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Bacteria all around us


Photo: NAID via Wikimedia Commons

Last week we sat in on a discussion hosted by CUESA and Kitchen Table Talks (a joint project of 18 Reasons and Civil Eats) about the unseen and largely unknown world of bacteria, a subject near and dear to FARMcurious.

Moderator Dr. Daphne Miller, family physician and author of Farmacology andThe Jungle Effect, kicked off the conversation by noting that it was only about 150 years ago that scientists first described these microorganisms and at that time the focus was on germs and eradication. It wasn’t until 2007 and the launch of the Human Microbiome Project that we really began to understand the extent of microbial communities. Only 7 years of research so far, wow!

This panel looked not only at the human microbiome, but life in the soil that we grow our food in and, of course, the action of bacteria on fermented foods. There were some interesting parallels.

Dr. Kate Scow, professor of soil science at UC Davis, soil microbial ecologist, and director of the Russell Ranch Sustainable Agriculture Facility, explained that microbes break down matter and liberate nutrients in healthy soil. In order to do this they need carbon (plant matter) to feed on, which is added in manure and compost in organic farming but is not part of chemical fertilizers. As a result, conventional farms have reduced microbial communities, both in quantity and diversity.


Photo: Christian Guthier via Flickr cc

Kathryn Lukas, local kraut maven and founder of Farmhouse Culture had a similar story to tell. She says that industrial kimchi and kraut makers have tried to culture bacteria to produce more controlled and consistent results with their ferments but found that the naturally occurring bacteria communities on vegetables created the best flavor, possibly because of diversity that can’t be reproduced in the lab. They work with a microbiologist to learn more about the ways a balanced system of microbes transform produce, freeing up vitamins like B12, making easier to digest food and creating flavors that appeal to humans.

Kristen Earle, a researcher and graduate student at Stanford’s Sonnenburg Microbiology Lab, weighed in with evidence that fiber (plants again!) is vital to healthy digestion.  Bacteria do their work as we learned with soil and food, further disassembling, releasing nutrients and making it easier for us to digest and absorb what we eat. With reduced fiber it takes just 10 days before a significant loss of diversity can be measured in the gut and, alarmingly, the remaining bacteria will start feeding on the host (that’s you!). Reintroduction of fiber has been shown to increase diversity, but some species will never be recovered once lost. Fermented foods have been shown to introduce diverse microbes that colonize the gut while probiotic supplements add specific species that work as they pass through but tend not to stick around.

photo by Katie Stoyka for FARMcurious

Photo: Katie Stoyka

All three panelists noted the importance of balanced systems. “Bad” microbes are out there and when we make changes in how we handle the soil, food preparation or our diet the balance can shift, creating unwanted (and unpleasant) results.

How do we keep it balanced? Well, more research is required. There are still a lot of mysteries waiting to be solved! The exciting second stage of the Human Microbiome Project is now underway and looking at the role of the human microbiome in health and disease. The study ends in 2015 and while I wait for  the results I’ll be feeding the microbiome in my garden with compost and the one in my gut with fermented foods and fiber!

(this post originally appeared on the FARMcurious blog 24 Nov 2014)

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Some thoughts on fermenting

Fermentation was one of humanity’s first forays into food preservation. Long before mason jars and ice boxes, the Babylonians were exploring new flavors and extending the life of perishable foods at least 5000 years ago. What we are just discovering now is that they were likely also extending their lives.

100 trillion little buddies

Jump ahead to the late 1990s. As scientists began to study the micro-organisms associated with the human body (we call those organisms the ‘human microbiome’), they found that shifts in naturally occurring microbes on and in the body were often related to disease. Essentially, when the microbiome population wasn’t thriving, harmful bacteria could make inroads. Furthermore, as Michael Pollan states in his ground-breaking article Some of My Best Friends are Germs “Our resident microbes also appear to play a critical role in training and modulating our immune system, helping it to accurately distinguish between friend and foe and not go nuts on, well, nuts and all sorts of other potential allergens. Some researchers believe that the alarming increase in autoimmune diseases in the West may owe to a disruption in the ancient relationship between our bodies and their “old friends” — the microbial symbionts with whom we coevolved.”

The alchemy of fermentation

So back to the Babylonians, they were onto something! Fermenting transforms food, allowing it to keep longer, but it also changes the food structure, breaking down sugars, releasing certain nutrients and even producing new ones. It creates an environment that both deters pathogenic bacteria (the ones that make you sick) and favors good bacteria (the ones that make fermented food taste good and help our digestion), so you can see why the technique stuck around. In other words, it helps keep that microbiome healthy and balanced. The magic happens when live cultures (bacteria, yeast, mold) are combined with fresh food, converting sugars to acid or alcohol and changing the chemical composition of the original ingredients.

Easy cheesy

An estimated 75% of the world’s population have some degree of lactose intolerance, meaning their body can’t digest dairy products easily (or at all). The good news? Lactose is a sugar, and fermenting breaks it down before you eat it. This is why many people can still enjoy aged cheese, which is what happens when milk is fermented long enough for the lactobacillus cultures to digest most of the lactose in it.

Nutritional springboard

You might think with micro-organisms munching through fermented foods, that some of their nutritional value would be lost. In reality, B vitamins including folic acid, riboflavin, niacin, thiamin, and biotin show a measured increase during the fermenting process. Vegetable ferments like sauerkraut and kimchi often have higher vitamins C and A than unfermented cabbages do, and K vitamins also jump up in vegetable ferments when compared to their fresh counterparts.

But wait, there’s more: bacteria and enzymes in fermented foods break down the components of the ingredients, making them easier to digest and increasing the healthy enzyme and bacteria population (probiotics) in your microbiome. All of this makes it easier to absorb the vitamins, minerals and other nutrients in fermented foods, as they are ‘pre-digested’.

Gut feeling

Several recent studies have begun to tie the health of the intestinal microbiome to brain chemistry, most notably depression, anger and anxiety. Findings included links between gastrointestinal diseases, such as irritable bowel syndrome and anxiety and depression, and correlations between reduced social anxiety and consumption of fermented foods. It turns out that microbes put out the same chemicals our brains use to communicate (collectively called GABA) and sure enough, increased levels of GABA are connected with positive mood. As it becomes clearer and clearer that the gut is connected with the brain, questions arise about conditions originally classed as mental that could in fact be gastrointestinal imbalances. More research is necessary to answer these questions, but in the meantime fermented foods are useful in supporting a balanced gut microbiome.

Cultural foods

Today nearly every culture includes some kind of fermented food in its cuisine. From its earliest function preserving food, fermenting has created unique regional flavors, thanks to indigenous flora. Cheese made in Parma, Italy has a special taste and texture because the microorganisms that ferment it are local, hanging out in the milk and air, and transforming the cheese as it ages into what is now a trademarked name: Parmigiano-Reggiano. Same story with that sparkling wine from Champagne, France. It’s the local yeast that gives it a flavor and effervescence different than any you could produce anywhere else.

It has taken millennia to get from regional specialties to probiotics and the microbiome, but along the way fermented foods have held their own and treasured recipes have been passed down through generations. If you don’t have your own family recipe, there are plenty of excellent cookbooks focusing on fermented foods, such as Sandor Katz’s The Art of Fermentation or Fermented Vegetables by Kirsten and Christopher Shockey. Be heappy, be healthy and support your microbiome!


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Ginger Beer

Ginger is native to tropical Southern Asia (India? China? No one really knows!). What we do know is that it was used as a tonic for common ailments by Arabic, Indian and Asian healers as far back as 5,000 years ago, and as a cooking spice long before that. Around 2000 years ago, Romans traveling on the Spice Route brought it back to Europe and from there it traveled on to the Caribbean and West Africa, adding a spicy kick to their culinary traditions.19348935333_1d7f042e7a_z

Above ground ginger is a beautiful plant with straps of green leaves and flower spikes sprouting small yellow blossoms. Ornamental varieties have spectacular pink or red flowers, but it’s underground where we find the most enchanting part of the plant. Here is the rhizome, a thick hand-shaped stem that spreads outward from the main plant to send up new shoots and descend roots below. Its papery coating reveals the spicy juicy “root”. This relative of turmeric and cardamom no longer grows wild, but is cultivated in tropical areas around the globe because of the culinary and medicinal value of its rhizome.

Modern research shows that ginger is effective at reducing nausea and vomiting after surgery. There is also evidence that it can reduce menstrual pain and lessen arthritic pain. It may also alleviate the symptoms of morning sickness although we always suggest consulting a physician before taking any herb during pregnancy.

You know what else is wonderful about ginger? It has an exotic refreshing taste, perfect to sip in this all-natural homemade soda. This recipe is based on one that appeared in BUST Magazine.

Ginger beer soda

Yield: 2 gallons or about 8 flip top soda bottles or 22 six-pack size beer bottles

Time: 2 hours + 1-2 days to carbonate (active time 30 minutes)


2 ¾-3 cups honey

6 Tablespoons fresh ginger, roughly chopped

4 lemons, juiced

1 lime, juiced

6 Tablespoons pineapple juice

¼ teaspoon dry active yeast (or champagne yeast)


Visit your local homebrewing supply store for a selection of bottles, caps and cappers, which are inexpensive, support a local business and a great investment for future beverage projects. While you’re there grab a packet of champagne yeast for tiny bubbles in your brew.

Alternatively, you can rescue bottles from the recycling bin! Swing-top glass soda or beer bottles or 2-liter plastic soda bottles & caps all work well and beer bottles with pry-off caps just need a trip to the homebrew supply store for fresh caps and a capper.

Note that you will need at least 1 plastic soda bottle (small size is fine) with a cap.


Fill a large pot with 2 gallons of water and stir in the honey until it dissolves. Add the chopped ginger, bring to a boil and simmer for 5-10 minutes, skimming off any foam that appears. Turn off heat and cover.

If you are in a rush you can fill up the sink with cold water and set the pot in an ice bath to cool it down quick, but you can also just let it sit on the stove while you walk the dog or whatever and come back to it later.

While the brew is cooling, wash your bottles with hot soapy water and rinse them really well (no one wants soapy soda). Squeeze your lemons and lime, and measure your pineapple juice and yeast. You can use the dry yeast packets you get in the grocery store but if you can get your hands on some champagne yeast it does make the prettiest bubbles.19781843818_99f5c0ceec_z

You want to be sure the brew is lukewarm (around 70-75F is ideal) before you add the yeast because yeast is what gives your brew bubbles and it doesn’t perform well at high temperatures. Sprinkle it into the pot, add the juices and give it a stir or two.

Line up your bottles on a rimmed baking sheet to corral any spills. Using a strainer, funnel and ladle, fill the bottles, leaving an inch of space at the top of each. Some sediment will go through the strainer. If you want clearer soda, line the strainer with cheesecloth. Cap the bottles and put them inside a box in a cool dark place to carbonate.

A couple times a day, press in on the sides of the plastic bottle. As the carbonation builds, it will become hard and have no give when you press it. When this happens (usually about 2 days) it’s time to put the soda in the fridge. This stops the carbonation and the soda is ready to enjoy!

Carbonation is a little tricky, which is why keeping the bottles in a box while the yeast does its work is a good idea. If the pressure builds too much you can end up with gushing bottles (also a good idea to open them over the sink, just in case). Sometimes the opposite is true. If you open your first soda and it seems flat, pull the rest out of the fridge for a bit so the yeast can make a few more bubbles. As long as you use a plastic bottle and check it regularly as described, there’s usually no problem!

The more ginger you add, the more heat and spice you will have in your soda, so experiment to see what suits you best. This recipe can easily be halved or doubled depending on your fridge space.


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Mexico City

Practiced hands softly slapped the blue corn masa back and forth forming flattened torpedoes and placing them on the comal for cooking. The smoke and steam mixed with the sweet smell of the corn as she waited for my order. Tempted by the exotic looking huitlacoche (corn smut), I opted instead for the vivid yellow and green squash blossoms which were cooked alongside the tlacoyo and then piled on top with a sprinkle of cheese and handed to me with a smile. I savored the first delicious bite knowing there was no better way to experience Mexico City.

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7 Ways to Connect with What You Eat

“They’re growing!” My friend reported to me that a mushroom-growing kit I’d given her had, in fact, made mushrooms. “Now what do I do with it?” she inquired. “You eat them.” I replied. “Are you sure they are OK?” she asked with some trepidation.


Don’t put that in your mouth, you have no idea where its been! We’ve all heard that before, right? But most of us frankly give little thought to where our food has been. It could have come from Tulsa or Timbuktu, but safely wrapped in plastic or sealed in a can and marked with a ‘best by’ date, we have come to trust what is packaged more than what we make ourselves.

So how do we reconnect with the food that has become so distant from us?

  1. Touch it. Knead some dough, slather on some sauce, snap the stems off. My personal favorite is massaging salt into vegetables and then packing them tightly into jars for fermenting. It teaches you a lot about texture and freshness.
  2. Compare it. Go to your local farmer’s market and pick a few standard vegetables (carrots, zucchini, onions, whatever). Then go to the supermarket and get the same items. How do they stack up? What is the difference between the texture, the freshness and taste? For extra credit cook with them separately and compare results.
  3. Identify it. What do artichokes and broccoli have in common? Or potatoes and radishes? Each pair is the same part of the plant. How about ham and drumsticks? How many other foods can you say what part of the animal or plant they are?
  4. Grow it. If you don’t have the space for a full-scale vegetable garden, even a small herb pot on your kitchen windowsill helps remind you where your food comes from when you grow it from a tiny seed.
  5. Source it. Pick an item that you buy regularly and find out where it came from. Another state? Another country? How big is the company? My favorite hot sauce is made 397 miles from here at a company with 50 employees. They make over 20 million bottle a year!
  6. Learn it. Ever wonder what happens between milk and mozzarella or cucumbers and pickles? Get the story and skills at a cheese making class and spread the word.
  7. See it. There are farmers, bakers, ranchers and other makers all over the place and many have regular tours. Make a trip to visit them and see how they produce food and where it goes next.



Ask plenty of questions about the food you are eating, where it came from and how it was made. Savor the stories along with your meal!