Composting and Human Digestion: the Interdependency of Microbiome Systems

By Qihui Jin - July 28, 2021

 Qihui Jin, LAc, Kimberlie Wilson, LAc, DACM,and Yichao Rui, PhD

Classical Chinese medicine (CCM) perceives the body through a paradigm of the rot-and-ripen function of the stomach, the transform-and-transport function of the spleen, the combustion function of the lungs, and the descension of waste through the u organs. All of these functions are essential elements of the process of making nutrients available to the human body. Composting, the microbial-mediated decomposition process that converts raw organic materials into readily available and biologically active carbon and nutrients, has similar mechanisms to CCM’s theory of how food is processed in the human body. This article will discuss the similarities between composting and human digestion, and the link between the composting process and its product with the health of human beings, both internally and externally. By placing these two theoretical frameworks in conversation with each other, a broader understanding of the dynamics of nutrient processing emerges. Similar to a healthy and functioning human digestive system that acts directly upon the human body, high-quality compost provides biologically available carbon and nutrients that promote strong plant-microbe associations, therefore supporting the physical and mental health of the human body directly by influencing the nutrient quality of food grown and the gut microbiomes it associates with.

Composting: An Ancient Practice with Modern Implications

Composting is the controlled aerobic decomposition of organic materials that has been around for many centuries. Ancient civilizations such as China and India utilized compost to replenish soil fertility and crop yields that sustained high density of populations (King, 1911; Howard and Wad, 1931). In the modern era, Rodale Institute was the first to introduce composting as a scientific pursuit into the United States in the 1940s (Rodale, 1960). During the composting process, microorganisms turn food scraps, animal manures, leaves and straw into biologically active carbon and nutrients. Therefore, composting can provide effective waste management and address the common on-farm needs of soil quality/fertility by improving soil biodiversity, nutrient cycling, disease suppression, and soil structure (Scotti et al., 2016). Because it is a biological process that is carried out by microorganisms, creating an ideal environment for microorganisms is key to the efficiency of composting and the quality of its product. An ideal compost recipe of carbon-rich and nitrogen-rich materials, a good amount of moisture, a free flow of air, and the initial size of the materials all play important roles. Effective chopping, mixing, turning, sifting, and curing can create a very complex and diverse environment for macro- and micro- organisms to reside and thrive (Gershuny, 2018). A wide variety of beneficial organisms can produce diverse compost products that will support the plants in a profound way, including their immune systems and their source of nutrition (Noble and Coventry, 2005). Plants that are grown in fertile and biologically active soils will form stronger associations with microbes and be less reliant on synthetic fertilizers (Minz et al., 2010). Plants with the complex and nutritive components derived from that soil then greatly influence the human gut biome and absorption of nutrition for human health.

The Connection Between Composting and Human Digestion

COMPOST Leading into CCM

The discovery of the relationship between composting and digestion, soil health, and gut health leads to the interpretation that healthy soil produces healthy foods, and healthy foods make healthy humans. This implies that if, as a society, there is a commitment to the regeneration of degraded soil, this will eventually promote better wellness in human beings. The connection between composting and human digestion is more direct and important than at first glance. A healthy composting biome promotes a healthy human gut biome which in turn promotes a healthy balanced emotional state. This homeostatic state is the cornerstone to CCM’s paradigm of health. From a CCM perspective, human digestion consists of reception, rot-and-ripen, transform-and-transport, combusting and synthesis. (Li, 2004, p.26)

The endeavor of composting as an empowering action promotes balance in a person’s life (Mayer et al., 2015). Compost provides nutrients to the soil microbes, plants, and other creatures in the soil, as well as improves the soil structure and texture, prevents erosion and drought, and improves aeration. This human endeavor then supports the internal biome of the human digestive tract. This can be seen in the CCM theory that a person can eat dirt from their indigenous area to protect their digestive tract, when travelling to foreign lands, from non-acclimatization when in a different biome. (Deng, 2011)

From the CCM viewpoint, the stomach is a fu organ that stores impure substances. It transforms ingested food and drinks by fermentation which is described as rot-and-ripen, and it is the most active place to break down and liquify food. (Li, 2004, p.65-73) Similarly to composting, the volume of matter decreases over time due to decomposition, and leachate is produced. The yin and yang aspects of digestion consolidate ingested matter over time using fermentation as well, liquefaction and decomposition. The yin aspect of the stomach, including digestive enzymes and microbiomes in the gut, stomach lining, bile, insulin, hydrochloride (stomach acid), and pancreatic enzymes, supports digestion with a material basis, comparable to the physical and chemical decomposers in composting. (Yuen, 2003, p.22-23) Thus the yang aspect of the stomach increases the metabolism and creates optimal temperature conditions for gut bacteria to function (Li, 2004, p.65-73). The heat present in composting acts in a similar fashion, encouraging thermophilic bacteria to help decompose.

The stomach is also the origin of fluids, while compost increases soil’s moisture retaining capability (Yuen, 2003, p. 53-54). If a compost pile is too dry or cold, it will result in extremely slow decomposition, while too wet of a pile will create an anaerobic environment, producing odor and causing problems. In the human gut, if the environment is too dry and too cold, food not being broken down properly will result in food stagnation; dampness in the body can cause diarrhea (Li, 2004, p.59-63).

The CCM paradigm is similar to the composting process in that the stomach represents the enzymatic activity, therefore the stomach prefers dryness while it hates dampness, and in CCM, the spleen acts as metabolic force—like the anaeration of the compost when it enhances microbial activity. Therefore the spleen prefers dampness while it hates dryness (Yuen, 2003, p.53-54). Through this mechanism, called homeostasis, the balance between heat and moisture can be managed. Similarly, in composting, there is a balance between heat (enzymatic activity and its by-product, fermentation) and moisture (anaerobic reaction). If a pile of compost is too damp, then dry (carbon-rich) materials need to be added; if too dry, then more water needs to be added to make sure decomposition happens properly. Heat will be generated when the moisture level matches the biological needs of microbiomes and is still allowing adequate airflow, while moisture is balanced from rot by active enzymatic activity. Heat, in human digestion, is from pancreatic enzymes and acids (Yuen, 2003, p.54-60). Dampness or moisture is the environment preferred by the good bacteria and flora of the gut. Ultimately, in CCM theory, heat is within the stomach and dampness is within the spleen paradoxically; the yin (more moist) of the stomach is the agent of fermentation and the yang (more heat) of the spleen is responsible for the transform-and-transporting of bolus (Yuen, 2003, p.22-24).

According to CCM theory, it is always recommended not to over-consume raw or cold foods so the spleen and stomach are not damaged by cold, causing food stagnation (Li, 2004, p.26-27). This can also be applied to composting. The cold composting method usually doesn’t require a lot of turning and is not particular about the carbon-to-nitrogen ratio, as compared to the hot composting method, so it has relatively slow microbial activity, long processing time, but it can be problematic and spread pathogens and weeds if managed improperly. There is no good or bad in terms of hot or cold composting, but as a human-managed activity, efficiency needs to be taken into account; it is a matter of time and labor. Cold composting usually takes more time while less labor than hot composting. Whether cold or hot, composting can be distinguished by whether the pile enters the thermophilic stage in temperature ranging from 105°F to 150°F (Gershuny, 2018). This is the same in digestion and absorption, influencing the body to utilize nutrients and produce energy, which must be efficient and sustainable. Warm food is easier to digest compared to cold food, simply because most chemical reactions proceed at a faster rate as temperature increases (Li, 2004, p.17-19).

In addition, there are similarities between the process of digestion and the procedure of composting. A meal requires food to be chewed. Chewing allows food to be physically broken down and increases surface area of the particles, as decreasing the size of food scraps makes the food more accessible to the organisms in the pile. The saliva mixed with food through the movement of the tongue creates a perfect recipe for chemical reaction, much as food scraps mixed with yard waste colonized with soil microbes create more room for decomposers. The food in the mouth is reformed as a bolus when swallowed into the esophagus. After being broken down by digestive juices, the bolus becomes chyme, which is assimilated with the humus of compost (Yuen, 2003, p.53-62). Along with the peristalsis of the gut, the chyme will sit in the stomach for three hours, after which the final bioavailable nutrients will be absorbed by the small intestine and distributed to body tissues through the bloodstream. When composting, regular “turning” action is sometimes recommended during the active composting stage, and “curing” is the last stage for compost to mature to make it less acidic (Pace, 1995). The curing process within both human digestion and composting is very important for the pH balance (Yuen, 2003, p.53-62).

The Role of Microbiomes in Composting and Digestion

Elizabeth Thursby stated that “intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens.” 90% of microbes in the body are found in the gut and the rest are on the skin, in the mouth, throat, lungs and other areas (Rinninella et al., 2019). Wei or defensive qi, in the context of CCM, derives from food (gu) qi produced in the Stomach. The wei qi flows between structures within the interstitial fluids and helps microbes distribute throughout the digestive tract (Maciocia, 2005). Interestingly, soil microbes also help plants resist disease (Kuchment, 2020). They act as the immune system of the soil, and therefore plants. This state of health in humans is the foundation of jin fluids and wei qi, which are the cornerstone of the human immune system (Yuen, 2003, p.22-24).

Time is another important component in composting and digestion that is not paid enough attention. Fermentation is a way to cheat the timeline of both composting and human digestion. Fermentation, as an old food preserving method, not only makes nutrients more available to the human body but also helps the body maintain the biodiversity of the gut microbiome by adding probiotic bacteria to the gut. Adding just a little fermented food into each meal can boost our digestion and absorption (Katz, 2016). In the same way, bokashi, a fermentation process to partially break down organic matter through anaerobic reaction, utilizing effective microorganisms (EM) to break down organic matter, is well-known to hasten the nutrient recycling and composting by adding it to soil or compost pile.

Impact of Composting on Environmental and Human Health

Composting has many benefits for humans on environmental and biological levels. A healthy composting routine allows the interaction with good bacteria to strengthen the immune system and digestive system. This interaction can include breathing the air filled with good bacteria, good bacteria touching human skin, smelling rich earth, and so on. Furthermore, in addition to the physical benefits, when modern human beings contribute to our communities and the planet, they become part of something bigger than themselves. When humans are mindful of the resources used, say, by composting food waste or collecting cans for recycling, they pay more attention to their community. This can result in a greater sense of meaning and purpose. Dr. Jared Scherz, a gestalt therapist, describes this as the “best antidote” to anxiety and depression (O’Reilly, 2016). Because the gut and brain influence one another (Mayer, 2015), the impact of composting to human health can be systemic, but the direct impact needs to be further studied and analyzed.

Additionally, composting indirectly impacts the surrounding aqueous system, air, and soil. It helps create a low chemical exposure and more balanced micro-ecosystem around the site of the composting bin. The ecosystem and the growth of healthy plants also depend on the soil biodiversity, which is improved by composted soil (Wall, 2015). Local food produced out of compost is more nutritionally dense and contains an abundance of beneficial bacteria. Modern technology such as irradiation destroys most of the beneficial bacteria and lowers the vitamin level in the food (Woodside, 2015). In a similar way, the more diverse the microbiota is in a person’s gut, the more robust and resilient digestive system they may have (Yuen, 2003, p. 53). Therefore, when nutrients are put back into the soil through composting, and a more biodiverse environment is created in comparison to using ecosystem-destroying pesticides and synthetic fertilizers, the nutrient-dense food produced provides human being with bioavailable nutrients that support healthy growth and healing (Singh, 2018).

The Importance of Diet and Microbiota Diversity

What we eat changes our population of gut microbiota: not only does it bring bacteria into our gut, but the nutrient content also changes the habitat of gut bacteria. This can also reveal the potential cause of infectious disease (Harris, 2019). The key to a healthy gut is to maintain the biodiversity of gut microbiota. In most cases, antibiotics, chemical residues in foods, and other environmental stressors have a great negative impact on gut microbiota (Dudek-Wicher, 2018). To rebuild and maintain a healthy gut, eating a variety of local, seasonal, nutrient-dense, and organically farmed foods is very important, just like the multicultural practice in farming. Although probiotics are widely considered “good” for gut health, they can potentially influence the gut microbiota as a monoculture does the soil, which decreases biodiversity. It is important to create and maintain a beneficial and balanced environment in the human gut that includes a broad spectrum of organisms, not just probiotics (Bush, 2020).

As this article has shown, the relationship between composting and digestion, soil health, and gut health is intimate and dynamic. Healthy soil produces healthy foods, and healthy foods make healthy humans. This implies that if we can regenerate degraded soil, we will eventually promote better wellness in human beings as humans are intrinsically linked to their environments. The sciences of soil biology and CCM have developed into similar paradigms. Now, there is an opportunity to work together to create a broader understanding of the human gut biome and the environment that could support healthier practices.


Bush, Zach. “Why Probiotics Don’t Always Work.” Holistic Primary Care, 20 Mar. 2020,

Deng, Z.(2011). Chinese Herbal Formulae Lecture Notes of Deng Zhongjia. People’s Medical Publishing House.

Dudek-Wicher, R. K., Junka, A., & Bartoszewicz, M. (2018). The influence of antibiotics and dietary components on gut microbiota. Przeglad gastroenterologiczny, 13(2), 85–92.

Gershuny, G., & In Martin, D. L. (2018). The Rodale book of composting: Simple methods to improve your soil, recycle waste, grow healthier plants, and create an earth-friendly garden.

Harris, E. V., de Roode, J. C., & Gerardo, N. M. (2019). Diet–microbiome–disease: Investigating diet’s influence on infectious disease resistance through alteration of the gut microbiome. PLoS pathogens, 15(10), e1007891.

Katz, S. E. (2016). Wild fermentation: The flavor, nutrition, and craft of live-culture foods.

Kuchment, O. (2020, April 08). How soil microbes help plants resist disease. Retrieved January 17, 2021, from:,a%20broad%20range%20of%20pathogens.

Li, G., & Flaws, B. (2004). Li Dong-yuan’s Treatise on the Spleen & Stomach: A Translation of the Pi Wei Lun. Blue Poppy Press.

Maciocia, G.(2008). The Foundations of Chinese Medicine: A Comprehensive Text for Acupuncturists and Herbalists. Second Edition.Churchill Livingstone.

Mayer, E. A., Tillisch, K., & Gupta, A. (2015). Gut/brain axis and the microbiota. The Journal of clinical investigation, 125(3), 926–938.

Minz, D., Green, S. J., Ofek, M., & Hadar, Y. (2010). Compost microbial populations and interactions with plants. Microbes at work, 231-251.

Noble, R., & Coventry, E. (2005). Suppression of soil-borne plant diseases with composts: a review. Biocontrol Science and Technology, 15(1), 3-20.

O’reilly, K. (2016, September 21). Mental Health Benefits of Going Green. Retrieved January 31, 2021, from

Pace, M.G., Miller, B.E., & Farrell-Poe, K.L. (1995). The Composting Process.

Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G., Gasbarrini, A., & Mele, M. C. (2019). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, 7(1), 14.

Singh, V., Arulanantham, A., Parisipogula, V., Arulanantham, S., & Biswas, A. (2018). Moringa olifera: Nutrient Dense Food Source and World’s Most Useful Plant to Ensure Nutritional Security, Good Health and Eradication of Malnutrition. European Journal of Nutrition & Food Safety, 8(4), 204-214.

Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. The Biochemical journal, 474(11), 1823–1836.

Wall, D. H., Nielsen, U. N., & Six, J. (2015). Soil biodiversity and human health. Nature, 528(7580), 69–76.

Woodside, J. V. (2015). Nutritional aspects of irradiated food. Stewart Postharvest Review, 11(3), 1-6.

Yuen, J., & Chin, P. (2003). Luo Vessels: Class Notes. Swedish Institute. 22-24, 53-62.

Featured Posts:

Qihui Jin headshot

Qihui Jin

Mr. Qihui Jin, LAc, a graduate of Pacific College of Health and Science, is a licensed acupuncturist and Master Composter in New York City. Dr. Kimberlie Wilson, LAc, DACM a graduate of Pacific College of Health and Science, is a licensed acupuncturist in New York City. She also is faculty at Pacific College of Health and Science. Dr. YiChao Rui, PhD is a soil scientist at Rodale Institute.

Is a Career in Acupuncture Right for You? Take The Career Readiness Quiz