It smelled amazing. Walking there among the barrels that housed the most popular stout in America, I couldn't believe that anything was wrong. I felt like I was wrapped up in a blanket next to a warm fire, drinking a stout as my companion opened a bourbon. That woody, musty smell would make anyone feel at home.

But, of course there was something wrong. Goose Island's Bourbon County stouts were infected -- with Lactobillicus acetotolerans, a substance that was only months ago shown to be a threat to good-tasting beer. That little bacteria was the source of the company's biggest recall in 28 years.

Some day, a brewer may use that bacteria on purpose, since it isn't harmful to humans and creates a souring effect, but right now, the company is considering their options for the popular line going forward. According to one source, it's down to a choice between a deep clean and a pasteurization process.

Most brewers would probably favor a deep clean. Cleaning is a critical part of any brewing process, and in a facility that houses both sours in wine barrels (in a temperature-controlled environment to manage the souring) and also stouts in bourbon barrels (non temperature-controlled, so that the wood breaths the beer in and out), it's even more important.

You don't want the sour bacterias getting into the stouts. That may not describe exactly what happened here, and if you look closely around the facility, you'll notice that there are two sets of everything in order to keep this from happening. Here are some "BCS" hoses, for example. A deep clean would just be a re-set, and a hope that the bacteria doesn't come back, but it would be a normal part of the process.

Pasteurization is more controversial, but there are proponents of the practice.

Anchor Steam pasteurizes, and their brewer answered questions about it. He affirmed that nobody in his organization could tell the difference in taste before and after the process, and pointed out why Anchor Steam had chosen to flash pasteurize their beers.

The basic purpose of pasteurization is to ensure that there are no microorganisms in the packaged beer that could cause it to spoil over time. In modern times, strict adherence to high levels of industrial sanitation in brewing has virtually eliminated the possibility bacterial contamination, but pasteurization continues as an extra level of quality control.

But the process of flash pasteurization seems iffy to some. It's not crazy to be worried about flash heating beer to kill the bacteria in it and then cooling it down -- changes in temperature are a crucial part of brewing beer, from beginning to end. Adding another temperature change might seem like a bad idea to some, even if fancy equipment like the below can cut the high-temperature time down to 20 seconds.

Even if it's only for a short time, and the beer is evenly heated, the beer is still being cooked for a short time, and that should be a concern for fresh beers. Albany Times Union beer blogger George de Piro once wrote:

Pasteurizing does indeed preserve beer from microbial spoilage, but at a very high price. The beer leaves the brewery tasting like it is already a few weeks old. Hop aroma and flavor will be more muted than the unpasteurized product, and there may be toffee-like or honey-like notes indicative of oxidation.

The science concurs. Craft Brewing Business actually ran the tests, and the results are fairly conclusive. Here's the first of their three case studies, which all found the same end. Flash pasteurization kills yeast in the beer.

Abita Brewing Co. Using a 71.5ºC and 20 seconds flash pasteurization regime. Production results for bottled beer from 154 samplings were averaging <40 yeast cells/100ml., <20 lactobacilli/100ml., <20 Pediococci/100ml. prior to flash pasteurization and <1 cell/100ml. of each after flash pasteurization.

There is one caveat for Goose Island. That extra honey/toffee taste listed above may be a feature in Goose Island stouts, rather than a bug. And since those stouts are aged for months in barrels anyway, the fresh hops flavor is not as integral to the taste of the beer. You don't want any yeast in a barrel-aged stout anyway, so maybe Pasteurization is the way to go here. Flash pasteurization may be a bad solution for some beers, and yet a good solution for Bourbon County Brand Stout.

On the other hand, BCBS Stouts have dominated our leaderboards since day one. They have been a well established brand with well established taste profiles. Does Goose Island want to risk that brand with a process that has been shown to kill compounds that affect flavor? Do they know if the infection came from the bottling line (after pasteurization) or earlier? If they pasteurize the bottles with Tunnel Pasteurization, which requires more time hot, will it affect the beer's taste more? Or do they want to start with a deep clean and risk damaging their brand with a return infection?

That's a difficult choice. Good luck to the Goose Island team in their ongoing debate.