Read the summary and the most important questions on 2.1: Gastrointestinal Microbes | Erwin. G. Zoetendal

• 1 Human GI tract

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• What is the triangle of GI tract interactions and how do they interact?

  Human host, diet & food and GI tract microbiota
  diet -> host: digestion and uptake, food components
  diet -> ubiota: conversion of non-digested food components
  host -> ubiota: a-ubial peptides, endogenous substrates, immune response
  ubiota -> host: vitamins, SCFAs, immune modulation

• Which 2 types of fermentation vessels/chambers do herbivores have?

  Foregut: rumen
  Hindgut: cecum

• What are the functions of the different parts of the GI tract? What is the distribution of ubiota?  

  Stomach: digestion; 10^3 bact/gram
  Small intestine: digestion, nutruent and water absorption; 10^5-10^7
  colon: ubial fermentation, metabolite and water absorption: >10^11

• Why is little known about SI ubiota? (5)

  1: limited knowledge due to sampling problems
  2: ubiota composition differs between humans
  3: compositions differs spatially: proximal - distal, lumen - mucosa
  4: composition flucutates over time
  5: some phyla dominate, difficult to sequence less abundant ubiota

• What are typical inhabitants of the SI and how do they interact?

  polysaccharides -> [Streptococcus] -> lactate -> [Veillonella] -> propionate/acetate
  polysaccharides -> [ E. coli] -> acetate -> [Clostridium] -> butyrate

   

• What are the products of ubial fermentation in the colon?

  production of SCFAs: propionate (liver); butyrate (gut epithelium); acetate (peripheral tissue)

• What are the pros (7) and cons (3) of ubiota?

  1: development of intestinal structure and function
  2: production of essential vitamins
  3: protection from pathogens (colonization resistance)
  4: deconjugation of bile salts
  5: bile pigment metabolism
  6: recycling valuable hormones
  7: cholesterol conversion
  cons: production of toxic, mutagenic and carcinogenic compounds

• What are examples, characteristics and functions of: Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia, Proteobacteria?  

  Firmicutes: Clostridium, Lactobacillus, Streptococcus
  low G+C Gram positives; conversion of carbohydrates into acetate, butyrate and lactate
  
  Bacteroidetes: Bacteroides, Prevotella
  Gram negatives; degrade complex carbohydrates
  
  Actiniobactera: Bifidobacterium, Colinsella
  high G+C Gram-positives; bifido is a lactate produces, beneficial/probiotic
  
  Verrumicrobia: Akkermansia
  Gram negative; muciniphila: mucus degrading bacterium
  
  Proteobacteria: E. coli, Campylobacter, Salmonella, Helicobacter
  Gram-negative; opportunisitic pathogens, sulphate reducing bacteria

• What are three characteristics of the ubiota of an adult?

  1: stable in composition and time
  2: host-specific composition
  3: complex composition

• What are characteristics of the ubiota of neonates?

  first colonizers are facultative anaerobics which convert the oxic GI tract into strictly anoxic
  afterwards: strict anaerobes colonize, mainly bifidobacteria (milk)
  after weaning: increasing ubial diversity, reaching adult complexity in 2 years time