Fermenting beer can at times appear unusual with its fluffy crown of yeast that looks like gargantuan cauliflower, and some of the solids that rise to the surface and adhere to the walls of the fermenter have a dirty appearance. But all of these compounds were either present in the wort prior to fermentation or were produced during fermentation from building blocks in the wort. And this dried ring of kräusen is no more appealing to spoilage bacteria than wort, fermenting beer, or fermented beer. The key to preventing bacterial problems in beer is to prevent bacteria from entering the beer environment.
Before our modern understanding of microbiology, some philosophers and scientists believed that some forms of life could spontaneously generate. In the fourth century B.C., Aristotle pulled earlier beliefs into a general idea termed abiogenesis or spontaneous generation. Anton van Leeuwenhoek, the Dutch merchant who invented the first modern microscope in the 1670s, made observations that seemed to confirm the notion of spontaneous generation. What he observed was yeast and/or bacteria growing in a sterilized media exposed to the environment. Scientists did not know at this time that air contained living microorganisms, so when life was observed sometime after exposing the media to air, and scientists concluded this life came from abiogenesis, Aristotle’s theory from 2,000 years earlier made sense.
As microbiological research continued, scientists began to question spontaneous generation and designed experiments to address their questions. In 1859, Louis Pasteur designed a method that definitively proved that spontaneous generation does not occur. His method used a flask with a swan’s neck shaped airlock to maintain a sterile environment. Two flasks of media were sterilized by boiling the media in these special flasks, one flask was left with the swan’s neck filled with water, and the airlock from the second flask was removed. Microbiological growth was observed in the flask without the airlock, but the flask with the airlock remained sterile. Pretty cool stuff because the airlock we use to keep our homebrew isolated from the environment is the same sort of airlock Pasteur used to disprove the theory of spontaneous generation.
The point to this review of history is to stress that you have the ability to keep bacteria out of your fermenter by controlling the environment. This is the key to bacteria-free beer. However, there are reasons to remove this brown stuff — commonly called “braun hefe” (brown yeast) by some brewers, and “brandt hefe” (burnt yeast) by others — associated with kräusen from your brew. Braun hefe is a mixture of trub, hop resins, and yeast. If you scrape off some of this residue and give it a taste you will probably agree that the flavor is less than pleasant. Brewers are a practical lot, so it is not surprising that brewers developed numerous methods to remove this unpleasant tasting and visually unappealing stuff from fermenting beer.
The simplest way to remove this “stuff” is to skim it from the surface of an open fermenter with a skimmer. This practice is still used today in commercial breweries using open fermenters. But Louis Pasteur’s research gave brewers a pretty good reason to consider using closed fermenters, which are the most common type used by home and commercial brewers today. However, this does not mean that braun hefe cannot be removed from the fermenter. There are numerous “self skimming” methods that remove braun hefe from beer using some sort of separation device that permits removal of the braun hefe without losing too much beer. Burton Unions and Yorkshire Squares from England are traditional fermentation methods that incorporate skimming into their design. Lager brewers also developed some pretty clever systems to allow kräusen from fermenting beer to foam over into a special chamber, and the beer to drain back in the fermenter.
You can skim at home by filling your fermenter high enough to ensure some blow-over. The down side to this is that you can lose a lot of beer, and if you do not use a large diameter blow-off tube you can blow the top off of your fermenter. If you ferment in a carboy with adequate headspace to contain the kräusen, a lot of the braun hefe will adhere to the walls of the carboy and not fall back into the beer after fermentation is complete.
Circling back to your question, you do not need to worry about braun hefe in relation to the microbiological stability of your beer.