intestinal microbes

• Introduction to the intestinal microbiota and metagenomics
• Intended learning outcomes
• Intended learning outcomes


  • List the major benefits conferred to us by our intestinal microbes
  • Explain how molecular phylogeny makes use of the 16S ribosomal RNA gene
  • Describe the major phyla of the human intestinal microbiota
• For many years, bacteria were viewed as nothing but bad guys
• But that view has changed recently
• Now we are told that keeping our intestinal microbes happy is one of the keys to good health
• Probiotics


  Living organisms that we ingest with the aim of increasing their numbers in the gut
• Prebiotics


  Non-digestible nutrients (esp. dietary fibre) that promote the growth of "friendly" bacteria
• Microbiota first recognised in 1683


  Leeuwenhoek's figures of bacteria from human mouth (17 sept 1683)
• Antoni van Leeuwenhoek


  Examined the dental plaque from his own teeth using the recently invented microscope
• He saw, for the first time, tiny microbes moving around
• He showed that drinking hot coffee stopped their movement, so they must be alive
• Animalcules


  What he called the microbes he saw
• They exist on our external surfaces, but not in our deeper tissues
• You have a unique microbiota on/in


  • Skin
  • Mouth
  • Pharynx
  • Respiratory system
  • Urogenital tract
  • Stomach
  • Intestinal tract
• Different communities of bacteria grow in the different niches of your body
• Epithelial cells


  Form a barrier between our microbes and tissues
• Some bacteria live in the outer layer of the mucous, but rarely penetrate the lower, thicker mucous layer to make contact with epithelial cells
• Metabolites produced by gut bacteria diffuse through the mucous for absorption
• Microbiota


  The micro-organisms that colonise normal, healthy individuals (used to be called "the normal flora")
• Microbiome


  The collective genomes of the organisms in the microbiota (although some people still use this term to mean the microbiota itself)
• By far the majority of your commensals are present in your gut
• The contents of the large intestine may contain up to 10^12 bacteria per gramme, possibly the densest bacterial population on earth
• Parasitism


  One species benefits at the expense of the other
• Commensalism


  One species benefits, but the other receives no benefit and is not harmed
• Mutualism


  Both species benefit from the relationship (symbiosis)
• Benefits conferred by our intestinal microbes

  • Digestion - they enable us to digest otherwise non-digestible plant polysaccharides, allowing us to extract more energy from food
  • Microbial antagonism - by taking up space and nutrients, and secreting anti-microbial agents, they prevent pathogens from taking hold
  • Vitamins - production of vitamins K and B12
  • Development - terminal differentiation of mucosa
  • Immune system - they are essential for proper development of the immune system early in life, and may also modulate immune function later in life
• Germ-free mice can be prepared by delivering pups by caesarean section into a completely sterile environment
• Effects of lacking intestinal microbes

  • They have a greatly enlarged caecum
  • They have poorly developed immune systems
  • They have very little body fat, but this is restored to normal levels on conventionalisation
• Your intestinal microbes are NOT evenly distributed!
• Small intestine ~10^8 bacteria
• Large intestine ~10^14 bacteria
• UK: 65 million people = 6 people
• pH and oxygen tension change greatly throughout the gut
• The pH and oxygen content of the different gut regions dictate which types of bacteria can grow there
• Low pH in stomach kills most ingested microbes
• Low oxygen in the large intestine prevents growth of aerobes
• Obligate aerobes


  Can only survive in the presence of oxygen, die without it
• Facultative anaerobes


  Can use and grow faster in oxygen, but don't need it to grow
• Aerotolerant anaerobes


  Don't use oxygen at all, but can tolerate its presence