Don’t Give Up the Funky Microbes in Your Life

June 2020

Don’t Give Up the Funky Microbes in Your Life


As a human evolutionary biologist, I’ve reached the point where I’m not totally sure what a human is — where our biology ends, and the environment begins. At the end of the day, we are holobionts — ecosystems unto ourselves — and we’ll have to understand these ecosystem interactions in order to better understand ourselves.” — Rachel Carmody, Harvard Department of Human Evolutionary Biology


Covid-19 has renewed our interest in the invisible, sometimes sinister, world of microbes. In the pre-pandemic era, gut health was just a digestive-health trend and superbugs were confined mostly to hospitals.


Post Covid-19 encouraged us to take deep dives into the world of fermentation, particularly sourdough starter, which certainly passed the time and created memories for many families. It also may have represented a frantic attempt to understand the very world of microbes that plagued us this spring, so we could possibly even tame them or whip them into submission. By controlling these microbes, we might control our own fates during these turbulent times.


Microbes matter because they’re everywhere and we can’t live without them. For thousands of years humans have learned to harness the power of microbes because, while pathogenic microbes can certainly infect and even kill us, microbes are more likely to feed and sustain us, even cure us.  Microbes are single-celled organisms categorized as fungi, bacteria, viruses, protozoan, archaea and algae.  Fungi and soil bacteria help break down and decompose dead plants, animals, waste, and food into smaller molecules made up of compounds and nutrients, including amino acids, fatty acids and sugars. There are more microbes in two ounces of soil than there are people on the planet Earth. Microbes and soil


The microbes in our gut function in a similar fashion. [see “Synthetics Are Not a Good Source of Sustenance“] Scientists believe that our bodies have evolved to live symbiotically with microbes and absorb the nutrients they need from them. In fact, humans are composed mostly of water and microbes, and some microbes, like fungi, are more similar to humans in their DNA than they are to plants. Our body’s microbes also help develop our immune system and protect us from other harmful microbes; for centuries their power has also been harnessed to treat diseases such as dysentery, sepsis, smallpox, and strep.


The recent gut-health trend is predicated on scientists’ understanding that us modern city folks have a diminished microbial diversity, thanks to our industrialized lifestyles and the processed foods we eat, not to mention our overuse of antibiotics.


The Food v. Supplement Debate: A lot of attention has been given to supplements that promise everything from mental acuity to gut health to immune-boosting properties. Americans are certainly accustomed to popping pills and powders in their mouths. Are supplements effective and can we even be sure that the ingredients in these supplements are safely sourced? According to The Mayo Clinic consumers need to consider many variables when selecting a supplement. As long as brands don’t purport to diagnose, treat, cure, or prevent illness, they can slide by with vague disclaimers about antioxidant properties and immune support. And the efficacy of many trending health and wellness substances aren’t backed by actual clinical studies on humans. Scientists attribute the success of many supplements to the placebo effect.


First, there is the issue of disclosure. Companies are not required by the FDA to disclose if its product contains what it says it does. For instance, some protein bodybuilding powders have been found to be mislabeled, containing Viagra and other erectile stimulants. In one 2017 study of reiki mushroom supplements, only five of the 19 mushroom supplements tested contained the reishi (mushroom) that the brand was promoting.


Second, there is the issue of sourcing. In terms of the supply chain, consumers can’t always be assured that the ingredients listed weren’t grown in contaminated soil or water. When selecting supplements, always look for a seal from one of the following certifying organizations:, NSF International, US Pharmacopeia (USP) or UL (Underwriters Laboratories). But even a certification isn’t a guarantee. Certified organic products, if they originated in other countries, might have been grown in contaminated soil or highly polluted areas. When it comes to sourcing, even the method of farming is important. For instance, there is a debate among scientists regarding the nutrients from fruiting body mushrooms versus mushrooms grown in a dark lab on grain (myceliated mushrooms), which could compromise nutrients but also reduces production costs. Mushrooms and Vitamin D


We need to feed our bodies good microbes and the best place to start is with the products we put in our mouths. In the same way we might laugh at someone who orders a hot fudge banana split and a diet coke, it doesn’t make much sense to pop powders and pills if we’re following a diet high in processed foods. We’ve all read that adequate sleep, a nutrient-dense diet and positive lifestyle choices, including stress reduction, probably lead to the best health and wellness outcomes. Whole foods, if consumed properly, provide us with the energy, fiber and water, and the many antioxidants and other compounds that our bodies need. That doesn’t mean that powders and extracts aren’t useful. Thousands of years of traditional practices such as ancient Chinese medicine, shouldn’t be overlooked. There’s much debate in the scientific community about the efficacy of nootropics and adaptogens, but let’s not forget the obvious, and well-studied, positive (and negative) effects of nootropics such as caffeine. For this reason, it’s always best to follow the science before choosing any supplement, nootropic or adaptogen. Always be your own advocate, do some research and make sure to consult with a doctor and certified dietitian. But where to start? The National Institutes of Health NIH Dietary Supplement Label Database is a repository of information for thousands of supplements sold in the United States.


Getting Funky with Fermented Foods

Food really is a pharmacy and fermented foods help promote those good microbes that we want in our corner, battling it out with the bad microbes and fighting disease. Fermented foods also break down the complex carbohydrates in our diet and synthesize many of the vitamins our bodies need. Getting down-in-the-trenches with sourdough is a fun introduction into the power of microbes as living organisms. Microbes drive fermentation and also preserve food and make it safer to eat, while amping up their flavor and aromas, as well as their textures.


Beyond the old standbys, like pickles and yogurt, and let’s not forget beer and the recent tequila craze (blue agave fermented with yeast and bacteria), our palates have come to enjoy some of the funkier umami flavors of miso, kimchi and kombucha. Many of these fermented foods are relatively easy to make if we’re willing to put in a little work each day.


Do This at Home:

The list of print and online sources, including online classes, covering fermentation is vast. Many of the classes can be quite expensive. Below are several recipes and some basic, yet comprehensive, pickling and fermentation guides that are designed for the home cook.



Grilled Sourdough Pizza with caramelized onions and pickled vegetables

Preserved Seaweed can be tossed into everything from pasta to pesto. It’s also a great way to amp up your avocado toast. Mix lightly with chopped or mashed avocado and serve on toast with sliced scallions and furikake (the Japanese version of Everything Bagel Salt)


Pickling and Fermentation Guides:

  1. The Complete Book of Pickling: 250 Recipes from Pickles and Relishes to Chutneys and Salsas by Jennifer Mackenzie is a thorough primer for everything from simple pickles to sauerkraut to salsa and martini olives, all the foods we love to enjoy. Simply tossing together veggie scraps with vinegar and salt and allowing them to pickle. With a little practice, fermenting foods in our kitchen can become second nature.
  2. The Art of Fermentation: An In-Depth Exploration of Essential Concepts and Processes from Around the World, by Sandor Katz. This book is a very comprehensive practical guide that covers everything to DIY to food safety, nutrition, tools, and equipment.
  3. The Noma Guide to Fermentation: Including Koji, Kombuchas, Shoyus, Misos, vinegars, garums, lacto-ferments, and black fruits and vegetables (Foundations of Flavor), by Rene Redzepi and David Zilber. As daunting as this title sounds, this guide takes us deeper into the wonderful world of fermentation. Each recipe is easy to follow, and steps are easily broken down into chunks, so you won’t ever need to devote your entire day to wrangling with microorganisms. The recipe for lacto-fermented mushrooms is easy and requires only time for the fermentation to take place. The resulting fermented mushrooms and the juice, which can be turned into a wonderful vinaigrette and oil, can be used in the caramelized mushroom and onion pizza below.
  4. Asian Pickles, by Karen Solomon.


Sourdough Guides:

  1.  King Arthur Flour Company is one of the best sources for baking guides, ingredients and equipment. Recipes are well tested and reliable. They also sell sourdough and French-style sourdough starter kits, with limited supply during the pandemic.
  2. Nancy Silverton’s Breads from the La Brea Bakery, by Nancy Silverton is over twenty years old and still the bible of bread making. She uses grapes to initiate the fermentation process. If you don’t have access to this book, which is still in print, you can find her sourdough starter guide online, along with other sources that make starters out of raisins, apricots and pineapple juice.
  3. Bien Cuit: The Art of Bread, by Zachary Golper and Peter Kaminsky (Bien Cuit also sells their eight-year-old starter online)


New York State Organic Grain Flours: Farmer Ground Flour

New Jersey Regenerative and Sustainable Flour: River Ground Community Grains


Food Science Reads:

On Food and Cooking: The Science and Lore of The Kitchen, by Harold McGee





Grilled Sourdough Pizza