Hello, my name is Metschnikowia pulcherrima

Eureka, back to spoilage yeasts. Today, I would like to introduce another spoilage yeast called Metschnikowia pulcherrima (anamorph Candida pulcherrima): A killer yeast with applications in the wine industry, available at Lallemand’s (aka Flavia MP346) and results from one of my countless (beer) split batch experiments. I hope there is something in here for everyone. Put on your science hats, take out your pencils & notepads and start reading. Spoiler alert: you have to interpret the results yourself.

Where do I work?

M. pulcherrima can be isolated from grapes, cherries, Drosophila spp. (fruit fly), flowers and spoiled fruits [Kurtzman et al, 2011]. A yeast commonly found in nature then. If you want to know more about M. pulcherrima and its role in the wine production, go to http://wineserver.ucdavis.edu.

What about beer?

I could not find a source where M. pulcherrima is linked to beer or discussed as potential spoilage yeast thereof. This might not be that surprising since beer is, first of all, commonly not brewed with fruits and second, it’s not really the most alcohol resistant nor metabolically advanced yeast in the universe. Apparently, M. pulcherrima seems to have an alcohol tolerance of about 5% [wineserver.ucdavis.edu, 2015]. Not really high compared to brewer’s yeast with levels of around 12% (or even higher).

What is so special about me?

One very special character of M. pulcherrima makes it a very interesting yeast for the food industry: It’s a killer yeast! The killer activity is affecting blue mold (Penicillium sp.), Botrytis cinerea (gray mold) and couple of bacteria, yeasts [Kurtzman et al, 2011]. This inhibition/killer activity seems to be linked to pulcherriminic acid which is able to form insoluble compounds ultimately depleting the medium of iron ions (which are essential for the growth of other microorganisms) [Oro et al, 2014]. Scientists therefore studied efficacies of M. pulcherrima as a biocontrol agent against the molds mentioned above to eventually prolong the storage times of fruits. If you want to know more about the killer activity and the science behind it, go to PubMed and have a look at the publication from M. Sipiczki. I think this is a very nice example to show people not affiliated with science, that spending money to investigate very odd microorganisms may even result in discoveries that can have an industrial application. Or even have an impact on drug developments against pathological molds. Or put the yeast on the radar of a yeast hunter…

Where can you find me?

As mentioned in the introduction, Lallemand sells a M. pulcherrima product called Flavia MP346. One of the few advantages to brew in Switzerland is the fact, that everything around me is about wine. And getting wine yeasts is therefore rather easy. I therefore got myself a package of said yeast and tried to investigate the impact on beer.

According to Lallemand, Flavia MP346 is a strain isolated from Chile with the speciality of α-arabinofuranosidase secretion to increase terpenes and volatile thiols to enhance the aroma of a wine. Overall increasing the aroma complexity (mainly fruit components) in the finished product. The yeast is commonly added to the must first followed by a Saccharomyces pitch 24 h later on.

To test if there is any (detectable) effect on aroma complexity in a malt based beverage like beer, I performed a simple split batch experiment. I started with a straight forward Belgian inspired recipe (3 kg Vienna malt, 3 kg Abbey malt and 0.5 kg CaraMunich 2; 24 IBU with Saazer; OG about 1.066, brewed 12. December 2014), and split the wort in two parts. One part fermented with a Saccharomyces (US-05) only, the second part with a dose of M. pulcherrima for 24 h before pitching the same Saccharomyces strain. I was really curious to try this yeast because an effect seemed very unlikely to me since the yeast can mainly ferment glucose (see below) and is incapable of fermenting maltose. Not to forget the rather low alcohol tolerance. Bottled on 12th of January 2015 (TG_control: 1.023 (5.9 ABV), TG_Metschnikowia: 1.024 (5.9 ABV)).

First tasting performed in June, 2015 (beer approximately five month in the bottle):

Control:

Aroma: Lots of dark fruits like figs, prunes. Caramel notes as well as burnt sugar components. Very nice!

Appearance: Red-brown color, slightly cloudy, off-white head (see picture on the left). Lots of carbonation.

Flavor: Very similar to aroma. Caramel and malts. Not much else going on (yeast character or whatever).

Mouthfeel: Light body, average carbonation, malty/sweet-caramel/bitter finish. Very nicely balanced.

Overall Impression: Nice bitter:body balance. Very classical and easy to drink. Most of the character originates from choice of malts (caramalts). Not much flavor picked up from US-05 yeast (as planned).

Metschnikowia partial ferment:

Aroma: Different (compared to control): Besides the malt character (caramel, dark fruits, burnt sugar) notes of raspberries, pepper and wild funk (mostly phenolic acids). Very pleasant aroma profile.

Appearance: Red-brown color, slightly cloudy, off-white head (see picture on the left). Lots of carbonation. Similar to control.

Flavor: Similar to aroma without the fruity components (mainly caramel & malt). Finishes with a bitter overhang (balance toward bitter).

Mouthfeel: Very light body (lighter than control), higher carbonation than control (gusher),

Overall Impression: Typical Belgian dark ale with hints of fruits as well as phenolic funk in the nose. Body on the lower end resulting in an overhang of bitterness (not very well-balanced). Seems to have attenuated more than the control resulting in a low body and over-carbonated beer. In the end, I prefer the control. Although the aroma profile of the Metschnikowia beer is nice, it’s a less drinkable beer (my opinion).

So far for the plain results. Lets put them into perspective. According to Lallemand, the yeast is used in wine to promote the fruit components. And I have the feeling that I was able to pick up such an effect in my experiment as well. The beer dosed with M. pulcherrima had pronounced notes of fruits which were not present in the control. The beer had a higher attenuation level resulting in a lower body and a bitter balanced beer.

Great! I will leave the interpretation of the experiment as well as other applications of this yeast to you. The only thing that I don’t recommend is to ferment a beer with M. pulcherrima only. Simply because of its incapability to ferment the most abundant sugars in wort (just in case someone tries that, goes horribly wrong and wants to sue me for that).

Some biochemical stats about me for yeast ranchers

First some micrographs:

Yeast grows on Sabouraud agar like any other Saccharomyces yeast. I however noticed one difference: M. pulcherrima seems to be non-cycloheximide resistant (according to http://wineserver.ucdavis.edu, 2015). I plated the Lallemand product on Sabouraud agar supplemented with + 10 mg L-1 cycloheximide and I could not detect any colonies. Now some stats summarized from Kurtzman et al (2011).

Systematic name:	Metschnikowia pulcherrima (anamorph Candida pulcherrima)
Synonyms:	There are a lots of accepted synonyms for this yeasts. Just some examples: Torula pulcherrima, Saccharomyces pulcherrimus
Growth on malt agar:	Cell morphology:	Globose to ellipsoid, 2.5 µm x 4-10 µm. Pulcherrimin (reddish-brown) pigment present & diffuses into media
	Clustering:	Not described
	Pseudohyphae:	Not described
	Pellicle formation:	Not described
Fermentation:	Glucose:	Positive
	Galactose:	Weak
	Sucrose:	Negative
	Maltose:	Negative
	Lactose:	Negative
	Raffinose:	Negative
	Trehalose:	Negative

That’s all for today. Thanks for reading.

Bibliography

• Kurtzman CP, Fell JW, Boekhout T (2011) The Yeasts, a Taxonomic Study. Volume 1. Fifth edition. Elsevier (Link to sciencedirect)
• Oro L, Ciani M, Comitini F (2014) Antimicrobial activity of Metschnikowia pulcherrima on wine yeasts. J Appl Microbiol. 116(5):1209-17
• wineserver.ucdavis.edu (2015) http://wineserver.ucdavis.edu/industry/enology/winemicro/wineyeast/metschnikowia_pulcherrima.html

Hello, my name is Hanseniaspora uvarum (aka Kloeckera apiculata)

Eureka, we are finally back to spoilage yeasts. Today, I would like to introduce another spoilage yeast called Hanseniaspora uvarum (anamorph Kloeckera apiculata). A very acid-tolerant yeast that can be found close to everywhere and is involved in various natural fermentations such as wine and even certain beer styles. Lets have a closer look at K. apiculata and some fermentations associated with this yeast.

Where do I work?

K. apiculata is present in early grape juice, cacao, coffee fermentation, malting barley, cider fermentation, spoiled figs, tomatoes, canned black cherries, can be isolated from fresh strawberries, black currants, wine grapes and various other fruits, fruit juices and fruit syrups [Pitt and Hocking, 2009, Kurtzman et al, 2011]. Furthermore, K. apiculata could be isolated from soil, fruit flies, caterpillars and even sea water (Florida USA) [Kurtzman et al, 2011]. In summary, K. apiculata is very abundant in nature. Lets have a look at some fermentations in more detail.

A study to investigate the microflora associated with wet Coffea arabica fermentation (pulped coffee is left to ferment under water) in Tanzania identified K. apiculata [Masoud et al, 2004]. The general idea is that K. apiculata, together with other yeasts, are involved in the degradation of the pulp of the coffee beans by secreting pectinases (pectin is a polysaccharide in plants found to give structural integrity). Making it possible to get the coffee bean without any pulp remainders. Another study investigating the microflora of wet fermenting Coffea arabica in Mexico could not identify K. apiculata [Avallone et al, 2001]. Same results performed on dry fermentation (pulped coffee is left to ferment exposed to air) of Coffea arabica in Brazil where the authors could not find any K. apiculata [Silva et al, 2008]. I don’t believe that K. apiculata is not present in Mexico and Brazil. I think it might be another example of the techniques used to identify yeasts may make a difference. Some techniques (especially molecular techniques such as PCR) can be more sensitive than agar plates. Furthermore, molecular techniques can pick up non-viable yeasts (as the DNA is still present) whereas one would miss these yeasts on agar plates as the yeasts are not viable (not growing) anymore.

Moving on to Irish Cider where K. apiculata is the predominant yeast in the first fermentation phase before Saccharomyces cerevisiae takes over [Morrissey et al, 2004]. In this case, the authors could identify the apples as the source for K. apiculata. Interesting to notice is the fact that the maturation phase is dominated by Brettanomyces/Dekkera (you are welcome, fellow Brett hunters).

What about beer?

Compared to some previous featured spoilage yeasts, Kloeckera apiculata can be found in beer. Very similar to the previous mentioned natural fermentations, K. apiculata is involved in a natural beer fermentation: The Belgian Lambics. After leaving the wort cool in a coolship and inoculation/mixing in tanks, the Lambic fermentation starts within a couple of days [Fig 1]. Beginning with an increase of Enterobacteriaceae and K. apiculata within the first days [van Oevelen et al, 1977]. Right before Saccharomyces sp. take over. What K. apiculata exactly contributes to the flavor composition of Lambics (and Geuze) is not really well understood. One study shows a minor impact on fatty acids and ester production where K. apiculata can increase C8, C10 and C12 fatty acids during fermentation [Spaepen M et al, 1978].

Fig 1: Microflora evolution in Lambic fermentation taken from van Oevelen et al, 1977

Although it is commonly accepted that K. apiculata is involved in Lambic fermentations, very recent studies to investigate the microflora at Cantillon as well as an American Coolship Ale facility (Allagsh?) don’t mention K. apiculata in their result section [Bokulich et al, 2012, Spitaels F et al, 2014]. Beside all these results, one can further pose the question how K. apiculata can even get into the wort in the first place? Maybe from the wine barrels?

What is so special about me?

K. apiculata is one of the dominant yeasts in several early natural fermentation stages. Beside that, the yeast seems to have some interesting enzymes such as beta-D-glucosidase and beta-D-Xylosidase which are key enzymes to release aromatic compounds in winemaking [Kurtzman et al, 2011].

Not only are enzymes interesting but flocculation seems to be an interesting research topic as well. As previously discussed, premature flocculation can lead to premature end of a fermentation. Studies showed that K. apiculata is able to pull down a poor flocculent S. cerevisiae strain [Sosa et al, 2008]. The authors mention a possible application such as removing any natural S. cerevisiae yeasts by co-flocculation from the grape must with K. apiculata (before fermentation). Then adding a well-defined S. cerevisiae culture for the main fermentation.

Where can you find me?

In theory and taking all the various sources into consideration where one can find K. apiculata, isolating K. apiculata from various natural sources should be rather easy. Furthermore to notice, K. apiculata is not an important human pathogen although isolates exist [Kurtzman et al, 2011].

Some biochemical stats about me for yeast ranchers

Fig 2: Kloeckera apiculata (sample received from SuiGeneris)

Data summarized from Kurtzman et al (2011).

Systematic name:	Hanseniaspora uvarum (anamorph Kloeckera apiculata)
Synonyms:	There are a lots of accepted synonyms for this yeasts. Just some examples: Hanseniaspora apiculata, Kloeckera brevis
Growth on YM agar:	Cell morphology:	Apiculate, spherical to ovoid, 1.5 -5 µm x 2.5-11.5 µm [Fig 2]
	Clustering:	Occurring as single cells or pairs
	Pseudohyphae:	May be observed
	Pellicle formation:	Not described
Fermentation:	Glucose:	Positive
	Galactose:	Negative
	Sucrose:	Negative
	Maltose:	Negative
	Lactose:	Negative
	Raffinose:	Negative
	Trehalose:	Negative

Since K. apiculata is negative for maltose fermentation and actually only capable of fermenting glucose, it is very unlikely that a single K. apiculata beer fermentation would work (as mainly maltose is present in wort). K. apiculata however should work very well with Cidre and other natural fruit juices where the most dominant sugar is glucose. That’s everything I got for Kloeckera apiculata.

Bibliography

• Avallone S, Guyot B, Brillouet JM, Olguin E, Guiraud JP (2001) Microbiological and Biochemical Study of Coffee Fermentation. Current Microbiology, Vol 42, p 252-256
• Bokulich NA, Bamforth CW, Mills DA (2012) Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale. PLoS ONE, Vol 7(4)
• Kurtzman CP, Fell JW, Boekhout T (2011) The Yeasts, a Taxonomic Study. Volume 1. Fifth edition. Elsevier (Link to sciencedirect)
• Masoud W, Cesar LB, Jespersen L, Jakobsen M (2004) Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis. Yeast, Vol 21(7), p 549-56
• Morrissey WF, Davenport B, Querol A, Dobson ADW (2004) The role of indigenous yeasts in traditional Irish cider fermentations. Journal of Applied Microbiology, Vol 97, p647-655
• Pitt JI, Hocking AD (2009) Fungi and Food Spoilage. Springer Science & Business Media
• Silva CF, Batista LR, Abreu LM, Dias ES, Schwan RF (2008) Succession of bacterial and fungal communities during natural coffee (Coffea arabica) fermentation. Food Microbiology, Vol 25, p 951-957
• Spaepen M, van Oevelen D, Verachtert H (1978) Fatty Acid And Esters Produced During The Spontaneous Fermentation Of Lambic And Gueuze. J. Inst. Brew, Vol 84, p 278-282
• Spitaels F, Wieme AD, Janssens M, Aerts M, Daniel H-M, van Landscoot A, de Vuyst L, Vandamme P (2014) The Microbial Diversity of Traditional Spontaneously Fermented Lambic Beer. PLoS ONE, Vol 9(4)
• Sosa OA, de Nadra MCM; Farias ME (2008) Behaviour of Kloeckera apiculata flocculent strain in coculture with Saccharomyces cerevisiae. Food Technology And Biotechnology, Vol 4, p 413-418
• Van Oevelen D, Spaepen M, Timmermans P, Verachtert D (1977) Microbiological Aspects Of Spontaneous Wort Fermentation In The Production Of Lambic And Gueuze. J. Inst. Brew, Vol 83, p 356-360

Hello, my name is Kluyveromyces marxianus

Eureka, we are back to spoilage yeasts. Today, I would like to introduce another spoilage yeast called Kluyveromyces marxianus (anamorph Candida kefyr). A yeast first described by EC Hansen in 1888 and named Saccharomyces marxianus after Marx, the person who originally isolated K. marxianus from grapes [Fonseca et al, 2008].

Where do I work?

K. marxianus can be isolated from dairy products, kefir, yoghurt, fermented milk, pozol (Mexican fermented corn dough), sorghum beer, cheese, prickly pear, decaying plants and insects. And a study reveiled, that K. marxianus is even involved in coffee fermentation [Jeong H et al, 2012; Kurtzman et al, 2011; Masoud et al, 2004; Vieira-Dalode G et al, 2007].

What about beer?

I could not find a study where K. marxianus could be identified/isolated from barley based beers. Nevertheless, there is more than just barley based beers. I would like to quickly discuss another malt based beverage called gowé made in Bénin, West Africa. This beverage is available as a cooked paste which gets diluted with milk and water leading to a sweet beverage [Vieira-Dalodé et al, 2007]. Never tried gowé myself and honestly haven’t heard about it before either.

A study to identify micro-organisms involved in the production of sorghum gowé identified K. marxianus as a dominant yeast species [Vieira-Dalodé et al, 2007]. Gowé is made from malted sorghum (Sorghum bicolour) according to the work flow shown in Fig 1. The sorghum grains are cleaned and divided into two parts. 25% of the grains get soaked, drained and left for germination before sun dried. A process very similar to the malting process used to make barley malt. The malted sorghum gets milled and kneaded with water. This mixture is left for a primary fermentation. The 75% part of sorghum is left nonmalted and 15% is combined with hot water to form a slurry which is re-combined with the remaining 60% of the nonmalted sorghum and the fermenting dough to form a mixture with a temperature of about 50-60°C. This mixture is left for a secondary fermentation resulting in gowé.

Fig 1: Production of gowé. Figure taken from Vieira-Dalodé et al, 2007

Vieira-Dalodé et al took samples during primary and secondary fermentation to identify the lactic acid bacteria and yeasts involved in the fermentation of gowé. The authors could identify K. marxianus, Pichia anomala, Candida krusei and Candida tropicalis during the fermentation. K. marxianus as well as P. anomala were present from an early stage on and the most important species during the first hours of primary fermentation. C. krusei and C. tropicalis peaked after 12 h.

What is so special about me?

K. marxianus has several biotechnological applications and is used to produce beta-galactosidase, inulinase or pectinase [Jeong et al, 2012].. Since this is yet another yeast with biotechnological applications, its genome was sequenced in 2012 by Jeong et al. The authors sequenced strain KCTC 17555 using Illumina Genome Analyzer IIx and assembled a 10.9 Mb genome allocated into eight chromosomal groups. Of 4,998 predicted proteins, 91% were also present in Kluyveromyces lactis. Furthermore, key enzymes for xylose assimilation are also present (as previously discussed in Pichia kudriavzevii) suggesting this yeast can be used for biofuel production as well [Jeong et al, 2012].

Where can you find me?

As K. marxianus is present in dairy products and many other sources, it is very likely one could pick up this yeast from these sources. The challenging part would be to identify K. marxianus from all the possibly isolated yeasts.

Some biochemical stats about me for yeast ranchers

Data summarized from Kurtzman et al (2011).

Systematic name:	Kluyceromyces marxianus (anamorph Candida kefyr)
Synonyms:	There are a lots of accepted synonyms for this yeasts. Just some examples: Saccharomyces marxianus, Kluyveromyces bulgaricus, Hansenula pozolis
Growth on YM agar:	Cell morphology:	Ellipsoidal to cylindrical, 2-6 µm x 3-11 µm
	Clustering:	Occurring as single cells, pairs or short chains
	Pseudohyphae:	Observed
	Pellicle formation:	May form a thin pellicle
Fermentation:	Glucose:	Positive
	Galactose:	Weak
	Sucrose:	Positive
	Maltose:	Negative
	Lactose:	Variable
	Raffinose:	Positive
	Trehalose:	Negative

Since K. marxianus is negative for maltose fermentation, it is very unlikely that a single K. marxianus beer fermentation would work (as mainly maltose is present in wort). So far for the theory. If anyone out there silly enough to try this yeast for a beer fermentation, please let me know. Over and out.

Bibliography

• Fonseca GG, Heinzle E, Wittmann C, Gombert AK (2008) The yeast Kluyveromyces marxianus and its biotechnological potential. Appl Microbiol Biotechnol, Vol 79(3), p 339-54
• Jeong H, Lee DH, Kim SH, Kim HJ, Lee K, Song JY, Kim BK, Sung BH, Park JC, Sohn JH, Koo HM, Kim JF (2012) Genome sequence of the thermotolerant yeast Kluyveromyces marxianus var. marxianus KCTC 17555. Eukaryot Cell, Vol 11(12):1584-5. doi: 10.1128/EC.00260-12, http://www.ncbi.nlm.nih.gov/pubmed/23193140
• Kurtzman CP, Fell JW, Boekhout T (2011) The Yeasts, a Taxonomic Study. Volume 1. Fifth edition. Elsevier (Link to sciencedirect)
• Masoud W, Cesar LB, Jespersen L, Jakobsen M (2004) Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis, Yeast, Vol 21(7), p 549-56
• Vieira-Dalode G, Jespersen L , Hounhouigan J, Moller PL, Nago CM, Jakobsen M (2007) Lactic acid bacteria and yeasts associated with gowé production from sorghum in Bénin, Journal of Applied Microbiology, Vol 103, p 342–349

Insight into the genome of Saccharomyces carlsbergensis

Eureka, another yeast genome got recently published (May 2014) by scientists at the Carlsberg Laboratory in Denmark: Saccharomyces carlsbergensis, the world’s first pure lager yeast used in production since 1883. I would like to review the published article and point out some interesting results. Below the full reference of the paper I am talking about.

Walther A, Hesselbart A, Wendland J (2014) Genome Sequence of Saccharomyces carlsbergensis, the World’s First Pure Culture Lager Yeast, G3, 4:783-793; doi:10.1534/g3.113.010090, http://g3journal.org/content/4/5/783.full

The scientists sequenced the genome using next generation sequencing techniques and compared the genome with Saccharomyces cerevisiae (top-fermenting yeast) and Saccharomyces eubayanus (likely to be a parent of the lager yeasts). Lager yeasts are hybrids and resulted from an interbreeding event between a top fermenting S. cerevisiae yeasts parent as well as a non-cerevisiae parent (likely to be S. eubayanus). This means, the genome of lager yeasts consist of parts of the S. cerevisiae genome as well as parts of a non-cerevisiae parental genome.

Beside S. carlsbergensis, the authors re-sequenced another lager yeast (Weihenstephan WS34/70) for comparative reasons. Lager yeasts can be grouped into group I (Saaz-type lager yeasts) and group II (Frohberg-type lager yeasts). Members of the two groups reflect geographic associations with breweries like group I (Czech and Carlsberg) and group II (Weihenstephan and Heineken). The sequenced S. carlsbergensis strain (CBS1513) belongs to group I whereas WS34/70 belongs to group II. Comparing the two genomes therefore might give some insight into genetical differences between the two lager yeast groups.

Loss of parental S. cerevisiae DNA in S. carlsbergensis

The authors found substantial genome size differences between the two lager yeasts (about 3.5 Mb). A previous investigation showed, the Weihenstephan lager yeast contains two complete parental genomes (S. cerevisiae and S. eubayanus) with some losses at chromosome ends [Nakao et al, 2009]. To address how much of the S. carlsbergensis genome is from S. cerevisiae and S. eubayanus, the authors mapped the obtained S. carlsbergensis genome to the two parent yeast genomes. The comparison revealed, the genome of S. carlsbergensis does not contain information of the S. cerevisiae chromosomes VI, XI and XII (Fig 1, left), harbours some translocated S. eubayanus chromosomes (II, IV and VIII and XV) (Fig 1, right) as well as loss of heterozygosity in some S. cerevisiae chromosomes (Fig 1, right, chromosomes IV, XIII, XV and XVI). This lack of chromosomal information of S. cerevisiae chromosomes VI, XI and XII as well as some loss of heterozygosity is sufficient to explain the smaller genome size of S. carlsbergensis in comparison with the Weihenstephan lager yeast.

Fig 1: Pairwise comparison of S. carlsbergensis genome with sub-genome of S. cerevisiae (left) and S. eubayanus (non-cerevisiae) sub-genome (right). Taken from Walther et al, 2014

Summarized, S. carlsbergensis (group I) lost some S. cerevisiae DNA which is still present in the Weihenstephan lager yeast (group II).

Chromosomal map of S. carlsbergensis

The authors generated a chromosomal map for S. carlsbergensis strain CBS 1513 which consists of 29 different chromosomes (Fig 2). Whereas the Weihenstephan lager yeasts harbours 36 different chromosomes (not shown). The individual chromosomes either contain only chromosomal information from the parental S. cerevisiae (parts in blue) or S. eubayanus (orange parts) yeasts or contain information from both yeasts (translocated chromosomes).

Fig 2: Chromosomal map of S. carlsbergensis strain CBS 1513. Blue parts represent S. cerevisiae sub-genome, orange parts the S. eubayanus sub-genome. Taken from Walther et al, 2014

To investigate if group I lager yeasts resulted from a hybridization event of two haploid (one copy of each chromosome) S. cerevisiae and S. eubayanus cells, the authors determined the copy numbers of each chromosome present in the S. carlsbergensis genome. If this would be the case, one would expect to find a 1:1 ratio of S. cerevisiae and S. eubayanus chromosomes in the S. carlsbergensis genome.

Surprisingly, the S. carlsbergensis genome seems to be triploid (three copies) with one copy of S. cerevisiae and two copies of S. eubayanus genome (1:2 ratio). The complete S. carlsbergensis genome therefore consists of a total of 47 chromosomes (Fig 2). In comparison, the Weihenstephan lager yeasts is tetraploid (4 copies) with two S. cerevisiae and two S. eubayanus genomes (1:1 ratio).

The comparison showed a clear distinction between lager yeast group I and II with loss of S. cerevisiae DNA in group I. In terms of origin, one may suggest that group I lager yeasts were generated by a fusion event of a haploid S. cerevisiae with a diploid S. eubayanus yeast cell whereas group II lager yeasts originated from a diploid-diploid fusion generating tetraploid group II lager yeasts. Three conserved translocation events in both sequenced lager yeasts may however suggest a common ancestor of both lager yeast groups. And a DNA elimination event may have created group I lager yeasts afterwards.

There you have it. A pretty cool research project. I would like to finish with yet another astonishing result. The authors addressed the level of diversity of possibly one of the original S. carlsbergensis yeast strain isolated by Emil Chr. Hansen in the late 19th century (obtained from Carlsberg bottles of the late 19th century) with the strain deposited at CBS in 1947. The yeasts present in the bottles were identical with the CBS deposited yeast strain. “This suggests very limited evolution of pure cultured yeast strains under industrial fermentation conditions” [cited from Walther et al, 2014]. Pretty cool, right?

I hope you enjoyed reading my short review. Please have a look at the original genome paper as well. I think it is very well written publication. Hope to see some new lager yeast genomes coming out soon.

Bibliography

Nakao Y, Kanamori T, Itoh T, Kodama Y, Rainieri S et al (2009) Genome sequence of the lager brewing yeast, an interspecies hybrid. DNA Res. 16:115-129

Hello, my name is Debaryomyces hansenii

Eureka, we are back to spoilage yeasts. Today, I would like to introduce another spoilage yeast called Debaryomyces hansenii (anamorph Candida famata). This yeast was originally isolated from saline environments and is maybe one of the most osmotolerant (can tolerate high levels of salt and sugar) yeasts in existence [Kumar, 2012]. This yeast is very common in various food products and has a big biotechnological potential. It is therefore of no surprise that two strains of this yeast, CBS767 and MTCC 234, have been previously sequenced and their genomes are published [Lépingle, 2000; Kumar, 2012].

Older publications talk of two yeast varieties of D. hansenii: D. hansenii var. hansenii and D. hansenii var. fabryi with differences in their 26S rRNA gene as well as their temperature preferences [Breuer, 2006]. The current nomenclature reinstated D. fabryi as a separate family based on the genetical differences between the two varieties. I will therefore only discuss D. hansenii: D. hansenii var. hansenii in this post.

Where do I work?

D. hansenii is the most prevalent yeast in dairy and meat products as well as early stages of soy sauce fermentation [Kurtzman, 2011]. Various isolates exist originating from cheese, sake moto, edomiso, rennet, psoriasis, infected hands and salmon [Kurtzman, 2011]. In general, D. hansenii can be found in habitats with low water activity as well as in products with high sugar concentrations [Breuer, 2006]. Although D. hansenii is considered a non-pathogenic yeast, various clinical cases of D. hansenii exist.

What about beer?

I could not find a source discussing the use of D. hansenii in the production of beer.

What is so special about me?

As already mentioned, D. hansenii can tolerate very high levels of salt. Some sources cite salinity levels up to 24% whereas Saccharomyces cerevisiae commonly tolerate levels up to 10% [Lépingle, 2000]. Such high tolerances are not that common in living organisms and can be used on industrial scale by cultivating D. hansenii at high salt levels to prevent the growth of other yeasts (quasi non-sterile production conditions). Beside dealing with high osmolarities, D. hansenii secrete toxins capable of killing other yeasts [Breuer, 2006].

Although this yeast is already an extremophile in terms of osmolarity, it does not stop there. Besides the normal sugars, D. hansenii is capable of metabolizing n-alkanes, melibiose, raffinose, soluble starch, inositol, xylose, lactic acid and citric acid [Breuer, 2006; Lépingle, 2000; Kumar, 2012]. Furthermore, this yeast can form arabitol as well as riboflavin (vitamin B2) [Génolevures, 2014]. D. hansenii is therefore used on industrial scale to produce vitamin B2 and has a big potential for other biotechnological processes.

D. hansenii is a very common yeast in cheeses and seems to have a major impact on the development of the microflora as well as the taste [Lépingle, 2000]. As previously mentioned, D. hansenii can metabolize lactic acid, citric acid and galactose. The assimilation of lactic acid by yeasts has been shown to have an impact on the bacterial flora of the cheese in types such as Limburger, Tilsiter, Port Salut, Trappist, Brick and the Danish Danbo [Breuer, 2006]. Furthermore, D. hansenii forms volatile compounds associated with a “cheesy” flavor [Breuer, 2006]. For example, D. hansenii seems to have a major role in the development of Cheddar and Camembert cheese by synthesizing S-methylthioacetate (most prevalent volatile sulphur compound found in cheese) [Breuer, 2006].

Summarized, D.hansenii is involved in various dairy products and has some very unique biochemical properties. This makes this yeast very interesting for biotechnological processes such as the production of toxins as therapeutic agents, produce xylitol (as already discussed in the previous post about Pichia kudriavzevii), manufacturing chemical compounds and the production of vitamin B2.

As soon as a yeast gets interesting on industrial scale, a genome sequencing project gets commonly initiated to get more insight into the organism you want to deal with. However, very often such genomes do not get published to keep the obtained information a secret. Luckily for us, the two draft genomes of D. hansenii can be accessed by anyone.

D. hansenii strain CBS767 (isolated from Sherry in Denmark) has been sequenced by the Génolevure project. The obtained assembly consists of 7 chromosomes (assembly size of 12.2 Mb). 205 tRNA genes could be found corresponding to a set of 43 tRNAs. D. hansenii uses an alternative genetic code and uses the codon CAG for serine instead of leucine and carries a single copy tRNA-Ser CAG.

D. hansenii strain MTCC 234 (isolated from New Zealand soil) has been Illumina sequenced and assembled using Velvet 1.1.06 into a draft genome consisting of 542 contigs and a N50 contig length of 68,507 bp [Kumar, 2012]. The authors furthermore predicted 5,313 proteins and could find matches (E-value cutoff of 10-6) in the nr NCBI database for >99.5% of the predicted proteins.

Where can you find me?

In theory, it should be easy to pick up D. hansenii from dairy products if one follows the protocol mentioned in the section below.

Some biochemical stats about me for yeast ranchers

Breuer et al mention a simple protocol to pick up D. hansenii: Cultivate yeasts at 10% NaCl and 5% glucose to discriminate between D. hansenii and other ascomycetous yeasts. Below a summary of the biochemical properties of D. hansenii. Data is summarized from Kurtzman et al (2011).

Systematic name:	Debaryomyces hansenii (anamorph Candida famata)
Synonyms:	There are a lots of accepted synonyms for this yeasts. Just some examples: Saccharomyces hansenii, Debaryomyces gruetzii, Pichia hansenii
Growth in malt extract:	Cell morphology:	Spherical to short-ovoid form, 2-7 µm x 2-9 µm
	Clustering:	Occurring as single cells, pairs or short chains
	Pseudohyphae:	Poor formation
	Pellicle formation:	Not described
Growth in malt extract:	Colony morphology:	After 4 weeks: Grayish-white to yellowish, glistening or dull, butyrous and smooth or wrinkled
Fermentation:	Glucose:	Weak
	Galactose:	Weak
	Sucrose:	Weak
	Maltose:	Weak
	Lactose:	Negative
	Raffinose:	Weak
	Trehalose:	Weak

That’s all about Debaryomyces hansenii. In summary, Debaryomyces hansenii is involved in the maturation process of various food products such as cheese, sausages, various other fermented products as well as industrial applications such as the production of vitamin B2.

Although this extremophilic yeast sounds really interesting, I would not use D. hansenii as a single yeast species to ferment a beer. Simply because it is a very weak fermenter of maltose and glucose, the main sugars present in wort. On the other hand, one can only guess its impact if used as a secondary or bottling strain. Maybe use this yeast for a Imperial Gose with a salt content of about 20%? Let me know if there is someone crazy enough to make such a big Imperial Gose similar to sea water…

Bibliography

• Breuer U, Harms H (2006) Debaryomyces hansenii – an extremophilic yeast with biotechnological potential. Yeast, Vol 23, p.415-437
• Génolevures, Debaryomyces hansenii entry (via http://genolevures.org/deha.html), accessed April 2014
• Kumar S, Randhawa A, Ganesan K, Raghava SG, Mondal AK (2012) Draft Genome Sequence of Salt-Tolerant Yeast Debaryomyces hansenii var. hansenii MTCC 234. Eukaryotic Cell, Vol11(7), p.961-962, (via NCBI)
• Kurtzman CP, Fell JW, Boekhout T (2011) The Yeasts, a Taxonomic Study. Volume 1. Fifth edition. Elsevier (Link to sciencedirect)
• Lépingle A, Casaregola S, Neuvéglise C, Bon E, Nguyen HV, Artiguenave F, Wincker P, Gaillardin C (2000) Genomic Exploration of the Hemiascomycetous Yeasts: 14. Debaryomyces hansenii var. hansenii. FEBS Letters, Vol 487, p.82-86

Hello, my name is Pichia kudriavzevii

Eureka, we are back to spoilage yeasts. Today, I would like to introduce another spoilage yeast called Pichia kudriavzevii (anamorph Candida krusei). This yeast was first described by V.I. Kudryavtsev in 1960 as Issatchenkia orientalis but was classified as P. orientalis in 1964 and to P. kudriavzevii in 1965. P. kudriavzevii is a very abundant yeast in the environment and can be found in soil, fruits and various fermented beverages. So far, P. kudriavzevii is mainly associated with food spoilage to cause surface biofilms in low pH products [Kurtzman, 2011].

Where do I work?

Since this yeast is very abundant, P. kudriavzevii could be isolated from various sources: fruit juice, berries, sourdough, butter-like products, culture of Tanzanian fermented togw, African fermented cassava lafu, Ghanaian fermented cocoa bean heap, sake, champagne, ginger beer, tea beer, baker’s yeast, chicken egg, human heart blood, sputum, swine waste and human feces [Kurtzman, 2011; Chan 2012]. Well this does not sound very appetizing. And in fact, this strain is not really appetizing at all. Not only are various isolates from humans and animals of P. kudriavzevii available but many clinical cases support the idea that P. kudriavzevii (Candida krusei) is a species of clinical importance. In fact, Candida krusei is the 5th most common cause of candidemia [Kurtzman, 2011]. A kind of fungi infection which can affect immunocompromised patients (such as AIDS patients). Since we are already speaking of Candida, Candida albicans another species within the Candida family is one of the most pathogenic yeasts around and leads to Candidiasis. If you want to know how the symptoms of these medical conditions look like, feel free to google. But be warned, its nasty!

Back to the possible applications of P. kudriavzevii. As I already mentioned, P. kudriavzevii can be isolated from various sources and has been found in sourdough and further research needs to be performed to elucidate its possible function [Meroth 2003; De Vuyst, 2005]. Beside sourdough, P. kudriavzevii accounted for about 30% of the isolated yeasts in a cocoa bean heap fermentation and might be involved in the citrate assimilation during the fermentation [Daniel, 2009].

What about beer?

One existing association to beer is CBS strain 5148 which was isolated from a beer wort. Beside the “traditional” beer, one publication covers the isolation of P. kudriavzevii from tchapalo, a sorghum beer brewed in Côte d’Ivoire [N’guessan, 2011]. Whether P. kudriavzevii has any benefits for the production of beer like many other non-Saccharomyces strains has yet to be determined.

What is so special about me?

What is quite remarkable in my opinion is the fact that a draft genome assembly exists for a P. kudriavzevii strain (M12). Meaning the genome of this yeast has been sequenced and the information of the DNA sequences are known, published and available to everyone. Since DNA sequencing and the assembling process requires some financial investments as well as time (been there), there have to be certain reason(s) why such a research project is initiated and funded. And that’s where it gets interesting. Apparently, P. kudriavzevii contains some neat enzymes which make this strain very interesting in biotechnology for processes such as the production of bioethanol and phytases used to increase the uptake of phosphorus by plants (biofertilizer) [Chan, 2012]. Below is a simplified pathway of the Xylose pathway including the three enzymes found in P. kudriavzevii. Xylose by the way is a sugar molecule found in wood and not that many yeasts are capable of metabolizing this kind of sugar.

Xylulose-5-phosphate can then be input into the pentose phosphate pathway (PPP) to be converted into fructose 6-phosphate which can be passed to the glycolysis pathway. Under the right conditions, one might use P. kudriavzevii strain M12 to form alcohol from wood which is a very neat way of producing bioethanol.

Where can you find me?

Don’t know any commercial sources for P. kudriavzevii. This is for sure not a bad thing as I don’t want to have people playing around with possible infectious yeasts at home anyway…

Some biochemical stats about me for yeast ranchers

Below a summary of the biochemical properties of P. kudriavzevii. Data is summarized from Kurtzman et al (2011). Since this yeast can mainly ferment glucose, its spectra of sugars is very limited. For sure not suitable to ferment an entire batch of beer wort which contains a lot of maltose which cannot be utilized by P. kudriavzevii.

Systematic name:	Pichia kudriavzevii (anamorph Candida krusei)
Synonyms:	There are a lots of accepted synonyms for this yeasts. Just some examples: Saccharomyces krusei, Issatchenkia orientalis
Growth in malt extract:	Cell morphology:	Ovoid to elongate form, 1.3-6 µm x 3.3-14 µm
	Clustering:	Occurring as single cells or in pairs
	Pseudohyphae:	Moderate formation
	Pellicle formation:	Heavy, dry climbing pellicles are formed
Growth in malt extract:	Colony morphology:	After 3 days: Butyrous and light-cream color
Fermentation:	Glucose:	Positive
	Galactose:	Negative
	Sucrose:	Negative
	Maltose:	Negative
	Lactose:	Negative
	Raffinose:	Negative
	Trehalose:	Negative

That’s all about Pichia kudriavzevii so far. In summary, Pichia kudriavzevii seems to be involved in various beverage and food fermentations and is of clinical importance. Although the clinical importance mainly affects people with a suppressed immune system. It is not clear at this point if only a certain type of strain(s) (mainly the ones isolated from animals or humans) are potentially pathogenic or all the Pichia kudriavzevii strains.

Due to the potential pathogenic character as well as the limited range of sugars Pichia kudriavzevii can utilize, I don’t see any reasons to intentionally try this yeast for beer production. Furthermore, I do not support the idea to try the yeast for any beverages. Even if you could make beer out of wood…

Bibliography

• Chan GF, Gan HM, Ling HL, Rashid NA. (2012) Genome sequence of Pichia kudriavzevii M12, a potential producer of bioethanol and phytase. Eukaryot Cell, 11(10)
• Daniel HM, Vrancken G, Takrama JF, Camu N, De Vos P, De Vuyst L (2009) Yeast diversity of Ghanaian cocoa bean heap fermentations,FEMS Yeast Research, 9, 774–78
• De Vuyst L, Neysens P (2005) The sourdough microflora: biodiversity and metabolic interactions. Trends in Food Science & Technology, 16, 43–56
• Kurtzman CP, Fell JW, Boekhout T (2011) The Yeasts, a Taxonomic Study. Volume 1. Fifth edition. Elsevier (Link to sciencedirect)
• Meroth CB, Hammes WP, and Hertel C (2003) Identification and Population Dynamics of Yeasts in Sourdough Fermentation Processes by PCR-Denaturing Gradient Gel Electrophoresis. Applied and Environmental Microbiology, 69(12)
• N’guessan KF, Brou, K, Jacques N, Casaregola S, Dje, KM (2011) Identification of yeasts during alcoholic fermentation of tchapalo, a traditional sorghum beer from Côte d’Ivoire, Antonie van Leeuwenhoek, Vol99(4), 855-864