microbiology – Science and Food

Tag Archive for: microbiology

Elaine Hsiao

April 28, 2016/in Profiles/by Grant Alkin

Dr. Elaine Hsiao is an assistant professor at UCLA’s Department of Integrative Biology & Physiology and UCLA’s Department of Medicine, Digestive Diseases. In addition to her many distinctions, she was elected to the Forbes’ 2014 “30 Under 30 in Science & Health Care” and served on the White House Office of Science and Technology Microbiome Forum. Her research studies how changes to microbes inside our bodies impact our health and behavior and may influence various neurological disorders like autism, depression, and Parkinson’s disease.

See Dr. Elaine Hsiao speak on May 11 2016 at “Microbes: From Your Food to Your Brain”

Check out some of her previous talks and interviews

TEDXCaltech – “Mind-Altering Microbes: How the microbiome affects brain and behavior”

In her talk, Dr. Hsiao explains how the microbes in our gut can affect our brains by altering our production of neuroactive molecules and the potential applications of this research

Media Evolution – “Brain, Heart, gut – what drive us, really”

Here Dr. Hsiao shows how mouse models are used in her research. Specifically, she explains how she and her team experimentally determined gut microbes influence autistic-like behaviors in the mice.

Autism Speaks – “Investing in Talent: Predoctoral Fellow Elaine Hsaio”

In this interview, Dr. Hsiao talks about her previous work investigating how infections during pregnancy impact the risk of Autism.

For more information check out her Lab’s Website here

Gutopia: A Microbial Paradise

April 26, 2016/in Science & Food/by Grant Alkin

The development of the microscope in the 17^th century magnified our awareness of a microbial universe previously invisible to the naked eye. Anton van Leeuwenhoek, a Dutch textile draper and science hobbyist, was one of the first individuals to glance into the microbial looking glass and identify unicellular organisms (so-called animalcules) such as protozoa and bacteria [1]. His colleague, Robert Hooke, went on to publish the seminal text, Micrographia, which described his observations of microfungi [2]. Two centuries later, Louis Pasteur validated the role of microbes in fermentation. However, Pasteur also gave weight to Ignaz Semmelweis’ controversial germ theory of disease stating that microbes have the capacity to cause pathological effects on our human health [3].

Early microbial drawings by Anton Van Leeuwenhoek [Photo Credit: Yale University Press]

These early studies in microbiology have provided significant insight on the human-microbe interaction characterized by either mutually beneficial or lethal outcomes. The duality of microbial behavior has dramatically impacted our perception of these microorganisms. Our cultural germophobia often precludes our ability to recognize the naturally transformative and symbiotic properties of microbes from the fermentation of grape juice into wine to their invaluable role in human digestion.

Michael Pollan, author of Cooked, explores a myriad of cooking traditions including those that directly involve the action of microbes such as bacteria and yeast. In his depiction of ancient sourdough recipes, he lists four ingredients: whole grain flour, water, salt, and the repertoire of microbes in the air [4]. The microbes catalyze slow-fermentation reactions (taking up to 24 hours) that leaven the bread while transforming molecules into digestible nutrients for us to absorb.

Whether we can stomach it or not, we all possess unique microbial signatures that are composed of trillions of microorganisms living both inside our bodies and on the surface of our skin [5]. These microbial communities, referred to as the human microbiome, cohabitate in our various mucosal, gastrointestinal, and epidermal surfaces. Symbiotic microbes are tolerated by our immune system and work collaboratively with our own bodies to digest the foods that we eat at the molecular level.

Our evolutionary history with bacteria is fueled by the currency of nutrition. In other words, our diet has a significant impact on the composition of our gut microbiota. Food consumption habits can either encourage the intestinal bloom of beneficial bacteria or opportunistic, disease-causing bacteria. Certain foods contain vital prebiotic molecules that encourage the expansion of beneficial bacterial species in the gut. High fiber foods including whole grains (brown rice, oats), vegetables (broccoli, peas) and legumes (lentils, black beans) contain an invaluable source of metabolic substrates that are converted into short-chain fatty acids by bacteria [6]. These short-chain fatty acids, such as butyrate, help to propagate microflora such as Bifidobacterium and Lactobacillus and maintain gastrointestinal tissue health [7].

If we were to design a perfect microbial habitat–a Gutopia, if you will, it would be a homeostatic organ city of diverse symbiotic microbiota that is rich in fiber economy and free of any harmful pollutants. However, our dietary choices can tip the balance of this intestinal paradise and create a dystopic environment suitable for the expansion of pathogenic microbes.

Contemporary eating habits that are characteristically high in fat and carbohydrates are responsible for the emergence of modern diseases such as diabetes, colorectal cancer, and inflammatory bowel diseases [8-11]. Recent studies suggest that compositional changes in the intestinal microbiome can encourage the bloom of disease-causing microflora. The dramatic alteration of today’s eating behavior introduces gastrointestinal disturbances or challenges that our bodies and microbial counterparts have not evolved to accommodate. For example, a study investigating the consumption of different dietary fats in immunocompromised IL-10^–/^– mice identified the expansion of B. wadsworthia; a gram-negative, sulfur-reducing species of bacteria flourished in mice fed a diet high in saturated fat , but not in low-fat or polyunsaturated fat diets [12-13]. The bloom of B. wadsworthia was attributed to the unregulated production of a bile salt known as taurocholic acid brought about by the overconsumption of saturated fat.

Imbalanced dietary intake and overconsumption of foods high in saturated fats can impact the ecology of gut microbiota [Illustration by Grace Danico]

Taurocholic acid is an important source of sulfur that can stimulate the growth and maintenance of the pathogenic B. wadsworthia in these mice. The presence of this bacterium activates murine proinflammatory immune defense mechanisms that compromise the permeability of gut mucosal tissue causing intestinal inflammation. This pathogenic etiology of gut inflammation is implicated in the onset of Crohn’s disease and ulcerative colitis [12-13].

Much like any city there are complications that arise, which can tip the balance between utopic and dystopic environments. In the case of our gut health, we should imagine ourselves as landscape architects cultivating the balanced ecology of our microbiome. If we feed our intestinal gardens with the right balance of foods we can foster the growth of symbiotic bacteria while discouraging the bloom of pestilent, pathogenic microbial weeds.

The human microbiome not only affects our gut health but can have some profound effects on our behavior and brain function. Dr. Elaine Hsiao, Assistant Professor in the Department of Integrative Biology and Physiology at UCLA, investigates the interplay between our commensal microbes and their role in neurological development and function. Her work has linked the perturbations in gut microbiota with the onset of neurological disorders such as autism [14].

As we continue to study the ecology and diversity of microbes living within and around us, we are faced with many fundamental challenges in testing the dynamics of these microbial communities. From a clinical perspective, physicians and researchers alike have utilized human fecal samples to identify unique microbial gut profiles in their patients. These samples serve as powerful investigative tools in our pursuit to understand how certain commensal microbes can cause or serve as diagnostic readouts. The power of the sequencing technology used to characterize microbes in stool samples (16s RNA sequencing) comes from its level of coverage-the ability to identify the majority of bacteria in a sample. However, sequencing depth-the resolution at which a species can be identified remains challenging. Additionally, many microbial species have been challenging to culture in vitro, making it difficult for researchers to repeatedly perform experiments in a laboratory setting and gain a deeper mechanistic understanding of microbial behavior and ecology.

Dr. Rachel Dutton, Assistant Professor in the Division of Biological Sciences at UCSD, addresses some of these technological limitations by studying the establishment and maintenance of microbial communities in different types of cheeses. With this model, her lab can investigate the interactions of different types of microbes to better understand them as ecological systems [15-16].

Science & Food is honored to host Elaine Hsiao and Rachel Dutton for the 2016 UCLA Science & Food public lecture series to elaborate on their findings. They will be accompanied by Sander Katz, author of Wild Fermentation, who will discuss the transformative properties of microbes in the production of foods like sauerkraut.

Join us on Wednesday, May 11^that 7PM in Schoenberg Hall at UCLA for “Microbes: From Your Food to Your Brain” to learn more about the intriguing world of microbes!

References cited

Gest H. “The discovery of microorganisms by Robert Hooke and Antoni Van Leeuwenhoek, fellows of the Royal Society”. Notes Rec R Soc Lond. 5 (2004). 187-201.
Hooke R. “Micrographia” Jo. Martyn & Ja. Allestry (1665).
“The History of the Germ Theory” The British Medical Journal. 1 (1888).
Pollan M. Cooked: A Natural History of Transformation. Penguin Books. (2013).
Abbott A. “Scientist bust myth that our bodies have more bacteria than human cells” Nature. (2016).
Leone V, Chang EB, Devkota SD. “Diet, microbes, and host genetics: the perfect storm in inflammatory bowel disease” J. Gastroenterol 48 (2013). 315-321.
Sartor RB,.“Microbial influences in inflammatory bowel disease: role in pathogenesis and clinical implications” Elsevier (2004). 138-162.
Hotamisligil, GS. “Inflammation and metabolic disorders” Nature. 444 (2006). 860-867.
Parkin DM, Bray F, Ferlay J, et al. “Global cancer statistics” CA Cancer J Clin. 55. (2005). 74-108.
Loftus EV Jr. “Clinical epidemiology of inflammatory bowel disease: incidence, prevalence, and environmental influences” Gastroenterology 126. (2004). 1504-1517.
Molodecky NA, Soon IS, Rabi EM, et al. “Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systemic review” Gastroenterology 142. (2012). 46-54.
Devkota SD, Wang Y, Musch MW, et al. “Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10^-/- mice” Nature. 487 (2012). 104-108.
Devkota SD, Chang EB. “Diet-induced expansion of pathobionts in experimental colitis” Gut Microbes. 4:2 (2013). 172-174.
Hsiao E.Y., “Gastrointestinal issues in autism spectrum disorder”, Harv Rev Psychiatry, 22 (2014). 104-111.
Wolfe BE, Dutton RJ. “Fermented Foods as Experimentally Tractable Microbial Ecosystems” Cell. 161(1) (2015). 49-55.
Wolfe BE, Button JE, Sanarelli M, Dutton RJ. “Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity” Cell. 158 (2014). 422-433.

About the author: Anthony Martin received his Ph.D. in Genetic, Cellular and Molecular Biology at USC and is self-publishing a cookbook of his favorite Filipino dishes.

Read more by Anthony Martin

Fermentation Revival & Mind-Altering Microbes

April 21, 2016/in What We're Reading/by Grant Alkin

Sandor Katz and Dr. Elaine Hsiao will be joining us at our next 2016 public lecture, Microbes: From Your Food to Your Brain. Get to know them beforehand, as Sandor Katz talks about his book, The Art of Fermentation, on NPR: Fresh Air and Dr. Hsiao shares her fascination with the microbiome at a TedxCaltech talk.
Read more

Kombucha Brewing: The Process

November 10, 2015/in DIY Kitchen Science/by Grant Alkin

Photo credit: Mgarten (Wikimedia Commons)

At first glance, making kombucha sounds straightforward. After all, kombucha is fermented tea, which tells all you need to know about making it: take some tea and ferment it. Unfortunately, brewing kombucha is not that simple, as evidenced by the plethora of information and recipes found on the Internet. For those who have ever contemplated or even decided to begin brewing kombucha for the first time, don’t let the wealth of kombucha information intimidate you. Here, we break down the process of kombucha brewing and experimentation, supplying you with the scientific rationale for each step. Understanding the science of each stage may allow for a more successful and experimental brewing without having to rely on a recipe.

1. Making the tea base.

The tea base is nothing more than sweetened tea, so it is easy enough to make. However, the amount of tea and sugar used will affect the flavor of the resulting kombucha. The exact proportion of water to tea to sugar can be modified to suit personal tastes. For the varieties of teas and sugars suitable for making kombucha, check out our previous post on the ingredients that go into making kombucha.

In general, for every 1 cup of boiled water, steep 1 tea bag or 1 ounce of loose leaf tea; this should be left to steep for 3 – 5 minutes, with deviations depending on the type of tea and desired tea strength. Certain teas, such as green and white teas, have subtle flavor profiles that may result in a bland-tasting kombucha. To obtain a more concentrated flavor with delicate teas, use more tea bags, do multiple infusions, or combine the green or white teas with a more robust black tea.

If you use tea bags, adding more of them can help increase the amount of flavor compounds in the brewed tea, creating a more concentrated green or white tea flavor. Avoid steeping the teas for too long; steeping teas longer than the recommended time results in the extraction of more bitter compounds. This over-extraction will create a more bitter tea base. The same caution equally applies to loose leaf teas.

If you use loose leaf teas, multiple infusions will help concentrate the flavor without the risk of over-extraction. A proper method for multiple infusion involves steeping a large amount of tea leaves for 20 – 45 seconds in just enough hot water to cover the leaves. The brewed tea is removed, and another small amount of hot water is added to the leaves and steeped for another short amount of time. This can be repeated 3 – 15 times, depending on the type of tea. This method uses twice the amount of tea leaves with half the amount of hot water [1], essentially concentrating the flavor compounds that diffuse out of the tea leaves. Multiple infusions may not be as effective with tea bags; the tea fannings used for tea bags have small surface areas, and so most, if not all, of the flavor compounds will have quickly diffused into the water in the first steeping.

Sugar can be added to the boiling water before or after steeping the tea, as long as the sugar source completely dissolves. Typically, 1 cup of sugar is added for every 4 cups of boiled water.

2. First fermentation.

Once the tea is finished steeping and the sugar is dissolved, remove the tea bags or strain out the leaves – this is the completed tea base. Tossing the SCOBY (Symbiotic Culture of Bacteria and Yeast) into this freshly-completed tea base willy-nilly will negatively affect the fermentation process, as the microbes within SCOBY thrive best at specific temperatures and pH levels. To ensure a successful fermentation, the tea base has to be adjusted for temperature and pH create a suitable environment for the SCOBY.

Optimum temperature. Recall that SCOBY is alive; wait for the tea base to cool down to at least below 90°F (32°C) before adding SCOBY. A hot tea base would destroy the SCOBY microorganisms, resulting in a complete lack of fermentation. Conversely, do not add SCOBY to a tea base that has been refrigerated to below room temperature, as this would encourage the microbes to go into a dormant state, leading to a very sluggish fermentation process. The optimal temperature to add the SCOBY is between 77°F (25°C) and 90°F (32°C); , as this is the range which SCOBY microorganisms such as Acetobacter and yeast grow best [2,3].
Optimum pH. SCOBY bacteria are acidophiles, meaning that these bacteria thrive in acidic environments. Excluding herbal teas, the teas used for kombucha generally have low pH ranging from 2.9 to 6.3 [4,5]. While this is considered acidic, the pH of the tea base may not be at the optimal range for the Lactobacillus and Acetobacter that inhabit SCOBY, which thrive around pH 5.0 – 6.3 [6,7]. To remedy this, a starter liquid is added to the tea base, which is the liquid that the SCOBY was stored in. Since the starter liquid houses both Lactobacillus and Acetobacter, which produce acid by oxidizing sugar to lactic acid and ethanol to acetic acid, the starter contains a mixture of lactic and acetic acid at a buffered pH that is ideal for the SCOBY. In general, 1 cup of starter liquid is used for every 2 cups of tea base. If there is not enough starter liquid, then plain, store-bought kombucha can be used in lieu of the starter.

SCOBY is added to the tea base in a wide-mouthed container, often a glass jar, to allow for gas exchange and left to ferment for 7 to 10 days at room temperature. During this first fermentation, oxygen has to be abundantly available for Acetobacter, which requires oxygen to grow (it is an obligate anaerobe) [7]. However, leaving the container uncovered puts the kombucha at risk for contamination by fruit flies. Covering the jar with a tightly-woven cloth or paper towel and an elastic band can keep out fruit flies while permitting oxygen availability for the fermenting kombucha. The longer the fermentation period, the more vinegary the flavor and the lower the sugar content.

Kombucha undergoing the first fermentation. Photo credit: Amy Selleck (amyselleck/Flickr)

3. Remove the SCOBY.

To end the first fermenation, simply remove the SCOBY from the kombucha. From here, there are two options: reuse the SCOBY for another batch of kombucha or store it for later brewing.

Reuse: Make another tea base. For the starter liquid, it would be easiest to use the kombucha that the SCOBY was previously removed from.

Store: Store the SCOBY in a tea base/starter liquid mixture. This can be kept at room temperature for up to three weeks, depending on the volume of the storage mixture, before the microbes exhaust the nutrients. For longer storage, place the SCOBY mixture in the refrigerator. SCOBY become dormant in cold temperatures, but this does not mean the microbes cease activity altogether. Rather, in dormancy, cell division halts and the microbes’ metabolism slows significantly [9]. In storage, the SCOBY will continue to ferment its storage mixture, albeit at a slower rate than if left at room temperature. To maintain SCOBY viability, replenish the storage mixture every 4 – 6 weeks by removing 50 – 80% of the liquid and replacing that with new sweetened tea [8]. The main idea is to provide continuing fuel for the microorganisms. It is also possible to simply add ¼ cup sugar per quart of storage mixture every 4 – 6 weeks [8], but keep in mind that the dormant microbes are still carrying out cellular functions which require nutrients and water. The stored SCOBY will reduce the volume of its storage mixture, and so additional tea is required to prevent the storage mixture from drying up.

4. Second fermentation.

Pour the kombucha into bottles and cap them, leaving the bottles out at room temperature. If a flavored kombucha is desired, this is the step to add flavoring ingredients. Although SCOBY was removed at the end of the first fermentation, not all the microorganisms were attached to the cellulose matrix, especially if the microbes were newly-cloned during that previous fermentation period. There will still be kombucha microbes present to perform a second fermentation.

As this second fermentation occurs in a closed system, CO₂ produced from the yeast cannot escape the kombucha as it did during the first fermentation. As a result, the kombucha becomes carbonated during this step. Further, the kombucha microbes will continue to metabolize any remaining sugar to produce lactic acid, acetic acid, ethanol, and CO₂, so the kombucha will become less sweet but tangier.

After 1 to 3 days, depending on how quickly carbonation occurs, store the kombucha in the fridge. This stops fermentation and carbonation because the significantly decreased temperature causes the microbes to go into a dormant state. And voilá! You have your first batch of kombucha!

Photo credit: thedabblist (64636759@N07/Flickr)

While making kombucha is a lengthy process that can take up to two weeks to complete one batch, and perfecting the recipe to your own taste will involve making many batches, there is perhaps nothing more satisfying than a successful and delicious kitchen experiment.

The process described in this post was based off of kombucha recipes from The Kitchn and Food52.

References cited

Thoughts on Re-steeping. Teatrekker’s Blog. 22 Sept, 2013.
Science of Bread: Yeast is Fussy about Temperature. Exploratorium.
McGee, Harold. On Food and Cooking: The Science and Lore of the Kitchen. New York: Simon & Schuster, 1997.
pH Values of Common Drinks. Robert B. Shelton, DDS MAGD.
Singh, S., Jindal, R. Evaluating the buffering capacity of various soft drinks, fruit juices and tea. Journal of Conservative Dentistry, 2013; 13(3): 129-131.
Rault, A. Bouix, M., Béal, C. Fermentation pH Influences the Physiological-State Dynamics of Lactobacillus bulgaricus CFL1 during pH-Controlled Culture. Applied and Environmental Microbiology, July 2009; 75(13): 4374-4381.
Hwang, J. W., Yang, Y. K., Hwang, J. K., Pyun, Y. R., Kim, Y. S. Effects of pH and dissolved oxygen on cellulose production by Acetobacter xylinum BRC5 in agitated culture, 1999; 88(2): 183-188.
Take a Break from Making Kombucha Tea. Cultures for Health.
Lahtinen, S. J., Ouwehand, A. C., Reinikainen, J. P., Korpela, J. M., Sandholm, J., Salminen, S. J. Intrinsic Properties of So-Called Dormant Probiotic Bacteria, Determined by Flow Cytometric Viability Assays. Applied and Environmental Microbiology, July 2006; 72(7): 5132-5134.

About the author: Alice Phung once had her sights set on an English degree, but eventually switched over to chemistry and hasn’t looked back since.

Read more by Alice Phung

Kombucha Brewing: The Ingredients

November 3, 2015/in DIY Kitchen Science/by Grant Alkin

Kombucha with SCOBY. Photo credit: thedabblist (64636759@N07/Flickr)

Craving some kombucha without the grocery store prices? Why not try brewing your own kombucha? As a fermented tea drink that is brightly effervescent, deliciously tangy, and slightly sweet, having some kombucha on hand could add a little spring to these cold seasons. On top of that, the brewing and fermentation involved in kombucha-making requires a little scientific know-how and quite a bit of trial and error to perfect the flavor to your liking. Think of it as having a science experiment in your kitchen!

At first glance, making kombucha appears fairly simple, as there are only four basic ingredients that go into it: water, tea, sugar, and a “Symbiotic Colony of Bacteria and Yeast,” SCOBY. If a flavored kombucha is desired, specific flavor ingredients can be added too. A cursory investigation into each ingredient, however, may bring up some questions. What type of tea makes the best-tasting kombucha? What is SCOBY and where can you source it? Is it possible to brew a sugar-free kombucha? Here is your scientific guide to making kombucha. We provide some scientific information regarding each component to help make an informed decision in choosing the ingredients that would create the kombucha that best aligns with your preferences.

SCOBY

What is it?

SCOBY is the most important component of kombucha, since it is the only thing standing between ordinary, sweetened tea and kombucha. Other fermented foods which utilize a similar symbiotic culture include kefir, ginger beer, vinegar, and sourdough. SCOBY is a grayish-white or beige, squishy mass floating within the brewed culture, and it is responsible for the distinct vinegar-like flavor, trivial alcohol content, and characteristic carbonation of kombucha. However, to call this leathery, stringy mat a symbiotic colony of microbes is a scientific misnomer. Biologically, a colony implies a coexisting group of individuals within the same species; a microbial colony is a cluster of microorganisms which have descended from a single cell, a common ancestor. SCOBY, on the other hand, is a symbiosis of multiple bacterial and yeast species cohabiting a cellulose matrix [1]. It may be more accurate to describe SCOBY as a biofilm, a colony of several microbial species attached to one another on a surface.

A symbiotic culture of bacteria and yeasts. Photo credit: Robert Anthony Provost (twon/Flickr)

As the name implies, SCOBY is alive. A study on the microbial populations existing in SCOBY reveals that the bacterial genus Gluconacetobacter is the most abundant [1]. Gluconacetobacter is responsible for the biosynthesis of the cellulose matrix that the SCOBY microbial population resides within. In other words, this genus of bacteria enables easy handling by creating the solid, stringy, floating mass that SCOBY is visually famous for. The next most abundant SCOBY bacteria belong to the genera Acetobacter and Lactobacillus [1], both of which give kombucha its acidic, vinegary taste by oxidizing ethanol to acetic acid and sugar to lactic acid, respectively. The yeast population of SCOBY primarily consists of the genus Zygosaccharomyces [1], which is notable for its high sugar, high alcohol, and high acid tolerance [2]. Yeasts in SCOBY generate CO₂ and thus provide carbonation; they also produce alcohol, some of which is metabolized by Acetobacter into acetic acid. It is worth noting that the microbial composition of SCOBY may vary over time [1], possibly due to rapid growth, contamination, and/or random mutations. This compositional change may lead to flavor differences among different batches that have used the same SCOBY.

Where do I get it?

Home-brewing stores and online marketplaces are the more common places to buy SCOBY. For the more ambitious, there is also the option to culture SCOBY at home. Given that it is a collection of living organisms, you need to start with some pre-existing collection of kombucha microbes.

To make SCOBY at home, a modest amount of store-bought or homemade, unflavored and unpasteurized kombucha is required. Kombucha often contains a small amount of SCOBY left behind from the brewing process. To begin, place about 1 cup of kombucha with 7 cups sweet tea in a covered container and store for 1 to 4 weeks. In storage, the SCOBY microbes multiply and aggregate, with Gluconacetobacter synthesizing the cellulose that enables the microorganisms to grow together in that signature rubbery mass. For more detailed instructions, check out The Kitchn’s recipe for home-grown SCOBY.

Teas

Which tea?

Kombucha would not be kombucha without tea, but with so many varieties and forms to choose from, it’s easy to get lost. In general, teas are categorized by how the tea leaves (from the plant, Camellia sinensis) were processed, which affects the flavor, caffeine content, and color of the brewed liquid. Varieties among the basic tea categories arise from the geography of C. sinensis, growing conditions, time of harvest, and production processing, giving rise to notable flavor differences. The type of tea chosen will influence the prominent flavor profile of the finished kombucha. For the adventurous, different teas can be mixed together to create a unique kombucha flavor base.

Left to right: green tea, yellow tea, oolong tea, and black tea. Photo credit: Haneburger (Wikimedia Commons)

Black: The most common choice for brewing kombucha, black teas undergo full enzymatic oxidation during production, which gives the drink a dark brown color [3]. Furthermore, complete oxidation of the tea leaves gives black teas a deep malt, caramel, or toasty flavor. This rich tea flavor enables a quick brew without flavor loss during kombucha fermentation.
Oolong: Literally translating to “black dragon tea”, oolong teas are partially oxidized, ranging from 8-85% oxidation depending on the tea producer. Oolong flavor profiles fall between the robustness of black teas and the delicacy of green teas, with tones ranging from smoky and buttery to floral and fruity, depending on the amount of oxidation the tea leaves were processed.
Green: During production, the oxidation process is stopped early; the tea leaves undergo minimal oxidation, giving green tea a more grassy, floral flavor when compared to other types of teas [3]. Due to their light and subtle flavors, green teas may have to be steeped many times for full flavor, and kombucha with a green tea base may have to be brewed longer.
White: Unlike the other teas, white teas are made using only the buds of the C. sinensis plant. Additionally, some white tea varieties use buds that have been steamed or baked, which inactivates enzymatic oxidation. The minimal or absence of oxidation gives white teas a very delicate and subtle grassy flavor, and so this tea may have to be steeped multiple times and a kombucha with a white tea base may have to be brewed for a long time.
Pu-erh: Pu-erh stands apart from other teas that use sinensis leaves by an additional fermentation step after the leaves are dried. Fermenting the tea leaves gives pu-erh teas a complex, sweet, earthy flavor profile that the other teas do not have [3].
Herbal: Unlike the above four categories, herbal teas rely on steeping plant parts that do not come from sinensis. Herbal teas are strongly advised against for kombucha brewing, as the plants that are used often contain volatile oils that have anti-microbial and/or anti-fungal activity. Some common anti-microbial volatile oils found in herbal teas include lavender oil (from lavender teas), peppermint oil (peppermint teas), and eugenol oil (chai teas) [4], all of which can destroy the bacteria and yeast in SCOBY. A damaged SCOBY will not be able to ferment or carbonate the kombucha batch.

Loose leaf or tea bags?

Tea bags are cheaper and easier to find at the grocery store, but tea bags typically contain fannings or tea dust, which are broken remnants of tea leaves. These remnants were either purposefully crushed for packaging into tea bags or are the leftover fragments after the loose leaf teas are packaged. In contrast, loose leaf teas cost more than their tea bag counterparts and are primarily found in tea specialty stores, but the leaves are much bigger than the fannings found in tea bags. The primary difference between loose leaf and tea bags are the size of the tea leaves, which will affect taste and brew time. Tea leaf sizes do not always correlate to the quality of the tea [5].

Where tea brewing is concerned, fannings have a much greater surface-area-to-volume ratio due to the small particle size, and so will brew much quicker than loose leaf teas. Furthermore, crushed tea leaves may increase the strength of the brewed tea [5]. However, loose leaf teas generally offer more complex, nuanced flavor profiles which tea bags lack. The form of tea to use for brewing kombucha overall depends on personal taste preferences.

Sugar

Which sugar?

At first glance, white sugar seems like the only option, given its ubiquity. For those wishing to experiment a little further, there is no reason to try other sugar sources, since the sugar-metabolizing microbes in SCOBY are not sucrose-specific. There are a couple of notes to consider when choosing the type of sugar:

Brown sugar is sucrose sugar that contains molasses, which may add a molasses flavor to the kombucha.

Raw sugar tend to have bigger crystals, since it is less refined. Bigger sucrose particles may affect its ability to completely dissolve in the kombucha, especially at or below room temperature. If the sugar crystals are not completely dissolved, there may be less sugar in solution available for the bacteria and yeast to metabolize. This could perhaps lead to a more yeasty, rather than fizzy kombucha.

Honey is a mixture of glucose and fructose, with its golden color deriving from non-sugar components such as pollen. Other microorganisms may also be found in honey [6], so using honey for brewing kombucha runs the risk of microbial contamination which may affect SCOBY efficacy.

Sugars extracted from plants or trees other than beets and sugar canes are fair game for brewing kombucha. A few examples include maple syrup, coconut sugar, and palm sugar. Agave nectar, despite health claims, contains a higher fructose content by weight than high fructose corn syrup [7].

Sugar substitutes, such as stevia, xylitol, and glycerol, are sugar alcohols. SCOBY is unable to metabolize sugar alcohols, and so adding artificial sweeteners would not be effective at all in brewing kombucha.

How much sugar?

In kombucha, sugar is used as a food source for the SCOBY, not as a sweetener as in many other recipes. The end product has far less sugar than was originally added to the first fermentation period, as the SCOBY has metabolized most of it to create the vinegary flavor and carbonation. Therefore, adding sugar is necessary for successful fermentation.

Too little sugar, and the SCOBY does not have the necessary fuel to undergo prolonged fermentation, leading to an unsweet, not very acidic, and possibly flat kombucha. Too much sugar may cause the yeast to over-proliferate, outnumbering the other SCOBY microbes. This both decreases the efficacy of the SCOBY and decreases the flavor and carbonation of the resulting kombucha. The exact amount of sugar varies among recipes, and can be experimented with to suit personal preferences.

Flavorings

For a more unique kombucha, flavors are often added near the end of the kombucha brewing process, after the batch has undergone its initial fermentation period. Just like every other component that goes into kombucha, the choices for flavoring are abundant.

Herbs and spices: Since herbs and spices tend to have strong flavors, adding a little bit can go a long way. Keep the amount to a minimum, as some herbs and spices may contain antimicrobial activity, and adding too much may harm the microbes on SCOBY, making the second fermentation period unlikely to occur successfully.

Fruits: Whether fresh fruit or fruit juice is used, be sure to keep an eye on the batch after adding the fruits. Fruits and fruit juices introduce an extra sugar source for the SCOBY during the second fermentation period; the yeast cultures in the SCOBY go into “overdrive” with this added amount of sugar. While this may lead to a fizzier kombucha, the increased carbonation will create a pressure-build up within the container. Opening the container may risk a small kombucha explosion or the container may burst open from the pressure built up.

Kombucha flavored with raspberries. Photo credit: Lukas Chin (Wikimedia Commons)

Extracts and infused waters: Like herbal teas, be sure that the extracts are oil-free as to avoid volatiles that contain anti-microbial activity. A few examples of water-based extracts would be lemon extract (not lemon oil), almond extract, and vanilla. Infused waters include rose water and orange blossom water.

With a little bit of background knowledge, kombucha brewing could become your favorite science project. Explore the possibilities!

References cited

Marsh, A. J., O’Sullivan, O., Hill, C., Ross, R. P., Cotter, P. D. Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples. Food Microbiology, April 2014; 38:171-178.
C. Fugelsang, “Zygosaccharomyces, A Spoilage Yeast Isolated from Grape Juice.”
Types of Tea. TeaSource. 2013.
Thosar, N., Basak, S., Bahadure, R. N., Rajurkar, M. Antimicrobial efficacy of five essential oils against oral pathogens: An in vitro European Journal of Dentistry, Sept 2013; 7:71-77.
Does the size of your tea leaf matter? Octavia Tea. 18 November, 2011.
Olaitan, P. B., Adeleke, O. E., Ola, I. O. Honey: a reservoir for microorganisms and an inhibitory agent for microbes. African Health Sciences, Sept 2007; 7(3):159-165.
Bowden, Jonny. Debunking the Blue Agave Myth. Huffington Post. 17 April, 2010.

About the author: Alice Phung once had her sights set on an English degree, but eventually switched over to chemistry and hasn’t looked back since.

Read more by Alice Phung

Food Genomes & Food Safety

July 30, 2015/in What We're Reading/by Grant Alkin

In more than two-thirds of cases arising from food-borne illnesses, the cause of the illness is never identified. However, the Food and Drug Administration has recently been using whole genome sequencing to track down the pathogens responsible for tainted foods in an effort to thwart outbreaks. Researchers at IBM Research and Mars Incorporated are also undergoing a project to sequence the DNA of the food supply chain to get a baseline of safe food ingredients.
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Microbes & the Future

July 2, 2015/in What We're Reading/by Grant Alkin

The vanillin (major flavor compound in vanilla beans) found in most food products on the market is derived from a three-step synthetic process that converts the molecule guaiacol to vanillin. Both natural and chemical methods for this conversion has shown to be expensive and environmentally burdensome, but biotech company Gen9 is providing a more promising route to synthesize vanillin that begins with glucose, using yeast to “ferment it just like beer.” David Chang of Momofuku and microbiologist Ben Wolfe further elaborate on how microbes may very well be the future of food.
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International Variations of Yogurt: A Cultural Exploration of Milk

June 30, 2015/in Science & Food/by Grant Alkin

Photo credit: Robert Koehler

It’s a dessert, it’s a condiment, it’s a breakfast staple. Yogurt can be consumed in a myriad of ways; there also exist several variations of yogurt around the world that differ dramatically in taste and texture.

It all begins with milk—be it from a cow, sheep, buffalo, donkey, or goat. In standard western forms of yogurt, the art of yogurt-making begins by heating milk to 85°C and holding for 30 minutes or at 90°C for 10 minutes. Applying heat denatures the whey protein, lactoglobulin, and plays a pivotal role in determining the yogurt’s final creamy texture. Without this protein denaturation, the milk proteins won’t set together in an organized matrix, but will instead cluster together and form curds.

In the second phase, fermentation, milk is first cooled to a temperature within the range of 30°C-45°C, a range well tolerated by the microbes that play a role in fermentation. Traditional yogurt-making in the western world relies on bacterial cultures containing Lactobacillus bulgaricus and Streptococcus thermophilus, which can be directly added to milk in the form of a packaged starter (similar to yeast) or taken from a previously-made batch of yogurt. The bacteria then convert the milk sugar, lactose, into lactic acid, which firms the yogurt and provides it with its tart and tangy taste.

Fermentation conditions heavily influence the flavor and consistency of the final product. Different types of bacteria thrive in different temperature ranges and can produce several variations in consistencies, ranging from smooth and creamy to thick and jelly-like. At lower temperatures, bacteria produce lactic acid much more slowly and it can take up to 18 hours for the yogurt to set; by contrast, lactic acid bacteria working at higher temperatures can set the milk proteins in just two or three hours. A rapid, high-temperature gelling will result in a firm yogurt, whereas a low-temperature, slow gelling will produce a more delicate, tightly packed protein network. [1]

Throughout the world, we’ll find several different kinds of yogurt or yogurt-like products. Significant textural or taste changes can be made with simple tweaks in the preparation or fermentation process, and we’ll explore a few of these here.

Greek yogurt

Greek yogurt has become ubiquitous in grocery stores over the past decade and is loved for its rich flavor and thick consistency. The secret behind its popularity lies in the straining step. Straining allows the liquid whey component of milk to drain away and also removes some of the lactose, leaving behind a product with reduced sugar and nearly double the protein when compared to its non-strained counterparts. Although not actually of Greek origin (its origins still remain unclear), this strained yogurt is also popular throughout the Middle East and Central Asia [1,2].

Viili

This slimy dairy product topped with mold may sound like a failed kitchen experiment, but is in fact a yogurt-like product held dear to many Scandinavians. Known as viili to the Finnish, långfil to the Swedes, or tättemjölk to those in Norway, this ropy milk product is so thick that it needs to be cut with a knife when served. The main culprit in viili’s ropiness is a mesophilic strain of lactic acid bacteria called Lactococcus lactis subspecies cremoris. During fermentation, this strain of lactic acid bacteria produces long strands of slimy sugars known as exopolysaccharides that create the characteristic texture and flavor profile of viili. On its surface, you’ll find a velvety layer of mold formed from G. candidum, which lends this dairy product fruity and savory notes. The mold also consumes lactic acid, reducing the acidity of viili, giving it a relatively mild acidic flavor. To make viili, you’ll need milk and a viili starter, which contains both Lactococcus cremorisx and G. candidum [3].

Kefir

Although not technically yogurt, kefir is a bubbly, mildly alcoholic, Russian-derived equivalent. What distinguishes kefir from yogurt is that instead of relying solely on lactic acid bacteria for fermentation, it’s made from kefir grains, which are large cauliflower-like complexes composed of lactobacilli bacteria and yeasts. Kefir also sets itself apart from other fermented milk products in that its fermenting microbes exist in these relatively large, popcorn-sized ‘grains,’ instead of being evenly dispersed throughout the milk. While bacteria are busy converting a portion of the lactose into lactic acid, yeasts from the kefir grains also convert lactose into ethanol and carbon dioxide. The result is a tangy, yeasty, and effervescent beverage [4]. Kefir boasts higher probiotic activity than typical yogurts, making it a fermented dairy product of choice among health enthusiasts.

Kefir grains. Photo credit: Chiot’s Run (chiotsrun/Flickr)

Ayran

This national drink of Turkey is made by diluting natural yogurt with ice water and salt. Throughout Turkey, different regional variations of ayran exist, with the most well-known version originating from a town called Susurluk. In Susurluk, local variations of ayran are made from a mixture of cow, buffalo, and sheep’s milk, giving it a distinctive creamy and foamy quality. A notable feature of Ayran is its lower shelf-life when compared to other fermented milk products. Stabilizers are added to ayran to prevent the water and milk mixture from separating, but salt hinders the effects of stabilization [5].

Yakult

Photo credit: Dezzawong/Wikimedia Commons

Now found all over the world and most notably in vending machines throughout Asia, Yakult is a probiotic drink that was developed in Japan. Japanese microbiologist, Minoru Shirota, was searching for a strain of bacteria that would benefit digestive and overall health. His work led him to Lactobacillus casei Shirota, which he cultivated and used to develop Yakult. Yakult is made from adding this unique bacteria strain to skim milk, water, and sugar, and is often enjoyed for its sweet and fruity natural flavors. As seen above, Yakult can also be found in several flavor variations as well.

Cultured milks are a culinary marvel, especially when you consider how many different forms it can take. Head to the dairy aisle and try a new variation of yogurt, or why not attempt making some at home in your own kitchen? With all the different forms out there, you’ll surely find one you enjoy.

References cited:

McGee, Harold. On Food and Cooking. The Science and Lore of the Kitchen. New York: Scribner, 2004. Print.
Lalime, Jennifer. “How to Make Greek-Style Yogurt“. The Feed.
Salminen, Edith. “There Will be Slime“. Nordic Food Lab.
Farnworth, E. R. Kefir—a complex probiotic. Food Science and Technology Bulletin.
“Fame of Foamy Ayran Goes Beyond Borders“. Hurriyet Daily News.

About the author: Mai Nguyen is an aspiring food scientist who received her B.S. in biochemistry from the University of Virginia. She hopes to soon escape the bench in pursuit of a more creative and fulfilling career.

Read more by Mai Nguyen

Cheese Microbes & Pizza Math

March 26, 2015/in What We're Reading/by Grant Alkin

Researchers at the American Academy of Microbiology answer the FAQs of cheese-making and Carl Friedrich Gauss, a famous 19th century mathematician, explains the best way to hold a pizza slice–using math, of course.
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Beer Yeast & Flavor

March 11, 2015/in What We're Reading/by Grant Alkin

Want beer foam that doesn’t dissipate right away? Microbiologist Tom Villa made a genetic discovery in yeast that could create beers with longer-lasting beer foam. This yeast, however, doesn’t quite affect the taste, so find out where beer flavor comes from.
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