settore ricerca e sviluppo

Biodiversity: Microbes, Fermentation and Human Health

A Research Project by Laura Ann Bocon

Master of Gastronomy at University of Gastronomic Sciences of Pollenzo
Intern at Civran Azienda Agricola

(La traduzione in italiano della ricerca è attualmente accessibile attivando i sottotitoli in italiano dei video di ogni capitolo)

This is a gastronomy research project on biodiversity applied to Civran Azienda Agricola, that can be analyzed on different angles:

  • in the field (plant biodiversity, microbiota soil richness and diversity, use of microorganisms as a field nourishment, etc.);
  • in the guts (human microbiome and health);
  • in the laboratory (microbial transformations and “almost unpredictable” flavors that occur via spontaneous fermentation).

The aim of the research is to create useful content and cultural dissemination to our farm’s audience.

Part 1 - Microbes, Ecosystems and Biodiversity

Chapter 1.1: Microbes

Chapter's transcript below.

What do plants and animals, even the soil or a jar of fermented sauerkraut have in common? It’s life.
Life, often unseen to the naked eye, is teeming all around us in the form of microbes, or microscopic organisms. When important topics like biodiversity, sustainability and nutrition are discussed, microbes play a very important role in helping us achieve a sustainable and healthy lifestyle. Life on earth is very old. Microbial life, particularly bacteria, are the oldest life forms on earth dating back 3.5 to even 4 billion years ago. Microbes are everywhere, inhabiting some of the most uninhabitable places on earth. There are more microbes on earth than stars in the universe.

When scientists were first attempting to categorize life on earth, the plant and animal kingdoms reigned supreme. As technology improved and new scientific discoveries emerged, scientists continually rethought their categorization. Today, the tree of life is categorized into three main domains: Bacteria and Archaea—both of which fall under the category of prokaryotae—and eukaryota—which includes a widely diverse range of life from plants and animals to protists and fungi. Two of the domains of life are occupied solely by two types of Prokaryotes. This illustrates just how extensive and important microorganisms are to our planet. There are three main categories of microorganisms: those are prokaryotes, eukaryotes and viruses.


Prokaryotes were the first signs of life to emerge on the earth almost 4 billion years ago. Prokaryotes can be found in just about every habitat on earth. They generally have a simpler cellular structure than that of eukaryotes. Most are single celled organisms that don’t contain a nucleus. Prokaryotes can be further classified into bacteria and archaea—both of which are very diverse groups of organisms.


Bacteria can be found in soil, in bodies of water—such as oceans—and in, on or around plants, animals, humans and other organisms. Bacteria play many crucial roles for both the environment and for humans. While not all bacteria are beneficial for the earth and humans, it would be a mistake to disregard them.

One of the oldest organisms in earth’s recorded history is cyanobacteria, also known as blue-green algae. Like other bacteria, they are single celled organisms but will often exist in colonies that are large enough to see with the naked eye. Cyanobacteria often cooperate as if they were a multicellular organism, working together to photosynthesize sunlight and carbon dioxide into energy and oxygen. Because of their size, records of their existence have been discovered in the form of fossils. These date back almost 3.5 billion years. Cyanobacteria are very important to earth’s history. Cyanobacteria contributed to the oxygen atmosphere that we depend on to today because of their ability to produce oxygen through photosynthesis. They are also the precursors to plants. Cyanobacteria perform important functions for soil and plant health, including nitrogen fixation. We wouldn’t be where we are today without the contributions of cyanobacteria to the ecological functions of our planet.


Archaea were only just classified as such in the late 1970s. Prior to that, they were thought of to be another type of bacteria. While archaea initially appear to be similar to bacteria, as they are also single celled organisms that contain no nucleus and can be found in similar environments, they are also evolutionarily very different. They can survive in much more extreme environments compared to bacteria in such places as the freezing waters of the Arctic ocean or in steaming hot springs. These particular species of archaea are known as extremophiles. Archaea are also found on our skin and within our gut. Another remarkable thing about archaea is that they are not known to cause any diseases in humans.


Eukaryotes make up the third (and largest) domain of life and include eukaryotic organisms like algae, fungi and protists.


Protists consist of everything else that cannot be easily classified. Some protists include Protozoa, amoebas, and algae.


Many algae come in a wide range of shapes and sizes; some can be single celled and microscopic while others may be multicellular and macroscopic. Algae can exist alone or may form chains in colonies that may be seen seen with the naked eye, such as an algae bloom. Algae live in both fresh and saltwater environments. While most algae are eukaryotic organisms, there is one type of algae which is actually a prokaryotic organism. It is known as blue-green algae, or cyanobacteria. All other types of algae, including green algae, are a type of eukaryotic organism. Green algae is primarily an aquatic organism which includes the many species of seaweed. However, despite the different types of algae, all contain chlorophyll and thus can create their own food through photosynthesis.


Unlike plants which make their own food through photosynthesis and carbon dioxide, fungi cannot make their own food. Instead they may get their nutrients through one of three ways. Fungi may absorb nutrients from decaying plant or animal matter. Other fungi will feed on living organisms rather than dead and decaying hosts, these fungi are considered parasitic. Lastly, some fungi live with other organisms in a mutually beneficial relationship. This is called a mutualistic relationship in which two species live harmoniously and benefit from one another. Since fungi cannot move to obtain their food, they instead grow in order to cover more surface area to increase their access to potential food sources. Fungi can be single celled or multicellular and contain a nucleus. Types of fungi include yeasts, molds and mushrooms. 

Molds secret digestive enzymes that break down organic matter. This fungi grows on surfaces such as mildew or mold. Having mildew grow on damp surfaces in our homes can be unappealing and damaging to our health. However, there are some favorable molds such as those that contribute to the delicious pungency of blue cheeses. Other types of fungi form large fruiting bodies known as mushrooms. 

Mushrooms come in all shapes and sizes and can be very delicious or very deadly to humans.

Yeast are single celled microscopic organisms about the same size as a red blood cell. They reproduce when daughter cells “bud” or break off of the parent cell. Yeasts play a very important role in the fermentation process of certain foods including beer, wine and bread. One of the more commonly recognized yeast strains is Saccharomyces cerevisiae.

Fungi live mostly on land, in soil or on dead plant matter. Fungi play indispensable roles in breaking down  plant matter which is important to carbon cycling. As the carbon contained in the cell walls of plants is likewise broken down, this vital nutrient is made more readily available to be taken up by plants, thus returning an important nutrient back into the surrounding environment. Some fungi however cause fungal infections such as athlete’s foot, yeast infections or cause diseases on plants.


Lastly, there are viruses. Viruses are the smallest of all microbes and are made up of nucleic acids, proteins and lipids. They only exist to reproduce. What is interesting about viruses is that they are only alive when they are infecting and reproducing through a host. Viruses can only reproduce by infecting prokaryote or eukaryote cells. They burrow inside of their host cell and use the cell’s genetic code to complete the act of replicating for them. As we all know too well with the coronavirus pandemic plaguing the world today, viruses can be truly dangerous and deadly to mankind. 

Why do microbes matter?

Still many more microbes exist and thousands more have yet to be discovered. What is undeniable is the power microbes have to affect the earth and all life within it. They are vitally crucial to the stability and productivity of environmental ecosystems as well as for the functioning of the human body and for sustaining our health. Microbes also perform important functions that transform the food we eat. Without microbes, we wouldn’t be able to enjoy a cup of tea, a slice of bread and a bowl of yogurt before we start our day.


Shige Abe. “The Three Domains of Life.” Astrobiology at NASA, 2001.

Aparna Vidyasagar. “What Are Algae?” Live Science, June 4, 2016.

Shannon Brescher Shea. “Behind the Scenes: How Fungi Make Nutrients Available to the World.”, 2018.

CK-12: Biology Concepts. “8.10: How Fungi Eat.” Biology LibreTexts, September 29, 2016.

Rob Guralnick, Allen Collins, Ben Waggoner, and Brian Speer. “Life on Earth.”, 1994.

Microbiology Society. “What Is Microbiology?” , 2019.

Kenneth Todar. “Overview of Bacteriology.” Online Textbook of Bacteriology, 2012.

Chapter 1.2: Microbial Communities

Chapter's transcript below.

Microbial life is often examined by the ecosystems they inhabit. Like all life in nature, examining only one piece of the puzzle rather than how it fits into its surrounding environment will severely limit our understanding of the functions and significance microbes have on our environment and our health. Microbial communities are called microbiomes. Micro of course, refers to microorganisms, but what is a biome? 


As we discover the world of microorganisms and microbiomes, we must first look at biomes. Biomes are classified as communities characterized by the dominant vegetation and organisms that inhabit it. Biomes will also vary across climates and whether they are on land or underwater. There are six major types of biomes. Those are freshwater, marine, desert, forest, grassland and tundra. Few biomes across the globe have been spared from human influence. Humans have vastly impacted our natural landscape through agriculture by depleting resources and the natural biodiversity and have increased carbon emissions. Nurturing and supporting natural and diverse ecosystems, both large and small, is essential to sustaining life on this planet.


Microbiomes often refer to the worlds unseen by the naked eye. In a jar of sauerkraut, in the soil under our feet and even within our gut, microorganisms inhabit these areas in diverse and expansive microscopic ecosystems. As people are becoming increasingly aware of the roles microbes play in our environment and our bodies, further research and initiatives are being conducted to explore their full potential. One such example is the The Earth Microbiome Project, a collaborative initiative to collect and study data on microbes and their functions in different ecosystems. The Human Microbiome Project likewise is a collaborative initiative aimed at studying human microbiota and its impact and role in human health and disease.


Most microbial life resides in biofilms. That is, microbes like bacteria will often clump together and even cooperate as if they were a multicellular organism rather than a collection of many single celled organisms. Microbes in biofilms adhere to a surface. Biofilms exist within humans as well such as within our mouths and in our digestive tract. Biofilms have the potential to be both beneficial and harmful for the environment or our health. Dental plaque is an example of a biofilm that forms on the surface of teeth. Tooth decay and gum disease are a result of bacteria’s metabolism within the plaque biofilm. Within our digestive tract, biofilms help protect us from pathogenic invaders. Likewise, in our environment biofilms have the potential to help or harm.

Plants and Microorganisms

As I stated in chapter 1, microbes can be found inhabiting even the most uninhabitable regions of our earth. One location that microbes inhabit holds particular significance to agriculture, crop production and the nutrient value of the plants that we consume. Microbes live within the soil and in, on and around plants. The relationship between plants and microorganisms is intricate, codependent and essential to all plant life.

There are a few terms used to describe this relationship. Holobiont is a term which refers to the host and its endocelluar, or internal, microbiome and extracellular, or external, microbiome. Another term is plant microbiome—microbiome as we know is used to describe the community of microorganisms living in a defined habitat. Lastly is the phytobiome (which consists of the plant, or “phyto”, and it’s “biome” which consists of the environment and all organisms living in, on or around it. The plant’s microbiome may consist of several types of microbes including bacteria, archaea, fungi, viruses and protozoa.

Microbes perform important functions for its health and growth. Such functions include protection against harmful pathogens, nutrient acquisition, regulation of the immune system and stress tolerance. Plants may experience stress from both biotic and abiotic sources. Biotic stresses are those caused by living organisms. This can include other microorganisms such as bacteria, yeasts, viruses or fungi, insects, parasitic nematodes, invasive plants or weeds.

Abiotic stresses are caused by nonliving entities such as essential nutrient deficiencies, exposure to toxic substances or environmental stresses such as extreme weather conditions. In agriculture, these stresses can drastically harm a crop and even cause crop failure.

A plant’s ecosystem

There are different microbiomes surrounding a plant. There is the rhizosphere, which includes the soil around the roots of a plant. This is one of the most complex ecosystems on earth. The phyllosphere is the region above ground and on and around the stems and leaves of the plant. Certain fungi called mycorrhizal fungi shared a symbiotic relationship with plant roots known as a mycorrhiza. This relationship is also mutualistic as it benefits both the host and fungi. Fungi feed off the glucose produced by the plant through photosynthesis and the fungi improves the plant’s access to mineral nutrient and water absorption by increasing the surface area of the plant’s root system. The endosphere is within the plant tissue itself.

These three microbiomes, similar to the microbial ecosystems that thrive in humans, are associated with the health of the host organism itself. Essential roles of microbes in these ecosystems include protecting the host against pathogens and increasing nutrient uptake in the host. This relationship is a symbiotic, mutualistic one. For example, roots extract compounds into the soil that microbes may utilize. In turn, microbes in the rhizosphere may help make nutrients such as phosphorus and nitrogen accessible to the plant.

While certain microbes, including various species of bacteria may form harmonious and mutualistic relationships with their plant hosts, there are many that may cause harm. There are parasitic bacteria, also known as pathogens, that may feed off the host or in other ways damage or kill the host in the process.


“Abiotic Stress.” ScienceDirect. Accessed May 17, 2021.

Biomes Group, Biology 1B class, section 115. “The World’s Biomes.” UC Museum of Paleontology, 1996.

“Biotic Stress.” ScienceDirect, n.d.

CK-12: Biology Concepts. “8.10: How Fungi Eat.” Biology LibreTexts, September 29, 2016.

Marilyn Cummins. “What Is a Phytobiome?” Noble Research Institute, 2020.

Frances Gilman. “Beyond Food: Fermentation and Microbiology’s Role in Farming and Agriculture.” Perfumer & Flavorist, 2020.

“NIH Human Microbiome Project.” , 2021.

Joan B. Rose. “Biofilms: The Good and the Bad.” Water Quality and Health Council, December 2, 2011.

“The Earth Microbiome Project.” The Earth Microbiome Project, 2017.

Micaela Tosi, Eduardo Kovalski Mitter, Jonathan Gaiero and Kari Dunfield. “It Takes Three to Tango: The Importance of Microbes, Host Plant, and Soil Management to Elucidate Manipulation Strategies for the Plant Microbiome.” Canadian Journal of Microbiology 66, no. 7 (July 2020): 413–33.

Chapter 1.3: Microbes role in biogeochemical cycles

Subtitles in English and Italian available on Youtube video's settings
Chapter's transcript below.

Microbes play a vital role in biogeochemical cycles. These cycles involve the recycling of primary elements that are essential to all living systems. Examples of these include the carbon, oxygen and nitrogen cycles. A biogeochemical cycle is the pathway an element takes through the environment: passing through the earth’s biosphere (all living organisms), atmosphere (the body of gases that surround earth), hydrosphere (bodies of water on or near earth’s surface) and lithosphere (the earth’s mantle and crust, including all rocks on earth). Microbes’ involvement in these cycles is indispensable. These cycles are essential to the functioning of our planet and human’s impact on our planet is affecting these cycles. Today’s agricultural practices, for example, have been significantly impacting our environment. Nitrogen and phosphorus fertilizers flow in runoff into waterways, carbon is being released into the atmosphere due to carbon emissions particularly from agriculture and livestock farming, including emissions from transportation.


The carbon cycle

In the carbon cycle, microbes perform what is known as CO2 fixation. In carbon fixation, photosynthetic organisms take CO2 from the atmosphere and convert it to organic matter. Such organisms include cyanobacteria and planktonic algae which are responsible for almost half of the carbon fixation production. Likewise, organic matter may be broken down by microorganisms by way of the metabolic processes of fermentation and respiration. The organic matter is converted into CO2 which then returns to the atmosphere. Carbon is vital to the survival of most microbes which consume carbon contained in organic matter from plants or the waste products or bodies of other organisms. 

A study was conducted to discover if there was a way to improve carbon sequestration in order to improve agricultural sustainability by manipulating the soil through an application of various farming techniques and through the manipulation of the soil microbiome. Researchers are interested in finding ways in which microbes may be utilized to help soils regain lost carbon and to curtail carbon emissions which impact climate change. But more research and experimentation need to be done regarding this as this is important to the future of agriculture and the health of our planet.

Intensive agricultural practices degrade soil quality and often have a negative impact on our environment. When plants are harvested during agricultural production, organic matter and nutrients and even topsoil are lost which impacts the soil health. Two common agricultural practices: tillage and drainage, have led to increased aeration of the soil and increased exposure of normally protected organic matter. This in turn, leads to accelerated decomposition of organic matter, subsequently releasing carbon into the atmosphere at an accelerated rate. 

But what can we do to improve soil quality and increase carbon sequestration in the soil? There are various agricultural practices that can improve soil health and reduce the loss of topsoil and nutrients in the soil. These include cover-cropping and intercropping, composting, and to increase the production of plants that have extensive root systems that reach deep into the soil. Another method is with the application of biochar, a type of charcoal that helps in carbon sequestration.


Nitrogen cycle

There are multiple processes which occur in the nitrogen cycle as nitrogen transforms and travels through organic matter, into the soil and water and back into the air.microorganisms are essential to some of these processes. Nitrogen is essential to plant growth and therefore to humans. Despite this, overuse of nitrogen fertilizers can have serious implications for environmental health and sustainability. Nitrogen must be fixed to another compound in order to be accessible by plants and other organisms. Microbes play an essential role in the biological processes by which nitrogen (N2) is converted into various forms of nitrogen compounds such as ammonia, nitrites and nitrates.



Nitrogen fixation

In biological nitrogen fixation, which is the most common process of nitrogen fixation, certain bacteria convert atmospheric nitrogen into a fixed form of nitrogen (such as ammonia, nitrites and nitrates) which may be then taken up by organisms that require the substance. Only some bacteria have the ability, these bacteria may freely live in the soil or share a symbiotic relationship with plants or other organisms.


Microbes consume and decompose organic matter from crops and within the soil. The nitrogen within is converted into ammonium.


Microorganisms convert ammonium to nitrate to use as a source of energy. Nitrate is the most widely available form of nitrogen for plants but can be easily leached from the soil, especially after harvest. Nitrate will easily move from the soil in water, especially if soil drainage is high.


Denitrification is as it sounds, a reserve of nitrification and involves certain bacteria converting nitrate into gaseous forms of nitrogen which return back into the atmosphere.


Within the soil there is also competition for nitrogen. Both microbes and plants use nitrogen and ammonia for energy. Immobilization occurs when there is a high demand for nitrogen and is not readily available for plants. However, as microbes die, that nitrogen will be released back into the soil. 


Managing nitrogen levels

To minimize these nitrogen losses and manage the nitrogen in the soil, as in the case of nitrate leaching, farmers may apply nitrogen fertilizers. However, applying too much or too little during the growing season can have adverse effects and may cause chemical imbalances in the soil and increase greenhouse gas emissions. Other factors may impact crop intake of nitrogen including the temperature, moisture of the soil or whether the nitrogen was applied when the plants are taking it up. Timing is important. 

There are negatives to the use of nitrogen fertilizers however. Overuse is a risk, especially if it is leached from the soil and enters waterways. When bodies of water, both freshwater and saltwater, are over saturated with nutrients like nitrogen, algae blooms can occur. Although algae blooms occur naturally, when formed by nutrient pollution, they can impact the natural ecosystem and produce toxins. Changes in nutrient supply in the water and soil such as this can impact the local plant and animal populations as well as the microbial populations.

Improving and maintaining soil health is vital to sustaining the world’s food supply while supporting sustainable agricultural practices. The use of nitrogen fixing cover crops are also great methods for improving soil health, preventing runoff and topsoil loss and for fixing nitrogen into the soil. Such crops include legumes like clover or certain cereal crops such as winter rye.


Oxygen cycle

Microorganisms also play an essential role in the oxygen cycle. We can thank photosynthetic microorganisms, that is microorganisms that produce their own energy through photosynthesis, for a significant proportion of the world’s oxygen. Photosynthetic microorganisms like algae and cyanobacteria (also known as blue green algae) produce 50% of the oxygen in our atmosphere. Cyanobacteria similarly play a crucial role in the nitrogen cycle.


“Biogeochemical Cycles.” UCAR Center for Science Education, 2011.

Cary Institute of Ecosystem Studies. “Biogeochemistry at Core of Global Environmental Solutions: Coupled-Cycles Framework Key to Balancing Human Needs with Earth’s Health.” ScienceDaily, 2011.

Gougoulias, Christos, Joanna M Clark, and Liz J Shaw. “The Role of Soil Microbes in the Global Carbon Cycle: Tracking the Below-Ground Microbial Processing of Plant-Derived Carbon for Manipulating Carbon Dynamics in Agricultural Systems.” Journal of the Science of Food and Agriculture 94, no. 12 (March 6, 2014): 2362–71.

Huang, L., C.W. Riggins, S. Rodríguez-Zas, M.C. Zabaloy, and M.B. Villamil. “Long-Term N Fertilization Imbalances Potential N Acquisition and Transformations by Soil Microbes.” Science of the Total Environment 691 (November 15, 2019): 562–71.

Johnson, Courtney, Greg Albrecht, Quirine Ketterings, Jen Beckman, and Kristen Stockin. “Nitrogen Basics – the Nitrogen Cycle Agronomy Fact Sheet Series.” Cornell University, 2005.

Lowenfels, Jeff, and Wayne Lewis. Teaming with Microbes : The Organic Gardener’s Guide to the Soil Food Web. Portland, Oregon: Timber Press, 2016.

Miyamoto, Chie, Quirine Ketterings, Jerry Cherney, and Tom Kilcer. “Nitrogen Fixation Agronomy Fact Sheet Series.” Cornell University, 2008.

Todar, Kenneth. “Impact of Microbes on the Environment.” Textbook of Bacteriology, 2012.

Vidyasagar, Aparna. “What Are Algae?” Live Science. Live Science, June 4, 2016.

Chapter 1.4: Biodiversity

Chapter's transcript below.

Industrialization, technological innovations and the streamlining of food production and agriculture have significantly impacted our environment. 

Overexploitation from hunting or fishing has led to deforestation and to habitat loss for many species of flora and fauna and in worse cases, has led to outright extinction of many plant and animal species. This has also been exacerbated by rapid expansion of agricultural farmland. The introduction of non-native species of flora or fauna have similarly negatively impacted and disrupted natural ecosystems. Increased agricultural production and modern farming methods have led to the loss of topsoil and soil contamination, increased greenhouse gas emissions and the resulting global warming. These are all threats we face today regarding the health of our planet and of ourselves.

Biodiversity is important for many reasons. A wide variety of plants or crops in a given region or agricultural plot increase the species, genes and potential biological functions of the area. The diversity of components may improve the biological stability and productivity, especially in regards to the performing of vital ecosystem functions.

Ecosystem functions

Ecosystem functions are defined as processes performed by plants, animals and microorganisms and how they impact their surrounding physical and chemical environment. Essential ecosystem functions include resource capturing, biomass production, decomposition and nutrient cycling. 

Loss of biodiversity, particularly across trophic levels, that is across species along the food chain, will also impact ecosystem functions. A diverse habitat of organisms like plants, animals, insects and microorganisms with a diverse range of traits and functions will increase the productivity of the area especially in regards to particular ecosystem services. For example, the variety of plant litter and other biological waste may improve decomposition and recycling.  These services provide humans with essential resources. 

Ecosystem services

These are the benefits that our ecosystem provides to humanity. There are four which include provisioning, regulating, supporting and cultural services.

Provisioning involves the production of renewable resources such as food, wood, medicines and freshwater. Increasing the biodiversity across species in a given area increases productivity, like in the case of commercial crop yield. Greater biodiversity will increase the products obtained through provisioning services.

Supporting services are those which support other ecosystem services. These include pollination, nutrient cycling and species adaptability to changing climates—such as tolerance to frost or high temperatures, drought or heavy rains. How well these services perform may improve productivity. If insects pollinate farmland that is rich in diverse plant life, crop yield will also increase. Pollination also improves climate conditions by aiding in carbon sequestration. Pollinators help both crops and wild and native plant life reproduce.

Regulating services help regulate environmental change. These include air and water purification, the detoxification of soils and erosion prevention and mitigating the negative impacts of climate change. Increasing biodiversity in a region, will lessen the risk of the spread of invasive plant species and the spread of plant pathogens such as viral and fungal infections. Carbon sequestration is increased as a result of a rich biomass production. Biomass is the debris originating from plants, animals and agricultural production.

Humans hugely impact the biodiversity of regions and it is imperative that we take care in restoring the natural ecosystems or agroecosystems and their biodiversity to improve the ecosystem services since human life depends on it.

Monocropping vs biodiversity

Monocropping came about to simplify the production of certain high demand commodity crops such as corn, wheat, and soy in the production of food, biofuels, fibre and more. This allowed growers to specialize in the production of one crop and to increase the output. However, such tactics can lead to biodiversity loss. There is also a greater risk of continuation due to use of agrochemicals in industrial monocropping.

With monocropping comes a greater risk of losing crops to disease or blight. Higher biodiversity offers greater stability. Organically grown vegetables have been shown to have a higher biodiversity of microbial populations than conventionally grown. More than likely, greater diversity of crops will also diversify the microbes present in the soil. Similarly, a diverse range of native deep-rooted plants offer greater stability to the soil and a more diverse and rich microbial population. The results of which I will discuss in the next chapter.

Microbes aid in the productivity of these services as well. It is possible that no multicellular organisms function completely without the aid of or interaction with microorganisms.

Sources: Editors. “Trophic Level.” Biology Dictionary, November 26, 2016.

“Biomass – an Overview.” Science Direct, 2016.

Blum, Winfried E.H., Sophie Zechmeister-Boltenstern, and Katharina M. Keiblinger. “Does Soil Contribute to the Human Gut Microbiome?” Microorganisms 7, no. 9 (August 23, 2019): 287.

Cardinale, Bradley J., J. Emmett Duffy, Andrew Gonzalez, David U. Hooper, Charles Perrings, Patrick Venail, Anita Narwani, et al. “Biodiversity Loss and Its Impact on Humanity.” Nature 486, no. 7401 (June 2012): 59–67.

Cary Institute of Ecosystem Studies. “Biogeochemistry at Core of Global Environmental Solutions: Coupled-Cycles Framework Key to Balancing Human Needs with Earth’s Health.” ScienceDaily, 2011.

Chivian, Eric, and Aaron Bernstein. Sustaining Life : How Human Health Depends on Biodiversity. Oxford ; New York: Oxford University Press, 2008.

El Serafy, Ghada, and Pedro J. Leitão. “Ecosystem Function – GEO BON.” GEO BON: The Group on Earth Observations, n.d.

Helmenstine, Anne Marie, Ph. D. “What Is Fixed Nitrogen or Nitrogen Fixation?” ThoughtCo, 2018.

Orr, Matthew R., Kathryn M. Kocurek, and Deborah L. Young. “Gut Microbiota and Human Health: Insights from Ecological Restoration.” The Quarterly Review of Biology 93, no. 2 (June 2018): 73–90.

Rosenberg, Matt. “What Are the 4 Spheres of the Earth?” ThoughtCo, 2020.

Sekercioglu, Cagan H. “Ecosystem Functions and Services.” In Conservation Biology for All. Oxford University Press, 2010.

“Why Is Pollination Important?” U.S. Forest Service, 2019.

Chapter 1.5: The Role of Microbes in Maintaining Soil Health

Chapter's transcript below.

Current issues

Improving and ensuring the health of our soil can increase the productivity and quality of our agricultural output. Modern agricultural practices and human intervention have impacted the health of our soils. Such issues include loss of topsoil, exposure to contaminants and pollutants, nutrient loss and desertification, or the transformation of healthy soil into sandy soil. Sandy soils contain less micro and macro nutrients and have low fertility and low water retention. These qualities make for poor growing conditions in plant cultivation. 

As forests are cut down to increase farmland, the risk of soil erosion also increases. This could mean a loss of nutrient rich and healthy topsoil. In some areas, soil is being lost at a much faster rate than it can be generated. Arable soil is a vital and often underappreciated resource.

Soil and Microbes

In modern day crop cultivation, widely diverse native crops have been replaced by fewer higher yield shallow-rooted staple crops. As I stated in the previous chapter, monocropping and other modern day agricultural practices have resulted in decreased soil health, soil erosion, and decreased biodiversity, which not only impact flora and fauna populations but the microbial populations as well. 

Soils are home to a great many microorganisms, from protozoa, bacteria and archaea to fungi and algae. These microorganisms provide many essential functions that improve soil and plant health. They recycle dead plant and animal matter into nutrients and nullify pathogens. Microbes in the soil also have the ability to store gases such as CO2 that would otherwise contribute to greenhouse gas emissions. Soil microbes can store up to 1.8 times more carbon and 18 times more nitrogen than plants, making them vital elements to slowing down and even preventing greenhouse gas emissions.

Improving and maintaining soil and plant health is vital to sustaining the world’s food supply while supporting sustainable agricultural practices. There are various microbe-assisted methods currently being used or tested to improve soil health and quality.

Soil Management Methods


Phytoremediation is a method of removing contamination in soil and ground water using plants. Plants may be grown in areas that are contaminated and then harvested, aiding in the removal of pollutants. The plants act as filters or traps, breaking down, filtering or containing organic or metal contaminants. Phytoremediation via microbes is a new but underutilized technology.

AMF: Arbuscular Mycorrhizal Fungi

These particular fungi colonize plant roots to form a symbiotic relationship. These fungi help protect the plants against pathogens and certain stresses, promote growth and yield and help protect the health of the plant and ecosystem. Utilizing these fungi may be a sustainable and environmentally friendly method which may replace certain chemical fertilizers. Utilizing AMF to improve soil conditions is one such example of the potential microbe-assisted phytoremediation methods.

However, there are downsides to this method. AMF may compete for nutrients in the soil and could decrease the microbial richness and diversity in the soil. Combining AMF with organic fertilizers could potentially counteract this. Bacteria, such as nitrogen fixers, may also be inoculated into the soil. As I stated in chapter 1.3, nitrogen fixing bacteria convert nitrogen from the atmosphere into ammonia or other nitrogen compounds that plants may take up more readily. Nitrogen increases plant growth and yield.

Organic fertilizers

The use of organic fertilizers improve the quality and stability of soil and may aid in changing soil’s physicochemical properties, increase nutrient uptake by plants and reduce pests. 


Microbes can be utilized to increase crop yield and plants’ resistance to disease or may be able to prevent disease altogether. It is important to promote microbiome health to keep the soil and plant healthy and to increase the nutritional value of the plant. Microbial products may go by various names depending on their intended use. Such products include soil inoculants, like nitrogen fixing bacteria which are used to stimulate root or plant growth and may also be referred to as biostimulants. Others include biofertilizers, biopesticides or probiotics. These products may be added to the soil or seed. 

The need for substitutes for harsh chemical fertilizers and pesticides which have contributed to environmental contamination due to runoff are driving research into alternative solutions. Microbes are also used to detoxify or to clean industrial wastewater. Through a system called bioremediation, microorganisms are used to break down pollutants in the wastewater. Compared to conventional methods, this method is much more cost effective, environmentally sustainable, and creates no waste byproduct.

Microbial soil inoculants have the potential to be a sustainable and environmentally conscious alternative. That said, it is not without its faults or challenges.


Doley, Khirood, and Mahesh Borde. “Arbuscular Mycorrhizal (AM) Fungi: Potential Role in Sustainable Agriculture.” Fungi Bio-Prospects in Sustainable Agriculture, Environment and Nano-Technology 1 (2021): 203–25.

Huang, L., C.W. Riggins, S. Rodríguez-Zas, M.C. Zabaloy, and M.B. Villamil. “Long-Term N Fertilization Imbalances Potential N Acquisition and Transformations by Soil Microbes.” Science of the Total Environment 691 (November 15, 2019): 562–71.

M Habte, N W Osorio, and University Of Hawaii At Manoa. College Of Tropical Agriculture And Human Resources. Arbuscular Mycorrhizas : Producing and Applying Arbuscular Mycorrhizal Inoculum. Honolulu: College of Tropical Agriculture and Human Resources (CTAHR), 2001.

NEPIS. “Phytoremediation Resource Guide.” United States Environmental Protection Agency. , 1999.

Rani, Nisha, Pritam Sangwan, Madhavi Joshi, Anand Sagar, and Kiran Bala. “Microbes.” Microbial Wastewater Treatment, 2019, 83–102.

Sekercioglu, Cagan H. “Ecosystem Functions and Services.” In Conservation Biology for All. Oxford University Press, 2010.

Tosi, Micaela, Eduardo Kovalski Mitter, Jonathan Gaiero, and Kari Dunfield. “It Takes Three to Tango: The Importance of Microbes, Host Plant, and Soil Management to Elucidate Manipulation Strategies for the Plant Microbiome.” Canadian Journal of Microbiology 66, no. 7 (July 2020): 413–33.

Zhang, Zhechao, Zhongqi Shi, Jiuyang Yang, Baihui Hao, Lijun Hao, Fengwei Diao, Lixin Wang, Zhihua Bao, and Wei Guo. “A New Strategy for Evaluating the Improvement Effectiveness of Degraded Soil Based on the Synergy and Diversity of Microbial Ecological Function.” Ecological Indicators 120, no. 106917 (January 2021): 106917.

Part 2 - The Human Ecosystem and Microbiome

Chapter 2.1: The Human Microbiome

Chapter's transcript below.

The Human Microbiome

Similar to the microbiomes and ecosystems that permeate the earth, microbes also inhabit a variety of diverse ecosystems within and on humans. The human microbiome is the counterpart to the human genome. Microbial genes outnumber the genes in our genome 100 to 1. These microbial communities are made up of bacteria, fungi, archaea, protists and viruses. In the GI tract (i.e. gastrointestinal tract) alone, there are up to 100 trillion microbes. It has the highest known cell densities of any microbiome on earth.

Microbes can be found on and within the human body: in our mouths, intestines and even in women’s vaginal canals and on our skin and teeth. Microbes that live in our mouths attach themselves to our teeth through a sticky adhesive known as a biofilm. These microbes are adapted to the moist and warm environment of our mouths and survive off of food particles, oxygen, water and our saliva. Our skin accommodates a wide variety of microbes that exist in various climates. The surface of our skin may be oily, dry, moist or exposed to much or little sunlight. Microbes that exist in these various climates are adapted to survive these conditions. However, less microbes thrive in the oily parts of our skin since oil is often antimicrobial. 

There are many abiotic, or non-living factors, that influence and impact the microbes that make us their homes. Such factors include temperature, diet, pH, oxygen, water, nutrients and UV light. Microbes that thrive in the various ecosystems that exist within and on the human body must be adapted to such. Any changes our bodies experience can likewise impact the microbial communities that live there. 

Another factor that impacts our microbial residents is age. Babies who are born vaginally will be coated in a film of microorganisms from their mothers whereas babies who are born by cesarean section will be colonized by skin microbes. Where babies are born will also impact by which microbes they are colonized. Babies who breastfeed will take in oligosaccharides present in breast milk. These sugars are actually beneficial to microbes rather than the babies directly. Microbes will consume these sugars and help build up babies’ immune systems. As we grow up, the variety and amount of microbes in and on our bodies changes. There are also significant stages in our lives and events that occur which will impact microbial populations. Such significant events include puberty, pregnancy and menopause. Sickness, antibiotic use, stress, injury, climate and significant changes in diet will also impact our microbiomes.  

We share different relationships with the microbes that reside within or on us. One such relationship is called commensalism. In this relationship, one organism, whether it is us or the microbes, will benefit from the other without causing it harm. Reversely, parasitism is a relationship in which one organism, considered a parasitic organism, benefits off the other, referred to as the host organism, causing it harm. Mutualism is a relationship in which both organisms benefit from each other.

Microbes and Health

Microbes play a variety of roles within our bodies. Some microbes make vitamins our bodies alone cannot. For example, in the large intestine, microbes produce B vitamins which are essential co-enzymes for DNA synthesis and repair. Vitamin B12, which can only be made within our bodies by bacteria and archaea, help build healthy blood and brain tissue. Diets deficient in vitamin B12 and folate, another B vitamin, are associated with depression.

Microbes protect us from infection by helping to decrease inflammation and train the immune system to fight off infections, attacking harmful invaders and sparing the good microbes. Microbial biofilms protect us from harmful invaders, both inside and out. Particularly within our intestines, how we eat will influence how healthy our biofilms are and how well they can protect us. They also influence the functions of our organs and often act as important signals during metabolic processes. However, as I stated in Section 1, not all biofilms are beneficial to humans with dental plaque being one such example. Of course, only a few of the hundreds of microbes that make up the biofilm that forms on our teeth actually cause cavities. Brushing cleans away the bad along with the good. Eating less sugar and processed foods can change the microbes that live in the plaque biofilm. 

Some microbes help us to digest our food. Up to 10% of the calories we absorb are made available by microbes. When trying to improve someone’s health and gut microbiota, it’s an easier solution to target someone’s diet since food has a large impact on one’s microbiota but changing it doesn’t require a huge and expensive medical intervention. A diet that is high in calories, carbohydrates and processed sugars and fats, is usually associated with less diversity of gut microbiota. Microbes help us to digest carbohydrates like sugars, starches and fiber and release nutrients that would otherwise pass through our digestive system. In turn, microbes also feast on the food we consume. Different diets support different microbial communities. A healthier diet means a healthier gut. 

Microbes within our gut may also influence our brains. Nervous tissue surrounds our gut. This collection of neurons is connected to the brain via the vagus nerve. Bacteria in our gut make molecules that transmit signals to the brain. Some microbe related intestinal issues are associated with the symptoms of certain mental disorders such as anxiety or depression. Certain diets, such as the mediterranean diet, which contains fermented foods, can keep our microbes happy and protect our physical and mental health.


Aslam, Hajara, Jessica Green, Felice N. Jacka, Fiona Collier, Michael Berk, Julie Pasco, and Samantha L. Dawson. “Fermented Foods, the Gut and Mental Health: A Mechanistic Overview with Implications for Depression and Anxiety.” Nutritional Neuroscience 23, no. 9 (November 11, 2018): 1–13.

Genetic Science Learning Center. “The Human Microbiome.” University of Utah: Learn Genetics, 2000.

Chapter 2.2: Soil and Gut Connection

Chapter's transcript below.

Soil’s connection to the human microbiome

The human gut microbiome and soil microbiomes are more connected than one would think. Both contain around the same amount of active microorganisms yet soil is much more diverse than our gut. In fact, our gut only contains about a 10th the microbial diversity than that of soil. However, unlike within the human gut, most of the cells contained in the soils are actually inactive.

Despite any similarities or differences in the microbial and cellular make of soil and the human gut, it is important to understand how the health of our soils impact the health of our gut. After all, we consume the plants that were grown in them. Modern agricultural practices and our modern diet have changed how and what we eat. Microbial populations in the soil have changed as a result of modern agricultural practices like in the case of monocropping and with the use of pesticides and other treatments. Likewise, our gut microbiota diversity has changed as we consume more highly processed foods and less fresh organically grown produce. Even among animals, it is believed that domesticated animals harbor a less diverse gut microbiome than their wild counterparts.

Humans have also had less contact with soil in recent decades. Where our ancestors often produced their own food or lived in rural environments, our population increase in the last century has contributed to growing cities as a great proportion of our population leaves the countryside for work or other opportunities. In fact, over 50% of the world’s population now resides in cities and that percentage is only expected to grow in coming years.

But why should this matter? Diverse and rich gut microbiota contribute to human health. Likewise, species richness in the soil can reduce the risk of pests and pathogens and can increase the nutritional value of the crops produced. Modern agricultural practices that promote monocropping and heavy use of agrochemicals may limit biodiversity and species richness in soils and affect the nutritional quality of the food produced. Farms that promote sustainable and biodiverse agriculture may promote a richer soil microbiota and more nutritionally rich crops. Children that interact with such an environment and consume the foods that are produced in the soils there, may be less likely to develop autoimmune diseases later in life.

Our ancestors, many of whom toiled the fields to raise their own fruits, vegetables, grains and legumes and practiced animal husbandry, also practiced fermentation. Fermentation is another method of introducing beneficial microbes into our bodies and gut. However, similar to how agricultural practices have drastically transformed in the last century, so too have our culinary ones. Where our ancestors may have fermented foods to store them over the winter months, the modern era has seen other food preservation methods gain favor over fermentation including refrigeration, pasteurization and canning. As factory foods became mainstream, consumers were encouraged to purchase these safe and convenient foods regardless of health and quality. I will discuss this topic more in section three.


Aslam, Hajara, Jessica Green, Felice N. Jacka, Fiona Collier, Michael Berk, Julie Pasco, and Samantha L. Dawson. “Fermented Foods, the Gut and Mental Health: A Mechanistic Overview with Implications for Depression and Anxiety.” Nutritional Neuroscience 23, no. 9 (November 11, 2018): 1–13.

Genetic Science Learning Center. “The Human Microbiome.” University of Utah: Learn Genetics, 2000.

Katz, Sandor Ellix. The Art of Fermentation. Vermont: Chelsea Green Publishing, 2012.

Matthew R. Orr, Kathryn M. Kocurek, and Deborah L. Young, “Gut Microbiota and Human 

Health: Insights from Ecological Restoration,” The Quarterly Review of Biology 93, no. 2 (June 2018): 78-9,

Blum, Winfried E.H., Sophie Zechmeister-Boltenstern, and Katharina M. Keiblinger. “Does Soil 

Contribute to the Human Gut Microbiome?” Microorganisms 7, no. 9 (August 23, 2019): 287.

Terefe, Netsanet Shiferaw. “Emerging Trends and Opportunities in Food Fermentation Abstract.” Reference Module in Food Science, 2016.

Part 3 - Microbes, Food and Fermentation

Chapter 3.1: Fermentation

Chapter's transcript below.


Some of the first processed and preserved foods made and consumed by humans were ferments. All sorts of foods have the potential to be fermented such as meats in the form of dry-fermented sausages, fish such as in fish sauce, dairy in the form of certain cheeses or yogurt, fruits and vegetables like sauerkraut and kimchi and legumes such as soy in the production of miso, natto and soy sauce.

Our ancestors may have been aware, to a certain extent, that our diet is essential to our health and overall well-being and as such, food was often part of medical treatments. Through humanities rapid growth, expansion and industrialization, much of the world disconnected food, medicine and health.

As one of the oldest forms of food preservation, fermentation and fermented foods are deeply embedded in our food cultures and traditions. Although some of those traditions have faded or been lost in recent decades, they are making a resurgence due to health-conscious consumers and creative artisans.


Fermentation is a chemical process that occurs by way of microorganisms or enzymes as they break down organic matter. Carbohydrates in the substrate are converted into alcohol and acids. Of course, our ancestors didn’t understand the science behind the processes involved when they were salting crocks of cabbage to preserve the fresh vegetable for the winter months or as they watched the milled wheat flour and water rise and bubble with microbial activity before preparing a hearty loaf of bread, more nutritious and easily digestible than when it started. 

The microorganisms at play in the fermentation process are bacteria, mainly LAB, also known as lactic acid bacteria, as well as fungi, yeasts, and even some molds. Fermentation of fresh foods likely occurred naturally long before humans understood how to utilize it for their benefit. Despite this, humans figured out how to utilize fermentation to make foods more digestible and nutritious, like in the case of bread or to increase the shelf life, such as with certain cheeses, meats and lacto fermented vegetables. Alcoholic beverages such as wine or beer were created not only as celebratory beverages but also safer ones. 

Fermentation also changes the texture, taste and smell of the original substrate. Milk fermented into yogurt is thicker and tangier than when it started all while gaining a longer shelf life. It may also be a carrier of probiotics. Probiotics are live microorganisms that humans consume in probiotic “functional” foods such as yogurt or sauerkraut. When consumed, these microorganisms are believed to be beneficial to human health. They promote helpful bacteria over harmful ones and may even enhance our immune systems and protect against gastrointestinal diseases by maintaining healthy gut microflora. 

There are two basic types of fermentation processes, which I will describe more in the next two sections. One is LAB fermentation, or lactic acid fermentation, that can occur spontaneously like when making sauerkraut or through the use of a starter culture like in yogurt production. The other type of fermentation is alcoholic fermentation in which yeast, such as the ubiquitous Saccharomyces cerevisiae, and bacteria transform sugars in the substrate into ethanol and CO2, like in the case of bread production. This process occurs anaerobically, or in the absence of oxygen. Much of the food and drink that we consume today, from chocolate to wine, wouldn’t be possible without the fermentation processes conducted by these bacteria and yeasts.

Fear of Microbes

In the last two hundred years, for those who’ve adopted a more “modern” diet and lifestyle (also referred to as the “Western diet”), how we cook and what we eat has changed considerably. In some societies, fermented foods are still regarded as staples, particularly in the East and developing nations. However, in many Western nations, fermentation has been sidelined in favor of other food processing and preservation methods. Particularly, with the rise of refrigeration, sterilization and pasteurization, the need of fermenting foods for preservation has lessened. 

As populations grew and people migrated to cities for work or convenience, less people grew their own food or worked as farmers. Instead of farmers and local tradesmen who sold us artisan crafted cheeses, meats, dairy products and bread, consumers could purchase a wide variety of factory-made standardized food commodities at a single supermarket. Sandor Katz, an avid fermenter and successful author, described two significant scientific and technological advancements that contributed to the decrease of fermentation practices, particularly in the West. Canning, a form of sterilization, revolutionized food preservation in the 19th century and is still a widely practiced food preservation technique used in the United States. The other is what he coined, “the war on bacteria” which emerged as microbes, specifically bacterial pathogens, were identified and treatments like antibiotics were developed.

While these discoveries have been invaluable, we have often been conditioned to fear microbes—just look to antimicrobial soaps and disinfecting sprays that promise to kill 99.9% of germs as examples of this. We have been told that germs are something unclean and unwanted when in fact, humans have been coevolving and cohabitating with microbes since we’ve walked this earth. For many, the idea of leaving food on one’s counter to ferment for days or even weeks from beyond the safe confines of the fridge is frightening. We’ve grown accustomed to a whole new set of “rules” regarding food production, health and safety. Unfortunately for many, fermentation practices were disregarded in some cultures, especially in the west, in favor of others which were viewed as safer or more efficient such as sterilization (i.e. canning), freezing, pickling and refrigeration. However, unlike some of these food preservation methods, fermentation offers exploration into new flavors and textures which are quite different from the original substrate.


Campbell-Platt, Geoffrey. “Fermentation.” In Encyclopedia of Food and Culture, edited by  Solomon H. Katz and William Woys Weaver, 630–31. Charles Scribner’s Sons, 2002.

Chan, Miin, Robyn Larsen, and Kate Howell. “Fermented Foods, the Gut Microbiome and Human Health.” Food Australia, 2020.

Hill, Colin, Francisco Guarner, Gregor Reid, Glenn R Gibson, Daniel J Merenstein, Bruno Pot, Lorenzo Morelli, et al. “Expert Consensus Document. The International Scientific Association for Probiotics and Prebiotics Consensus Statement on the Scope and Appropriate Use of the Term Probiotic.” Nature Reviews. Gastroenterology & Hepatology 11, no. 8 (2014): 506–14.

Katz, Sandor Ellix. The Art of Fermentation. Vermont: Chelsea Green Publishing, 2012.

Swain, Manas Ranjan, Marimuthu Anandharaj, Ramesh Chandra Ray, and Rizwana Parveen Rani. “Fermented Fruits and Vegetables of Asia: A Potential Source of Probiotics.” Biotechnology Research International 2014, (May 2014): 1-19.

Tamang, Jyoti Prakash, Paul D. Cotter, Akihito Endo, Nam Soo Han, Remco Kort, Shao Quan Liu, Baltasar Mayo, Nieke Westerik, and Robert Hutkins. “Fermented Foods in a Global Age: East Meets West.” Comprehensive Reviews in Food Science and Food Safety 19, no. 1 (January 2020): 184–217.

Terefe, Netsanet Shiferaw. “Emerging Trends and Opportunities in Food Fermentation Abstract.” Reference Module in Food Science, 2016.

Chapter 3.2: Lacto-fermented foods

Chapter's transcript below.

Lacto-fermented foods

As I stated previously, there are two main types of fermentation, alcoholic fermentation and lactic acid fermentation. Lacto fermented foods can be produced from all sorts of different substrates, transforming milk into yogurt, cabbage into sauerkraut or kimchi or fish into fish sauce—which was once a popular condiment, also known as a garum, in ancient Rome. 

Sauerkraut is one such example of a fermented vegetable product. At its most basic, is shredded cabbage mixed with salt which is then fermented. However simple sauerkraut may appear, its popularity, long history and nutritional transformation it undergoes during fermentation can attest to its importance in culinary culture and tradition and human health.


Fermented vegetable staples, fermented cabbage in particular, have existed in human history for thousands of years with fermenting practices developing independently and simultaneously around the world. The word sauerkraut comes from the German words sauer meaning sour and kraut meaning herb or cabbage. At its most basic, sauerkraut is a fermentation of cabbage and salt. Cabbage was a cheap and nutrient rich staple crop since it was easy to propagate throughout parts of Europe. Fermenting cabbage assured its longevity throughout the winter months to provide sustenance and nourishment and was a way to preserve a surplus crop that would otherwise quickly wilt and rot without the aid of refrigeration.

Fermentation Process

White or green cabbage and even red cabbage is commonly used in the production of sauerkraut. Cabbage is rich in nutrients such as vitamins, folate, carotenoids, flavonoids and phenolic compounds. In sauerkraut production, fresh cabbage is shredded and then mixed with 2% to 3% salt ratio. The cabbage is layered in a crock or glass jar, covered with a cloth and lid which is weighed down to prevent air from reaching the cabbage. Salt is essential for sauerkraut production—as with the production of other lacto-fermented fruits and vegetables—as it promotes the production of beneficial microbes and inhibits the growth of spoilage microbes by creating anaerobic conditions during fermentation. The amount of salt used may depend on a variety of factors including the temperature at which the ferment is kept and the desired outcome. Salt also impacts the sensory properties of the final ferment as well as the microbial populations. Sauerkraut can be fermented for just one week or several months and can last for several months beyond that. 

Fermentation wouldn’t be possible without the aid of microbes. LAB, or lactic acid bacteria transform raw cabbage, bringing out more of its potential nutritional benefits. Lactic acid bacteria and a variety of other microbes, both beneficial and harmful, are present in raw cabbage. During sauerkraut production, salt is added and the cabbage is pressed down, covered and weighed down to remove any air, after which anaerobic fermentation begins. These anaerobic conditions favor the lactic acid bacteria.


Sauerkraut is traditionally made by spontaneous fermentation but can also be made by way of backslopping or by use of a starter culture. A starter culture allows for a more stable and homogenous product which can be useful in commercial production. Regardless of which method is used, fermentation transforms the substrate in many ways. The taste is altered as carbohydrates are transformed into lactic acids giving sauerkraut its characteristic tangy flavor. Sauerkraut also retains a satisfying crunchy texture early in the fermentation process slowly becoming softer the longer it ferments.

Health Benefits

While preservation may have been the original motivation for fermenting cabbage, our ancestors understood the health benefits of fermented cabbage to a certain extent before science revealed its true potential. The English navigator and explorer, Captain James Cook, recognized sauerkraut’s ability to prevent scurvy in his sailors and brought barrels of it on long voyages as it also kept without the need of refrigeration.

During fermentation, cabbage’s chemical composition undergoes a transformation. The final product is rich in vitamins such as vitamin E and C, folic acid, phenolic compounds and antioxidants—the antioxidant context actually increases 3-4 times during fermentation. Sauerkraut contains acids such as lactic, acetic and malic acids as well as ethanol. And is also an important source of phytochemicals. Eating fermented vegetables like sauerkraut may improve digestion and may even exhibit anticarcinogenic properties making it potentially beneficial in preventing cancer. Sauerkraut may also be probiotic. Certain strains of lactic acid bacteria, when consumed live, may impart health benefits on the consumer.


As a consumer selecting the best jar of sauerkraut that will offer the best flavor, texture and potential health benefits, it is always important to read the fine print. The development and adaptation of modern food production techniques has improved food quality standards ensuring consumers a standardized, safe and hygienic product. Pasteurization, a technique named after its founder, Louis Pasteur, revolutionized food safety for mass production. Despite the relative safety of fermented products, when implemented on a mass production level, they are often subject to various preservation techniques such as pasteurization or sterilization to ensure safety, stability and to increase shelf life and to decrease the risk of spoilage. Unfortunately, during pasteurization, which involves subjecting the product to a thermal treatment, beneficial microbes may be significantly reduced. It may also impact the texture and freshness of the product. Another form of preservation may involve the addition of preservatives to ensure the safety, stability and longevity of the product. Such preservatives include sorbic and benzoic acids, potassium sorbate and sodium benzoate. Sodium benzoate, used in some fermented or fresh products, is specifically added to inhibit bacterial growth, especially lactic acid bacteria. Consumers searching out probiotic or unpasteurized, naturally fermented products must navigate an often overwhelming variety of deceptive marketing, unsubstantiated health claims and pasteurized and preservative laden products.


Aslam, Hajara, Jessica Green, Felice N. Jacka, Fiona Collier, Michael Berk, Julie Pasco, and Samantha L. Dawson. “Fermented Foods, the Gut and Mental Health: A Mechanistic Overview with Implications for Depression and Anxiety.” Nutritional Neuroscience 23, no. 9 (November 11, 2018): 1–13.

Barbara Rolek. “Sauerkraut Packs a Punch in Many Eastern European Recipes.” The Spruce Eats, October 2, 2019.

Katz, Sandor Ellix. The Art of Fermentation. Vermont: Chelsea Green Publishing, 2012.

Mayo Clinic Staff. “Folate (Folic Acid).” Mayo Clinic, 2017.

Medina-Pradas, Eduardo, Ilenys M. Pérez-Díaz, Antonio Garrido-Fernández, and Francisco Noé Arroyo-López. “Review of Vegetable Fermentations with Particular Emphasis on Processing Modifications, Microbial Ecology, and Spoilage.” In The Microbiological Quality of Food (2017): 211–36.

Özer, Ceren, and Hatice Kalkan Yıldırım. “Some Special Properties of Fermented Products with Cabbage Origin: Pickled Cabbage, Sauerkraut and Kimchi.” Turkish Journal of Agriculture – Food Science and Technology 7, no. 3 (March 12, 2019): 490–97. 

Peñas, Elena, Cristina Martinez-Villaluenga, and Juana Frias. “Sauerkraut: Production, Composition, and Health Benefits.” Fermented Foods in Health and Disease Prevention, 2017, 557–76.

Sadowski, Jan, and Chittaranjan Kole. Genetics, Genomics and Breeding of Vegetable Brassicas. Boca Raton (Fla.): Crc Press, 2011.

Science History Institute. “Louis Pasteur.” Science History Institute, January 17, 2018.

Sieving Kelly, Shirley. “The History of Sauerkraut: The Art of Fermenting Foods Has Been around for Centuries.” Countryside and Small Stock Journal 97, no. 6 (2013): 68.

Swain, Manas Ranjan, Marimuthu Anandharaj, Ramesh Chandra Ray, and Rizwana Parveen Rani. “Fermented Fruits and Vegetables of Asia: A Potential Source of Probiotics.” Biotechnology Research International 2014, (May 2014): 1-19.

Tamang, Jyoti Prakash, Paul D. Cotter, Akihito Endo, Nam Soo Han, Remco Kort, Shao Quan Liu, Baltasar Mayo, Nieke Westerik, and Robert Hutkins. “Fermented Foods in a Global Age: East Meets West.” Comprehensive Reviews in Food Science and Food Safety 19, no. 1 (January 2020): 184–217.

Walther, B., and A. Schmid. “Effect of Fermentation on Vitamin Content in Food.” In Fermented Foods in Health and Disease Prevention, edited by Cristina Martinez-Villaluenga and Elena Peñas, 131–57. Elsevier, 2017.

Chapter 3.3: Alcoholic Fermentation

Chapter's transcript below.

Alcoholic Fermentation

The second type of fermentation is known as alcoholic fermentation. In the absence of oxygen, bacteria and yeasts work in tandem, transforming the sugars in the substrate into ethanol and CO2. Wine, beer and bread are all examples of alcoholic fermentation. For this segment, we will be looking at how alcoholic fermentation transforms wheat flour and water into a nutritional loaf of sourdough bread.

Sourdough Bread

There are many kinds of fermented grain staples that have prevailed around the world for centuries. However, few have risen to the heights of worldwide stardom that wheat and bread hold. Bread produced by starter cultures such as sourdough have been staples among mankind for thousands of years. It is important to examine the microbial transformations that take place during fermentation that make this bread more digestible and improve nutrient bioavailability.

 Unlike sauerkraut, the microbes in sourdough bread expire as they are baked but impart health benefits through pre-digestion of the substrate and increase nutrient content in the final loaf. Sourdough bread is made using a natural starter, also known as a mother, which is teeming with microbial life. A great loaf of sourdough can be as simple as water, wheat flour and salt but through the fermentation process develops deep and complex flavors and its characteristic sour tang. Sourdough is only just one example of a huge variety of leavened breads humans have been enjoying for millennia. 

A simple mixture of water and flour, when fermented, results in a sourdough starter that is alive with microbes. Lactic acid bacteria, or LAB, and wild yeasts such as the fermentation superstar Saccharomyces cerevisiae, live in harmony in the slurry. When a starter is periodically fed with fresh water and flour, it rises and bubbles with activity as the yeasts and LAB consume sugars present in the flour. As in the case of LAB fermented sauerkraut or yogurt, the bacteria convert the lactose into lactic and acetic acids. This lowers the pH of the starter and gives the bread that characteristic sour taste. Lactic acid fermentation in sourdough also improves the texture, flavor and volume of the final loaf. The naturally occurring acids, alcohols and bacteria that are the by-products of microbial activity of sourdough production extend the shelf life of the bread and will mold and go stale less quickly as a result.

As I said, the texture, flavor and smell of the bread transforms as a result of the fermentation and baking. Once the first rise of the dough occurs, the gluten present in wheat flour—a protein which provides the chewy texture in the final loaf—relaxes and allows the microbes present to consume the sugars present in the flour. Yeast produces alcohol as well as carbon dioxide which gets trapped in pockets in the dough allowing it to rise. Those air pockets are baked into the dough resulting in a final loaf that is airy and chewy. A longer fermentation process also contributes to deeper and more complex flavors once the bread is baked.

Health Benefits

Unlike with lacto-fermented products such as yogurt or sauerkraut, which contain live microbes which impart health benefits in the form of probiotics, the microbes in bread are no longer active as a result of the baking process. However, that doesn’t lessen their significance in improving the health benefits in sourdough. Whole grains, that is flour with the germ and bran intact, are rich in dietary fiber, vitamins, minerals including calcium, potassium, magnesium, iron, zinc, phosphorus, phytochemicals and endogenous enzymes. During fermentation these enzymes are activated and impact the nutritional quality of the final product. 

However, the presence of phytate, or phytic acid, in wheat flour can potentially impair mineral absorption in humans. Fortunately, due to the lower pH achieved during fermentation, phytate content is lowered and the mineral bioavailability is increased. Fermentation can also improve the retention of vitamins during the baking process as yeast favors the formation of folates, also known as vitamin-B9, and thiamine, or vitamin-B1. Furthermore, sourdough fermentation has also been shown to lower the glycemic index of wheat bread. Glycemic Index, or GI, is a measurement of how quickly blood glucose levels rise after eating certain foods. During fermentation, microbes pre-digest the substrate which improves the digestibility of the final product for human consumption.

Beyond Sourdough

Sourdough starters can be used beyond the production of bread, giving life and new flavors to pancakes or even cookies. The science behind a starter also has the potential to improve gluten free products on the market. Celiac disease is a growing problem among wheat lovers. Some argue that the use of vital gluten in baked goods, over consumption of wheat, and modern wheat breeding has led to increased levels of celiac disease although this is still debated. Thankfully, gluten free options continue to improve and the application of sourdough fermentation methods open up more possibilities for improving the flavor, texture and nutritional value of gluten free products.

Commercial Production

Through scientific achievements, what was once a wild microbe, transforming our food unbeknownst to us, was identified and reproduced into a commercial yeast cake and later, was sold as the dry shelf stable form we know today. Commercial yeast, along with modern farming and milling practices, led to the expansion of mass produced commercial white bread.  In many ways, a pre-industrial loaf of crusty sourdough bread bears little resemblance to the modern loaf of fluffy, soft, plastic wrapped white bread. To achieve the desired texture, airiness and whiteness of a commercial bread loaf, it was necessary to add emulsifiers, preservatives and other chemical additives that improve texture and lengthen the shelf-life of commercial breads. Mass produced breads have become the standard in most countries where homemade bread was once the norm.

Sourdough bread production is a time and labor-intensive process due to the longer fermentation required because of the lower yeast levels in a wild sourdough starter. A sourdough starter is much more complex than the commercial yeast one can find on grocery stores shelves which is a dehydrated form of Saccharomyces cerevisiae. Commercial yeasts may speed up the fermentation process but the slow fermentation of sourdough production yields a deeper and more complex flavor, often with that trademark acidity due to increased presence of acids and contains more naturally occurring bacteria.

Humans have made great strides in producing wheat to feed a growing population and commercial yeast to simplify the time consuming process of making bread. However, with that convenience and abundance has come certain trade offs.


Aslam, Hajara, Jessica Green, Felice N. Jacka, Fiona Collier, Michael Berk, Julie Pasco, and Samantha L. Dawson. “Fermented Foods, the Gut and Mental Health: A Mechanistic Overview with Implications for Depression and Anxiety.” Nutritional Neuroscience 23, no. 9 (November 11, 2018): 1–13.

Cappelli, Alessio, Noemi Oliva, and Enrico Cini. “Stone Milling versus Roller Milling: A Systematic Review of the Effects on Wheat Flour Quality, Dough Rheology, and Bread Characteristics.” Trends in Food Science & Technology 97 (March 2020): 147–55.

Chawla, Snigdha, and Shweta Nagal. “Sourdough in Bread-Making: An Ancient Technology to Solve Modern Issues.” International Journal of Industrial Biotechnology and Biomaterials 1, no. 1 (2015): 1–10.

Franklin,  Peter S. “Bread.” In Encyclopedia of Food and Culture, edited by Solomon H. Katz (Charles Scribner’s Sons, 2004): 235-241. 

Jones, Stephen S., and Bethany F. Econopouly. “Breeding Away from All Purpose.” Agroecology and Sustainable Food Systems 42, no. 6 (January 29, 2018): 712–21.

Kasarda, Donald D. “Can an Increase in Celiac Disease Be Attributed to an Increase in the Gluten Content of Wheat as a Consequence of Wheat Breeding?” Journal of Agricultural and Food Chemistry 61, no. 6 (January 31, 2013): 1155–59.

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