Coming to understand the bugs in our yogurt and in our guts

In many ways, medicine is remarkably similar to farming.  The ancient Romans and Chinese, for example, knew that rotating crops and spreading manure in their fields would vastly improve yields.  These farmers didn’t know the underlying biology, and it didn’t matter: these practices worked, and they worked well.  Often, medicine is little different.  Insulin was given before knowing that it spurred the movement of glucose transporters to the edge of muscle cells, and exactly how acetaminophen relieves headaches has remained elusive.  The bacteria that thrive in yogurt and kefir, otherwise known as probiotics, are the modern day equivalent of manure.  But researchers are beginning to get a grasp of the microbial world in our tummies.   

In a paper published last month, Jeffrey Gordon’s team at Washington University in St. Louis identified how probiotics may influence gut health.  The scientists inoculated a sterile mouse model with 15 strains of bacteria that normally reside within the human colon.  The mice were then given probiotics and studied for changes in gut function.

Source: Wikipedia.  The model bacteria e. coli viewed by electron microscopy

The most interesting finding was that the probiotics hardly changed the composition of the bugs in the gut.  That is, the beneficial bacteria didn’t simply displace the ones already residing in the animals’ intestines.  And this makes sense to Gordon, who when interviewed said that the bacterial-colonization idea was analogous to “pouring a gallon of Kool-Aid into your swimming pool and expecting it to turn red.”

Instead, the new bacteria apparently vary the gene expression of the native ones.

Human cells and all of the microbes that inhabit the body have individual sets of genes.  A combination of spontaneity, interactions with other genes, and environmental triggers causes the genome to produce chains of messenger ribonucleic acid (mRNA). The “expressed” mRNA, in turn, is converted, or “translated,” into chains of amino acids (proteins) that do all the wonderful things that cells – or bacteria – do.  If genes were sheet music, the mRNA would be the specific keys, or group of keys, that produce the distinct musical notes or chords.  Probiotics changed the frequency that the bacteria’s genes produced mRNA, like a pianist using fewer C’s and more major scales.  Different levels of gene expression, like different musical composition, produce different effects.

Source:  Wikipedia.  Gene coding a protein.

The most noticeable shift in expression was seen in genes that dictate carbohydrate metabolism, specifically molecules known as xylooligosaccharides that are commonly found in plants.  Importantly, the probiotics manipulated the same genes in the bacterial community of human subjects.  It’s these sudden manipulations that may explain the known benefits of friendly microbes.

Gut bacteria influence the entire body.  Clinical trials have consistently shown improved gut function in people taking probiotics, where the benefits are especially pronounced in those afflicted with diarrhea.  When mice are fed probiotics, the brain produces chemical critical for regulating anxiety.  Conversely, eliminating native bacteria can be detrimental.  Some scientists are considering the over-use of antibiotics as a contributor to the rising incidence of allergies, asthma, and inflammatory bowel disease because the drugs indiscriminately wipe out the pathogenic and helpful bugs.  And eating bacteria isn’t the only way to get them into the gut.

Fecal transplant is the most remarkable bacterial therapy, if not the grossest.  As the name makes obvious, the treatment takes feces and the billions of resident bacteria from one person and transplants it into someone else.  It has been used in several different conditions, but the most dramatic results have been shown in c. difficile infections, a relentless hospital acquired bug that is rapidly resisting more antibiotics.  The stomach-churning therapy resolves a whopping 9 out of 10 c. difficile cases with virtually no side effects, and apparently, no smell.  What this frontier of probiotics will evolve into, though, is still an open question. 

Both scientists and marketers are pushing the frontier of probiotics.  “Contains live active cultures” is plastered on every dairy product from yogurt to ranch dressing.  Unfortunately, promise before understanding is a simple recipe for bad nutrition.  Bacteria could become the new snake oil, like high-dose antioxidant supplements.  But microbiologist Jeffrey Gordon’s experiments offer a model to begin rigorously investigating how probiotics work, optimal combinations of bacterial strains, and appropriate doses. 

The great 20^th century physicist Richard Feynman once said that “what I cannot create, I do understand.”  It looks like the science of probiotics is taking a step in the right direction.

   

Food Science: What happens when you rinse kefir grains?

So, ignore the name of my blog for this post.  That's right.  It's time for some food science.  But in my defense, it involves traditional food (kefir) and good ol' falsifiable science.  That's right.  I did a an experiment to determine whether or not one should rinse kefir grains before adding them to a fresh batch of milk.

Kefir is not a popular food, at least not compared to its yogurt-y cousin.  So when you decide to go out and make it on your own, you have to rely on what you can dig up on the internet.  And true to the internet's reputation, you can find any possible answer for whatever question you are asking.  One simple question that I had was whether or not I should be rinsing the grains between batches.  The information I received with my grains said I should not rinse them.  However, Nourishing Traditions seems to suggest that they should be rinsed.  There was only one way to find out.  I hypothesized that rinsing the grains would blunt their capacity for producing kefir, and therefore produce a milder kefir.

Fig 1.  Separated and weighed to 10 grams

Methods

The grains were rinsed and randomized.  Two groups, each weighing 10 grams (g) and containing 18 grains (Fig 1), were formed.  Most batches were made with 8 ounces of organic pasteurized whole milk; the last couple of batches were a bit over 8 ounces to accommodate the increased fermentation.  Fermentation was 12-14 hours per day. Clean jars were used each time.

Fig 2.  Kefir preparation.  Clean jars, 8 oz. milk, cover with paper towel. 

The time and temperature were not always consistent.  However, because the jars were adjacent to each other at all times, any day-to-day variation would affect each group equally, and would therefore not bias the results.  The only difference between the groups was that the experimental (washed) group was rinsed under cold tap water in a stainless steel strainer until curds were removed, roughly 10 seconds.  The control group was simply placed in a new batch of fresh milk.  The experiment ran for 11 days, and on the 7th and 11th days, both groups of grains were washed and weighed, and the two different batches were tasted by a blind taster a.k.a. the girlfriend.

Results

Both groups increased in weight at the same rate.  However, the grains in the unwashed group were more dense than the washed group on day 7 (0.67 g/grain vs. 0.48 g/grain) and on day 11 (0.74 g/grain vs. 0.51 g/grain).  Thus, rinsing reduced the density of the grains by 30%, and produced many small grains (Figs. 3-5).

Fig 3. Unwashed (left) and washed (right) groups at the end of the study.

Fig. 4 Results of control (unwashed)

Fig 5.  Results of experimental (washed) group.

Tasting results were consistent between the 7th and 11th day.  Both batches of kefir reportedly tasted as kefir should, and both batches were similarly thick, both in the glass and in mouthfeel.  However, the unwashed kefir was "definitely more sour."  Furthermore, the washed kefir had a lighter effervescence with smaller bubbles and "a more full kefir taste."  The unwashed group appears to ferment faster, as there was usually more whey present (Fig 6).

Fig 6.  The unwashed (left) was usually more fermented.

Discussion

This experiment demonstrates that rinsing kefir grains between batches produces more and smaller grains than when grains are left unwashed.  Furthermore, these rinsed grains tend to produce a milder kefir.  While I can surmize that this occurs because the unwashed grains produce kefir at a faster rate (and therefore make a more kefir, kefir), that will require another experiment.

I'm definitely confident in these results, but I would love to hear other peoples' experience with washing their grains.  The results might have been more dramatic had I not rinsed and weighed the grains mid-experiment, but then again, this added a bit of reproducibility within the study.  Unfortunately, I was not blinded to the treatment group.  And come to think of it, the kefir wasn't blinded with a placebo.  I already anthropomorphize my kefir grains enough as it is, but perhaps they knew what group they were in...

So, what can we take away from this bit of food science?  There are likely many recommendations for treating kefir grains because there is no obvious best way.  While I would argue that the density produced by leaving the grains unwashed is evidence of "healthier" grains, if you prefer the taste of a mild kefir, then you would be better off rinsing them, at least occasionally.  Or, as I've started doing, rinse the grains on warmer days or when you might make it home late and risk over fermenting the kefir.  Either way, it's between you and your kefir.

Now, it's time for a kefir smoothy.  Theory into practice, I suppose.  Cheers!

This post is shared on Real Food Whole Health's Traditional Tuesdays.

How I make Kefir

You didn't think that I would write an entire post on kefir without sharing how I make it, did you?  From what I've been able to find, the fundamentals of making kefir are universal, but everyone has their own take on the proportions, time, and processing.  Here's how I've been doing it.

1.  Remember, this is a continual process from the previous batch of kefir.  After straining the kefir, I set the grains aside and thoroughly wash the glass jar I used for fermentation.  I use about two tablespoons of kefir grains for every 12-14 ounces of milk, which is more concentrated than typically called for.

I don't wash the grains, but some people do.  Over several batches, the grains will accumulate a polysaccharide gel known as kefiran, and many writers purport that this enhances the kefir making process - I'll talk about this in a later post.  

Kefir grains

2.  Place the kefir grains into a large jar and add 12 ounces of whole fat milk.  I add a couple tablespoons of cream for good measure.  I use this as an afternoon snack, so it needs plenty of calories to hold me over.

I do my best to buy organic milk, especially if I am more confident that the cows are mostly grass-fed.  Remember, organic cows can still be on a feedlot.  I try my best to use the pasture-based animal products since it's better for the cows and doesn't perpetuate the over-use of antibiotics in cattle feed.  And grass-fed organic cow's milk is probably somewhat more nutritious than conventional grain fed cow's milk.  After all, cows evolved eating grass and not corn.  However, the major problem with organic milk is that it is usually ultra pasteurized (UHT) rather than conventionally pasteurized.  Thus, it tends to have a cooked taste.  I was pleased to find conventionally pasteurized organic milk at Sprout's.  This particular dairy does not have to rely on excessive pasteurization to prevent early spoilage because it is local and travels a shorter distance.   

Bath-time for the grains

Organic and pasteurized, not UHT.

3.  Allow the mixture to ferment for roughly twenty-four hours at room temperature.  Cover with a towel.  Keep in mind that the ambient temperature will change the rate of fermentation.  Hotter days/nights will speed up the process.

Kefir-ing.

4.  The kefir is ready when it has small pockets of clear-yellow whey and small bubbles.  It smells of yogurt (due to the lactic acid producing bacteria) with a hint of sourdough bread (due to the yeast).  Pour the mixture through a strainer and bump the shaker with your hand until you are left with kefiran-covered kefir grains.

Notice the small bubbles at the surface.

Strain into a large-ish bowl to prevent a mess.

5.  Pour the kefir into a jar and let it chill in the refrigerator.  It will continue to ferment in the refrigerator because of the residual microorganisms, but it will be much slower at this lower temperature.  I like to drink it straight, especially with a touch of sweetener.  But there are many other things you can do with it...

Kefir goodness

Introducing Kefir

Kefir

After coming across various blog posts on fermented dairy (yogurt, kefir, cultured butter), I was intrigued.  I placed an order for kefir grains from The KefirLady and started a batch as soon as they arrived in the mail.  Once you start fermenting your own dairy, you've crossed into a another world of hippie-locavore-homecooking that you cannot return from.

Kefir is simply fermented milk.  Its origins have been traced to Caucasus, where the Muslim population regarded kefir as a gift from Allah.  The fermentation is achieved by inoculating a container of milk with a combination of bacteria and yeast, collectively known as kefir grains. The grains metabolize the nutrients in the milk - the lactose and some fatty acids - and in-turn produce carbon dioxide, lactic acid, and small amounts of a host of other compounds, including ethanol.  These benign microorganisms out-compete and actually fend-off pathogenic bacteria, thus preserving the milk without refrigeration.  Kefir is unique because it contains both bacteria and yeast, unlike yogurt which only contains bacteria, and because the grains are re-used again and again with each new batch.  Similar to other fermented foods, kefir is considered a probiotic.

Kefir grains

A probiotic is defined as "microbial cell preparations or components of microbial cells that have a beneficial effect on the health and well being of the host."  Many of the purported health benefits of fermented products are commonly attributed to improved gut health and modulation of the immune system (via the gut), although some have investigated possible anti-cancer properties. While everyone is familiar with probiotics because of the yogurt craze, the idea that fermented foods are healthful is not new.  As implied above, the people of Caucasus had much appreciation for kefir.  But despite the precedence, we cannot yet call probiotic foods a panacea. 

The Cochrane Collaboration has found no benefit in probiotics for inducing remission or maintaining remission in Crohn's disease, which perhaps argues against how strongly probiotics can modulate the immune response.  In regard to general gut health, Cochrane did find limited evidence for reduced c. dificile re-infection and minor improvements in childhood diarrhea.  These trials commonly used isolated  probiotics, so perhaps whole food probiotics are more beneficial.

There is some evidence that yogurt and the lactobacillus bacteria it contains can improve gut health in humans.  However, the most compelling evidence seems to be in regard to relieving constipation, particularly in children and women.  From what I can gather, lactobacillus containing yogurt does appear to relieve constipation, although not necessarily with the consistency asserted by advertisments.  To be sure, my cursory review of the literature does not warrant a definitive assessment for or against the benefits of probiotic foods, but I think there are a few things to keep in mind.  

The whole area of probiotic research suffers from inconsistant trial design, inconsistent use of bacteria and probiotic sources, and trouble defining exactly what "gut health" is.  The role of gut bacteria and health is compelling, but our understanding is still in its infancy.  We know that illness is associated with different gut microflora, such that obese children and those with Crohn's disease have different gut microflora composition than normal controls.  And as I learned from this past weekend's American Diabetes Association conference, these microflora are partially malleable e.g bariatric surgery changes the prevalance of different bacteria within the same individual.  However, we still do not understand what these associations and changes mean.  And while this research will likely provide improved treatment for gut disorders and diseases, we are still unsure how readily one food (kefir, yogurt, fermented vegetables) will change our gut bacteria and subsequently our health.  But I still think trying kefir is worthwhile.

From my experience, and I know that I am not alone, conventional medicine does a poor job with general gut health.  Conventional medicine clearly has a grasp on serious digestive diseases such as colon cancer, but more nuanced problems, such as food intolerances or sensitivities, usually evoke eye-rolling or a psycho-somatic diagnosis.  The diagnosis-by-exclusion Irritable Bowel Syndrome is likely a symptom of this general ignorance.  Although to be fair, I am not convinced that alternative medicine understands gut health as much as it purports to.  So given that fermented foods are both traditional and whole foods (avoid sugar containing yogurts!), and given their potential benefit, I think they are absolutely worth trying.  And because I make the kefir myself, I know that it has the probiotics that it is supposed to.  And if it is nothing but nutritional mysticism, at least it is low carb mysticism (the bacteria eat the milk sugar so that I don't have to).  And hey, instead of a cat to keep me company, now I have kefir grains to come home to.