Bacteria: A Very Short Introduction – Sebastian G. B. Amyes

Thoughts: Amyes doesn't shy away from using technical terms, yet with the exception of the last chapter or two (lots of acronyms!), I found Bacteria: A Very Short Introduction to be pretty readable and generally well written. I don't know that I learned a great deal of new information, but it brought back and solidified many bits of knowledge that I had heard at some point but had forgotten.

(In contrast to many other book notes on this site, these chapter summaries were written from memory immediately after finishing each chapter. They may contain inaccuracies - in fact, I'm almost certain they do! The idea was to impress the book's ideas in memory rather than to produce a faithful summary of the information contained within. I'm sharing this bit of "learning exhaust" in case it inspires others to try something similar.)

Amyes, Sebastian G. B. 2013. Bacteria: A Very Short Introduction. Oxford UP.

• Chapter 1 - origins:
  • Amyes speculates a bit about the origin of life, and notes that bacteria first emerged about 1.5 billion years after the formation of the earth (4bya?). About 2?bya, photosynthesizing bacteria emerged. About 1.5?bya, aerobic bacteria emerged. About 1bya, bacteria become much less plentiful in the fossil record, suggesting something may have begun predating on them around this time. Also around 1bya, eukaryotic cells emerge, though Amyes doesn’t explicitly connect these two facts.
  • Bacteria are much smaller than eukaryotic cells (the average length of a bacterial cell being approximately 1/15 the length of the average eukaryotic cell). Whereas eukaryotic cells contain distinct structures/organelles and a nucleus, there is no such structural definition in bacteria.
  • some scientist named Gram invented a test to distinguish between double–cell walled gram-positive bacteria and single–cell walled gram-negative bacteria. Bacteria are often grouped first under these two broad categories. It’s unclear which group evolved first.
  • Many eukaryotic cells have either chloroplasts or mitochondria, organelles which have their own genomes and are roughly the same size as bacteria. They probably have their origin in bacterial cells which were ingested by archaea but not killed.
• Chapter 2 - evolution
  • Bacteria often exchange DNA with bacteriophages, which sometimes incorporate parts of bacterial genomes into their own, and sometimes incorporate themselves into bacterial genomes, lying dormant until a mutation in some DNA sequence suppressing their replication allows them to proliferate anew.
  • Bacteria participate in the carbon cycle, the nitrogen cycle, and other biogeochemical cycles like the sulfur cycle.
  • Bacteria live in mutualist and commensal relationships with many other organisms. Amyes recounts how several bacterial aid in animal digestion, regulate immune function, and help prevent infections by pathogenic bacteria.
• Chapter 3 - discovery
  • Antony von Leeuwenhoek was the first person to observe bacteria
  • Louis Pasteur was one person among several who contributed to the development of germ theory
  • The research and advocacy of Joseph Lister (of Listerine fame, presumably?) and Ignaz Semmelweiss contributed to great reductions in post-surgical infections by promoting sterilization
  • Robert Koch identified many bacterial pathogens and laid out Koch’s Postulates, still used, in variously modified forms, to demonstrate that some specific organism causes some specific disease
  • Escherichia coli is found in abundance in people’s digestive systems, where it’s usually benign, but new strains, or existing local strains to which a visitor’s immune system is not yet accustomed, can cause illness. It is the daphnia of bacteriological research
• Chapter 4 - Environment and civilization
  • Amyes outlines various preservation methods that can be used to prevent food spoilage at the hands of bacteria and fungi, including salting, smoking, preserving with alcohol and with honey. He outlines how bacteria aid in the production and preservation of various foods, including vinegar (where bacteria convert alcohol into acid), cheese (where cheesemakers generally use a primary bacterial culture before adding an adjunct bacterial or fungal culture, sometimes as a wash), and yogurt. Bacterial species useful to cheesemaking often include Lactobacillus and ??Lactococcus species, whereas yogurt tends to involve Bifidobacterium species
  • Amyes then pivots to talk briefly about probiotics, noting that their principal health benefits likely derive from displacing pathogenic organisms, especially following, e.g., a course of antibiotics
  • Amyes finally talks about how bacteria in cesspools, septic tanks and sewage treatment plants work to decompose and detoxify human waste, how bacteria can be used to compost organic matter, and how bacteria decompose animal (including human) bodies. In all these processes, the presence or absence of oxygen allows aerobic or anaerobic species to proliferate.
• Chapter 5 - Bacterial Pathogenesis
  • there are four main classes of proteins (or just compounds?) that allow bacteria to infect and proliferate within hosts. These four virulence factors are
    • invasins - allow bacteria to move within the body
    • aggressins - build physical structures that block the host’s immune system from reaching the bacteria
    • impedins - directly interfere with components of the host’s immune system
    • adhesins - allow bacteria to bind to advantageous locations within a host’s body
  • although symptoms of bacterial infections are often mostly caused by the immune system’s response to them, some pathenogenic bacteria are toxic. These toxins can usefully be grouped into endotoxins (which are part of the bacteria themselves - often cell walls - and become toxic when a bacterial cell dies and disintegrates) and exotoxins (which are released by the bacteria)
  • Amyes lists a number of bacterial pandemics and epidemics, including the Black Death, tuberculosis, and cholera, as well as a number of sexually transmitted diseases, including gonnorrhea and chlamydia
• Chapter 6 - Antibiotics
  • humans have used antibiotic substances for millennia, including, e.g., quinine, which inhibits the pathogen that causes malaria (which I thought was a small animal rather than a bacterium??)
  • Several antibiotics and classes of antibiotics were discovered and developed over the course of the first few decades of the 20th century, among which penicillin was the first. Many antibiotic compounds are effective only on gram-positive or on gram-negative bacteria
  • some antibiotics kill bacterial cells, causing them to lyse, while others simply prevent bacterial cells from replicating, which can then be cleaned up by the immune system. Bacteria-killing antibiotics may likely be preferred in situations where the patient’s immune system is weakened/suppressed such as in transplant patients, whereas antibiotics that prevent replication may be preferred when the bacterium has endotoxins which might be released by the destructive action of bactericidal antibiotics
  • bacterial cells in biofilms are much more resistant to antibiotics - Amyes mentions a factor of 1000(!)
• Chapter 7 - Antibiotic resistance
  • many antibiotic-resistant traits are encoded on plasmids, which are free-floating, smaller sequences of DNA that are sometimes exchanged between bacterial cells, more often between organisms of the same species but sometimes between organisms of different species. Sometimes these plasmids contain sequences encoding several different proteins each of which confers resistance to a different antibiotic. Sometimes, DNA sequences on plasmids can be transposed into bacteria’s main chromosomes
  • many resistant traits are already found in bacteria, particularly soil bacteria, which have to cope with the offensive strategies of other microorganisms. Often, it’s DNA from these species that provide the raw material for sequences that confer high levels of resistance, rather than novel mutations.
  • Amyes lists several conditions in developing countries which tend to conflow to lead to the evolution of antibiotic resistant strains: people living in regular close contact with soil and with animals, antibiotics being available for general purchase, especially in insufficient quantities to complete a full course, or not manufactured up to standard so that concentrations are lower than necessary, poor sanitary conditions leading to frequent infection and reinfection.
• Chapter 8 - The Future
  • some directions of research likely to be explored in the future
    • the discovery of more species of bacteria, and the repeated sequencing of the DNA of known species, should shed light on the evolutionary relationships between bacterial clades
    • genetic engineering - scientists have succeeded in adding sequences to bacterial genomes, allowing, e.g., the production of insulin in a culture of E. coli, as well as the creation of “synthetic” bacteria in which a bacterial cell’s existing DNA was excised and a new genome was inserted; the resulting cell was able to replicate. Such experiments come with ethical complexities, as techniques can be used to intentionally cause harm or might lead to unintended consequences if something escapes from a lab