By Walter Sorochan Emeritus Professor San Diego State University

Posted May 15, 2013; updated October 16, 2021.   Disclaimer  The information presented here is for informative and educational purposes only and is not intended as curative or prescriptive advice. 

  • We are 1/10 human and 9/10 bacteria! [ 10 times more bacteria cells than human cells ]
  • We carry between 3-4 pounds of live bacteria inside and outside our bodies.
  • Bacteria do not, cannot, attack healthy tissue. If they did, then we would all be dead.
  • Healthy persons eating a healthy diet will have about 80% good bacteria and 20% bad bacteria.
  • You need to eat good healthy food for two organisms .... yourself and maintain the good bacteria in your gut. 
  • About 70% of immunity is regulated by bacteria in the digestive system
  • Bacteria form an invisible skin shield to protect us [like an invisible stealth bomber]
  • Most bacteria make us healthy, but a few can make us sick
  • Human health should now be thought of controlled by bacteria living in us
  • Bacteria give off exotoxins when they die. These exotoxins can make us sick
  • Bacteria decompose dead cells and organic matter, converting them into nature's reusable chemicals
  • 90% of known pathogens enter the body through the gastrointestinal tract
  • Bacteria communicate with each other
  • Bacteria are better in preventing fighting among each other than humans

Few know that many bacteria not only coexist with us all the time, but help us do an amazing array of useful things like make vitamins, decompose  plants, decompose sewage in sewage plants, decompose garbage in garbage dumps, eat up dead animals and humans, and even maintain our atmosphere.  All this should be simple enough to understand, in spite of skeptics who may be startled with all this information about bacteria. Eat humans?  Then how come we are still alive?  The statement said that bacteria eat dead humans and animals, not living ones!

It is often bewildering to read how mass-media and web-sites describe bacteria in so much scientific and technical prose that the simple common sense things about bacteria are lost and written in a scary manner.

For example:  Bacteria were unknown to people until the 1600s, when Antony van Leeuwenhoek first observed them in his newly-made microscope.  Today, medical scientists give us incorrect and misleading information about bacteria as causing infections and diseases, when it is really the waste products of bacteria or toxins that are poisonous and really causing most of our human misery.  There is a parallel between what people knew about bacteria before 1600's,  and what we are manicured to know today. Pollan: germs are best friends 2013   Sorochan: Dig sys-immunity-bacteria-connection 2013  Baker: Man's new friend 2008  Flam: Bacteria & people 2012

It is our experience that far fewer biomedical scientists are as informed about the revolution that has occurred in the last 20 years that has transformed our thinking about bacterial pathogenesis as they are about our understanding of human disease. Blaser: Bacterial polymorphisms 2001

Here is what you should know about bacteria:

hands Where are bacteria found:   Bacteria [ including fungi ] can be found virtually everywhere. They are in the air, the soil, and water, and in and on plants and animals, including us. 100 trillion microbes live on and inside  each of us, symbiotically helping to keep us healthy.  A single teaspoon of topsoil contains about a billion bacterial cells [ and about 120,000 fungal cells and some 25,000 algal cells ]. The human mouth is home to more than 500 species of bacteria.  Microbe World

The human gut alone contains on average: 40,000 bacterial species,7 to 9 million unique bacterial genes and 100 trillion microbial cells.  According to Asher Mullard, “The bacteria in our bodies harbor millions of genes, compared with the paltry 20,000 estimated in the human genome." Microbes in the human body

The illustration below displays a few places where a few bad and good bacteria may be found in the home and how germs may be inadvertently spread:

germs family2bugs
Bad germsgermbad1  germbadguy3  germbadguy2 Good germs germgood3

There are approximately ten times as many bacterial cells in the body [ human flora ] as there are human cells, with large numbers of bacteria on the skin and as   The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, and a few are beneficialWiki: bacteria

Germ theorists estimate that an average of 14,000 germs pass into the nose in an hour's breathing. In the subway and in a crowded building, we probably get this many into our noses in a few minutes. Many more are taken in in food and drink. Microbial populations abound throughout nature.

germs mom baby You acquire most of the initial microbes in your gut community from your parents, but others are picked up from the environment. Pollan: germs are best friends 2013

We normally eat food or drink liquids that contain bacteria and digest these as we do apples and bread.

Microorganisms are a natural part of our environment.  We need them as much as they need us.

Bacteria are social and communicate with each other:

Ted Video by Bonnie Bassler:  How Bacteria talk: length: 18 mns

You can view this video in English, Spanish or any other language.


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  • Click para Espanol: Bonnie Bassler habla sobre cómo se comunican las bacterias
  • Click for English:  Bassler: How bacteria talk
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Bacteria are decomposers: Decomposers eat anything dead and once they are finished they put the converted chemical nutrients from the dead object or plant back into the ground to grow new plants. Bacteria help us by doing something really good.

Some bacteria are not only useful, but are essential to life.  Waste food garbage [ organic fertilizers ] is broken down by bacteria into materials that can be used by plants. Decomposed vegetable and animal matter is thus transformed into nutrients that are absorbed through the roots of other plants.

Many species of soil bacteria fix nitrogen; that is, they convert atmospheric nitrogen into nitrates, compounds that are readily absorbed by plants. Some of these good bacteria live in colonies in the roots of legumes, such as peas, clover, and alfalfa.  UC Berkely: Bacteria history

Various commercial processes depend on bacteria. Anaerobic bacteria [ require no oxygen ], that ferment certain substances, are used in the production of vinegar and some drugs, and in the aging process of cheeses. Some bacteria produce waste products that are useful to humans. One such waste product is lactic acid, which is produced by intestinal bacteria and promotes digestion in humans. It is grown commercially and is added to certain foods such as yogurt.

Bacteria are also used to chemically break down the tough, woody tissues of flax, jute, hemp, and coconut. Modern methods of sewage disposal often make use of bacteria to decompose organic wastes. In a process known as bioremediation, bacteria are added to water or soil to convert toxic pollutants, such as pesticides and oil, into harmless substances. Through genetic engineering, bacteria have been developed for bioremediation and also to produce drugs and other chemicals.

Most germs are saprophytes; that is, they live off dead inorganic matter.

How bacteria eat:

Bacteria do not have a mouth. They make proteins called enzymes inside the cell and these travel through the cell wall into the surrounding medium. Todar: Bacterial toxins  These enzymes chop the food into tiny subunits that then come into the bacteria cell by osmosis or active transport. Active transport is the process by which the cell grabs a molecule of glucose or other food and pulls it in thru the cell wall. Many specialized proteins and other molecules made by the bacterium are involved in this active transport process. Different bacteria use different enzymes to eat surrounding food.  Thus, in processing waste, we might use a "mixed bacteria culture" to work as a consortium able to digest the waste foods at the various stages of decomposition.  BluePlanet: how bacteria eat

What Bacteria Eat: Diet: Germs live off of dead matter. They are . . . decomposers [saprophytes], and are busily engaged in reducing dead organic matter [ like dead animals and  plants ] to the dust from whence it came.  Bacteria are vital in recycling nutrients, with many steps in nutrient cycles.

Bacteria have a wide range of diets. Some are heterotrophs [they eat other organisms] and others are autotrophs [they make their own food].

Most heterotrophic bacteria are saprobes [they absorb dead organic material like rotting flesh]. Some of these parasitic bacteria kill their host while others help their host. Wiki: bacteria

There are hundreds of species of bacteria and it is possible to find a bacterium able to eat anything from sugar, to corn proteins, to soybean oil, to iron nails, to sulfur, to the compounds in wood.  In fact, it has long been known that bacteria were involved in transforming soluble iron ions into the insoluble compounds of iron ores and iron rust.

A few blue-green bacteria [some times called blue-green algae or spirulina] have chlorophyll and can make their own food from light energy + carbon dioxide. Other bacteria can digest proteins down to amino acids and break down complex carbohydrates such as starches and table sugar down to simple sugars. Some bacteria can make their own amino acids and vitamins from carbohydrates.  Eddleman: Microbes 1998

Infection:  Microorganisms that live naturally in the body are not considered as infections. For example, bacteria that normally live within the mouth and intestine are not infections. An infection occurs when existing bacteria grow into very large numbers, or when bacteria from their normal living location, like the mouth, invade a new location like an open cut on the skin, or when new bacteria invade the body in large numbers faster than the immune system can kill them.

"The deadly bacteria [germ] on the hands, lips, drinking cups, -- in fact, found anywhere and everywhere--is not deadly until it gets mixed up with man's deadly, dirty, filthy physical and mental habits." Germs do not become toxic until they get into a toxic environment.

A germ attempts to assist in the removal of undesirable material, like dead skin cells, by liquifying it. [ exotoxin ].  This exotoxin is what can make us feel sick if it is not removed quickly from the body.

An example of a mild skin infection: A lot of these skin cells are shed inside the pores themselves. Mild infection occurs often when bacteria begin eating dead skin cells in skin pores.

A blocked skin pore also contains bacteria. They feed off the dead skin cells and the clogged sebum within the pores and produce toxins that damage the lining of the pores. As these bacteria grow and multiply, they invade the area surrounding the pore, which can lead to a bacterial infection.

A blocked pore initially turns red because blood rushes to the site, which is one of the ways our body responds to an infection. Then, white blood cells—a type of blood cell responsible for fighting infection—destroy bacteria, build up below the surface of the skin, and die.

These dead white blood cells, along with dead skin cells and some bacteria, form a white liquid known as pus. A pimple forms when the excess sebum and dead skin cells clog up and block the opening of the pore. This type of pimple is called a whitehead.

Another type of pimple, called a blackhead, appears when sebum and dead skin cells clog the pore but not the opening, as in a whitehead. While the pore is clogged, its surface remains open. A blackhead appears black because melanin in the dead skin cells reacts with oxygen from the air, which changes the melanin’s color from brown to black.

If the infection worsens, a painful cyst may develop under the skin. A cyst is a fluid-filled sac that is the most severe type of acne.

How bacteria cause disease video by Dr. Warren Levinson MD, UCSF School of medicine: [Length is 1.30 hours]

Levinson: bacteria-disease 2006

Body Defense against invading bacteria:   Invading bacteria are recognized by the immune system as foreign objects and are attacked by macrophages as illustrated in the video: YouTube animation illustrating macrophages releasing cytokines
Source: Nucleus Medical Art, www.

"Bacteria cause tissue injury primarily by releasing exotoxins. All humans are infected covered with bacteria [the normal flora] living on their external surfaces [including the skin, gut and lungs].  Normally due to our host defenses most of these bacteria are harmless. In compromised patients, whose defenses are weakened, these bacteria often cause opportunistic infectious diseases when entering the bloodstream [ as after surgery, catheterization or other treatment modalities ]. When initiated in the hospital, these infectious diseases are referred to as nosocomial. Some common bacteria found in the normal flora include Staphylococcus aureus, S. epidermidis and Propionibacterium acnes [ found on the skin ] and Bacteroides and Enterobacteriaceae found in the intestine [ the latter in much smaller numbers ]." [Fox: bacterial pathogenesis 2010 no longer on internet].

If you and epidemiologists think that you have all the answers about bacteria, think again. Baker: Man's new friend 2008 There was a lot unknown about bacteria over 100 years ago and there still is today.  The new medical-health buzz is about the connection between the digestive system, the immune system and bacteria. Researchers since 2000 have identified over 400 good and bad bacteria living in the large intestine or colon.  If the normal balance of 80 - 85% good and 15 - 20 % bad bacteria is disrupted, then the bad bacteria multiply and can cause many of our illnesses and diseases. Sorochan: Dig sys-immunity-bacteria-connection 2013

Bacteria usually do not attack healthy human tissue. If they did, then we would all be dead.  But this was not always common sense!  Case in point:

In the early days of medicine and microbiology, controversy raged about how diseases were spread.  This was especially true about  typhoid fever and especially cholera.  Dr. John Snow in 1854 proved that cholera was spread by well water and a German medical scientist Dr. Koch, identified cholera was caused by a microorganism. One of their opponents, Dr. Max Pettenkofer, hypothesized that it took more than an microorganism to cause cholera.  Wiki: Pettenkofer life

It is now well documented by epidemiologists that cholera caused sever diarrhea that dehydrates the victim and causes death. Medical doctors during 1850 - 1900 also observed that not all persons who got sick from cholera died.  Adding to the controversy was the famous experiment that Dr. Max Pettenkofer, professor of bacteriology, at the University of Vienna, who tried to demonstrate to his class that cholera germs did not cause "disease." He was a proponent of the "ground water theory" regarding the spread of epidemic Asiatic cholera.  On October 7, 1892, while instructing his class in the bacteriological laboratory, he startled his students by picking up a glass tube containing millions of living cholera bacilli and swallowed the entire contents before the astonished students. There were enough millions of wriggling comma germs in this tube to infect a regiment, but Pettenkofer only growled through his beard: 'Now let us see if I get cholera.'  The results of this experiment were misinterpreted by many scientists of that day, including Dr. Shelton:

"Mysteriously, nothing happened that day and the failure of the mad Pettenkofer to come down with cholera remains to this day an enigma without even the beginning of an explanation." Shelton: Bacteria

After swallowing one cubic centimeter of contaminated cholera water, Dr. Max experienced abdominal colic with severe gas pains and mild diarrhea.  The diarrhea lasted for a week and he never became seriously ill.  Today's interpretation of all this is that he escaped with a mild form of cholera.  Many had contracted the mild form and not the killer form.  To this day, we do not have an accepted understanding nor a valid explanation for the two forms of cholera.  Altmann: Pettenkofer experiment update 1998  This cholera phenomenon is further explained today by Guerney as "quorum sensing." [ view Guerney in reference below ]  Gurney: Pettenkofer & cholera 2012  

SO .... does bacteria attack healthy human tissue? For more on the mystery about cholera, check out the info below in the reference under Colwell: Colwell: mystery research on cholera

An old controversy revived:

The explosion of new information about bacteria, and how bacteria adapt has caught "most medical doctors with their pants down!" Doctors who graduated from medical school 10 years or more were probably never made aware of the controversy that existed during Louis Pasteur days about monomorphic and polymorphic bacteria.  Bacteria that retain their shape are called monomorphic [ as today's Western Medicine is practiced ]; those that do not are called polymorphic.  This controversy has resurfaced once again to confuse medical doctors.

This is especially true between monomorphic and polymorphic bacteria and how bacteria may be changing shape as an adaptation to different environments.  I Blaser: Bacterial polymorphisms 2001

Substantial polymorphism exists within exogenous organisms such as Streptococcus pyogenes, Borrelia species, and Neisseria meningitidis, and amongst indigenous bacteria such as Escherichia coli and Helicobacter pylori. Diversity per se is not an indication of virulence, since, for example, Mycobacterium tuberculosis is relatively clonal and H. pylori highly polymorphic. Other types of polymorphic bacteria include Rickettsia rickettsii, which causes Rocky Mountain spotted fever, and Bacillus anthracis, which causes anthrax.  Blaser: Bacterial polymorphisms 2001  This issue is a hot one and we leave further discussion of it for another day.  You can find more information about this controversy and the affect of gut bacteria on well-being in: Sorochan: Dig sys-immunity-bacteria-connection 2013

It should be obvious by now that different cultures eat different foods and hence have different bacteria colonize their digestive systems.  Here is a sample of what people eat in different regions of the world: What the world eats


Abt Michael C., Lisa C. Osborne, Laurel A. Monticelli, Travis A. Doering, Theresa Alenghat, Gregory F. Sonnenberg, Michael A. Paley, Marcelo Antenus, Katie L. Williams, Jan Erikson, E. John Wherry, David Artis, "Brothers in Arms: Commensal Bacteria Help Fight Viruses," Journal of Immunity, 2012.  Article no longer valid

Altmann Lawrence K., Who Goes First? Book, University Of California Press, Berkely, California, 1998.  Altmann: Pettenkofer experiment update 1998

Baker Mitzi, "Man's best friend-New take on infection-causing bugs," Stanford medical magazine, Summer, 2008. Article no longer active.

Blaser Martin J. and James M. Musser, "Bacterial polymorphisms and disease in humans," J Clin Invest. February 15,2001, 107(4): 391–392.  Blaser: Bacterial polymorphisms 2001

Blue Planet, "How bacteria eat."  Article no longer active.

Colwell Rita and Anwarul Huq, "Cholera-Carrying Copepod." National Science Foundation.    Colwell: mystery research on cholera

cholera vibro

Her ongoing research has disproved many commonly held theories about the bacterium, including how it travels the world, how it transmits to humans, and in particular, where it goes between outbreaks. Scientists had long questioned how V. cholerae could seemingly disappear-undetected in water samples; no new cases reported--and then almost spontaneously arise again? Solving this mystery became a primary focus of Colwell's research.

Colwell discovered if conditions are not right for replication, V. cholerae's metabolic rate will plummet, causing it to shrink 15- to 300-fold and go into a dormant, spore-like state. This nonculturable state is essentially a survival tactic for the bacterium, enabling it to live in a wide range of conditions and habitats, including seawater, brackish water, rivers, and estuaries. Additionally, Colwell discovered that the bacteria are just as infectious in the dormant state. Exactly what awakens the bacterium from their dormant state is unknown, but it is thought to involve a combination of the "right" conditions such as water temperature and water salinity. For example, Colwell found that a graph compiled from satellite data showing seasonal peaks in sea surface temperature in the Bay of Bengal correlates with the seasonal peaks in admissions for cholera in local hospitals. Not long after the rise in sea temperature comes a rise in cholera admissions.

Flam Faye, "Bacteria and people: In it together," Philadephia Enquirer, June 25, 2012.    Gurney: Pettenkofer & cholera 2012

Quorum sensing: "how did Pettenkofer survive or at least come out with his trousers clean! Allow me to put forward my own pet theory, V. cholerae has a interesting life style. It is highly infection at low levels. Once the level of V. cholerae bacteria builds up in an infected person a change occurs in the biology of the bacteria. Instead of becoming more virulent (how sick a bacteria makes you) V. cholerae turns off its virulence; it shuts down its toxin production and turns on its little out board motor known as flagellum and swims off down stream off to infect another person. I’ve mentioned this process before, its known as quorum sensing. Bacteria release a small molecule into the environment (soil, petri dish or intestines), they use these molecules as a census in which they chose how to act as a group. Most bacteria, to our knowledge, use these molecules, and many use it in order to work out when to become virulent. V. cholera however works the other way around; it counts these votes and when a certain level is reached it turns off its virulence."

So Pettenkofer could have survived by this little biological trick without being aware of quarum sensing.

Eddleman Harold, "Study of Microbes." 1998. President, Indiana Biolab, 14045 Huff St., Palmyra IN 47164.  Article no longer active.

Jeananda,Col, "Enchanted Learning," 1996.  Jeananda

Levinson Warren, "How bacteria cause disease," video, UCSF School of medicine, October 24, 2006.  Levinson: bacteria-disease 2006

Lozupone Catherine A., Jesse I. Stombaugh, Jeffrey I. Gordon, Janet K. Jansson & Rob Knight, "Diversity, stability and resilience of the human gut microbiota," Nature, September 13, 2012, 220–230.  Lozupone: gut microbia 2012

Microbes in the human body.  Microbes in the human body

Pollan Michael, "Some of My Best Friends Are Germs," The New York Times magazine, May 15, 2013.  Pollan: germs are best friends 2013

Sorochan Walter, "The Immune - Digestive System Connection,", January 29, 2013.  Sorochan: Dig sys-immunity-bacteria-connection 2013

Todar Kenneth, "Bacterial Protein Toxins," Online textbook of Bacteriology,   Todar: Bacterial toxins

Turnbaugh, P. J., Backhed, F., Fulton, L. Gordon, J. I., "Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome," Cell Host Microbe, 2008, 213-223.  Turnbaugh: bacteria & obesity link 2008

University of California, "Bacteria: Life history and ecology."  UC Berkely: Bacteria history

Wilder Bee, "False Information About Die-Off Symptoms & Herxheimer Reactions," Healing Naturally by Bee.  Wilder: Bacteria info

Wikipedia, "Bacteria."  Wiki: bacteria

Wikipedia, "Infection."  Wiki: infection

Wikipedia, "Max Joseph von Pettenkofer."  Bavarian chemist and hygienist.  Wiki: Pettenkofer life

Willyard Cassandra, "Microbiome: Gut reaction," Nature, November 24, 2011479, S5–S7.  Willyard Ggut reaction 2011

"Today scientists are trying to unravel the relationship between changes in lifestyles in recent decades, changes in our microbiota, and the skyrocketing prevalence of allergies in the developed world.

The immune cells in the gut are in constant contact with a diverse microbial milieu, and “the human gut has more immune cells than the rest of the body put together,” says David Artis, a microbiologist at the University of Pennsylvania in Philadelphia. To an immune cell, beneficial or harmless bacteria (known as commensals) look much like harmful ones, but the beneficial bugs have developed methods of shaping the function of the immune system, so that their presence doesn't provoke an immune attack. “These bugs are flipping switches,” says Sarkis Mazmanian, a microbiologist at the California Institute of Technology in Pasadena. If these beneficial microbes fail to colonize our guts early in life, or if they succumb to a course of antibiotics, then switches don't get flipped and the immune system can become hypersensitive, attacking harmless microbes and other substances such as pollen, pet dander or shellfish — or so the thinking goes."

200 scientists published a most ambitious survey of the human microbiome. Known as the Human Microbiome Project, it is based on examinations of 242 healthy people tracked over two years. The scientists sequenced the genetic material of bacteria recovered from 15 or more sites on their subjects’ bodies, recovering more than five million genes.