Microbes are everywhere. They perform functions essential for biological life and survival on earth. Yet they are simple celled organisms, invisible to the naked eye, and extremely promiscuous. You may not realize it, but we have been harnessing their power for centuries to make and preserve our food and beverages. In fact, some of our most beloved and iconic things to eat and drink are a direct result of the action of microbes. You should be thinking now about beer, bread, cheese, and sausages. And it doesn’t stop there… nowadays microbes are involved in making food dyes, flavor compounds, and even act as sensors in packaging to detect contamination. Hopefully now it is apparent that these tiny organisms hold tremendous influence over food as we know it today. But how do they do this and what does the future look?


Take a look outside your window - hopefully you have a view of something green. In school we were taught the recipe for growing plant: seeds, sunlight, water, and soil. But they forgot an important ingredient. They forgot the microbes! Soil is teeming with microorganisms that are constantly at work breaking apart some compounds and building different ones. Plants make good use of this skill and uptake these byproducts via their roots and give back to the bugs as well. It is a true symbiotic relationship. This relationship is so dependent that some plants cannot grow if certain microbes are absent from the soil. Farmer and researchers have been working together for a long time to unravel and optimize these relationships for agricultural purposes. And their work doesn’t only apply to plants, but also the popular animal products found in the supermarket: milk, eggs, chicken, bacon, and beef. Some research has shown that chickens are healthier and produce better eggs if they have certain microbes in their guts. Same story for the pigs and cows when it comes to giving birth to healthy young. For something so small, that is quite some influence and the pipeline science shows that we may be able to further positively impact agriculture through utilization of microbes.


Back to your window view and cup of tea. Or is it coffee? Well it doesn’t matter as other microbes have played a role in the making of either beverage through fermentation. Have you had fondue recently or a perhaps cheese pizza or a rich bowl of yogurt with fruit? You can also thank microbes for these. We mostly think of fermentation and alcoholic beverages but microbes have a direct and irreplaceable role in fermented products whether it is beer, sauerkraut and sausage or wine with cheese and mustard. Once again, it has to do with making and breaking down molecules in the raw ingredients. They are responsible for the foam in beer and the fizzy bubble in fermented sodas (precursors of soda pop and colas) because of their utilization and conversion of sugars to carbon dioxide. Fermentation was a way of preserving food before refrigeration existed but it has evolved in something with more meaning as scientists are showing the positive influence such food and drinks has on our bodies including features ranging from better digestion and gut health to improved immune system responses and positive neurological signals.


So how do microbes actually do all of these things and what makes them so special? There are two parts to that answer and the first lies in their how their genes are turned on and off. Each microbe has a set of genes, or life instructions if you will, that enable it to grow, divide, thrive, and die under specific conditions. In fact, some microbes possess up 3.3 million genes which seriously dwarfs our 23,000 human ones. In fact, if all the DNA in bacterial genes were unpacked and lined up in a single row, it would be over a kilometer long! With so many genes that are easily turned on and off, microbial behavior can be quite promiscuous and depends largely on their environment (suitable temperature, food or nutrients that they can use, etc.), their neighbors (friendly or hostile microbes), and their unique set of genes.


We all recognize that off-smell when food is spoiled; this means that bacteria are taking advantage of their circumstances and creating an environment that suited them for growing and dividing. Some microbes prefer an acidic environment and will work hard to create that by converting compounds around them into acids. We take advantage of this preference to make yogurt or other fermented dairy products. Others need high amounts of sugar to grow and divide, else they will remain dormant and even starve, like the bacteria and yeasts for wine and beer-making. That intense butter flavor on your popcorn is a direct result of bacterial production of short chain fatty acids such as butyric and oleic acid under the right conditions. Some microbes that live in our intestines can even signal the digestive tract to move faster or slower to optimize their chances of a good meal; talk about symbiosis with humans!


The second reason why bacteria are special is because of their strength in numbers. All things microbial are geared towards reproduction and survival. While one bacteria may not be able to make a wheel of cheese on its own, it can signal and activate neighboring microbes to turn on certain genes via chemicals that it secretes (kind of like instant messaging). These neighbors then activate and brainwash their neighbors and so on until billions of bacteria are synced and coordinated towards a particular function, all because that first bacteria sensed an opportunity. One bacteria can divide and copy itself in about 20 minutes, so within a few hours, a small army of the original bacteria can exist. The possibilities of these innate properties have had scientists drooling for many decades: an organism that can replicate itself quickly, signal its peers, and can itself be manipulated is a useful tool and a fascinating thing to study.


Okay, so the question in your mind as you continue to sip your beverage is probably: “All of this sounds nice but why should I really care?” Well, can you imagine a future without wine or coffee? Do you want to have healthy farm animals and nutritious crops that grow well? The time may come soon where your food might be labeled, “made in part by microbes” to acknowledge the immense contributions these tiny organisms have on all parts of the food chain. Though invisible to the unaided eye, microbes are truly amazing and the food industry will continue to harness their combined power.



7000 BC

Evidence is found that the Babylonians used fermentation to manufacture beer.  Wine appeared in about 3500 BC.  In early civilizations (and even today in underdeveloped countries where modern sanitation is lacking), alcoholic beverages like beer and wine were much safer to consume than the local water supply, because the water was often contaminated with intestinal microorganisms that caused cholera, dysentery and other serious diseases.


3000 BC

Egyptians manufactured cheese (fermentation) and butter (fermentation, low aw).  Again, fermented foods such as cheese and sour milk (yogurt) were safer to eat and resisted spoilage better than their raw agricultural counterparts.  Several cultures also learned to use salt (low aw) to preserve meat and other foods around this time.


1000 BC

Romans used snow to preserve shrimp (low temp), records of smoked and fermented meats also appear. Even though early human cultures discovered effective ways to preserve food (fermentation, salt, ice, drying and smoking), they did not understand how these practices inhibited food spoilage or food borne disease.  Their ignorance was compounded by a belief that living things formed spontaneously from nonliving matter (Theory of Spontaneous Generation).



In the first Chinese handbook of emergency medicine, alchemist Ge Hong documents the use of orally administered feces to cure food poisoning and severe diarrhea.


Mid 1500s

Suleiman the Magnificent of Turkey sends a physician to France to prescribe yogurt as a cure for King Francis I’s diarrhea.


Late 1500s

The Microscope is invented, finally revealing parts of the microbiological world.


An Italian physician by the name of Francesco Redi demonstrated that maggots on putrefying meat did not arise spontaneously but were instead the larval stages of flies (put meat in container capped with fine gauze so that flies couldn’t get access to deposit eggs).  This was the first step away from the doctrine of spontaneous generation.



Anton van Leeuwenhoek from the Netherlands examined and described bacteria through a microscope.  At about the same time, the Royal Society was established in England to communicate and publish scientific work, and they invited Leeuwenhoek to communicate his observations.  He did so for nearly 50 years until his death in 1723.  As a result, Leeuwenhoek’s reports were widely disseminated and he is justifiably regarded as the person who discovered the microbial world.



An Italian man named Spallanzani tried to disprove the theory of spontaneous generation of life by demonstrating that beef broth which was boiled and then sealed remained sterile.  Supporters of the theory discounted his work because they believed his treatment excluded O2, which they thought was vital to spontaneous generation.


Captain James Cooke leaves England for the South Pacific with 7,860 pounds of sauerkraut onboard. Sauerkraut is made from thinly sliced cabbage preserved in its own juices. Once ferm- ented, the cabbage can last for over a year. The fermentation process creates vitamin C as a byproduct of the bacteria digesting the cabbage. Vitamin C prevents and cures scurvy, which at the time was a common disease, killing approximately two million sailors between 1500 and 1800.


The French government offered 12,000 francs to anyone who could develop a practical way to preserve food.  A French confectioner named Nicholas Appert was issued the patent after showing that meat could be preserved when it was placed in glass bottles and boiled.  This was the beginning of food preservation by canning.


Schwann demonstrates that healed infusions remain sterile in the presence of air (which he passed in through heated coils), again to disprove spontaneous generation.  It is interesting to note that although Spallanzani and Schwann each used heat to preserve food, neither man apparently realized the value of turning these observations into a commercial method for food preservation.  (Critics suggest heating somehow changed the effect of air as it was needed for spontaneous generation.)



The first person to really appreciate and understand the causal relationship between microorganisms in infusions and the chemical changes that took place in those infusions was Louis Pasteur.  Through his experiments, he convinced the scientific world that all fermentative processes were caused by microorganisms and that specific types of fermentations (e.g. alcoholic, lactic or butyric) were the result of specific types of microorganisms. In 1857 he showed that souring milk was caused by microbes.



In 1860, he demonstrated that heat destroyed undesirable microbes in wine and beer.  The latter process is now used for a variety of foods and is called pasteurization.  Because of the importance of his work, Pasteur is known as the founder of food microbiology and microbiological science.  He demonstrated that air doesn’t have to be heated to remain sterile using his famous swan-necked flasks that finally disproved spontaneous generation. From the time of Pasteur, microbiological discoveries and developments began to proceed more rapidly.  Microbes were implicated in several diseases, heat-resistant spores were discovered, toxins were identified, and by the late 1800s, governments began to enact legislation to protect the quality of food.



Elie Metchnikoff hypothesizes that yogurt and other fermented dairy products could add beneficial bacteria to the guts of elderly people, which would aid digestion and maintain bowel health as well as prolonging life. Metchnikoff and his colleagues began drinking sour milk to populate their digestive tracts with the lactobacillus, marking the introduction of probiotics as dietary supplements.



Minoro Shirota developed a yoghurt based drink which contained his probiotic strain; Lactobacillus casei Shirota. He called this product; Yakult, one of the first commercially available probiotics.


Microbiota: The collective community of microorganisms present in a given environment.

Microbiome: An entire environment including the microorganisms that are present, their genomes and the prevailing environmental conditions.

Bacteria: Single-celled organisms that can be rod, spherical or spiral in shape. They have symbiotic and parasitic relationships with animals and plants, and are found in soil, water, and seemingly inhospitable places like radioactive waste. Different species of bacteria are involved in important processes like nitrogen fixing, infection and diseases, fermentation, decay, rotting, and the production of chemicals.

Enterotype classification: a classification system that breaks humans into three groups based on bacterial populations in the gut. Humans with high levels of Bacteroides are classified
as type 1 and generally have high diets high in protein. Type 2 have high amounts of Prevotella and diets high in carbohydrates and dietary fiber. Ruminococcus is found in high quantities in the gut of type 3.

Entero-: Relating to the intestine

Bifidobacteria: Discovered by Henry Tissier in 1899 and used as one of the first probiotics, they are particularly abundant in infants and are believed to benefit human health in many ways.

Fermentation: Energy-yielding metabolism of complex substrates to simpler products, including short chain fatty acids, under anaerobic conditions.

Lactate: A metabolite that is formed as a byproduct during the fermentation process (as bacteria convert glucose into cellular energy).

Prebiotics: Non-digestible food ingredients that beneficially affect the host by selectively stimulating the growth and/ or activity of one or a limited number of bacteria.

Probiotics: Live microorganisms that, when administered in adequate amounts, confer a health benefit to the host.

Spontaneous generation: The hypothetical process by which living organisms develop from nonliving matter. Many believed in spontaneous generation because it explained such occurrences as the appearance of maggots on decaying meat.







Title: 1869 Abbe Kondensor | Author: ZEISS Microscopy | Source: Flickr

Title: Micro spectroscope and polariscope | Author: unknown | Source: Flickr

Title: Io microscope and accessories | Author: unknown | Source: Flickr

Title: Fig. 82. Reicher Vs. Microscope | Author: Richards & Co. | Source: Flickr

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