New Mailer System!

Mailer showing dividing lines, numbering & yeast deposited
on spots 1, 3, 6, 8, 9 and 11. Click for larger image.

As many of my readers know, I run an extensive yeast bank and frequently exchange yeasts with other homebrewers from around the world. In the past I've used a simple mailer system that allows yeast to be sent by letter mail. While this system worked very well, it had two major drawbacks. Firstly, it was a lot of work to prepare the mailers, taking me about an hour to prepare enough mailers to exchange 48 or so yeasts. Secondly, they did not always pack nicely into envelopes, leading to a few envelopes being returned by the post for being too thick for letter mail.

For my last few exchanges I've used a modified form of this mailer system. It is much easier to setup than the old mailers (enough mailers for hundreds of yeasts can be prepared in the time needed to make enough of the old mailers for a dozen yeast), and packs very nicely into envelopes. The only downside is that it is a little more work on the end of the recipient, as multiple yeast are now packed onto a single card.

Full details of the new mailer system can be found below the fold.

New Video - Freezing Yeast

After 8 long months I have finally completed the next video in my "Your Home Yeast Lab Made Easy" series - this one on using refrigeration and freezing for storing yeast. Both methods use materials readily available around your home.

There is not much to add in this post to complement the video. If you have any questions or comments, post them here or on the video.



My YouTube Channel
Your Home Yeast Lab Made Easy Series

Easy Home Yeast Banking - and a Video!

Wow, two videos in as many weeks - that has to be a new production record for me! This time around the video is on my most requested topic - an easy to implement home yeast banking system. The video outlines a method, based on the use of slants, to store yeast for future use. Managed carefully this method will allow the average home brewer to easily maintain stocks of up to 2 dozen strains with minimal cost or effort.

Because of the length of the video, and the presence of multiple separate methods, I have provided written instructions, below, to complement the video.

At long last, a new video!

A frequent question I receive here on my blog, and on other forums, is what microscope I would recommend for home use. This is a difficult question for me - I'm a medical researcher by profession, with microscopy representing the bread and butter of my lab (a bit of eye-candy from my labs work can be found near the beginning of the video). While on the surface this would appear to make me an ideal person to offer advice on microscope selection, alas, its not really true. Because I work with research-grade scopes (which are very pricey) I'm not really experienced in the cheaper, consumer-grade microscopes that are cost-effective for home use.

So in lieu of a video recommending specific models, I've instead put together a video discussing features to look for, along with comparison images to give you an idea of what the various features add to a microscope.

Also, I apologize for the crummy audio; I'm experimenting with screen casting as a way to speed video production (which, in my case, is excruciatingly slow), and haven't quite figured out how to properly balance my mic.

Yeast v Bacteria

I occasionally get e-mails (and forum posts) asking questions about identifying yeast versus bacteria in microscopy images. I'm just posting this here as an example of what an average yeast looks like compared to an average bacteria.

At the top of the image is a cluster of a normal yeast strain - Wyeast 1007 (German ale). They are slightly out-of-focus as I was trying to get the bacteria into focus. At the bottom of the cluster are two budding yeasts, in the middle is another budding yeast which is budding upwards (hence why the small bud is in-focus) and there is a non-budding yeast in the upper-left corner of the cluster. The "strand" extending upwards is a clump of trub.

The bacteria is an 'average' bacteria (E. coli, which you hopefully will never see in your beer), but which I added to this sample as a comparator.

Happiness is a Full Test-Tube Rack

Twenty-six new yeasts for the yeast bank!

Thank you fellow yeast farmers.

Top: 6 bottle cultures
Middle: 14 wild & 6 commercial yeast strains
Bottom: Cryovials to store them all

Purifying Yeast from Infected Cultures - Part 2

A couple of days ago I put up a post describing the first step in purifying a contaminated yeast culture. In that post I described a simple method (requiring some specialized reagents) which allows a contaminated sample to be depleted of a contaminating bacteria, and also to provide semi-pure cultures of Saccharomyces and Brettanomyces. But as far as that method goes, it doesn't ensure complete depletion of the contaminants, nor pure cultures of Sacc or Brett.

So how do we get a totally pure culture? The answer...streak plating, followed by a quick screen to ensure purity.

Details below the fold.

Purifying Yeast from Infected Cultures - Part 1

Mixed Saccharomyces (large ovoid cells) and Brettanomyces
(elongated cells) yeast culture contaminated with cocci
(top-centre "string") and rod-shaped bacteria

One of the most requested topics I receive is how to clean up an infected yeast sample. I've alluded to the use of streak plates, and basic identification of organisms, etc, for cleaning up yeast previously, but despite that I've yet to give a detailed example of how I go about cleaning up a contaminated yeast sample.

Provenance has smiled down on me, in the form of an infected attempted bottle culture of a mixed sacch and brett fermented saison from The Bruery, provided to me by a local home brewer. The contamination was not a "good" one - i.e. not a lactic acid bacteria contamination - but rather one that produced a rather putrid sulphur/brimstone aroma.

So how do we fix that...and how can we easily get pure strains of the brett and sacc strains used in the beer?

In this, the first part of a 2-part post (part 2 can be found here), I will go through a basic procedure to enrich the Saccharomyces and Brettanomyces from the infected culture using a selective/differential media and culture conditions to enable the growth of the desired yeast species while inhibiting the growth of the undesired bacteria and yeast. In part 2, hopefully posted later this week, I'll go through a final clean-up procedure to ensure the resulting cultures are, in fact, clean of the contaminating yeast and bacteria.

As always, details are below the fold...

BREAKING NEWS - White Labs Official Statement on Brett trois.

As the followers of my blog are likely aware, there has been a growing body of evidence that WLP644 (Brettanomyces trois) is, in all likelihood, a Saccharomyces (conventional brewing) species. I, and other bloggers did a series of genetic tests that pretty firmly nailed down the genus  of WLP644 as Saccharomyces (although the exact species remains somewhat nebulous).

Many brewers have been directing questions at White Labs about this, and their reply to-date has been rather guarded. Today, they broke their silence (PDF), and confirmed that trois is, indeed, a Saccharomyces. Ironically, they've based this on a far less robust measure than the data myself and others have generated - they determined the genus simply by looking at the size of one of the regions myself, and others, sequenced to ID this yeast.

White Labs has an extensive sequencing project on-going which I expect will reveal to us some exciting (and perhaps upsetting) data on the yeast strains we know and love. While WLP644 is clearly a Saccharomyces, the exact species remains unclear - indeed, one of the sequences we have floating around suggests it may be something all together new. Indeed, white labs is rather guarded in their conclusions (they call WLP644 a "brux-like Trois"), which makes me suspect they too didn't get a clean species ID on the yeast.

More updates to come as more information becomes available.

Previous Posts:

• Brett Trois - A riddle, wrapped in a mystery, inside an enigma
• A (sort-of) update on Brett trois

A (sort-of) update on Brett trois

Some of my readers will be aware that I and several others have done some genetic analyses that suggest that WLP644 (Brett trois) may in actuality be a Sachharomyces. For those not familiar with this issue, or who need a refresher, my post covering both my work and some of the work done by others can be found here: Brett Trois - A riddle, wrapped in a mystery, inside an enigma.

Chris White talked briefly about the "controversy" surrounding the true identity of Brettanomyces trois in a Cheers Charlotte podcast a few days ago (time stamp 28:45 to 30:05). He didn't give away the punchline, saying "it is too early to tell" and that "we have seen some signs it is Saccharomyces". He went on to state that the results he has seen are mixed and that it is not yet clear. Apparently, they are waiting for the whole genome sequence to determine what it is, and if it is a hybrid. But it sounds to me like he is leaning towards a Saccharomyces identification as well.

New Video! Identifying Wild Yeast & Bacteria

Finally, the last video in my "Hunting Wild Yeast" video series is complete. In this, the third and final video, I briefly discuss some of the things you can look for when assessing yeast/bacteria growing on an agar plate, in order to avoid potentially dangerous organisms and to increase your odds of identifying something good.

Both videos are based off of this years wild yeast hunt, whose methodology and results are summarized over two blog posts.

Brett Trois - A riddle, wrapped in a mystery, inside an enigma.

So recently a youtube viewer of mine (Dan Aba, whose youtube channel you need to check out if you haven't already) turned me onto a Facebook group dedicated to sour beers. Lo and behold, the first thread I see on the forum is one claiming that Brettanomyces trois is actually a Saccharomyces yeast! This info didn't just come from nowhere; Lance Shaner of Omega Yeast Labs sent of the strain to a friend for sequencing, and the sequence came back Saccharomyces. Unfortunately, the sequence quality was poor and the sample appears to be a mix of two strains - so I thought it was time to do my own investigation.

The process I followed was fairly straight forward:

1. I grew up B. trois from my yeast bank, overnight in a 37^oC shaking culture - 1.040 wort + penicillin and streptomycin (to ensure a bacteria-free culture, not because my stocks are dirty)
2. I took some images to assess morphology of the yeast
3. I isolated some DNA and sequenced the Internal Transcribed Spacer (ITS) and part of the small (18s) rRNA gene to identify the yeast, using an optimized version of what I was doing in my previous posts.

So what did these experiments show? . . . . . . . Answer (and details) below the fold.

Two New Videos!

Months after filming I've finally completed two videos in a three-part series on collecting & purifying wild yeast. These videos are part of my "Hunting Wild Yeast" series of blog posts, and go hand-in-hand with those posts.

The first video gives a quick overview of two ways to collect wild yeasts - namely, grabbing them off of fruits/veggies/plants/etc and collecting them from the air.

The second video shows a simple method for purifying individual strains of yeast and bacteria, in order to get pure strains for later use.

Both videos are based off of this years wild yeast hunt, whose methodology and results are summarized over two blog posts.

Video 1: Capturing Wild Yeast


Video 2: Purifying Wild Yeast

Serial Feeding

In my review of "Brewing Engineering" by Steven Deeds I mentioned that I had an issue with a recommendation of his that amounted to using serial feedings to get a single tube of yeast upto pitchable amounts without using a starter. This led to some discussion with Dennis of Life Fermented asking why serial feeding is bad and how it differs from sugar additions in Belgian brewing traditions. I began an answer to this question, and quickly hit the character limit for a comment. So here's the answer in full.

Just to provide a little more background, the procedure the author was recommending was to hold back a portion of your wort, such that you are pitching a tube of white labs/wyeast yeast into an appropriate volume of wort for the cell count. At a later timepoint you then add the remainder of the wort, under the (likely correct) assumption that you now have sufficient yeast for the batch.

The issue with this comes down to a few things - what drives yeast cell division (and thus, production of some off-flavours), how yeasts change to a changing fermentation environment, and how yeast process fermentables.

More below the fold...

Announcing a New Yeast Bank! & A successful Yeast Hunt

As readers of my bank know, I have an interest in wild brews and purifying wild yeasts. I have gone through a series of wild yeast collection attempts, and finally have some success to report (more on that below the fold). In addition, over the past few years I've acquired wild yeasts harvested by other brewers - including the infamous/famous Brettanomyces strains from DCYeast.

I'm splitting off the wild yeasts from my yeast bank of commercial (e.g. Wyeast/White labs/bottle cultured) yeasts. I realize this is a somewhat artificial division, as within the commercial yeasts are yeasts that breweries harvested from the wild, but regardless, I figured this was the best division. The new bank of yeast is still rather small, but it should grow quickly as I purify strains from some successful wild brews I have recently conducted (again, more below the fold). For those of you who like my yeast-culturing videos, you'll be happy to know that I'm using this year's wild-yeast hunt to prepare a video covering the process of isolating pure strains of wild-yeast from beginning-to-end, so watch out for that - it should be up soon.

My "vision" for the wild yeast bank is akin to that of Bootleg Biology, namely a terroir-style project, but in my case the goal is to gather these largely from Canada (although I'm happy to bank wild yeasts from any terroir).

One mystery solved...

As I mentioned yesterday I recently developed a persistent infection of part of my brewing setup. Thee batches that passed through my primary fermenter ended up infected (based on aroma/taste/texture); in the final beer I was able to confirm the infection directly by examining a wort sample in which I observed chains of highly elongated rod-shaped bacteria.

Aside from having no idea where the infection came from, I also had no idea what it was. The cell size and length:width ratio were too big for lactobacillus; the shape and formation of chains was inconsistent with both pediococcus and acetobacter. In other words, it isn't likely one of our usual suspects. So I ran a variation of the genomic sequencing method I've used previously to ID yeast, but this time with primers that recognize bacteria - producing the following sequence:

AGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGG GAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGA GTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAA TAGGGCGGTACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCC GCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGC GGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGG GGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGA TGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGA AAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGC TAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTG GGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGG AGCATGTGGTTTAATTCGAAGCA

For those who don't read DNA, that the sequence of Bacillus subtilis's ribosome. This explains...well pretty much everything. Bacillus are spore producing species and their spores are very nearly indestructible - they can survive transient exposure to bleach, are pretty much impermeable to sanitizers like starsan, and can even survive short period of boiling! Moreover, their spores stick to surfaces like crazy-glue, making them near-impossible to remove. The persistence of Bacillus spores, but killing of the vegetative (growing) form after sanitation, would lead to the situation I've experienced - stuff fermented briefly in the container appears normal until weeks after packaging, while beers fermented for longer periods show signs while still in the primary.

Of course, the question is where the heck did this come from? B. subtilis grows in the soil, and is a normal components of our guts - so it is comforting to think that it may be nothing more than an environmental contaminant. But I don't think that is the source - at the time I was developing a teaching lab - using B. subtilis - for an undergrad course that I am currently running.  I have a sneaking suspicion I may literally have brought my work home with me...

Your Home Yeast Lab Made Easy - Streak Plates

The fourth of my "Your Home Yeast Lab Made Easy" series is now up on youtube. This video covers an advanced topic - streak plating. I was not planing on covering this topic so early in my video series, but I was streaking yeast for another project and decided to take advantage of the situation.

Streak plating is used any time you need to purify a strain of yeast (or other microorganism). This method allows you to pull single, genetically pure strains of a microorganism out of a mixed culture. This mixed culture could be any number of sources - an old strain of yeast whose characteristics are starting to drift, a contaminated batch of yeast, a mixed culture (e.g. those made by Wyeast, or from a bottle of sour beer), or even from a wild ferment you started using yeast from your back yard!

The principal of streak plating is simple - a small amount of the source yeast is spread across an edge of a petri dish. The yeast/bacteria/etc concentration in this streak are at a high density, so you swipe a sterilized loop across the first set of streaks, picking up a small number of the organisms, and then streak over another portion of the plate. You repeat this two more times, each time diluting out the yeast/etc further.

Your Home Yeast Made Easy - Aseptic Techniques

The third of my "Your Home Yeast Lab Made Easy" series is now up on youtube! This video is the most important video I will produce as part of this series. The skills I discuss in this video are central to keeping yeast samples uncontaminated - are key and indispensable skill for any brewer interested in taking their yeast culturing activities beyond making starters and washing yeast. You must master these skills if you want to slant or freeze yeast, purify yeast strains, or engage in any form of advanced yeast culturing. In the world of yeast culture, these skills are the your tricycle - until you learn to "ride" these techniques you are not ready to ride the two-wheeler.

I've been trying to keep these video's short, and broke that rule with this one, but the length is for a good reason - these skills are critical for any intermediary or advanced yeast-culturing method, and a 5 minute video simply cannot do this topic justice.


I know my video's are not everyone's cup of tea, so here are some other good resources for those needing additional information, or who get put to sleep by me droning on for 10 minutes...

• Amrita Virtual Laboratory
• Nuffield Foundation's Aseptic Techniques
• Microguide
• Biotopics series on aseptic techiues
• American Society of Microbiology Aseptic Techniques (large PDF, highly technical)

New Video: Your Home Yeast Lab Made Easy

I've been asked many times here on my blog, on my YouTube channel, and in person, to do some videos and posts about how to employ some of the methods I use in my lab to culture yeast in the home. I've long been promising to prepare videos that do just that, and today I begin making good on that promise!

This is the first video in a planned series of 9 or 10 videos. The goal is to keep the videos short as to give the information in easily-digestible bites. This first video shows you how to set-up a workspace in your home for yeast culturing.


At this time I have video filmed for two additional episodes - how to make an alcohol lamp (a DIY Bunsen burner), and how to do a streak plate. Watch for these over the next few days! Future videos will include:

• Basic sterile techniques
• Preparation of starters
• Preparation & use of agar plates in the home lab
• Preparation & use of slants in the home lab
• Freezing yeast at home
• Purifying wild yeast

A Beautiful Sight

Eighteen new yeasts, all on agar, ready to be grown up and frozen down in the yeast bank.  Where did this bounty of yeastie goodness come from you ask?  The answer is brewers like you - these are the product of three exchanges with fellow yeast bankers.  Yeast exchanges are easy and cheap.  So common - share those yeasts!

And to Brian, Richie & Nick, I say thanks for the yeast!