Introduction to the Archaea

The Domain Archaea wasn't recognized as a major domain of life until quite recently. Until the ۲۰th century, most biologists considered all living things to be classifiable as either a plant or an animal. But in the 1950s and 1960s, most biologists came to the realization that this system failed to accomodate the fungi, protists, and bacteria. By the 1970s, a system of Five Kingdoms had come to be accepted as the model by which all living things could be classified. At a more fundamental level, a distinction was made between the prokaryotic bacteria and the four eukaryotic kingdoms (plants, animals, fungi, & protists). The distinction recognizes the common traits that eukaryotic organisms share, such as nuclei, cytoskeletons, and internal membranes.

CORYNEBACTERIA

The coryneform group of Gram-positive bacteria includes several genera of non-spore-forming rods which are ubiquitous in nature. We will consider only two of these genera in our discussion of clinically significant microorganisms: Actinomyces and Corynebacterium. The first genus, Actinomyces, will be presented later when we focus on anaerobic Gram-positive bacteria.

The second genus, Corynebacterium, is comprised of facultatively anaerobic bacteria which are normally saprophitic and harmless to humans. An exception is the bacterium C. diphtheriae which produces the toxin that causes diphtheria, a disease of the upper respiratory system in humans. Under the microscope (best viewed using Loeffler's methylene blue dye), C. diphtheria can be seen forming colonies which clump up or stick together. This is a characteristic associated with many higher forms of bacteria. Although other species of Corynebacterium can inhabit the mucous membrane, C.diphtheria is unique in its exotoxin formation. Treatment for the disease usually consists of administration of an antitoxin with penicillin.

LABORATORY INDICATIONS:

• Catalase +
• Nitrate +
• Glucose fermentation
• Non-motile

ERYSIPELOTHRIX

E. rhusiopathiae, the only species of this genus, is better known as a veterinary pathogen than as a human pathogen. When cultured on blood agar or some other nutrient medium, Erysipelothrix forms notably large colonies. This ubiquitous microbe has been found in many farm animals such as pigs, horses, and turkeys. Occasionaly, though, it can infect a human host and cause an inflammatory skin disease, Erysipeloid. Treatment usually consists of penicillin G, ampicillin, or cephalothin. Most clinical strains have been found to be resistant to the super-antibiotic, vancomycin.

LABORATORY INDICATIONS:

• Catalase -
• Non-motile
• TSI : H₂S +

LACTOBACILLUS

Most species of this non-spore-forming bacterium ferment glucose into lactose, hence the name Lactobacillus. The most common application of Lactobacillus is industrial, specifically for dairy production. This genus also contains several bacteria that make up part of the natural flora of the human vagina. Because of their ability to derive lactic acid from glucose, these bacteria create an acidic environment which inhibits growth of many bacterial species which can lead to urogenital infections. Lactobacillus is generally harmless to humans, rarely inciting harmful infections or diseases. Treatment of this vancomycin-resistant microbe usually consists of high doses of penicillin in combination with gentamicin.

LABORATORY INDICATIONS:

• Catalase -
• Lactic acid production from glucose
• Growth on tomato juice agar

BACILLUS

Bacillus represents a genus of Gram-positive bacteria which are ubiquitous in nature (soil, water, and airborne dust). Some species are natural flora in the human intestines. When grown on blood agar, Bacillus produces large, spreading, gray-white colonies with irregular margins. A unique characteristic of this bacterium is its ability to produce endospores when environmental conditions are stressful. The only other known spore-producing bacterium is Clostridium. Although most species of Bacillus are harmless saprophytes, two species are considered medically significant: B.anthracis and B. cereus.

LISTERIA

Listeria is a Gram-positive rod which is not capable of forming endospores. Although several species of this bacterium exist, our discussion will focus only on the two species of human pathogenic significance: L. monocytogenes and L. ivanovii. In particular, L. monocytogenes has been implicated in several food poisoning epidemics. This normal inhabitant of the gastrointestinal tract and of animal feces led to a 1986 outbreak in Massachusetts hospital patients. Those infected suffered from vomiting, nausea, and diarrhea. Apparently, the hospital patients contracted the microbe from the infected hospital food and were at high risk of infection. Those at high risk include newborns, pregnant women and their fetuses, the elderly, and persons lacking a healthy immune system. The bacterium usually causes septicema and meningitis in patients with supressed immune function. It also causes listeriosis which is an inflammation of the brain. Antibiotics are recommended for treatment of infection because most strains of Listeria are sensitive to ampicillin and gentamicin.

LABORATORY INDICATIONS:

• Catalase +
• Motile at room temperature
• Growth at 4 degrees Celsius
• Bile esculin hydrolysis
• Beta-hemolysis

STREPTOCOCCUS

The Streptococcus genus consists of Gram-positive, aerobic bacteria which appear as chains under microscopic observation. The organisms in this genus are characterized by a coccus appearance, a thick cell wall, and aerobic action on glucose. Four different classification systems exist for this important microorganism:

CLINICAL

• Pyogenic Streptococci
• Oral Streptococci
• Enteric Streptococci,

STAPHYLOCOCCUS

Clinically, the most important genus of the Micrococcaceae family is Staphylococcus. The Staphylococcus genus is classified into two major groups: aureus and non-aureus. S. aureus is a leading cause of soft tissue infections, as well as toxic shock syndrome (TSS) and scalded skin syndrome. It can be distinguished from other species of Staph by a positive result in a coagulase test(all other species are negative).

The pathogenic effects of Staph are mainly asssociated with the toxins it produces. Most of these toxins are produced in the stationary phase of the bacterial growth curve. In fact, it is not uncommon for an infected site to contain no viable Staph cells. The S. aureus enterotoxin causes quick onset food poisoning which can lead to cramps and severe vomiting. Infection can be traced to contaminated meats which have not been fully cooked. These microbes also secrete leukocidin, a toxin which destroys white blood cells and leads to the formation of pus and acne. Particularly, S. aureus has been found to be the causative agent in such ailments as pneumonia, meningitis, boils, arthritis, and osteomyelitis (chronic bone infection). Most S. aureus are penicillin resistant, but vancomycin and nafcillin are known to be effective against most strains.

MICROCOCCUS

Microcoocus is a Gram-positive, aerobic bacterium which is a member of the Micrococcaceae family. Micrococcus cells can be observed under the microscope as spherical cells forming pairs or clusters. If cultured in broth or on nutrient agar, the colonies may be red or yellow when observed unstained. Although these bacteria are a common human skin contaminant, they are relatively harmless to humans because they maintain a saprophytic lifestyle. They can also be found in freshwater environments or in soil. Three common species of Micrococcus are M. luteus, M. roseus, and M. varians.

GRAM-POSITIVE COCCI

The Gram-positive cocci are grouped together based on their Gram-stain reaction, thick cell wall composition, and spherical shape. Most of the organisms in these groups are members of the Micrococcaceae family All of the organisms in these groups are non-endospore forming chemosynthetic heterotrophs. We will discuss only the clinically relevent bacteria from Micrococcus and Staphylococcus of the Micrococcaceae family. Streptococcus and Enterococcus(formerly a species of Streptococcus) are discussed as well because of the many diseases they inflict on humans. The chart below shows the paths to identification of the genera discussed.

The Gram-Positive Cell

As previously mentioned, Gram-positive bacteria are characterized by their blue-violet color reaction in the Gram-staining procedure . The blue-violet color reaction is caused by crystal-violet, the primary Gram-stain dye, complexing with the iodine mordant. When the decolorizer is applied, a slow dehydration of the crystal-violet/iodine complex is observed due to the closing of pores running through the cell wall. Because the crystal-violet is still present in the cell, the counter stain is not incorporated, thus maintaining the cell's blue-violet color. If you recall, most cell walls contain peptidoglycan, a molecule made of amino acids and sugar. A distinguishing factor among Gram-positive bacteria is that roughly 90% of their cell wall is comprised of peptidoglycan and a Gram-positve bacteria can have more than 20 layers of peptidoglycan stacked together to form the cell wall. That's pretty thick! Examples of common Gram-positive cells are Staphylococcus aureus and Streptococcus cremoris, a bacterium used in dairy production.

FUSOBACTERIUM

Fusobacterium organisms are anaerobic, Gram-negative bacilli that bare a strong resemblance to certain Bacteroides species. Under the microscope, they are normally spindle-shaped cells with sharp ends. Both bacteria are normal gut inhabitants but are capable of causing serious infection. Fusobacterium species, the most common of which is F. nucleatum, are associated with pleuropulminary infections and disease. They are also capable of causing infection in the oral cavity (the mouth). F. nucleatum has been cited as one of the causes of gingivitis. Identification of these bacteria

 BACTEROIDES

The Bacteroides genus of anaerobic bacteria comprise the majority of microorganisms that inhabit the digestive tract. 50% of most fecal matter is actually Bacteroides fragilis cells! Bacteroides organisms are the anaerobic counterpart of E. coli except they are somewhat smaller. They grow well on blood agar, and under the microscope, they may contain large vacuoles that are similar in appearance to spores. Members of Bacteroides species are not spore-forming, but they do produce a very large capsule. Their pathogenicity is limited, however, because they possess no endotoxin in their cell membrane. Infection only occurs after severe trauma to the abdominal region. Infection could lead to abscess formation and possibly fever. Antibiotic treatment usually consists of metronidazole or clindamycin.

GRAM-POSITIVE BACILLI
(NON-SPORE-FORMING)

ACTINOMYCES

Actinomycetes are fungus-like bacteria that form filamentous branches. These Gram-positive obligate anaerobes are known to reside in the mouth and in the intestinal tract. Pathogenic proliferation of the organisms, which is usually a result of trauma to the region of infection, can lead to actinomycosis. The patient will form abscesses and swelling at the site of infection. A diagnosis can be made upon microscopic examination of pus. The fluid will have a granular texture which is caused by sulfur granules. These sulfur granuules are actually composed of the bacterium and its waste. The species of Actinomyces which is most commonly associated with actinomycosis is A. israelii, but several other bacteria in this genus are capable of causing the disease as well. Actinomycosis can often be treated with penicillin.

CLOSTRIDIUM

Members of genus Clostridium are Gram-positive, spore-forming rods that are anaerobic. These motile bacteria are ubiquitous in nature and are especially fond of soil. Under the microscope, they appear as long drumsticks with a bulge located at their terminal ends. A Gram-stain is a good method for identifying Clostridium because the cell incorporates the dye while the spore remains unstained. Clostridium shows optimimum growth when plated on blood agar at human body temperatures. When the environment becomes stressed, however, the bacteria produce spores that tolerate the extreme conditions that the active bacteria cannot. In their active form, these bacteria secrete powerful exotoxins that are responsible for such diseases as tetanus, botulism, and gas gangrene. The four clinically important species of Clostridium will be discussed here: C. tetani, C. difficile, C. perfringens, and C. botulinum.

Definition

An anaerobic infection is an infection caused by bacteria (called anaerobes) which cannot grow in the presence of oxygen. Anaerobic bacteria can infect deep wounds, deep tissues, and internal organs where there is little oxygen. These infections are characterized by abscess formation, foul-smelling pus, and tissue destruction.

Tuberculosis (TB)  

Tuberculosis (often called TB) is an infectious disease that usually attacks the lungs, but can attack almost any part of the body. Tuberculosis is spread from person to person through the air.

When people with TB in their lungs or throat cough, laugh, sneeze, sing, or even talk, the germs that cause TB may be spread into the air. If another person breathes in these germs there is a chance that they will become infected with tuberculosis.  Repeated contact is usually required for infection.

Gram Negative ( Gram- ) Bacteria

What Makes Some Bacterial Cells Stain Gram-negative?

Most bacteria have one of these two types of cell walls. The differential Gram stain uses two dyes to distinguish between bacteria based on cell wall structure.

Gram Positive ( Gram+ ) Bacteria

What Makes Some Bacterial Cells Stain Gram-positive?

Most bacteria have one of these two types of cell walls.The differential Gram stain uses two dyes to distinguish between bacteria based on cell wall structure.

Where They Live

Our Challenge: Name at least three places microbes live. Can you think of any places that microbes might not live?

Microbiologists have found microbes living just about everywhere: in the soil, water and air; in animals, plants, rocks and even us!

Virus Or Bacterium?

Our Challenge: Determine the ways that viruses and bacteria are different.

Because bacteria and viruses cause many of the diseases we're familiar with, people often confuse these two microbes. But viruses are as different from bacteria as goldfish are from giraffes.

For one thing, they differ greatly in size. The biggest viruses are only as large as the tiniest bacteria.

Another difference is their structure. Bacteria are complex compared to viruses.

What is a Microbe?

Microbes are single-cell organisms so tiny that millions can fit into the eye of a needle.

They are the oldest form of life on earth. Microbe fossils date back more than 3.5 billion years to a time when the Earth was covered with oceans that regularly reached the boiling point, hundreds of millions of years before dinosaurs roamed the earth.

Without microbes, we couldn’t eat or breathe.

 Many of us know bacteria only as “germs,” invisible creatures that can invade our bodies and make us sick.

Some microbes live on our skin and protect us from many harmful agents. The drier areas, like the back, have few microbes; moist areas, such as under the arm, have many more.

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, break down some garbage, and even maintain our atmosphere.

Archaea and Other Extremists

Types of Archaea There are three main types of archaea: the crenarchaeota (kren-are-key-oh-ta), which are characterized by their ability to tolerate extremes in temperature and acidity. The euryarchaeota (you-ree-are-key-oh-ta), which include methane-producers and salt-lovers; and the korarchaeota (core-are-key-oh-ta), a catch-all group for archaeans about which very little is known. Among these three main types of archaea are some subtypes, which include: Methanogens (meth-an-oh-jins) — archaeans that produce methane gas as a waste product of their "digestion," or process of making energy. Halophiles (hal-oh-files) — those archaeans that live in salty environments. Thermophiles (ther-mo-files) — the archaeans that live at extremely hot temperatures. Psychrophiles (sigh-crow-files) — those that live at unusually cold temperatures