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4.1 Prokaryote Habitats, Relationships, and Microbiomes

  • Prokaryotes are unicellular microorganisms whose cells have no nucleus.
  • Prokaryotes can be found everywhere on our planet, even in the most extreme environments.
  • Prokaryotes are very flexible metabolically, so they are able to adjust their feeding to the available natural resources.
  • Prokaryotes live in communities that interact among themselves and with large organisms that they use as hosts (including humans).
  • The totality of forms of prokaryotes (particularly bacteria) living on the human body is called the human microbiome, which varies between regions of the body and individuals, and changes over time.
  • The totality of forms of prokaryotes (particularly bacteria) living in a certain region of the human body (e.g., mouth, throat, gut, eye, vagina) is called the microbiota of this region.
  • Prokaryotes are classified into domains Archaea and Bacteria.
  • In recent years, the traditional approaches to classification of prokaryotes have been supplemented by approaches based on molecular genetics.

4.2 Proteobacteria

  • Proteobacteria is a phylum of gram-negative bacteria discovered by Carl Woese in the 1980s based on nucleotide sequence homology.
  • Proteobacteria are further classified into the classes alpha-, beta-, gamma-, delta- and epsilonproteobacteria, each class having separate orders, families, genera, and species.
  • Alphaproteobacteria include several obligate and facultative intracellular pathogens, including the rickettsias. Some Alphaproteobacteria can convert atmospheric nitrogen to nitrites, making nitrogen usable for other forms of life.
  • Betaproteobacteria are a diverse group of bacteria that include human pathogens of the genus Neisseria and the species Bordetella pertussis.
  • Gammaproteobacteria are the largest and the most diverse group of Proteobacteria. Many are human pathogens that are aerobes or facultative anaerobes. Some Gammaproteobacteria are enteric bacteria that may be coliform or noncoliform. Escherichia coli, a member of Gammaproteobacteria, is perhaps the most studied bacterium.
  • Deltaproteobacteria make up a small group able to reduce sulfate or elemental sulfur. Some are scavengers and form myxospores, with multicellular fruiting bodies.
  • Epsilonproteobacteria make up the smallest group of Proteobacteria. The genera Campylobacter and Helicobacter are human pathogens.

4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria

  • Gram-negative nonproteobacteria include the taxa spirochetes; the Chlamydia, Cytophaga, Fusobacterium, Bacteroides group; Planctomycetes; and many representatives of phototrophic bacteria.
  • Spirochetes are motile, spiral bacteria with a long, narrow body; they are difficult or impossible to culture.
  • Several genera of spirochetes contain human pathogens that cause such diseases as syphilis and Lyme disease.
  • Cytophaga, Fusobacterium, and Bacteroides are classified together as a phylum called the CFB group. They are rod-shaped anaerobic organoheterotrophs and avid fermenters. Cytophaga are aquatic bacteria with the gliding motility. Fusobacteria inhabit the human mouth and may cause severe infectious diseases. Bacteroides are present in vast numbers in the human gut, most of them being mutualistic but some are pathogenic.
  • Planctomycetes are aquatic bacteria that reproduce by budding; they may form large colonies, and develop a holdfast.
  • Phototrophic bacteria are not a taxon but, rather, a group categorized by their ability to use the energy of sunlight. They include Proteobacteria and nonproteobacteria, as well as sulfur and nonsulfur bacteria colored purple or green.
  • Sulfur bacteria perform anoxygenic photosynthesis, using sulfur compounds as donors of electrons, whereas nonsulfur bacteria use organic compounds (succinate, malate) as donors of electrons.
  • Some phototrophic bacteria are able to fix nitrogen, providing the usable forms of nitrogen to other organisms.
  • Cyanobacteria are oxygen-producing bacteria thought to have played a critical role in the forming of the earth’s atmosphere.

4.4 Gram-Positive Bacteria

  • Gram-positive bacteria are a very large and diverse group of microorganisms. Understanding their taxonomy and knowing their unique features is important for diagnostics and treatment of infectious diseases.
  • Gram-positive bacteria are classified into high G+C gram-positive and low G+C gram-positive bacteria, based on the prevalence of guanine and cytosine nucleotides in their genome
  • Actinobacteria is the taxonomic name of the class of high G+C gram-positive bacteria. This class includes the genera Actinomyces, Arthrobacter, Corynebacterium, Frankia, Gardnerella, Micrococcus, Mycobacterium, Nocardia, Propionibacterium, Rhodococcus, and Streptomyces. Some representatives of these genera are used in industry; others are human or animal pathogens.
  • Examples of high G+C gram-positive bacteria that are human pathogens include Mycobacterium tuberculosis, which causes tuberculosis; M. leprae, which causes leprosy (Hansen’s disease); and Corynebacterium diphtheriae, which causes diphtheria.
  • Clostridia spp. are low G+C gram-positive bacteria that are generally obligate anaerobes and can form endospores. Pathogens in this genus include C. perfringens (gas gangrene), C. tetani (tetanus), and C. botulinum (botulism).
  • Lactobacillales include the genera Enterococcus, Lactobacillus, Leuconostoc, and Streptococcus. Streptococcus is responsible for many human diseases, including pharyngitis (strep throat), scarlet fever, rheumatic fever, glomerulonephritis, pneumonia, and other respiratory infections.
  • Bacilli is a taxonomic class of low G+C gram-positive bacteria that include rod-shaped and coccus-shaped species, including the genera Bacillus and Staphylococcus. B. anthracis causes anthrax, B. cereus may cause opportunistic infections of the gastrointestinal tract, and S. aureus strains can cause a wide range of infections and diseases, many of which are highly resistant to antibiotics.
  • Mycoplasma spp. are very small, pleomorphic low G+C gram-positive bacteria that lack cell walls. M. pneumoniae causes atypical pneumonia.

4.5 Deeply Branching Bacteria

  • Deeply branching bacteria are phylogenetically the most ancient forms of life, being the closest to the last universal common ancestor.
  • Deeply branching bacteria include many species that thrive in extreme environments that are thought to resemble conditions on earth billions of years ago
  • Deeply branching bacteria are important for our understanding of evolution; some of them are used in industry

4.6 Archaea

  • Archaea are unicellular, prokaryotic microorganisms that differ from bacteria in their genetics, biochemistry, and ecology.
  • Some archaea are extremophiles, living in environments with extremely high or low temperatures, or extreme salinity.
  • Only archaea are known to produce methane. Methane-producing archaea are called methanogens.
  • Halophilic archaea prefer a concentration of salt close to saturation and perform photosynthesis using bacteriorhodopsin.
  • Some archaea, based on fossil evidence, are among the oldest organisms on earth.
  • Archaea do not live in great numbers in human microbiomes and are not known to cause disease.
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