The Gut Microbiome: The Soil Inside Us

What is the Human Microbiome?

The Invisible Universe Of The Human Microbiome | NPR from NPR on Vimeo.

The microbiome is the whole community of microorganisms that live in and on your body: the microbes themselves, their genes and the environment they live in.

The Gut Microbiome

The bacteria, yeasts and viruses living in your digestive tract, trillions of them, are called the "gut microbiome" or "gut flora." Many of these microbes are beneficial, and some are essential. Others can cause harm, especially when they overgrow.

Did you know you carry roughly as many microbial cells as human cells? Current research estimates about 38 trillion bacteria living alongside about 30 trillion of your own cells.^[1] Most of them live in your gut.

Every person has a unique microbial makeup, almost like a fingerprint, and these tiny residents are in constant conversation with the rest of your body, including your brain.^[2] Research increasingly links the health of the gut microbiome to digestion, immunity, mood and many chronic conditions, as well as overall well-being.

Terms to know

Commensal bacteria: bacteria that live with us without causing harm, and often protect us from harmful microorganisms.
Dysbiosis: an imbalance in the types and numbers of microbes in the gut. The prefix dys means "bad" or "abnormal." Dysbiosis is associated with many health problems.
Microbes: microscopic organisms, including bacteria, fungi, archaea, protozoa and viruses.
Microbiota: the microorganisms living in a given part of the body. Similar to "microbiome," but refers to the microbes only.
Opportunistic microbes: microbes that usually stay quiet but can cause problems when the immune system is weakened or the microbiome is disrupted.
Pathogenic microbes: bacteria, fungi, protozoa and parasites that can cause disease.
Prebiotics: fibers and food compounds we can't digest ourselves, which feed beneficial bacteria.
Probiotics: live beneficial microorganisms that, in the right amounts, can support health and digestion.
Synbiotic: a combination of probiotics and prebiotics.
Epigenetics: how our environment, food and lifestyle turn genes "on" or "off" without changing the genetic code itself.

Soil Diversity, Dis-ease and the Gut Microbiome

Dr. Zach Bush on Microbiome, Leaky Gut & Cancer at Bulletproof Biohacking Conference 2017 from thecoffeepanda on Vimeo.

The link between the gut microbiome and health

One of the most consistent findings in microbiome research is that diversity matters. A gut with many different kinds of microbes tends to be more resilient than one with only a few.

Think of a rainforest compared with a single-crop field. The rainforest, with thousands of species, bounces back from storms, pests and droughts. The monoculture field can be wiped out by one disease. Your gut works the same way: the more diverse the community, the better it can handle stress, illness and change.

Since World War II, the widespread use of antibiotics, processed food and farm chemicals has changed how we live and eat. Over the same period, conditions like inflammatory bowel disease, celiac disease, type 2 diabetes, obesity and allergies have become far more common. Dr. Zach Bush and others argue that a loss of microbial diversity, in our soil and in our guts, may be one of the common threads.^[3] The science is still developing, but it is one of the most exciting areas of health research today.

Many experts now call this "the decade of the microbiome." Thousands of studies are published every year, and almost every field of medicine is being touched by it. What this research has shown us is simple but profound: we are not just a collection of organs and tissues. We are an ecosystem, and the microbes living in and on us play a huge role in health and disease.

Farmer's Footprint: Regeneration

Farmer's Footprint: Regeneration – The Beginning, a full-length film from Farmer's Footprint, the coalition co-founded by Dr. Zach Bush that we proudly support. It follows farmers moving away from chemical agriculture and toward living soil.

Everyday Exposures We Choose to Avoid

A lot of what we're exposed to every day goes "under the radar." Most of us are naturally trusting: why would anyone put something harmful in our food, cleaning products or deodorant? But as consumers, we are the driving force behind what gets made. When we stop buying something, companies change what they produce. The responsibility falls on each one of us.

We can't clean up the world overnight, but we can make simpler, cleaner choices at home. Here's how we approach it:

Household cleaners

Read labels and keep it simple. Many conventional cleaners contain harsh ingredients that can irritate your skin, eyes and lungs, including ammonia, chlorine bleach, quaternary ammonium compounds ("quats"), 2-butoxyethanol and strong drain cleaners like lye. Some, like triclosan in "antibacterial" products, also harm aquatic life once they go down the drain. The FDA removed triclosan from antibacterial hand soaps in 2016 and says plain soap and water works just as well.^[5] Never mix cleaning products, especially bleach and ammonia, which creates toxic gas.^[6]

Our rule of thumb: if you wouldn't want to breathe it or touch it, look for a gentler option. Vinegar, baking soda, castile soap and plant-based cleaners handle most jobs.

Skin and personal care

Your skin is your largest organ, and some ingredients can pass through it. We prefer simple, organic, plant-based products with short ingredient lists we can understand. Some ingredients we personally choose to avoid or limit:

Undisclosed "fragrance" or "parfum," which can hide dozens of chemicals
Phthalates (often hidden in fragrance)
Some parabens and other preservatives
Formaldehyde-releasing preservatives
Oxybenzone in some sunscreens
Harsh sulfates, if they irritate your skin

Look for trusted certifications and brands that are transparent about what's in their products.

Medications and antibiotics

Medications and the microbiome affect each other in ways scientists are still mapping. Antibiotics in particular can save lives, no question about it, but they also disrupt beneficial gut bacteria, sometimes for months.^[7] The key is to use them only when truly needed, as prescribed, and to help your gut recover afterward with fermented foods, fiber and plants. Always talk with your doctor before stopping or changing any medication.

The Soil, Our Food and Our Gut

Food is the biggest lever we can pull for our health, and our microbiome. Here's what we focus on:

1. Food from living soil, not heavily sprayed monocrops
Many commodity crops, including genetically modified corn, soy, canola and sugar beets, are grown in chemically dependent monoculture systems and are commonly sprayed with herbicides such as glyphosate (the active ingredient in Roundup), now the most heavily used weed killer in history.^[8] Glyphosate works by blocking a pathway plants and many microbes use to make certain amino acids, which is why some researchers are studying its possible effects on soil and gut microbes.^[9] Choosing organic and regeneratively grown food where you can is one of the simplest ways to vote for living soil.

2. Fewer processed foods
Ultra-processed foods are built from cheap commodity ingredients, with lots of calories and very little nutrition. They're best kept to a minimum.

3. Fewer refined carbs and added sugars
Refined carbohydrates and additives tend to feed the less helpful microbes in your gut and crowd out the beneficial ones.

4. Just eat real food!
Real food comes from the ground, grown in good soil that is alive with beneficial microbes, ideally local and grown with love. This is how food used to be.

5. Mindful meat choices
Industrial animal farming raises animals in crowded conditions and uses large amounts of antibiotics. In the US, roughly two-thirds of medically important antibiotics sold each year go to food animals^[10]^[11], which contributes to antibiotic resistance, and manure from these systems often pollutes soil and water instead of feeding it. If you eat meat, choose animals raised on pasture by farms using regenerative practices. And when you can't find a clean source, enjoy a plant-based meal instead. We could all use more veggies and more diversity on our plates.

A Gentle Way to Reset Your Gut

Many people find it helpful to try an elimination diet. You take out common trigger foods for a few weeks so your gut can settle, then bring them back one at a time to see how your body responds. Common foods people remove include:

Gluten and wheat
Dairy
Caffeine
Refined sugar
Soy
Corn
Eggs
Peanuts and tree nuts
Shellfish

A common approach is to remove these foods for about 3 to 4 weeks, eating plenty of vegetables, herbs, spices and warming soups and broths in the meantime. Then add one food back every few days and notice how you feel. If a food doesn't agree with you, set it aside for a while. It may not need to be gone forever.

It may feel like work, but many people are surprised by how much better they feel, and how clearly their body tells them what works. If you have a health condition, are pregnant, or have a history of disordered eating, please do this with guidance from a healthcare practitioner.

Some nutrients and herbs often used to support the gut lining and microbiome include L-glutamine, zinc, glycine, quercetin, digestive enzymes, slippery elm, marshmallow root, licorice root, reishi mushroom, chlorella, apple pectin and magnesium. The right choice and amount is different for everyone, so talk with a qualified practitioner before starting new supplements. You can explore the products we trust in Heal the Gut.

Prebiotic foods that feed your good bacteria

Leeks, onions and garlic: rich in inulin, a fiber beneficial bacteria love
Asparagus: high in inulin and fiber
Jerusalem artichoke and chicory root: some of the richest sources of inulin
Fennel and ginger: traditional digestive aids
Bananas (especially slightly green): rich in resistant starch
Flaxseeds: a great source of fiber
Seaweed: rich in fibers that feed beneficial bacteria
Oats and sprouted whole grains

The simple daily rule

1 fermented food with each meal
1 prebiotic food with each meal
Eat the rainbow: foods of every color, every day

Many people worry they won't feel full eating this way. You will. When you feed your good bacteria, they produce short-chain fatty acids that nourish the cells lining your gut. It can take a week or two, but as you start to feel better, cravings for sugar, soda and extra coffee often fade on their own.

Build your meals around low-glycemic vegetables. They feed your microbes without spiking your blood sugar. Some favorites: leafy greens (kale, spinach, chard, arugula, lettuces, dandelion and mustard greens), broccoli, cauliflower, cabbage and Brussels sprouts, asparagus and artichokes, zucchini and summer squash, peppers, cucumbers and tomatoes, mushrooms, green beans and snap peas, celery, fennel and radishes, and onions, garlic, ginger, parsley and chives.

We Are the Soil, the Soil Is Us

In the race for higher yields, modern agriculture has become dependent on synthetic fertilizers and pesticides. Heavy tilling and bare fields are costing US farmland topsoil much faster than nature can rebuild it, and it can take over 1,000 years to form a single centimeter of soil.^[20]

Healthy topsoil is alive. A single teaspoon can hold more living organisms than there are people on Earth.^[21] It's full of fungi, bacteria and tiny creatures that deliver minerals and micronutrients to plant roots, protect plants from disease and hold water like a sponge. Plants feed this underground community in return, pushing sugars made by photosynthesis out through their roots. When we till, leave soil bare and spray chemicals designed to kill, we break this partnership. The result is weaker plants, more disease and less nutritious food. Studies comparing historical data suggest that the mineral and vitamin content of some fruits and vegetables has declined over the past several decades.^[19]

Healthy soil is also one of the best places to store carbon. That's why regenerative agriculture, with cover crops, minimal tilling, compost and diverse plantings, is increasingly seen as part of the climate solution.

The same story shows up in us. Researchers such as Dr. Sarkis Mazmanian and Dr. Martin Blaser have pointed out that people in traditional and non-industrialized communities tend to have more diverse microbiomes than people in the US, Europe and Japan.^[4] Their hypothesis is that modern life, with antibiotics, processed food and less contact with soil and nature, is causing us to lose certain microbes generation after generation, along with the benefits they provide.^[3]

"So how does life jump out of the soil is a huge question that I think heretofore has gotten way too little attention. It seems like probably the most important question we could ask is, as living beings, how does life start?"
— Dr. Zach Bush

"Life begins in the soil"

Life begins with clean water and living soil. Every chemical we add to farmland ends up somewhere: in the soil, in the water and eventually in us. Antibiotics fed to livestock contribute to antibiotic-resistant bacteria, and heavy herbicide use can change the balance of microbes and fungi in the soil. When we take care of the soil, we take care of ourselves.

Things You Can Begin Right Now!

1. Eat fermented foods (and consider a probiotic)

Kombucha

Fermented foods are a natural source of probiotics. Research suggests they can increase the diversity of your gut microbiome and lower markers of inflammation.^[12] Try adding these regularly:

Fermented and pickled vegetables
Kefir
Kimchi
Kombucha
Miso
Sauerkraut
Tempeh

Some people also choose a probiotic supplement. You can find the ones we trust in Heal the Gut.

Wild Fermented Foods from Restore4Life on Vimeo.

2. Eat prebiotic fiber

If probiotics are the seeds you plant in your inner garden, prebiotics are the compost that feeds them. Probiotics feed on fibers we can't digest ourselves, called prebiotics. Good sources include asparagus, bananas, chicory, garlic, Jerusalem artichoke, onions, oats and sprouted whole grains.

Prebiotic Foods for Microbiome from Fresh Holistic Health on Vimeo.

3. Eat less sugar and fewer artificial sweeteners

Diets high in added sugar and ultra-processed food are linked to less diverse, less healthy gut microbiomes. Some studies also suggest that certain artificial sweeteners can alter gut bacteria and affect how the body handles blood sugar.^[13]

4. Lower your stress

Your gut and brain are in constant conversation. Chronic stress, whether psychological stress, poor sleep, a disrupted daily rhythm, or constant noise and overstimulation, can shift the balance of your gut microbes.^[2] Breathing practices, meditation, yoga, time in nature and regular movement all help your body shift out of fight-or-flight.

Calm your nervous system →

5. Avoid unnecessary antibiotics

Antibiotics can be lifesaving, but they also affect beneficial gut bacteria, and some species may take months to recover. A course of antibiotics is a bit like a wildfire moving through a forest: sometimes necessary, but the ecosystem needs time and care to regrow. According to the CDC, at least 1 in 3 antibiotic prescriptions written in US doctor's offices and emergency rooms is unnecessary.^[14] Use them only when your doctor determines they're necessary, take them exactly as prescribed, and support your gut with fermented foods and fiber afterward.

6. Move your body regularly

Regular exercise supports heart health and healthy weight, and may improve gut health too. A 2014 study found that athletes had a more diverse gut microbiome than non-athletes, though diet likely played a role as well.^[15]

Yoga for Wellbeing - Yoga Namaskar from Sadhguru on Vimeo.

7. Get enough sleep

Good sleep supports mood, focus and gut health. Research suggests irregular or disrupted sleep can negatively affect the gut microbiome.^[16] Aim for at least 7 hours a night, and go to bed and wake up at about the same time each day.

8. Choose gentler cleaning products

Harsh disinfectants and cleaning chemicals may also affect the microbes we live with. Use simple, plant-based cleaners, and save the heavy-duty disinfectants for when you truly need them.

9. Eat more plants

Studies show clear differences between the gut microbiomes of people who eat mostly plants and those who eat a lot of meat, largely because plant-rich diets are packed with prebiotic fiber.^[17] A good goal is 30 different plants a week. The American Gut Project found people who ate 30 or more types of plants a week had more diverse gut microbiomes than those who ate 10 or fewer.^[18] And eating more plants is good for the planet too.

4 Ways Poor Gut Health Damages Your Health by Nourishme Organics from Nourishme Organics on Vimeo.

Heal the Soil Inside You, and the Soil Beneath You

Everything we offer at The Ninth Petal feeds one of the two. And every $5 you spend plants a tree.

Heal the Gut → · Heal the Soil → · Our Impact →

Sources

We believe good information should be open to everyone. Here are the studies and organizations behind this page, so you can read them yourself.

This page is for general education and inspiration. It is not medical advice and isn't meant to diagnose, treat, cure or prevent any disease. Please talk with a qualified healthcare provider before making major changes to your diet, starting supplements, or changing any medication, especially if you are pregnant, nursing or managing a health condition. *Statements about supplements have not been evaluated by the Food and Drug Administration.

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