BIO 102: Bacteria Identification and Classification

Identification of Bacteria

• Bacteria are diverse single-celled microorganisms characterized by unique cell wall structures and metabolic processes.
• Sample collection methods include clinical specimens (blood, urine, tissue), environmental samples (soil, water), food samples, industrial samples, and research samples.
• Culture-Based Methods involve using selective and differential media to encourage the growth of specific bacterial colonies.

Examination Methods

• Macroscopic Examination: Observations of colony morphology such as size, shape, color, texture, and margins can indicate bacterial identity.
• Microscopic Examination:
  • Gram Staining: Differentiates bacteria into Gram-positive (purple) and Gram-negative (pink) based on cell wall composition.
  • Observations of cell morphology and presence of structures like flagella/capsules.
• Biochemical Tests: Assess metabolic capabilities, including tests for catalase, oxidase, indole production, citrate utilization, coagulase, and sugar fermentation, with specific bacteria as examples.
• Molecular Techniques:
  • PCR: Amplifies bacterial DNA for identification.
  • 16S rRNA Sequencing: Analyzes conserved genetic regions for bacterial classification.
  • Whole Genome Sequencing (WGS): Provides extensive genetic information for accurate identification.
• Serological Methods: Use antibodies to detect bacterial antigens, including ELISA and Western Blotting.
• Anaerobic Culture Techniques: Specialized methods for bacteria requiring anaerobic conditions.

Types of Bacterial Isolation Media

• General Purpose Media: Nutrient Agar supports growth of diverse non-fastidious bacteria.
• Enriched Media: Blood Agar and Chocolate Agar support fastidious bacteria and differentiate based on hemolytic properties.
• Selective Media: MacConkey and Mannitol Salt Agar selectively grow certain bacteria and differentiate based on metabolic characteristics.
• Differential Media: EMB and XLD provide visual differentiation of lactose fermenters and specific pathogens.
• Specialized Media: TCBS for Vibrio and Lowenstein-Jensen Medium for Mycobacterium species.

Classification of Bacteria

• Based on Cell Wall Composition:
  • Gram-positive (e.g., Staphylococcus aureus) versus Gram-negative (e.g., Escherichia coli).
• Morphological Classification:
  • Cocci: Spherical bacteria (e.g., Micrococcus luteus, Neisseria gonorrhoeae).
  • Bacilli: Rod-shaped bacteria (e.g., Escherichia coli, Haemophilus influenzae).
  • Spirilla: Spiral-shaped (e.g., Spirillum minus).
  • Vibrios: Curved rod-shaped (e.g., Vibrio cholerae).
  • Pleomorphic: Variable shape (e.g., Mycoplasma pneumoniae).

Oxygen Requirements Classification

• Obligate Aerobes: Require oxygen (e.g., Mycobacterium tuberculosis).
• Obligate Anaerobes: Cannot survive in oxygen (e.g., Clostridium botulinum).
• Facultative Anaerobes: Can utilize both aerobic and anaerobic respiration (e.g., Escherichia coli).
• Microaerophiles: Require lower than atmospheric oxygen levels (e.g., Helicobacter pylori).
• Aerotolerant Anaerobes: Can tolerate oxygen but do not use it (e.g., Lactobacillus species).

Metabolic Characteristics

• Autotrophic Bacteria: Use inorganic substances (e.g., Nitrosomonas europaea).
• Heterotrophic Bacteria: Rely on organic compounds (e.g., Pseudomonas aeruginosa).

Ecological Roles

• Symbiotic Bacteria: Form relationships with hosts (e.g., Rhizobium leguminosarum).
• Pathogenic Bacteria: Cause diseases (e.g., Salmonella enterica).

Systematic Classification of Bacteria

• Domain: Bacteria
• Kingdom: Eubacteria
• Phylum Examples:
  • Firmicutes: Bacillus subtilis (produces antibiotics).
  • Proteobacteria: Includes various classes, each with significant examples (e.g., Neisseria gonorrhoeae in Betaproteobacteria).
  • Actinobacteria: Mycobacterium tuberculosis (common pathogen).
  • Cyanobacteria: Anabaena sp. (nitrogen fixation).
  • Spirochaetes: Borrelia burgdorferi (causes Lyme disease).

Identification and Classification of Bacteria

• Bacteria are single-celled microorganisms with diverse shapes and environments.
• Basic characteristics include cell wall structure, reproduction, and genetic diversity.

Sample Collection and Preparation

• Samples collected using sterile techniques from:
  • Clinical sources: blood, urine, sputum, cerebrospinal fluid, tissue biopsies, swabs.
  • Environmental sources: soil, water, air, healthcare surfaces.
  • Food sources: meats, dairy, fruits, processed foods.
  • Industrial sources: biofilms, fermentation products, waste.
  • Research sources: model organisms, genetically modified bacteria, environmental DNA.

Methods of Examination

• Culture-Based Methods: Use selective and differential media to promote growth of specific bacteria.
• Macroscopic Examination: Colony morphology provides initial identification clues based on size, shape, and color.
• Microscopic Examination:
  • Gram Staining differentiates bacteria into Gram-positive (purple) or Gram-negative (pink).
  • Observes cell shape, arrangement, and specific structures (e.g., flagella).
• Biochemical Tests assess metabolic capabilities (e.g., catalase test differentiates Staphylococcus from Streptococcus).
• Molecular Techniques: PCR amplifies bacterial DNA for identification.
• Serological Methods: Use antibodies to detect bacterial antigens (e.g., ELISA).
• Anaerobic Culture Techniques: Specialized methods for bacteria requiring low oxygen conditions.

Types of Bacterial Isolation Media

• General Purpose Media:
  • Nutrient Agar (NA) supports various non-fastidious bacteria.
• Enriched Media:
  • Blood Agar (BA) used for fastidious bacteria, identifies hemolytic properties.
  • Chocolate Agar (CHOC) supports growth of respiratory bacteria.
• Selective Media:
  • MacConkey Agar (MAC) selects for Gram-negative bacteria.
  • Mannitol Salt Agar (MSA) differentiates staphylococci.
• Differential Media:
  • Eosin Methylene Blue Agar (EMB) differentiates lactose fermenters.
  • Xylose Lysine Deoxycholate Agar (XLD) used for enteric pathogens.
• Specialized Media:
  • Thiosulfate-Citrate-Bile Salts-Sucrose Agar (TCBS) selects for Vibrio species.
  • Lowenstein-Jensen Medium (LJ) selects for Mycobacterium species.

Classification of Bacteria

• Based on Cell Wall Composition:

  • Gram-positive: e.g., Staphylococcus aureus, causes skin infections.
  • Gram-negative: e.g., Escherichia coli, can cause foodborne illness.

• Based on Morphology:

  • Cocci: spherical shapes (e.g., Streptococcus pyogenes).
  • Bacilli: rod shapes (e.g., Escherichia coli).
  • Spirilla: spiral shapes (e.g., Treponema pallidum).
  • Vibrios: comma-shaped (e.g., Vibrio cholerae).
  • Pleomorphic: variable shapes (e.g., Mycoplasma pneumoniae).

• Based on Oxygen Requirement:

  • Obligate Aerobes: need oxygen (e.g., Mycobacterium tuberculosis).
  • Obligate Anaerobes: cannot tolerate oxygen (e.g., Clostridium botulinum).
  • Facultative Anaerobes: can use oxygen or ferment (e.g., Escherichia coli).
  • Microaerophiles: need low oxygen levels (e.g., Helicobacter pylori).
  • Aerotolerant Anaerobes: tolerate oxygen, ferment energy (e.g., Lactobacillus).

• Based on Metabolic Characteristics:

  • Autotrophic: e.g., Nitrosomonas europaea, oxidizes ammonia.
  • Heterotrophic: e.g., Pseudomonas aeruginosa, opportunistic pathogen.

• Based on Ecological Roles:

  • Symbiotic: e.g., Rhizobium leguminosarum, aids plant nitrogen fixation.
  • Pathogenic: e.g., Salmonella enterica, causes salmonellosis.

Systematic Classification of Bacteria

• Bacteria classified into hierarchical categories based on evolutionary relationships.

• Domain: Bacteria, part of the three life domains: Bacteria, Archaea, Eukarya.

• Kingdom: Eubacteria.

• Phylum Examples:

  • Firmicutes (Bacilli): e.g., Bacillus subtilis.
  • Proteobacteria (Gammaproteobacteria): e.g., Escherichia coli.
  • Actinobacteria: e.g., Mycobacterium tuberculosis.
  • Cyanobacteria: e.g., Anabaena sp.
  • Spirochaetes: e.g., Borrelia burgdorferi.

Virus Overview

• Viruses are non-cellular infectious agents with genetic material (DNA or RNA) encased in a protein coating (capsid).
• Require host cells for replication, leading to illnesses like respiratory infections and STIs.
• Common viral infections include flu, COVID-19, chickenpox, and HIV/AIDS.
• Smaller than bacteria, viruses range from 20-300 nm.
• Cannot be classified as living or non-living due to characteristics of both.
• Enter the host through mucous membranes or breaks in the skin.### Classification of Viruses
• Classification based on nucleic acid presence: DNA viruses (single-stranded and double-stranded) and RNA viruses (single-stranded and double-stranded).
• Examples of DNA viruses:
  • Single-stranded: Picornaviruses, Parvovirus.
  • Double-stranded: Adenovirus, Herpes virus.
• Examples of RNA viruses:
  • Double-stranded: Reovirus.
  • Single-stranded: Poliovirus, Hepatitis A, Rabies virus, Influenza virus.
• Classification based on replication properties:
  • Replication in cytoplasm: All RNA viruses except Influenza.
  • Replication in nucleus and cytoplasm: Influenza virus, Poxvirus.
  • Replication predominantly in nucleus: All DNA viruses except Poxvirus.
  • Double-stranded DNA intermediate replication: All DNA viruses, retroviruses, some tumor-causing RNA viruses.
  • Single-stranded RNA intermediate: All RNA viruses except Reovirus and tumor-causing RNA viruses.

Host Range Classification

• Animal viruses: Infect animal cells; notable examples include Influenza virus, Rabies virus, Herpes virus.
• Plant viruses: Infect plant cells; examples include Potato virus, Tobacco mosaic virus.

Transmission Modes

• Airborne transmission: Through respiratory tract; examples include Swine flu and Rhinovirus.
• Fecal-oral route: Contaminated food or water transmission; examples include Hepatitis A and Poliovirus.
• Sexual transmission: Spread through intimate contact; examples include Retrovirus and Human papillomavirus.
• Transfusion-related transmission: Through blood transfusions; examples include Hepatitis B and HIV.
• Zoonotic transmission: Spread through animal bites; examples include Rabies virus and Ebola virus.

Major Virus Types

• Influenza viruses (Orthomyxoviridae): Cause flu; strains include A (avian flu, swine flu) and B.
• Human herpesvirus (Herpesviridae): Causes oral/genital herpes, chickenpox, shingles, Epstein-Barr virus.
• Coronaviruses: Include SARS-CoV-1, SARS-CoV-2 (COVID-19), and MERS; cause respiratory infections with serious outcomes.
• Human Papillomavirus (HPV): Causes warts and some cancers; casual transmission is primarily sexual.
• Enteroviruses: Affect intestinal tract; notable for causing polio and hand, foot, and mouth disease.
• Flaviviruses: Often spread by mosquitoes; examples include Zika, West Nile, dengue, yellow fever.
• Orthopoxviruses: Cause flu-like symptoms and rashes; examples include Cowpox and Mpox.
• Hepatitis viruses: Affect the liver, with variants A-E differing in transmission and severity.
• Oncoviruses: Can lead to cancer; include HPV and Human herpes virus 8 (HHV-8).

Types of Viral Infections

• Respiratory infections: Affect respiratory tract; examples include common cold, flu, COVID-19.
• Digestive system infections: Affect stomach/intestines; examples include Norovirus, Hepatitis viruses.
• Viral hemorrhagic fevers: Affect blood clotting; examples include Ebola and Yellow fever.
• Sexually transmitted infections: Spread through sexual contact; examples include HIV, HPV.
• Exanthematous infections: Cause skin rashes; examples include Measles, Chickenpox, Mpox.
• Neurological infections: Attack nervous system; examples include Polio, Rabies.
• Congenital infections: Passed from mother to child; examples include Zika, Rubella.

Common Viral Diseases

• Common cold: Caused primarily by Rhinoviruses, with symptoms including nasal congestion and cough.
• Influenza: Respiratory infection with sudden onset, fever, muscle aches; vaccination is crucial for at-risk groups.
• COVID-19: Caused by SARS-CoV-2, spread through respiratory droplets; severe cases require hospitalization.
• Respiratory Syncytial Virus (RSV): Common in children and the elderly, causing cold-like symptoms.
• Chickenpox: Highly contagious, causing itchy skin rash; preventive vaccines are available.
• Measles: Airborne disease with symptoms including fever and rash; vaccination provides effective protection.
• HIV/AIDS: Attacks immune system; transmitted sexually or through body fluids; management through antiretroviral therapy.
• Human Papillomavirus: Causes warts and can lead to cancer; vaccination and regular check-ups can prevent complications.
• Herpes infections: Painful blisters on skin, caused by HSV-1 and HSV-2; management is important though no cure exists.
• Polio: Can cause paralysis; vaccination is essential for prevention.
• Rabies: Transmitted via animal bites, leading to fatal outcomes without prompt treatment.
• Mpox: Caused by monkeypox virus, presenting with skin rashes and flu-like symptoms.
• Zika Virus: Mosquito-borne virus, asymptomatic in many cases but can cause birth defects in pregnancies.
• Hepatitis: Involves liver inflammation caused by several viruses, differing in transmission routes and disease severity.