[claponsie]

Just curious, why did you decide to start reusing yeast?

Besides the reasons others have mentioned, because it is const effective.  You don't consider the cost of a $7 vial of yeast when you brew 5 gallons, but when you brew 35 gallons it gets pretty costly.  We don't propagate our own yeast.  We purchase our yeast directly from WhiteLabs and it has been appropriately propagated for pitching into out 1bbl batches.  You can either propagate your own yeast for every batch, or you can reuse yeast from the previous batch.  Purchasing pre-propagated yeast for each batch is expensive.  They are essentially the same options with the same kinds of risks.

[claponsie]

You should be aiming to use enough yeast to wrap fermentation up in a week to 10 days - use the yeast pitching calc at www.mrmalty.com to make sure you are pitching enough yeast. 3 weeks is too long. Make sure you are aerating the cold wort properly before pitching. Make sure the wort is cooled below 70 before pitching. Preferably you don't want the temp of the fermenting beer to rise over 70 degrees for the first 2 or 3 days, but on your system that may not be possible, though it is certainly ideal.

I'd recommend harvesting yeast not long after fermentation is actually finished and keep the generation from 6-9 or less. Don't use yeast from higher gravity fermentation (not much higher than 1.065). Make sure your water has at least 50 ppms of calcium or you can have sluggish fermentations.

Fresh, healthy yeast and plenty of it. Aeration, yeast nutrients (I like the wyeast nutrient), and temp control are your keys to healthy fermentations.

Thanks, these are all good tips.  What do you think the chances are that I didn't pitch enough yeast if I reused the entire yeast slurry from the previous batch?  I'd like to get a microscope soon so that I can do some basic cell counting and pitch more accurate and consistent amounts.  We don't oxygenate our wort yet so that could be part of the problem.  I don't think the fermentation temps were the problem because they rarely fluctuate and every time I check the chamber temperature, we are at 69 degrees.  I've almost finished building my BrewPi though, so that will help with that.  We probably collected the yeast too late as the beer had been sitting on it for about 3 weeks when we collected it.  Thanks for the tips, they are much appreciated.

[narvin]

If you are not harvesting yeast, even at the 5 gallon level, your missing out.

Yes, but I'd add the caveat: harvest and reuse yeast *fresh*.  You can get away with storing it in the fridge, but even after only a couple of weeks you might want to make a starter.  Or you may have no problems using yeast slurry older than that, but there's no guarantee.  At the 5 or 10 gallon homebrew level, yeast is cheap, so the benefits are smaller.  I personally like to make so many different styles that unless I know I'm making a string of american ales or german lagers, I'm not going to bother saving yeast.  It is a great idea to plan a few beers in a row where you can reuse the yeast immediately and go from weaker to stronger beer... like Keith said, plan it so you make a high gravity beer after using a smaller beer to propagate.  However, I'm not always this organized (or patient).

Which brings me back to the OP: when did you harvest the yeast?  This sounds like a yeast health problem.  The cone of a conical get get hotter than the rest of the beer, especially if it's not cooled, and the longer beer sits on it, the less healthy it is.  If you follow Keith's advice, you should be good to go.

Edit: yes, this sounds like the issue.  You probably pitched unhealthy yeast, and without aerating growth of new yeast was further inhibited.

We probably collected the yeast too late as the beer had been sitting on it for about 3 weeks when we collected it.

[fmader]

Well maybe it's something I'll try.

Go for it! It's really not difficult nor that time consuming. I don't harvest yeast that I don't use often, but white labs 001 is a staple for my brew operation. I love my hobby and I love to do it often... So I need to be cost effective. I used to brew on a batch-by-batch basis, which can get expensive. I buy grain and hops in bulk and reuse yeast. That cuts cost nearly 50% per batch. If I can get six batches out on one $8 vile of yeast, I'm saving $40... That's a sack of grain! Also, the nearest places I can buy quality liquid yeasts are 45 minutes away, so it's convenient always having it on hand. It has also been mentioned that the yeast really comes into its own third or fourth time around. You don't need a conical fermenter to harvest yeast. I would investigate this practice... Well worth it

I will add that starters are necessary and I use Wyeast yeast nutrient in the starter and the actual brew.