Phylum Spirochaetes

Definition and Classification

Phylum Spirochaetes includes gram-negative, chemoheterotrophic bacteria.

It is classified into one class (Spirochaetes), one order (Spirochaetales), and three families (Spirochaetaceae, Serpulinaceae, Leptospiraceae).

There are currently 13 genera within this phylum.

Metabolism

Spirochaetes can be anaerobic, facultatively anaerobic, or aerobic.

They utilize various carbon and energy sources, including carbohydrates, amino acids, long-chain fatty acids, and long-chain fatty alcohols.

Morphological Characteristics

They are slender, long bacteria (ranging from 0.1 to 3.0 μm by 5 to 250 μm) with a flexible, helical shape.

The central protoplasmic cylinder contains cytoplasm and the nucleoid, surrounded by a plasma membrane and a gram-negative cell wall.

Two or more than a hundred flagella (axial fibrils or periplasmic flagella) extend from both ends of the cylinder, often overlapping in the middle.

Axial Filament and Outer Sheath

The axial filament, composed of periplasmic flagella, is located inside a flexible outer sheath made of lipid, protein, and carbohydrate.

The precise function of the outer sheath is unknown, but it is crucial for the survival of spirochaetes; they die if the sheath is damaged or removed.

The outer sheath of Treponema pallidum (the syphilis spirochaete) has few surface proteins, allowing it to evade host antibodies.

Unique Motility

Spirochaetes have a distinct mode of movement adapted for viscous environments.

The rotation of axial fibrils causes the outer sheath to rotate in the opposite direction, enabling a corkscrew-like movement through liquids.

This motility also allows for flexing and crawling on solid surfaces.

Ecological Diversity

Spirochaetes are ecologically diverse, inhabiting various environments from mud to the human mouth.

• Genera such as Spirochaeta: Free-living and typically grow in anaerobic muds.

Characteristics of Spirochete Genera

• Cristispira sp.: Marine spirochete found in mollusks (e.g., clams). Large, helical shape. Likely involved in mollusk digestion.
• Leptospira interrogans: Causes leptospirosis (zoonotic disease). Transmitted via contaminated water/soil. Thin, flexible spiral shape.

The Spirochetes

Spirochetes often form symbiotic relationships with other organisms. For example, spirochetes help move the flagellate Myxotricha paradoxa.

Symbiotic Associations

Pathogenic Spirochaetes

Several species are human pathogens, including Treponema pallidum (causative agent of syphilis) and the spirochetes responsible for Lyme disease.

Syphilis

Syphilis is a sexually transmitted disease caused by the bacterium Treponema pallidum subsp. pallidum (T. pallidum).

It enters the body through mucous membranes or minor skin abrasions.

The disease is not highly contagious, with only about a 1 in 10 chance of transmission from a single exposure to an infected partner.

Congenital syphilis occurs when the disease is transmitted from mother to fetus.

Stages of Syphilis

• Primary Stage: After an incubation period of 10 days to 3 weeks, a painless ulcer (chancre) forms at the infection site. It may heal on its own, but T. pallidum can enter the bloodstream and spread.
• Secondary Stage: A variable skin rash appears within 2 to 10 weeks of the primary lesion, along with symptoms like hair loss, malaise, and fever. Both the rash and chancre are infectious.
• Latent Stage: The disease becomes dormant and is typically not infectious, except for potential transmission from mother to fetus.
• Tertiary Stage: Occurs in 40% of untreated individuals, marked by degenerative lesions (gummas) in skin, bone, and the nervous system. Central nervous system involvement can lead to cognitive deficits, blindness, or insanity.

Lyme Disease

Lyme disease, also known as Lyme borreliosis, is caused by Borrelia spirochetes, primarily Borrelia burgdorferi, B. garinii, and B. afzelii.

Stages of Lyme Disease

• Stage 1 (Localized): Occurs 1-2 weeks after a tick bite. Symptoms include an expanding ring-shaped rash called erythema migrans and flu-like symptoms (fatigue, headache, fever, and chills).
• Stage 2 (Disseminated): Weeks or months later, symptoms may include neurological abnormalities, heart inflammation, and bouts of arthritis in major joints like the elbows or knees.
• Stage 3 (Late): Years after infection, individuals may develop neuron demyelination, with symptoms similar to Alzheimer's disease and multiple sclerosis.

Associated with Human Disease

Genus	Species	Disease
Treponema	Pallidum ssp. Pallidum	Syphilis
	Pallidum ssp. endemicum	Bejel
	Pallidum ssp. Pertenue	Yaws
	carateum	Pinta
Borrelia	Burgdorfi	Lyme disease (Borreliosis)
	Recurrentis	Epidemic relapsing fever
	Many Species	Endemic relapsing fever
Leptospira	interrogations	Leptospirosis (Weil’s Disease)

Primary Symptoms

• Painless sores (ulcers) in the mouth, lips, or on the skin, especially around the mouth area.
• The initial lesions might heal without treatment but signal the onset of infection.

Secondary Symptoms (appear weeks to months later)

• Rashes: Small, non-itchy rashes, often on the limbs, face, or trunk.
• Wart-like growths: Small, raised lesions called condylomata lata can appear on moist skin areas like the armpits or groin.
• Swollen lymph nodes: Particularly around the sites of infection.

Tertiary Symptoms (in untreated cases over years)

• Bone and joint pain: Due to bone lesions or chronic inflammation.
• Disfigurement: Severe cases may develop deformities in the nose and bones.

YAWS

Treponema carateum: Hypopigmented skin lesions of Pinta. Depigmentation is commonly seen as a late sequel with all treponemal diseases.

Borrelian vincenti - Vincent Angina: Is a mouth commensal but may, under predisposing conditions such as malnutrition or viral infection, give rise to ulcerative gingivostomatitis or oropharyngitis.

Symptoms:

• Intense Gum Pain: Severe pain in the gums, which may intensify while eating or drinking.
• Ulceration and Necrosis: Ulcers form along the gum line, often with dead tissue and bleeding.
• Grayish Membrane on Gums: A gray or yellowish-white film can form over the ulcers, which can be peeled off to reveal bleeding tissue.
• Foul Breath: Due to bacterial overgrowth and tissue decay, there is often a strong, unpleasant odor.
• Swelling and Redness: The gums become swollen, red, and bleed easily, with tissue degeneration in advanced cases.
• Fever and Malaise: Some patients may experience fever, fatigue, and swollen lymph nodes.

Phylum Chlamydiae

Obligate intracellular parasites

Hosts: Humans, animals, and even protozoa

• Extremely limited metabolically, relying on their host cells for key metabolites since chlamydiae cannot catabolize carbohydrates or synthesize ATP.
• Nonmotile, coccoid bacteria
• Size: 0.2 to 1.5 µm

Characteristics

• Gram-negative, but cell wall differs since it lacks muramic acid and a peptidoglycan layer.
• They gram stain poorly, so Geimsa stain is used.

Biphasic Life Cycle

1. Elementary Body

• 0.2 to 0.6 µm in diameter
• Contain electron-dense nuclear material and a rigid cell wall
• Infectious; have minimal metabolic activity and cannot take in ATP or synthesize proteins. Designed exclusively for transmission and infection.

2. Reticulate Body

• 0.5 to 1.5 µm in diameter
• Have less dense nuclear material, more ribosomes than EBs, and more flexible walls
• Noninfectious; specialized for reproduction rather than infection.

Reproduction Process

1. Attachment of an elementary body (EB) to the host cell surface.
2. The host cell phagocytoses the EB, which is held in inclusion bodies where the EB reorganizes to form a reticulate body (RB).
3. About 8 to 10 hours after infection, the reticulate body undergoes binary fission and RB reproduction continues until the host cell dies. Although they undergo binary fission, Chlamydia is one of only a few bacteria that lacks the cell division protein FtsZ.
4. After 20 to 25 hours, RBs begin to differentiate into infectious EBs and continue this process until the host cell lyses and releases the chlamydiae EBs 48 to 72 hours after infection.

Survival Rate Outside Host

• Chlamydia EBs can survive short-term in moist environments like water or damp surfaces but are vulnerable to drying, heat, UV light, and extreme pH.

Species

1. Chlamydia trachomatis

• Serotypes A-C: Leading cause of infectious blindness worldwide
• Disease: Trachoma/Chlamydia conjunctivitis
• Mode of Transmission: Direct contact, clothes, insect

• Serotypes D-K: Result in genital infection, infant conjunctivitis, pneumonia
• Mode of Transmission: Sexual
• Diseases in Men: Urethritis and prostatitis
• Diseases in Women: Cervicitis, Pelvic Inflammatory Disease

An infected pregnant woman can transmit this bacterium to her infant, resulting in infant conjunctivitis and pneumonia.

• Serotypes L1-L3: Cause infection in lymph nodes (lymphogranuloma venereum).

Treatment:

Azithromycin or doxycycline.

Prevention:

• Safe sex practices
• Regular STI screening
• Sanitation in trachoma-endemic areas

Chlamydial Trachomatis: TRUE or FALSE

• 1. You can’t catch chlamydia from a toilet seat: TRUE
• 2. Chlamydia only affects females: FALSE
• 3. Oral contraception can protect against chlamydia: FALSE
• 4. You can’t get chlamydia through oral or anal sex: FALSE
• 5. Chlamydia infections can be prevented: TRUE
• 6. You can tell if you have chlamydia: FALSE
• 7. Chlamydia infections can’t go away on their own: TRUE
• 8. You can only get chlamydia once: FALSE
• 9. Getting tested for chlamydia is easy: TRUE
• 10. Chlamydia is difficult to treat: FALSE

2. Chlamydophila pneumoniae

Disease: Chlamydial pneumonia

Mode of Transmission: Primarily a human pathogen directly transmitted from human to human by droplet (respiratory) secretions.

Symptoms: Infections are generally mild, including pharyngitis, bronchitis, and sinusitis. Potentially linked to chronic diseases like asthma and atherosclerosis.

Treatment:

Azithromycin, doxycycline, or levofloxacin.

Prevention:

• Handwashing
• Avoiding close contact with infected individuals
• Wearing masks

3. Chlamydia psittaci

Disease: Psittacosis (ornithosis), a worldwide infectious disease of birds transmissible to humans.

Mode of Transmission: Handling infected birds or inhaling dried bird excreta containing viable C. psittaci.

After entering the respiratory tract, the chlamydiae are transported to the cells of the liver and spleen, where they multiply and then invade the lungs, causing inflammation, hemorrhaging, and pneumonia.

Treatment:

Antibiotics (Doxycycline or Azithromycin).

Prevention:

• Avoid exposure to bird droppings
• Practice hygiene in bird-handling environments

Phylum Bacteroidetes

Introduction to Phylum Bacteroidetes

Bacteroidetes is a diverse phylum of Gram-negative, non-spore-forming, anaerobic, rod-shaped bacteria. Well-known genera within Bacteroidetes include Bacteroides and Prevotella.

This group of bacteria is primarily found in the gut of humans and other animals, as well as in soil and marine environments.

Taxonomy Overview

Phylum: Bacteroidetes
Class: Bacteroidia
Order: Bacteroidales
Family examples: Bacteroidaceae, Prevotellaceae
Key genera: Bacteroides, Prevotella, Parabacteroides

Key Characteristics of Bacteroidetes

Gram-Positive vs. Gram-Negative Bacteria

Gram-Positive Bacteria:
Color: Purple
Reason: These bacteria have a thick cell wall made mostly of peptidoglycan. During the staining process, they retain the purple crystal violet dye strongly, so they appear purple under a microscope.

Gram-Negative Bacteria:
Color: Pink or Red
Reason: These bacteria have a thinner peptidoglycan layer and an additional outer membrane. They do not hold onto the purple dye well, so during the process, they lose the purple color but take up a pink or red dye called safranin, which is added as a counterstain.

The Gram Staining Process

• Crystal Violet Stain: Bacteria on a slide are stained with a purple dye called crystal violet, which enters all bacterial cells, making them purple initially.
• Iodine Solution: An iodine solution is applied, which binds with the crystal violet to form larger complexes inside the cell, helping the dye stick better.
• Alcohol Wash (Decolorization): The slide is rinsed with alcohol, which decolorizes the cells:
  • Gram-positive cells retain the purple color because their thick peptidoglycan cell wall traps the dye.
  • Gram-negative cells lose the purple color because their thinner cell wall allows the dye to wash out.
• Safranin Counterstain: A pink or red dye is added, staining gram-negative cells pink or red while gram-positive cells remain purple.

Ecological Role in the Human Gut

Positive Effects

• Aiding Digestion: Bacteroidetes, particularly Bacteroides species, are essential for breaking down complex carbohydrates, proteins, and fats.
• Immune System Modulation: They promote tolerance to beneficial microbes while preparing the immune system to defend against harmful pathogens.
• Preventing Pathogen Colonization: By occupying space and consuming nutrients in the gut, they help prevent harmful bacteria from establishing and growing.

Negative Effects

• Opportunistic Infections: Some Bacteroidetes, like Bacteroides fragilis, can become opportunistic pathogens if they escape the gut.
• Association with Diseases: Imbalances in Bacteroidetes are linked to diseases:
  • Obesity: Certain species may increase energy absorption from food, contributing to obesity.
  • Inflammatory Bowel Disease (IBD): Imbalances can aggravate Crohn's disease and ulcerative colitis.

Potential for Antibiotic Resistance: Some Bacteroidetes have genes that confer resistance to antibiotics, which they can potentially transfer to other bacteria in the gut.

Phylum CLOSTRIDIA

Overview of Anaerobic Bacteria

Bacteria are microscopic, single-celled organisms. There are thousands of different kinds, and they live in every conceivable environment all over the world. They live in soil, seawater, and deep within the earth’s crust. Some bacteria have been reported to live in radioactive waste.

Overview of Anaerobic Bacteria

Only a few kinds of bacteria always cause disease when present. They are called pathogens. Bacteria can be classified in several different ways. One way is based on whether they need oxygen to live and grow:

• Aerobic bacteria: Need oxygen
• Anaerobic bacteria: Have trouble living or growing when oxygen is present
• Facultative bacteria: Can live and grow with or without oxygen

General Characteristics

A group of gram-positive, anaerobic bacteria. Found in soil, intestines, and organic matter. Known for their ability to form spores and produce potent toxins.

Morphological Features

Rod-shaped, gram-positive bacteria (may lose stain with age). Form endospores resistant to heat, desiccation, and chemicals. Pleomorphic appearance in some species.

Sporulation in Clostridium

Life Cycle

C. difficile exists in two states—the vegetative (growth) form or the spore state. In the vegetative state, the bacterium is able to use nutrients to grow and divide. However, when conditions become unfavorable, C. difficile is able to enter a dormant state and form a highly resistant spore. Unfavorable conditions include deprivation of nutrients, exposure to a very acidic environment, or exposure to high temperatures. These spores are very resistant to heat, radiation, drying, chemicals, and even oxygen (for up to two years).

The spore is dormant, and a thick spore coat protects its genetic material. When conditions become favorable again, the C. difficile spore is able to return to its vegetative state. The bacteria’s ability to form spores enables its survival through the human digestive system. In addition to returning to the oxygenated environment, the bacteria re-enter the human host and transition back into the vegetative state.

Host Associated Species

• C. botulinum: Causes botulism, a serious form of food poisoning due to toxin production.
• C. tetani: Causes tetanus, leading to muscle stiffness and spasms.
• C. difficile: Can cause severe diarrhea and colitis, often in hospitalized patients after antibiotic treatment.

C. tetani

Route of Infection: Spores typically enter the body through wounds, especially deep punctures or cuts contaminated with soil or feces. The anaerobic environment of the wound allows the spores to germinate and multiply.

Types of Tetanus:

• Generalized: Affects the whole body.
• Localized: Limited to muscles near the infection site.
• Neonatal: Occurs in newborns, often due to infection of the umbilical stump.

C. botulinum

Botulism is a rare but serious illness. It is caused by a toxin that attacks the body's nerves and causes difficulty breathing, muscle paralysis, and even death.

• Foodborne Botulism: Caused by ingesting foods contaminated with preformed toxin (e.g., improperly canned or preserved foods).
• Infant Botulism: Occurs when spores are ingested, germinate, and produce toxin in the infant's intestine (often linked to honey).
• Wound Botulism: Arises when spores infect a wound and produce toxin under anaerobic conditions.

Industrial Applications

• Solvents
• Certain Pharmaceuticals

Study Material: Phylum Spirochaetes

Overview

Definition: Gram-negative, chemoheterotrophic bacteria.

Classification:

• One class: Spirochaetes
• One order: Spirochaetales
• Three families: Spirochaetaceae, Serpulinaceae, Leptospiraceae
• Includes 13 genera

Metabolic Characteristics

• Types: Anaerobic, facultatively anaerobic, or aerobic.
• Energy Sources: Carbohydrates, amino acids, long-chain fatty acids, and alcohols.

Morphological Features

Structure: Long, slender, helical shape (0.1–3.0 μm by 5–250 μm).

Components:

• Central protoplasmic cylinder: Cytoplasm and nucleoid.
• Plasma membrane & gram-negative cell wall.
• Axial filament: Enables corkscrew-like motility.
• Outer sheath: Essential for survival; damage leads to death.

Unique Motility

Adapted for movement in viscous environments via axial filament rotation, facilitating crawling on solid surfaces.

Ecological Diversity

• Habitat: Anaerobic muds (e.g., Spirochaeta), human mouth, mollusk digestion (Cristispira).
• Symbiosis: Aid in movement of flagellates like Myxotricha paradoxa.

Pathogenic Spirochaetes

1. Syphilis

• Causative Agent: Treponema pallidum.
• Stages:
  • Primary: Painless ulcer (chancre) at the infection site.
  • Secondary: Skin rash, hair loss, fever, infectious lesions.
  • Latent: Dormant; not infectious except for congenital transmission.
  • Tertiary: Degenerative lesions (gummas), cognitive and nervous system damage.
• Treatment: Penicillin; later stages may require higher doses.

2. Lyme Disease

• Causative Agents: Borrelia species (e.g., B. burgdorferi).
• Transmission: Bite of infected deer ticks (Ixodes scapularis).
• Stages:
  • Localized: Rash (erythema migrans), flu-like symptoms.
  • Disseminated: Neurological and cardiac symptoms, arthritis.
  • Late: Neuron demyelination; resembles Alzheimer’s/MS.
• Prevention: Tick removal, protective clothing, repellents (DEET, permethrin).

Other Diseases

Yaws

• Painless ulcers, wart-like lesions, bone and joint pain.
• Disfigurement in untreated cases.
• Gum necrosis, foul breath, grayish membrane on gums.

Noteworthy Facts

• Syphilis affected historical figures such as Al Capone, Nietzsche, and Oscar Wilde.
• Lyme disease has approximately 17,000 cases annually in the U.S.

Study Guide: Phylum Chlamydiae

Phylum Bacteroidetes Study Material

Overview

• Characteristics: Diverse phylum of Gram-negative, non-spore-forming, anaerobic, rod-shaped bacteria.
• Habitats: Found in the gut of humans and animals, soil, and marine environments.
• Key Genera:
  • Bacteroides: Important for gut health.
  • Prevotella: Often associated with oral and gut flora.

Taxonomy

• Phylum: Bacteroidetes
• Class: Bacteroidia
  • Example: Bacteroides fragilis (gut bacteria, breaks down complex carbohydrates).
• Class: Flavobacteriia
  • Example: Flavobacterium johnsniae (found in freshwater and marine environments).
• Class: Sphingobacteriia
  • Example: Sphingobacterium spiritivorum (associated with soil and plant surfaces).

Key Characteristics

• Gram-negative Bacteria:
  • Color: Pink or red (stained with safranin).
  • Structure: Thin peptidoglycan layer and an outer lipid membrane.
• Comparison with Gram-positive Bacteria:
  • Thicker peptidoglycan layer and retain purple crystal violet dye during staining.

Gram Staining Process

1. Crystal Violet Stain: Stains all cells purple.
2. Iodine Solution: Fixes the dye in the cells.
3. Alcohol Wash: Decolorizes Gram-negative cells, leaving them clear.
4. Safranin Counterstain: Stains Gram-negative cells pink/red.

Ecological Role in the Human Gut

Study Guide: Class Clostridia

Introduction to Anaerobic Bacteria

Definition: Microscopic, single-celled organisms living in diverse environments like soil, seawater, and radioactive waste.

Classification by Oxygen Requirement:

• Aerobic bacteria: Require oxygen.
• Anaerobic bacteria: Thrive without oxygen; oxygen inhibits growth.
• Facultative bacteria: Can survive with or without oxygen.

General Characteristics of Clostridia

• Type: Gram-positive, anaerobic bacteria.
• Habitat: Found in soil, intestines, and decaying organic matter.
• Key Features:
• Rod-shaped and pleomorphic (varied shapes in some species).
• Form endospores resistant to harsh conditions (e.g., heat, desiccation, chemicals).
• Known for producing potent toxins.

Life Cycle of Clostridium

1. States:
• Vegetative form: Actively grows and divides when conditions are favorable.
• Spore state: Dormant, highly resistant to adverse environments like acidity, heat, and lack of nutrients.
2. Survival Mechanism: Spores protect genetic material with a thick coat and return to vegetative form when conditions improve.

Host-Associated Species and Diseases

Clostridium botulinum

Disease: Botulism (nerve toxin leads to paralysis and difficulty breathing).

Types:

• Foodborne: Contaminated food (e.g., improperly canned goods).
• Infant: Germination in infants' intestines (linked to honey).
• Wound: Spore infection in wounds under anaerobic conditions.

Industrial Use: Produces solvents and certain pharmaceuticals.

Clostridium tetani

Disease: Tetanus (muscle stiffness and spasms).

Route of Infection: Spores enter through wounds; anaerobic environments promote germination.

Tetanus Types:

• Generalized: Affects the entire body.
• Localized: Limited to the area near the wound.
• Neonatal: Affects newborns, often via umbilical stump infections.

Clostridium difficile

Disease: Severe diarrhea and colitis, especially post-antibiotic use in hospitalized patients.

Spores: Survive in oxygenated environments and persist in the digestive system, transitioning between states.

Morphological Features

• Rod-shaped and pleomorphic.
• Endospores resist adverse conditions (heat, radiation, chemicals).
• May lose gram-positive stain with age.

Summary Points

• Clostridia are spore-forming, toxin-producing, gram-positive anaerobic bacteria.
• Their ability to form spores allows them to survive extreme environments.
• Key diseases include botulism, tetanus, and antibiotic-associated colitis.
• Industrial relevance includes producing solvents and pharmaceuticals.

Review Material

Mitochondria

• Final Quiz