Microbial ecology is the study of the relationship between microbes and their surrounding (environments).
Microbe have developed strategies which enable them to survive;
-           Survival and growth by structural adaptation eg alkaline soda lakes, saline lakes, hot springs, desert soils.
-           High reproduction rate allows survival
-           High nutrients enable rapid growth to out compete other cells
Microbes and Body surface.

Bacteria are consistently associated with the body surfaces of animals. There are many more bacteria cells on the surfaces of human (including the gastrointestinal tract) than there are human cells that make up the animal. The bacteria and other microbes that are consistently associated with an animal are called the normal flora, or more properly the “indigenous microbiota” of the animal.
            These bacteria have a full range of symbiotic interactions with their animal hosts. This relationship between microbes and animals is called symbiosis. In biology, symbiosis is defined as “life together” ie that two organisms live in an association with one another. Thus, there are at least three types of relationship based on the quality of the relationship for each member of symbiotic association.

1.         Mutualism: - Both members of the association benefit. For humans, one classic naturalistic association is that of the lactic acid bacteria that live on the vaginal epithelium of a woman. The bacteria are provided habitat with a constant temperature and supply of nutrient (glycogen) in exchange for the production of lactic acid, which protect the vagina from colonization and disease caused by yeast and other potentially harmfully microbes.
2.         Commensalism:- There is no apparent benefit or harm to either member of the association.
A problem with commensal relationships is that if you look at one long enough and hard enough, you often discover that at least one member is being helped or harmed during the association. Consider our relationship with staphylococcus epidermidis, a consistent habitant of the skin of humans probably; the bacterium produces lactic acid that protects the skin from colonization by harmful microbes that are less acid tolerance. But it has suggested that other metabolites produces by the bacteria are an important cause of body odors (good or Lad, depending on your personal point of view) and possibly associated with certain skin cancers.

3.         Parasitism:-
Parasite refers to an organism that grows, feed and is sheltered on or in a different organism while contributing nothing to the survival of its host. In microbiology, the mode of existence of a parasite implies that the parasites are capable of causing damage to the host. This type of a symbiotic association draws our attention because a parasite may become pathogenic if the damage to the host result in disease. Some parasitic bacteria live as normal flora of humans while waiting for an opportunity to cause disease. Other no indigenous parasites generally always cause disease if they associate with a non immune host.     
         In human, some of the normal bacterial flora (e.g staphylococcus aureus, streptococcus pneumonia, Haemophilus influenza) are potential pathogen that live in a commensally or parasitic relationship without producing disease. They do not cause disease in their host unless they have an opportunity brought on by some compromise or weakness in the host’s anatomical barriers, tissue resistance or immunity.
            The host in a host-parasite interaction is the animal that maintains the parasite. The host and parasite are in a dynamic interaction, the outcome of which depends upon the properties of the parasite and of the host. The bacterial parasite has its determinants of virulence that allow it to invade and damage the host and to resist the defenses of the host. The host has various degrees of resistance to the parasite in the form of the host defenses.  A healthy animal can defend itself against pathogens at different stages in the infections disease process. The host defenses may be of such a degree that infection can be prevented entirely, or if infection does occur, the defenses may stop the process before disease is apparent. At other times, the defenses that are necessary to defeat a pathogen may not be effective until infectious disease is well into progress.

Typically the host defense mechanisms are divided into two groups.
1.         Constitutive Defenses:  Defenses common to all healthy animals. These defenses provide general protection against invasion by normal flora or colonization, infection, and infectious disease caused by pathogens. The constitutive defenses have also been referred to as “natural” or “Innate” resistance, since they are inherent to the host.

2.         Inducible Defenses: 
Defense mechanism that must be induced or turned on by host exposure to a pathogen (as during an infection). Unlike the constitutive defenses, they are not immediately ready to come into play until after the host is appropriately exposed to the parasite. The inducible defenses involve the immunological responses to a pathogen causing an infection. The inducible defenses are generally quite specifically directed against an invading pathogen. The constitutive defenses are not so specific, and are directed toward general strategic defense. The constitutive defenses, themselves, may not be sufficient to protect the host against pathogens. Such pathogens that evade or overcome the relatively non-specific constitutive defenses are usually susceptible to the more specific inducible defenses, once they have developed.
Microbes that colonize the human body during birth or shortly thereafter, remaining throughout life, are refer to as normal flora. Normal flora can be found in many sites of the human body including the skin (especially moist areas such as groin and between the toes), respiratory tract (particularly the nose), the urinary tract, and digestive tract (primarily the mouth and colon). On the other hand, areas of the body such as the brain, the circulatory system and lungs are intended to remain sterile (microbe free).          
The human body provided may unique environments for different bacterial communities to live. Individual microbe may be carrying out important functions within our bodies that we have not yet discovered.
            Whether a host-microbe relationship is “positives” or “negative” depends on many factors. And in most cases the relationships well actually remain positive. The host provides a niches and nutrition for the colonizing microbe and the microbe occupies a space that a potential parasite or pathogen might otherwise colonize. In these cases microbial communities may even aid in digestion or synthesize nutrient for the host.
            However, life is not always perfect, and in certain situations good-standing members of your normal flora can cause disease or invading pathogens can displace them,    the result will be disease.
            Life on the surface, the skin:
Human skin is not a particularly rich place for microbes to live. The skin surface is relatively dry, slightly acidic and the primary source of nutrition is dead cells. This is an environment that prevents the growth of many microorganisms, but a few have adapted to life on our skin.
            Propionibacterium acnes is a gram positive bacterium that inhabits the skin. P. acnes are anaerobes, so they live in pores and glands where oxygen levels are lower. As the name implies, P. acnes causes the common skin condition called acnes. Although acne out breaks can result in emotional and physical discomfort, the infection is not life threatening. A point complemented by P. acnes performing an important role through occupying niches that might otherwise be colonized by more dangerous pathogens.
            Another prominent member of the skin flora is staphylococcus epidermidis. This is a highly adapted gram positive bacterium that can survive at many sites throughout the body. S. epidermidis can cause life threatening disease in hospital patients when invasive medical devices such as catheters are used. In such cases, S epidemics form antibiotic resistance biofilms along the catheter and enter the blood stream causing systemic infection that can be fatal.

            The human nose is home to the infamous Gram positive bacterium staphylococcus aurous, best known for its role in hospitals where it is a major cause of surgical wound and systemic infection.

500-600 different kinds of bacteria thrive on mucus and food remnants in the mouth. A predominant member of this community is the Gram positive bacterium streptococcus mutans. It grows in biofilms on the surface of teeth (plague) where it consumes sugar and converts it to lactic acid.
Lactic acid erodes the enamel on the surface of teeth, which leads to the formation of cavities.

The stomach has a highly acidic (pH 1-2) environment. One organism that has been discovered living in the human stomach is the gram negative bacterium called Halicobacter phylori.
            It creates a less acidic microenvironment. The bacteria achieve this by burrowing into the stomach’s mucosal lining to a depth where the pH is essentially neutral. In addition H pylori produce an enzyme called urease to convert urea produced by the stomach into ammonia and carbon dioxide. H pylori is the causative agent of gastric ulcers.
            Compared to the stomach, the small intestine is a relatively hospitable environment. However, the small intestine presents microbes with a new challenge – high flow rates. This makes it difficult for bacteria to colonize, the small intestine because they get washed out very quickly. As a result the concentration of bacteria in the small intestine remains relatively low and human enzymes carry out most of the digestion processes.
            In the colon, the show rate of food movement, gives bacteria in the colon time to reproduce so that they reach very high concentration (1012-1013 bacteria per ml). The colon is a holding tank for bacteria that participate in the end stages of food digestion. For it is here that bacteria are presented with polysaccharides that cannot be broken down by human enzyme. The process of polysaccharide degradation in the colon is referred to a colonic fermentation. Polysacchande fermentation results in the production of acetate, butyrate and propionate, which are used as a source of carbon and energy by mucosal cells of the colon. There is also evidence that E coli within the colon produce vitamin K, which the human body requires for the process of blood clothing.


Hentschel, U.M. Steinert and J. Hacker (2000). Common molecular mechanisms of symbiosis and pathogenesis trends             microbio/8:226-23.1   
Kenneth Todar (2009). The nature of Host-parasite relationships      between Bacteria and animals. University of Wisconsin     madison         department of Bacteriology.
Lansing M. Prescott, John P. Harlern Donald A. Klein (1999) general           microbiology MC Graw-Hill companies, inc. 4th edition pg 400,            405-407    
Michael J. Pelczar, JR.,  E. C. S. Chan, Noel R. Krieg (1999). Tata      McGraw-Hill Publishing Company Limited New Delhi 5th Edition       pg  687
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