have a look into the references, I find both articles relatively good to understand.

References:

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Well essentially the added Lactobacillus species ferment lactose and other sugars to lactic acid, thus lowering the pH of the product (they take up lactose use it as an energy source under anaerobic conditions and secrete lactic acid). This gives the kefir and other fermented milk products their sourness. Also the lower pH prevents many other bacteria from growing in the product so this is also serves as a natural preservation method. Further more the low pH can denature some of the protein in the milk/kefir resulting in a more solid form. Many of these Lactobacillus species or their relatives are natural part of our gut flora.

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