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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!