Learn more about Microbiology
In this module, you will learn more about
- Normal body flora/biota
- Opportunistic infections
- The differences between viruses, bacteria, fungi, moulds, protozoa and other parasites
- Infection cycle
- Anti-microbial agents and controlling microbial growth
1 Normal body flora/biota
What is normal microbial flora?
Sometimes referred to as normal biota or the microbiome, normal flora are the millions of microbes that reside on or in our body without causing harm.
The microbiome plays an important role in digestion, metabolism and production of important chemicals such as Vitamin K necessary for blood clotting.
The presence of normal flora also helps inhibit invasion of pathogenic microbes.
The composition of the microbiome differs from person to person and is dependent on factors such as the host’s genetic makeup, environment and the nutrient supply available.
Considerable research is underway to determine just how the biome impacts on our body’s weight, mental health and other chronic and inflammatory diseases.
Sometimes referred to as normal biota or the microbiome, normal flora are the millions of microbes that reside on or in our body without causing harm.
The microbiome plays an important role in digestion, metabolism and production of important chemicals such as Vitamin K necessary for blood clotting.
The presence of normal flora also helps inhibit invasion of pathogenic microbes.
The composition of the microbiome differs from person to person and is dependent on factors such as the host’s genetic makeup, environment and the nutrient supply available.
Considerable research is underway to determine just how the biome impacts on our body’s weight, mental health and other chronic and inflammatory diseases.
Examples of normal flora
2 Opportunistic infections: When do normal flora become pathogens?
Opportunistic infections result when normal flora move into an area of the body they don’t normally colonise.
For example, the kidneys, bladder and upper urethra usually have a sterile environment. Regular emptying of the bladder prevents bacteria from moving from the lower urethra up to the bladder or kidneys. However, contamination of the urethra from the bowel can facilitate E. coli moving up into the bladder resulting in a urinary tract infection (UTI). The urethra in females is quite a bit shorter than that of males and much closer to the anus so we see more UTIs in females than males.
For example, the kidneys, bladder and upper urethra usually have a sterile environment. Regular emptying of the bladder prevents bacteria from moving from the lower urethra up to the bladder or kidneys. However, contamination of the urethra from the bowel can facilitate E. coli moving up into the bladder resulting in a urinary tract infection (UTI). The urethra in females is quite a bit shorter than that of males and much closer to the anus so we see more UTIs in females than males.
3 The differences between viruses, bacteria, fungi, moulds, protozoa and other parasites
There are two main categories of microbes:
- Acellular microbes - viruses and prions;
- Cellular microbes – bacteria, fungi, protozoa
Acellular microbes – Viruses & prions
Viruses are acellular. That is, they do not have their own cellular structure, instead relying on the host cell’s machinery to produce new virus known as virions.
Viruses consist of either double or single stranded DNA or RNA, but not both, and it is the presence of DNA or RNA that designates the particular strain of a virus.
Each virus has a distinctive shape and structure; some will have an extra layer of covering named an envelope into which there are incorporated ‘spikes’ that help the virus particle attach to a new host cell
Viruses consist of either double or single stranded DNA or RNA, but not both, and it is the presence of DNA or RNA that designates the particular strain of a virus.
Each virus has a distinctive shape and structure; some will have an extra layer of covering named an envelope into which there are incorporated ‘spikes’ that help the virus particle attach to a new host cell
Viral replication
The viral DNA inserts into the host cell DNA causing the cell’s organelles to reproduce new virus particles and package them.
These new particles are then released to infect other cells.
Those viruses that have RNA at their core, like the Human Immunodeficiency Virus (HIV) carry the code to make an enzyme named reverse transcriptase. This enzyme enables the RNA to be transcribed into viral DNA and another enzyme, intergrase, then allows this to be inserted into the host DNA. Viral enzymes can be drug targets to prevent viral infection.
These new particles are then released to infect other cells.
Those viruses that have RNA at their core, like the Human Immunodeficiency Virus (HIV) carry the code to make an enzyme named reverse transcriptase. This enzyme enables the RNA to be transcribed into viral DNA and another enzyme, intergrase, then allows this to be inserted into the host DNA. Viral enzymes can be drug targets to prevent viral infection.
Prions
Prions are pieces of protein implicated in neuro-degenerative diseases such as Creutzfeld-Jacob Disease and Mad Cow disease. The infection may occur many years before symptoms appear.
Cellular microbes – Bacteria, protozoa, fungi
One of the important differences between bacteria and other cellular microbes is the cell structure.
Cell structures are classified as either:
Bacteria are prokaryotes whereas the moulds, fungi, algae and protozoa are eukaryotes which entails a more complicated cell structure with separate organelles within the cell. Animal cells are also eukaryotes. This is useful information because these two words tell us a lot about a cell structure and when looking at drug databases, drug descriptions will often refer to a drug being either being effective against prokaryotes or eukaryotes or both. A drug that is effective against a eukaryotic structure is more likely to have adverse effects against our body cells.
Cell structures are classified as either:
- prokaryotic, or
- eukaryotic.
Bacteria are prokaryotes whereas the moulds, fungi, algae and protozoa are eukaryotes which entails a more complicated cell structure with separate organelles within the cell. Animal cells are also eukaryotes. This is useful information because these two words tell us a lot about a cell structure and when looking at drug databases, drug descriptions will often refer to a drug being either being effective against prokaryotes or eukaryotes or both. A drug that is effective against a eukaryotic structure is more likely to have adverse effects against our body cells.
Prokaryotes: Bacteria
Bacteria have relatively simple structures with a cell membrane and outer cell wall. The cell wall provides the shape for the cell structure.
The most common bacterial shapes are spherical and rod-shaped. Spherical (round) bacteria are called coccus (plural: cocci) while rod-shaped bacteria are known as a bacillus (plural: bacilli). They can exist as single cells or in chains. Bacterial cells reproduce every 6 to 8 hours allowing a colony to develop very quickly.
Bacteria that cause disease in humans grow well in environments that match our body temperature.
Other factors that affect bacterial growth in the body include nutrient and oxygen supplies. With respect to oxygen, some bacteria known as anaerobes, do not reproduce in the presence of oxygen. Those that die in the presence of oxygen are termed obligate anaerobes. Conversely, the obligate aerobes have an absolute requirement for oxygen for cellular function. Mycobacterium tuberculosis, the bacteria that causes Tuberculosis (TB) is an obligate aerobe and so can colonise the lungs. In contrast, Clostridium perfringens is sensitive to oxygen levels so it thrives in oxygen-free (anaerobic) environments and is the cause of gas gangrene in deep wounds.
The most common bacterial shapes are spherical and rod-shaped. Spherical (round) bacteria are called coccus (plural: cocci) while rod-shaped bacteria are known as a bacillus (plural: bacilli). They can exist as single cells or in chains. Bacterial cells reproduce every 6 to 8 hours allowing a colony to develop very quickly.
Bacteria that cause disease in humans grow well in environments that match our body temperature.
Other factors that affect bacterial growth in the body include nutrient and oxygen supplies. With respect to oxygen, some bacteria known as anaerobes, do not reproduce in the presence of oxygen. Those that die in the presence of oxygen are termed obligate anaerobes. Conversely, the obligate aerobes have an absolute requirement for oxygen for cellular function. Mycobacterium tuberculosis, the bacteria that causes Tuberculosis (TB) is an obligate aerobe and so can colonise the lungs. In contrast, Clostridium perfringens is sensitive to oxygen levels so it thrives in oxygen-free (anaerobic) environments and is the cause of gas gangrene in deep wounds.
Eukaryotes: Fungi and parasites (worms and amoeba)
Fungi
Fungi are classified as either yeasts or moulds. Yeasts are single celled while moulds are filamentous, that is they have long filaments (called hyphae) that can form a dense mat. The fungal structure includes both a cell wall and a cell membrane. They are much larger than bacteria. Many fungal species have proven economically important such as the yeasts used to produce bread or beer. The mould species Penicillium gave us the antibiotic penicillin.
‘Mycosis’ is the term used to describe a fungal infection. Most fungal infections, such as tinea, are superficial or cutaneous. Ringworm and athlete’s foot (Tinea pedis) are both forms of tinea. The common fungi genera responsible are Microsporum, Trichphyton and Epidermophyton that use the keratin in dead skin cells as nutrients. Transmission is via person-to person contact or infection from shed skin cells or nails.
Systemic (within the body systems) fungal infections occur in people who are immune-compromised and the risk for morbidity is then high. Those at risk include the aged, people with leukaemia or an immune disorder and people prescribed immune-suppressive drugs such as chemotherapy or organ transplant patients.
‘Mycosis’ is the term used to describe a fungal infection. Most fungal infections, such as tinea, are superficial or cutaneous. Ringworm and athlete’s foot (Tinea pedis) are both forms of tinea. The common fungi genera responsible are Microsporum, Trichphyton and Epidermophyton that use the keratin in dead skin cells as nutrients. Transmission is via person-to person contact or infection from shed skin cells or nails.
Systemic (within the body systems) fungal infections occur in people who are immune-compromised and the risk for morbidity is then high. Those at risk include the aged, people with leukaemia or an immune disorder and people prescribed immune-suppressive drugs such as chemotherapy or organ transplant patients.
Protozoa
Giardia lamblia – a flagellate protozoan parasite responsible for causing the disease giardiasis; a diarrheal disease that results by ingestion of contaminated water. It is transferred through faecal contamination. Centres for Disease Control and Prevention Public Health Images Library http://phil.cdc.gov/phil/ (CDC PHIL ID #8698) Content provider CDC Dr. Janice Haney Carr (creation date N.D.)
Parasitism is when an organism benefits from a relationship with a host, at the expense of the host, either damaging it or killing it. Protozoans and worms that colonise the human tissue and gut are true parasites.
Protozoa are single celled organisms that may take in food by surrounding the particle with the cell membrane so that it forms a vacuole within itself (e.g. amoeba) or by ingesting it through a mouth into a digestive tract (e.g. paramecia). They are eukaryotes.
Examples of disease caused by protozoa are amoebic dysentery caused by Entamoeba histolytica, malaria caused by Plasmodium spp., vaginitis caused by Trichomonas vaginalis and giardiasis caused by Giardia spp. Infection occurs either through ingestion or, for example, in malaria where the protozoa is delivered from a mosquito through a blood sucking bite.
Protozoa are single celled organisms that may take in food by surrounding the particle with the cell membrane so that it forms a vacuole within itself (e.g. amoeba) or by ingesting it through a mouth into a digestive tract (e.g. paramecia). They are eukaryotes.
Examples of disease caused by protozoa are amoebic dysentery caused by Entamoeba histolytica, malaria caused by Plasmodium spp., vaginitis caused by Trichomonas vaginalis and giardiasis caused by Giardia spp. Infection occurs either through ingestion or, for example, in malaria where the protozoa is delivered from a mosquito through a blood sucking bite.
Worms
Another group of parasites are the worms, also termed helminths.
These microbes have three life-cycle stages: eggs, larvae and adults.
The definitive host is the species where the adult or mature worm will form whereas the cysts or larvae will be found in an intermediate host.
Humans become infected by ingestion of contaminated food or water and then shed eggs in their faeces.
Roundworms, Ascaris lumbricoides, hookworms such as Necator americanus, and tapeworms such as Echinococcus granulosis are examples of where humans become the host through ingesting the eggs of the worms. Strongyloides stercoralis is an example of a worm that infects by larvae penetrating the skin. Humans are the definitive host for this worm and they infect the intestine and other tissues. These examples are all found in Australia.
These microbes have three life-cycle stages: eggs, larvae and adults.
The definitive host is the species where the adult or mature worm will form whereas the cysts or larvae will be found in an intermediate host.
Humans become infected by ingestion of contaminated food or water and then shed eggs in their faeces.
Roundworms, Ascaris lumbricoides, hookworms such as Necator americanus, and tapeworms such as Echinococcus granulosis are examples of where humans become the host through ingesting the eggs of the worms. Strongyloides stercoralis is an example of a worm that infects by larvae penetrating the skin. Humans are the definitive host for this worm and they infect the intestine and other tissues. These examples are all found in Australia.
4 The infection cycle
The infection cycle is made up of six elements which link together to create a chain of infection.
Reservoirs of infection are the sources of microbes that cause infectious disease.
There are many different reservoirs of infection and they can be either living hosts, non-living objects (e.g. soil, water) or materials (fomites). The most important reservoir of human infections is other humans. Transmission of pathogens from human to human can occur in many different ways including via airborne droplets (usually from coughs or sneezes), via contaminated food/water and via skin-skin contact or mucous membrane-to-mucous membrane contact. Infection control practices are designed to remove or interrupt links in the infection cycle, thereby preventing transmission of infection. In the healthcare setting, hand washing or hand hygiene is widely recognised as the single-most effective means of reducing the spread of infections.
Reservoirs of infection are the sources of microbes that cause infectious disease.
There are many different reservoirs of infection and they can be either living hosts, non-living objects (e.g. soil, water) or materials (fomites). The most important reservoir of human infections is other humans. Transmission of pathogens from human to human can occur in many different ways including via airborne droplets (usually from coughs or sneezes), via contaminated food/water and via skin-skin contact or mucous membrane-to-mucous membrane contact. Infection control practices are designed to remove or interrupt links in the infection cycle, thereby preventing transmission of infection. In the healthcare setting, hand washing or hand hygiene is widely recognised as the single-most effective means of reducing the spread of infections.
5 Antimicrobial agents and controlling microbial growth
Distinguishing Microbes
Epidemiology is the study of the occurrence, spread and control of disease.
An understanding of which type of microbe that is causing an infection/disease and how it is spread helps determine appropriate treatments and the necessary infection control practices to prevent transfer of the infection to other people. For example, bacterial growth will not be changed by exposure to an antiviral drug and, conversely, an antibacterial drug will have no effect on virus production.
Illness, changes in diet and the ingestion of antibiotics can disrupt the microbiome. The body’s immune system is less able to combat microbial infections when it is busy responding to other pathogens or trauma. Immunosuppression refers to a reduction in the activation or efficiency of the immune system and it increases our susceptibility to microbes. For example, a person with chicken pox virus (Varicella zoster) active in their system is more susceptible to secondary infections such as bacterial meningitis (inflammation of the meninges of the central nervous system). In severely immunosuppressed patients, such as those undergoing chemotherapy, some microorganisms which would normally be harmless can cause serious or even fatal infections. The body’s capacity for defence against microbial disease is also related to age; immaturity of body systems in the young and aging of body systems in the elderly is reflected in increased susceptibility to infectious diseases.
An understanding of which type of microbe that is causing an infection/disease and how it is spread helps determine appropriate treatments and the necessary infection control practices to prevent transfer of the infection to other people. For example, bacterial growth will not be changed by exposure to an antiviral drug and, conversely, an antibacterial drug will have no effect on virus production.
Illness, changes in diet and the ingestion of antibiotics can disrupt the microbiome. The body’s immune system is less able to combat microbial infections when it is busy responding to other pathogens or trauma. Immunosuppression refers to a reduction in the activation or efficiency of the immune system and it increases our susceptibility to microbes. For example, a person with chicken pox virus (Varicella zoster) active in their system is more susceptible to secondary infections such as bacterial meningitis (inflammation of the meninges of the central nervous system). In severely immunosuppressed patients, such as those undergoing chemotherapy, some microorganisms which would normally be harmless can cause serious or even fatal infections. The body’s capacity for defence against microbial disease is also related to age; immaturity of body systems in the young and aging of body systems in the elderly is reflected in increased susceptibility to infectious diseases.
Controlling the growth of microbes
Sterilisation is the killing or removal of ALL microbes present whereas disinfection is killing of MANY (but not all) microbes present. Control of microbial growth involves the use of physical or chemical methods. The physical methods used for sterilisation and disinfection include:
Chemicals commonly used to control microbial growth include alcohols, chlorine, heavy metals, soaps and detergents. Antiseptics are chemicals used for disinfection of living tissue whereas disinfectants are chemical used for disinfection of inanimate objects.
- Dry heat (e.g. burning) or moist heat (e.g. boiling, pasteurisation)
- Heat and pressure – e.g. autoclaves
- Desiccation (removal of water)
- Radiation
- Filtration
Chemicals commonly used to control microbial growth include alcohols, chlorine, heavy metals, soaps and detergents. Antiseptics are chemicals used for disinfection of living tissue whereas disinfectants are chemical used for disinfection of inanimate objects.
Antimicrobial drugs
Drugs used to treat microbial infections include antibiotics for treatment of bacterial infections, anti-fungals for treatment of fungal infections, anti-helminthics for treatment of worms and anti-virals for treatment of viral infections. Treatment of any infection/infectious disease is dependent on detection and identification of the causative pathogen in clinical specimens.
The Gram stain is the initial step in identification of bacteria.
This staining technique differentiates bacteria into two groups: Gram-positive or Gram-negative depending on the thickness of the peptidoglycan layer in the bacterial cell wall. Antibiotics for bacterial infections include in their descriptions whether they are effective for Gram-positive or Gram-negative bacteria. If the gram stain is not absorbed it may be due to the presence of a waxy layer, for example, those belonging to the Mycobacterium genus, which includes the bacteria that causes tuberculosis (TB). In this circumstance an acid-fast stain is used.
This staining technique differentiates bacteria into two groups: Gram-positive or Gram-negative depending on the thickness of the peptidoglycan layer in the bacterial cell wall. Antibiotics for bacterial infections include in their descriptions whether they are effective for Gram-positive or Gram-negative bacteria. If the gram stain is not absorbed it may be due to the presence of a waxy layer, for example, those belonging to the Mycobacterium genus, which includes the bacteria that causes tuberculosis (TB). In this circumstance an acid-fast stain is used.
Antibacterial drugs
Antibiotic sensitivity test. Note the zones of inhibited microbial growth around antibiotic impregnated paper disks. The agar was contaminated with E.coli and Proteus sp. Centres for Disease Control and Prevention Public Health Images Library (CDC PHIL ID#3902 http://phil.cdc.gov/phil/) Content provider CDC, creation date 1971.
Different strains of microbes have different levels of susceptibility to different antibiotics so once the pathogen responsible for the infection has been identified, antibiotic susceptibility testing is used to determine the most appropriate antibiotic treatment for that particular patient.
Antibacterial drugs affect bacterial cell structures such as the cell wall, the bacterial ribosomes, or cellular metabolic processes.
These aspects of bacterial biology are different from human cells which helps limit the side effects of many of these drugs.
An example of a metabolic function that antibacterial drugs may target is the production of folic acid, a critical component needed for the building of DNA and RNA. By inhibiting production of folic acid in bacteria, or the maintenance and construction of cell walls, cellular reproduction is reduced or stopped.
Broad-spectrum antibacterial drugs, that is those effective against both gram-positive and gram-negative bacteria, damage many different types of bacteria including those of the normal flora.
Where possible drug choice should be targeted to the specific infecting bacteria type.
Antibacterial drugs affect bacterial cell structures such as the cell wall, the bacterial ribosomes, or cellular metabolic processes.
These aspects of bacterial biology are different from human cells which helps limit the side effects of many of these drugs.
An example of a metabolic function that antibacterial drugs may target is the production of folic acid, a critical component needed for the building of DNA and RNA. By inhibiting production of folic acid in bacteria, or the maintenance and construction of cell walls, cellular reproduction is reduced or stopped.
Broad-spectrum antibacterial drugs, that is those effective against both gram-positive and gram-negative bacteria, damage many different types of bacteria including those of the normal flora.
Where possible drug choice should be targeted to the specific infecting bacteria type.
Antiviral drugs
Viruses require a host cell to replicate. This makes it difficult to develop drugs that kill or inhibit a virus without also harming the host cell and consequently we have relatively few anti-viral drug choices.
Anti-viral drug targets include the cell receptors for viral attachment or the process for the creating or releasing of new virus particles (virions) by the infected cell.
An example of an anti-viral drug is interferon, a synthetically made version of human interferon. Interferon is released by infected cells and acts to alert cellular mechanisms to limit virus incorporation into unaffected cells. The drug form of interferon is used to prevent cellular infection.
Anti-viral drug targets include the cell receptors for viral attachment or the process for the creating or releasing of new virus particles (virions) by the infected cell.
An example of an anti-viral drug is interferon, a synthetically made version of human interferon. Interferon is released by infected cells and acts to alert cellular mechanisms to limit virus incorporation into unaffected cells. The drug form of interferon is used to prevent cellular infection.
Vaccines and vaccinations
Vaccination is the administration of a vaccine to produce immunity from particular disease. Vaccines act to stimulate the body’s immune system with a weakened (attenuated) or killed form of the causative microorganism. Examples of diseases for which vaccines are available in Australia include:
Some viruses such as the influenza virus undergo gradual mutations which result in alterations to the appearance of the outer viral surface. This is the reason that new flu vaccines need to be created each flu season.
- Polio
- Rotavirus
- Pertussis
- Tetanus
- Influenza
- Hepatitis A & B
Some viruses such as the influenza virus undergo gradual mutations which result in alterations to the appearance of the outer viral surface. This is the reason that new flu vaccines need to be created each flu season.
Microbial resistance
Antibiotic resistance has been an ongoing issue since shortly after the widespread introduction of the first antibiotic, penicillin, in 1944.
Bacterial cells contain both chromosomal DNA and a circular piece of DNA termed a plasmid. Plasmids can be exchanged between bacterial cells. Those cells that survive longest can pass the genes that enabled that longevity to their neighbours by exchanging plasmids. In this way a bacteria that survives a particular antibiotic drug can pass a resistance gene to another bacteria.
The number of microorganisms with resistance to multiple antibiotics has risen dramatically in recent years and now poses a serious worldwide threat to public health. Leading experts are warning that without urgent action, the world will be headed for a post-antibiotic era similar to the early 19th century where common infections may be untreatable.
Bacterial cells contain both chromosomal DNA and a circular piece of DNA termed a plasmid. Plasmids can be exchanged between bacterial cells. Those cells that survive longest can pass the genes that enabled that longevity to their neighbours by exchanging plasmids. In this way a bacteria that survives a particular antibiotic drug can pass a resistance gene to another bacteria.
The number of microorganisms with resistance to multiple antibiotics has risen dramatically in recent years and now poses a serious worldwide threat to public health. Leading experts are warning that without urgent action, the world will be headed for a post-antibiotic era similar to the early 19th century where common infections may be untreatable.