Chapter 11- The Prokaryotes: Domains Bacteria and Archaea

Early classification attempts of bacteria struggled as they didn’t fit into the existing taxonomic systems for plants and animals.
Initial classifications were based on observable features like morphology (e.g., rod shape, coccus) and reactions to stains, such as Gram staining.
Grouping bacteria based on physical characteristics proved limited, leading to misclassifications similar to grouping bats and birds solely by wing presence.
Advances in molecular biology have enabled the classification of bacteria using phylogenetic systems based on genetic information, specifically rRNA sequences.
- Example:
- Genera Rickettsia and Chlamydia were previously grouped based on intracellular growth requirements.
- Rickettsia is now classified in the phylum Proteobacteria, while Chlamydia belongs to its separate phylum.
Changes in classification may be unsettling for some microbiologists but reflect accurate evolutionary relationships among organisms.

Rapid identification is crucial for pathogenic bacteria causing infections, such as Streptococcus pyogenes.
- Clinical Case Example:
- Patients after cardiovascular surgery presented with red colonies of Gram-negative bacteria.
- Identified source was a scrub nurse with artificial fingernails.
- Red pigment production indicated a specific bacterium, suggesting the need for swift action to end the outbreak.

Prokaryotes are divided into two domains: Archaea and Bacteria, categorized into phyla, classes, orders, families, genera, and species based on various characteristics.
Bacteria can be further categorized as Gram-negative or Gram-positive.

Phylum: Proteobacteria (divided into classes)
- Alphaproteobacteria (Ehrlichia, Rickettsia)
- Betaproteobacteria (Bordetella, Burkholderia)
- Gammaproteobacteria (Vibrio, Salmonella, Helicobacter, Escherichia)
- Deltaproteobacteria (Bdellovibrio)
- Epsilonproteobacteria (Campylobacter, Helicobacter)
Other Gram-Negative Phyla
- Cyanobacteria: Oxygenic photosynthetic microbes; nitrogen-fixing capability.
- Chlorobi and Chloroflexi: Anoxygenic photosynthetic bacteria.
- Chlamydiae: Intracellular pathogens.
- Bacteroidetes: Significant in the human microbiome; role in digestion.
- Spirochaetes: Known for unique flagellar structure.
- Deinococcus-Thermus: Specialized for environmental resilience.

Phylum: Firmicutes
- Includes important genera like Clostridium, Staphylococcus, and Streptococcus.
- Endospore-Formers: Clostridium, Bacillus, with clinical relevance (e.g., causing tetanus, botulism).
Phylum: Actinobacteria
- Contains important pathogens and antibiotic producers.
- Group includes Mycobacterium (tuberculosis, leprosy), Corynebacterium (diphtheria).

Distinguished from bacteria by unique cell wall composition (no peptidoglycan).
Divided into five physiological groups based on environmental adaptations:
- Halophiles: Thrive in high saline conditions.
- Thermophiles: Prefer extremely high temperatures.
- Acidophiles: Grow optimally in low pH environments.
- Methanogens: Produce methane, found in anaerobic environments, including the human microbiome.

Clinical Case Example: Most bacteria that can cause disease in humans belong to larger groups, including Streptococcus pneumoniae and Neisseria meningitidis.
- Specific conditions such as meningitis from group B Streptococcus (GBS), which affects neonatal mortality, exemplify the clinical relevance of precise bacterial identification.

Current research indicates a vast microbial diversity that has not yet been fully characterized or identified.
- Molecular Techniques: Use of PCR has enhanced the ability to identify and catalog bacteria from environmental samples.
- New findings continue, reflecting a greater complexity in microbial life than previously understood.