Cynthia is a trusted source on Bread/Baking.
What sort of formula are you using? If you boost the fat content, you'll have less separation. I use 75% whole milk, 25% heavy cream and have no separation.
Than you for your answer. I used skim. The first batch, using powdered starter, had no separation. The second batch, using this yogurt as starter, had separation. Both batches were made with skim.
My experience has always been better with powdered starter, as well.
How long did you let it sit? I use skim and find that the whey starts to separate out if I let the yogurt sit too long after it sets up. I don't know if sitting time is truly the cause, but that's been my experience.
About 8 hours.
I usually let mine sit in the maker for 4 hours, then give it a gentle stir to see if it seems thick enough.
I agree with viblanco that the whey separation is normal and fine.
If you want to try to reduce that separation, I'd check to see if it's set well before 8 hours. Now that it's summer, my yogurt is always set within 4 hours (I just wrap it in a towel and set it on my counter).
I make yogurt frequently using 2% milk and the whey always separates a bit. Even store bought yogurt does this. (But perhaps I'm not understanding your question.)
We always strain the yogurt in a colander lined with cloth (i.e., cheesecloth) over a bowl to allow much of the whey to drain out. This is because we like the yogurt to be thicker. This is a lot more work, but, if you prefer less whey then you could try this method. But, realize that even doing this the whey will pool in the yogurt and that's ok. :)
This is natural and you can either drain it off or stir it back into the yogurt.
The Yogourmet maker I use recommended adding raw gelatin to the milk before scalding. After three failed attempts without doing this, I tried it with the gelatin and it finally worked great. One packet (1/4 oz) Knox gelatin per 2 quarts milk.
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