The human microbiome is the collection of microorganisms (such as bacteria and fungi) which live on and inside humans (on the skin, in the saliva and mouth, in the eyes, and in the gut and the rest of the gastrointestinal tract). Foreign microbes outnumber human cells in the body a wide margin; humans have about 100 trillion cells, and carry ten times as many microorganisms in the intestines alone.
Some of these organisms are useful for humans. However, most have no known effect; they are just symbionts and are referred to as the normal ‘flora.’ Studies in 2009 asked whether our health is damaged if we reduce this biota (collection of organisms in an ecosystem), which is certainly the case with gut flora (which can be restored by a ‘fecal transplant.’
Populations of microbes (such as bacteria and yeasts) inhabit the skin and mucosa. Their role forms part of normal, healthy human physiology, however if microbe numbers grow beyond their typical ranges (often due to a compromised immune system) or if microbes populate atypical areas of the body (such as through poor hygiene or injury), disease can result. It is estimated that 500 to 1000 species of bacteria live in the human gut and a roughly similar number on the skin. Bacterial cells are much smaller than human cells. Though members of the flora are found on all surfaces exposed to the environment (on the skin and eyes, in the mouth, nose, small intestine), the vast majority of bacteria live in the large intestine. Many of the bacteria in the digestive tract, collectively referred to as the gut flora, are able to break down certain nutrients such as carbohydrates that humans otherwise could not digest. The majority of these commensal bacteria are anaerobes, meaning they survive in an environment with no oxygen. Normal flora bacteria can act as opportunistic pathogens at times of lowered immunity.
Escherichia coli (a.k.a. E. coli) is a bacterium that lives in the colon; it is an extensively studied model organism and probably the best-understood bacterium of all. Certain mutated strains of these gut bacteria do cause disease. A number of types of bacteria live in the mouth, where they are part of a sticky substance called plaque. If this is not removed by brushing, it hardens into calculus (also called tartar). The same bacteria also secrete acids that dissolve tooth enamel, causing tooth decay. A small number of bacteria are normally present in the conjunctiva of the eye. The lachrymal glands continuously secrete, keeping the conjunctiva moist, while intermittent blinking lubricates the conjunctiva and washes away foreign material. Tears contain bactericides such as lysozyme, so that microorganisms have difficulty in surviving the lysozyme and settling on the epithelial surfaces. However, some pathogens able to attach to the conjunctival epithelium. Newborn infants are particularly prone to bacterial attachment.
The metabolic activity performed by these bacteria in the gut is equal to that of a virtual organ, leading to gut bacteria being termed a ‘forgotten’ organ. Bacteria make up most of the flora in the colon and 60% of the dry mass of feces. This fact makes feces an ideal source to test for gut flora for any tests and experiments by extracting the nucleic acid from fecal specimens. This form of testing is also often preferable to more invasive techniques, such as biopsies. Though thousands my exist, it is probable that 99% of the bacteria come from about 30 or 40 species. Fungi and protozoa also make up a part of the gut flora, but little is known about their activities. Research suggests that the relationship between gut flora and humans is not merely commensal (a non-harmful coexistence), but rather is a mutualistic, symbiotic relationship. Though people can survive with no gut flora, the microorganisms perform a host of useful functions, such as fermenting unused energy substrates, training the immune system, preventing growth of harmful species, regulating the development of the gut, producing vitamins for the host (such as biotin and vitamin K), and producing hormones to direct the host to store fats. However, in certain conditions, some species are thought to be capable of causing disease by causing infection or increasing cancer risk for the host.
The Daily Omnivore 